diff --git a/.flake8 b/.flake8 new file mode 100644 index 0000000..3a70fba --- /dev/null +++ b/.flake8 @@ -0,0 +1,20 @@ +[flake8] +--select = A,B,C,D,E,F,W,C90,FS +max-line-length = 93 +# For PEP8 error codes see +# http://pep8.readthedocs.org/en/latest/intro.html#error-codes +ignore = + D101, + D102, + D103, + D104, + D105, + D107, + F403, + F405, + F841, + FS, + W503 +# for compatibility with black +# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#flake8 +extend-ignore = E203 diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml new file mode 100644 index 0000000..0e76f61 --- /dev/null +++ b/.github/workflows/black.yml @@ -0,0 +1,30 @@ +--- +name: black + +on: + push: + branches: + - master + pull_request: + branches: + - '*' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + black: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: '3.12' + allow-prereleases: false + - name: Install black + run: python -m pip install --upgrade pip black + - name: Run Black + run: black --check --diff --color . diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml index c5e1604..63b4b53 100644 --- a/.github/workflows/codespell.yml +++ b/.github/workflows/codespell.yml @@ -2,21 +2,21 @@ name: Codespell on: - push: - branches: [master] - pull_request: - branches: [master] + push: + branches: [master] + pull_request: + branches: [master] permissions: - contents: read + contents: read jobs: - codespell: - name: Check for spelling errors - runs-on: ubuntu-latest + codespell: + name: Check for spelling errors + runs-on: ubuntu-latest - steps: - - name: Checkout - uses: actions/checkout@v4 - - name: Codespell - uses: codespell-project/actions-codespell@v2 + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Codespell + uses: codespell-project/actions-codespell@v2 diff --git a/.github/workflows/flake8.yml b/.github/workflows/flake8.yml new file mode 100644 index 0000000..2b6021d --- /dev/null +++ b/.github/workflows/flake8.yml @@ -0,0 +1,31 @@ +--- +name: flake8 + +on: + push: + branches: + - master + pull_request: + branches: + - '*' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + flake8: + name: run flake8 + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Setup python + uses: actions/setup-python@v5 + with: + python-version: '3.12' + allow-prereleases: false + - name: Install tox + run: python -m pip install --upgrade tox + - name: Run Flake8 + run: tox run -e flake8 diff --git a/.github/workflows/isort.yml b/.github/workflows/isort.yml new file mode 100644 index 0000000..d7bd3db --- /dev/null +++ b/.github/workflows/isort.yml @@ -0,0 +1,31 @@ +--- +name: isort + +on: + push: + branches: + - master + pull_request: + branches: + - '*' + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + isort: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: '3.12' + allow-prereleases: false + - name: Install isort + shell: bash {0} + run: python -m pip install --upgrade pip isort + - name: Run isort + run: isort --diff --check --settings-path pyproject.toml . diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 301dbc7..28c3d13 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -3,7 +3,7 @@ name: Test on: push: - branches: ['master'] + branches: [master] pull_request: branches: ['*'] @@ -16,7 +16,7 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - os: [ubuntu-latest, macOS-latest, windows-latest] + os: [ubuntu-latest, macOS-latest, windows-latest] python-version: ['3.8', '3.9', '3.10', '3.11', '3.12'] fail-fast: false steps: @@ -30,4 +30,3 @@ jobs: run: pip install tox - name: Run tests run: tox run -e tests - diff --git a/.gitignore b/.gitignore index c0ba852..eb5446c 100644 --- a/.gitignore +++ b/.gitignore @@ -21,4 +21,4 @@ debug.log test/data -.tox \ No newline at end of file +.tox diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a73479a..1d4053c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,43 +3,43 @@ # See https://pre-commit.com/hooks.html for more hooks repos: -# - repo: https://github.com/pre-commit/pre-commit-hooks -# rev: v4.5.0 -# hooks: -# - id: check-ast -# - id: check-case-conflict -# - id: check-json -# - id: check-merge-conflict -# - id: check-toml -# - id: check-yaml -# - id: end-of-file-fixer -# - id: mixed-line-ending -# - id: trailing-whitespace +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.5.0 + hooks: + - id: check-ast + - id: check-case-conflict + - id: check-json + - id: check-merge-conflict + - id: check-toml + - id: check-yaml + - id: end-of-file-fixer + - id: mixed-line-ending + - id: trailing-whitespace -# - repo: https://github.com/pycqa/isort -# rev: 5.13.2 -# hooks: -# - id: isort -# args: [--profile, black, --settings-path, pyproject.toml] +- repo: https://github.com/pycqa/isort + rev: 5.13.2 + hooks: + - id: isort + args: [--profile, black, --settings-path, pyproject.toml] -# - repo: https://github.com/asottile/pyupgrade -# rev: v3.15.0 -# hooks: -# - id: pyupgrade -# args: [--py38-plus] +- repo: https://github.com/asottile/pyupgrade + rev: v3.15.0 + hooks: + - id: pyupgrade + args: [--py38-plus] -# - repo: https://github.com/psf/black-pre-commit-mirror -# rev: 24.1.1 -# hooks: -# - id: black -# args: [--config, pyproject.toml] +- repo: https://github.com/psf/black-pre-commit-mirror + rev: 24.1.1 + hooks: + - id: black + args: [--config, pyproject.toml] -# - repo: https://github.com/adamchainz/blacken-docs -# rev: 1.16.0 -# hooks: -# - id: blacken-docs -# additional_dependencies: -# - black==23.9.1 +- repo: https://github.com/adamchainz/blacken-docs + rev: 1.16.0 + hooks: + - id: blacken-docs + additional_dependencies: + - black==23.9.1 - repo: https://github.com/codespell-project/codespell rev: v2.2.6 @@ -48,11 +48,11 @@ repos: args: [--toml, pyproject.toml] additional_dependencies: [tomli] -# - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt -# rev: 0.2.3 -# hooks: -# - id: yamlfmt -# args: [--mapping, '4', --sequence, '4', --offset, '0'] +- repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt + rev: 0.2.3 + hooks: + - id: yamlfmt + args: [--mapping, '4', --sequence, '4', --offset, '0'] - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks rev: v2.12.0 @@ -60,14 +60,14 @@ repos: - id: pretty-format-toml args: [--autofix, --indent, '4'] -# - repo: https://github.com/pre-commit/pygrep-hooks -# rev: v1.10.0 -# hooks: -# - id: rst-backticks +- repo: https://github.com/pre-commit/pygrep-hooks + rev: v1.10.0 + hooks: + - id: rst-backticks -# - repo: https://github.com/pyCQA/flake8 -# rev: 7.0.0 -# hooks: -# - id: flake8 -# args: [--config, .flake8, --verbose, nilearn, examples, maint_tools] -# additional_dependencies: [flake8-docstrings, flake8-use-fstring, flake8-functions] +- repo: https://github.com/pyCQA/flake8 + rev: 7.0.0 + hooks: + - id: flake8 + args: [--config, .flake8, --verbose, nidmresults, examples] + additional_dependencies: [flake8-docstrings, flake8-use-fstring] diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 15c8318..0000000 --- a/MANIFEST.in +++ /dev/null @@ -1,7 +0,0 @@ -include requirements.txt -include nidmresults/prefixes.csv -include nidmresults/owl/nidm-results_020.owl -include nidmresults/owl/nidm-results_100.owl -include nidmresults/owl/nidm-results_110.owl -include nidmresults/owl/nidm-results_120.owl -include nidmresults/owl/nidm-results_130.owl \ No newline at end of file diff --git a/README.md b/README.md index 3261d65..962eb29 100644 --- a/README.md +++ b/README.md @@ -23,5 +23,3 @@ Examples are available in the [examples](examples) folder. ## Contributing Thanks for your interest in contributing to nidmresults. All contributions are very welcome! If you experience difficulties using the library, please [open an issue](https://github.com/incf-nidash/nidmresults/issues/new) describing the problem. See the list of [current issues](https://github.com/incf-nidash/nidmresults/issues). - - diff --git a/examples/ex_read_nidm.py b/examples/ex_read_nidm.py index cd32e19..7829a13 100644 --- a/examples/ex_read_nidm.py +++ b/examples/ex_read_nidm.py @@ -1,22 +1,24 @@ -# Example: reading a NIDM pack available on NeuroVault -import os +"""Example: reading a NIDM pack available on NeuroVault.""" + import json -import nidmresults as nidm +import os import urllib.request +import nidmresults as nidm + # Download the NIDM pack locally -nidm_url = 'https://neurovault.org/collections/2210/fsl_default_130.nidm.zip' +nidm_url = "https://neurovault.org/collections/2210/fsl_default_130.nidm.zip" nidmpack = "2210_fsl_default_130.nidm.zip" if not os.path.isfile(nidmpack): - print(f'Downloading {nidmpack}') + print(f"Downloading {nidmpack}") urllib.request.urlretrieve(nidm_url, nidmpack) # Known issues with NIDM packs in collection 2210 to_replace = { - ' \\ntask': '\\\\n task', - ';\n nidm_coordinateVectorInVoxels: "null"^^xsd:string .': - '.'} + " \\ntask": "\\\\n task", + ';\n nidm_coordinateVectorInVoxels: "null"^^xsd:string .': ".", +} # Read the NIDM pack nres = nidm.load(nidmpack, to_replace=to_replace) diff --git a/nidmresults/__init__.py b/nidmresults/__init__.py index 1f69162..477c9ae 100644 --- a/nidmresults/__init__.py +++ b/nidmresults/__init__.py @@ -1,11 +1,13 @@ import os +from nidmresults._version import __version__ # noqa from nidmresults.load import load -from nidmresults._version import __version__ - latest_owlfile = os.path.join( - os.path.dirname(os.path.dirname(__file__)), 'nidmresults', 'owl', - "nidm-results_130.owl") + os.path.dirname(os.path.dirname(__file__)), + "nidmresults", + "owl", + "nidm-results_130.owl", +) -__all__ = ["load"] \ No newline at end of file +__all__ = ["load"] diff --git a/nidmresults/cli/nidm_mkda_convert.py b/nidmresults/cli/nidm_mkda_convert.py index 2e7d4e5..fe5b553 100644 --- a/nidmresults/cli/nidm_mkda_convert.py +++ b/nidmresults/cli/nidm_mkda_convert.py @@ -5,7 +5,6 @@ @copyright: University of Warwick 2013-2014 """ -from __future__ import absolute_import, division, print_function import argparse import os @@ -29,7 +28,7 @@ def main(argv=sys.argv): nargs="+", ) parser.add_argument( - "--version", action="version", version="{version}".format(version=__version__) + "--version", action="version", version=f"{__version__}" ) args = parser.parse_args(argv[1:]) @@ -56,7 +55,10 @@ def main(argv=sys.argv): nidmgraph = Graph(nidm_zip=nidmpack) con_ids = nidmgraph.serialize( - outfile, "mkda", overwrite=overwrite, last_used_con_id=max(con_ids.values()) + outfile, + "mkda", + overwrite=overwrite, + last_used_con_id=max(con_ids.values()), ) diff --git a/nidmresults/cli/nidmreader.py b/nidmresults/cli/nidmreader.py index ece974a..d2e9556 100644 --- a/nidmresults/cli/nidmreader.py +++ b/nidmresults/cli/nidmreader.py @@ -1,5 +1,6 @@ #!/usr/bin/python -"""Export neuroimaging results created with FSL feat following NIDM-Results specification. +"""Export neuroimaging results created with FSL feat \ + following NIDM-Results specification. The path to feat directory must be passed as first argument. @@ -7,7 +8,6 @@ @copyright: University of Warwick 2013-2014 """ -from __future__ import absolute_import, division, print_function import argparse import os @@ -21,7 +21,7 @@ def main(argv=sys.argv): parser = argparse.ArgumentParser(description="NIDM-Results reader.") parser.add_argument("nidm_pack", help="Path to NIDM-Results pack.") parser.add_argument( - "--version", action="version", version="{version}".format(version=__version__) + "--version", action="version", version=f"{__version__}" ) args = parser.parse_args(argv[1:]) diff --git a/nidmresults/cli/nidmresults.py b/nidmresults/cli/nidmresults.py index e703f6d..705310c 100644 --- a/nidmresults/cli/nidmresults.py +++ b/nidmresults/cli/nidmresults.py @@ -17,7 +17,7 @@ def main(argv=sys.argv): "-v", "--version", action="version", - version="{version}".format(version=nidmresults.__version__), + version=f"{nidmresults.__version__}", ) parser.parse_args(argv[1:]) diff --git a/nidmresults/exporter.py b/nidmresults/exporter.py index 14e36aa..59e183b 100644 --- a/nidmresults/exporter.py +++ b/nidmresults/exporter.py @@ -1,5 +1,4 @@ -""" -Export neuroimaging results created by neuroimaging software packages +"""Export neuroimaging results created by neuroimaging software packages \ (FSL, AFNI, ...) following NIDM-Results specification. Specification: http://nidm.nidash.org/specs/nidm-results.html @@ -8,31 +7,28 @@ @copyright: University of Warwick 2013-2014 """ -from prov.model import ProvBundle, ProvDocument -import os -import datetime -from nidmresults.objects.constants import * -from nidmresults.objects.modelfitting import * -from nidmresults.objects.contrast import * -from nidmresults.objects.inference import * -from io import open -import uuid import csv +import datetime +import json +import os +import sys import tempfile import zipfile -from builtins import input + # Needed for export using JSON-LD 1.1 import pyld as ld -import json -import sys +from prov.model import ProvBundle, ProvDocument + +from nidmresults.objects.constants import * +from nidmresults.objects.contrast import * +from nidmresults.objects.inference import * +from nidmresults.objects.modelfitting import * -class NIDMExporter(): - """ - Generic class to parse a result directory to extract the pieces of - information to be stored in NIDM-Results and to generate a NIDM-Results - export. - """ +class NIDMExporter: + """Generic class to parse a result directory \ + to extract the pieces of information to be stored in NIDM-Results \ + and to generate a NIDM-Results export.""" def __init__(self, version, out_dir, zipped=True): out_dirname = os.path.basename(out_dir) @@ -41,16 +37,16 @@ def __init__(self, version, out_dir, zipped=True): # Create output path from output name self.zipped = zipped if not self.zipped: - out_dirname = out_dirname+".nidm" + out_dirname = out_dirname + ".nidm" else: - out_dirname = out_dirname+".nidm.zip" + out_dirname = out_dirname + ".nidm.zip" out_dir = os.path.join(out_path, out_dirname) # Quit if output path already exists and user doesn't want to overwrite # it if os.path.exists(out_dir): - msg = out_dir+" already exists, overwrite?" - if not input("%s (y/N) " % msg).lower() == 'y': + msg = out_dir + " already exists, overwrite?" + if not input("%s (y/N) " % msg).lower() == "y": quit("Bye.") if os.path.isdir(out_dir): shutil.rmtree(out_dir) @@ -59,17 +55,25 @@ def __init__(self, version, out_dir, zipped=True): self.out_dir = out_dir if version == "dev": - self.version = {'major': 10000, 'minor': 0, 'revision': 0, - 'num': version} + self.version = { + "major": 10000, + "minor": 0, + "revision": 0, + "num": version, + } else: major, minor, revision = version.split(".") if "-rc" in revision: revision, rc = revision.split("-rc") else: rc = -1 - self.version = {'major': int(major), 'minor': int(minor), - 'revision': int(revision), 'rc': int(rc), - 'num': version} + self.version = { + "major": int(major), + "minor": int(minor), + "revision": int(revision), + "rc": int(rc), + "num": version, + } # Initialise prov document self.doc = ProvDocument() @@ -78,14 +82,11 @@ def __init__(self, version, out_dir, zipped=True): # A temp directory that will contain the exported data self.export_dir = tempfile.mkdtemp(prefix="nidm-", dir=out_path) - self.prepend_path = '' + self.prepend_path = "" def parse(self): - """ - Parse a result directory to extract the pieces information to be - stored in NIDM-Results. - """ - + """Parse a result directory to extract the pieces information \ + to be stored in NIDM-Results.""" try: # Methods: find_software, find_model_fitting, find_contrasts and # find_inferences should be defined in the children classes and @@ -123,9 +124,7 @@ def cleanup(self): shutil.rmtree(self.export_dir) def add_object(self, nidm_object, export_file=True): - """ - Add a NIDMObject to a NIDM-Results export. - """ + """Add a NIDMObject to a NIDM-Results export.""" if not export_file: export_dir = None else: @@ -136,21 +135,22 @@ def add_object(self, nidm_object, export_file=True): else: nidm_object.export(self.version, export_dir, self.prepend_path) # ProvDocument: add object to the bundle - if nidm_object.prov_type == PROV['Activity']: - self.bundle.activity(nidm_object.id, - other_attributes=nidm_object.attributes) - elif nidm_object.prov_type == PROV['Entity']: - self.bundle.entity(nidm_object.id, - other_attributes=nidm_object.attributes) - elif nidm_object.prov_type == PROV['Agent']: - self.bundle.agent(nidm_object.id, - other_attributes=nidm_object.attributes) + if nidm_object.prov_type == PROV["Activity"]: + self.bundle.activity( + nidm_object.id, other_attributes=nidm_object.attributes + ) + elif nidm_object.prov_type == PROV["Entity"]: + self.bundle.entity( + nidm_object.id, other_attributes=nidm_object.attributes + ) + elif nidm_object.prov_type == PROV["Agent"]: + self.bundle.agent( + nidm_object.id, other_attributes=nidm_object.attributes + ) # self.bundle.update(nidm_object.p) def export(self): - """ - Generate a NIDM-Results export. - """ + """Generate a NIDM-Results export.""" try: if not os.path.isdir(self.export_dir): os.mkdir(self.export_dir) @@ -167,8 +167,9 @@ def export(self): for model_fitting in self.model_fittings: # Design Matrix # model_fitting.activity.used(model_fitting.design_matrix) - self.bundle.used(model_fitting.activity.id, - model_fitting.design_matrix.id) + self.bundle.used( + model_fitting.activity.id, model_fitting.design_matrix.id + ) self.add_object(model_fitting.design_matrix) # *** Export visualisation of the design matrix self.add_object(model_fitting.design_matrix.image) @@ -180,95 +181,114 @@ def export(self): # drift model self.add_object(model_fitting.design_matrix.drift_model) - if self.version['major'] > 1 or \ - (self.version['major'] == 1 and - self.version['minor'] >= 3): + if self.version["major"] > 1 or ( + self.version["major"] == 1 and self.version["minor"] >= 3 + ): # Machine # model_fitting.data.wasAttributedTo(model_fitting.machine) - self.bundle.wasAttributedTo(model_fitting.data.id, - model_fitting.machine.id) + self.bundle.wasAttributedTo( + model_fitting.data.id, model_fitting.machine.id + ) self.add_object(model_fitting.machine) # Imaged subject or group(s) for sub in model_fitting.subjects: self.add_object(sub) # model_fitting.data.wasAttributedTo(sub) - self.bundle.wasAttributedTo(model_fitting.data.id, - sub.id) + self.bundle.wasAttributedTo( + model_fitting.data.id, sub.id + ) # Data # model_fitting.activity.used(model_fitting.data) - self.bundle.used(model_fitting.activity.id, - model_fitting.data.id) + self.bundle.used( + model_fitting.activity.id, model_fitting.data.id + ) self.add_object(model_fitting.data) # Error Model # model_fitting.activity.used(model_fitting.error_model) - self.bundle.used(model_fitting.activity.id, - model_fitting.error_model.id) + self.bundle.used( + model_fitting.activity.id, model_fitting.error_model.id + ) self.add_object(model_fitting.error_model) # Parameter Estimate Maps for param_estimate in model_fitting.param_estimates: # param_estimate.wasGeneratedBy(model_fitting.activity) - self.bundle.wasGeneratedBy(param_estimate.id, - model_fitting.activity.id) + self.bundle.wasGeneratedBy( + param_estimate.id, model_fitting.activity.id + ) self.add_object(param_estimate) self.add_object(param_estimate.coord_space) self.add_object(param_estimate.file) if param_estimate.derfrom is not None: - self.bundle.wasDerivedFrom(param_estimate.id, - param_estimate.derfrom.id) + self.bundle.wasDerivedFrom( + param_estimate.id, param_estimate.derfrom.id + ) self.add_object(param_estimate.derfrom) - self.add_object(param_estimate.derfrom.file, - export_file=False) + self.add_object( + param_estimate.derfrom.file, export_file=False + ) # Residual Mean Squares Map # model_fitting.rms_map.wasGeneratedBy(model_fitting.activity) self.add_object(model_fitting.rms_map) - self.bundle.wasGeneratedBy(model_fitting.rms_map.id, - model_fitting.activity.id) + self.bundle.wasGeneratedBy( + model_fitting.rms_map.id, model_fitting.activity.id + ) self.add_object(model_fitting.rms_map.coord_space) self.add_object(model_fitting.rms_map.file) if model_fitting.rms_map.derfrom is not None: self.bundle.wasDerivedFrom( model_fitting.rms_map.id, - model_fitting.rms_map.derfrom.id) + model_fitting.rms_map.derfrom.id, + ) self.add_object(model_fitting.rms_map.derfrom) - self.add_object(model_fitting.rms_map.derfrom.file, - export_file=False) + self.add_object( + model_fitting.rms_map.derfrom.file, export_file=False + ) # Resels per Voxel Map if model_fitting.rpv_map is not None: self.add_object(model_fitting.rpv_map) - self.bundle.wasGeneratedBy(model_fitting.rpv_map.id, - model_fitting.activity.id) + self.bundle.wasGeneratedBy( + model_fitting.rpv_map.id, model_fitting.activity.id + ) self.add_object(model_fitting.rpv_map.coord_space) self.add_object(model_fitting.rpv_map.file) if model_fitting.rpv_map.inf_id is not None: - self.bundle.used(model_fitting.rpv_map.inf_id, - model_fitting.rpv_map.id) + self.bundle.used( + model_fitting.rpv_map.inf_id, + model_fitting.rpv_map.id, + ) if model_fitting.rpv_map.derfrom is not None: self.bundle.wasDerivedFrom( model_fitting.rpv_map.id, - model_fitting.rpv_map.derfrom.id) + model_fitting.rpv_map.derfrom.id, + ) self.add_object(model_fitting.rpv_map.derfrom) - self.add_object(model_fitting.rpv_map.derfrom.file, - export_file=False) + self.add_object( + model_fitting.rpv_map.derfrom.file, + export_file=False, + ) # Mask # model_fitting.mask_map.wasGeneratedBy(model_fitting.activity) - self.bundle.wasGeneratedBy(model_fitting.mask_map.id, - model_fitting.activity.id) + self.bundle.wasGeneratedBy( + model_fitting.mask_map.id, model_fitting.activity.id + ) self.add_object(model_fitting.mask_map) if model_fitting.mask_map.derfrom is not None: self.bundle.wasDerivedFrom( model_fitting.mask_map.id, - model_fitting.mask_map.derfrom.id) + model_fitting.mask_map.derfrom.id, + ) self.add_object(model_fitting.mask_map.derfrom) - self.add_object(model_fitting.mask_map.derfrom.file, - export_file=False) + self.add_object( + model_fitting.mask_map.derfrom.file, export_file=False + ) # Create coordinate space export self.add_object(model_fitting.mask_map.coord_space) @@ -277,8 +297,9 @@ def export(self): # Grand Mean map # model_fitting.grand_mean_map.wasGeneratedBy(model_fitting.activity) - self.bundle.wasGeneratedBy(model_fitting.grand_mean_map.id, - model_fitting.activity.id) + self.bundle.wasGeneratedBy( + model_fitting.grand_mean_map.id, model_fitting.activity.id + ) self.add_object(model_fitting.grand_mean_map) # Coordinate space entity self.add_object(model_fitting.grand_mean_map.coord_space) @@ -287,33 +308,41 @@ def export(self): # Model Parameters Estimation activity self.add_object(model_fitting.activity) - self.bundle.wasAssociatedWith(model_fitting.activity.id, - self.software.id) + self.bundle.wasAssociatedWith( + model_fitting.activity.id, self.software.id + ) # model_fitting.activity.wasAssociatedWith(self.software) # self.add_object(model_fitting) # Add contrast estimation steps analysis_masks = dict() for (model_fitting_id, pe_ids), contrasts in list( - self.contrasts.items()): + self.contrasts.items() + ): for contrast in contrasts: model_fitting = self._get_model_fitting(model_fitting_id) # for contrast in contrasts: # contrast.estimation.used(model_fitting.rms_map) - self.bundle.used(contrast.estimation.id, - model_fitting.rms_map.id) + self.bundle.used( + contrast.estimation.id, model_fitting.rms_map.id + ) # contrast.estimation.used(model_fitting.mask_map) - self.bundle.used(contrast.estimation.id, - model_fitting.mask_map.id) - analysis_masks[contrast.estimation.id] = \ + self.bundle.used( + contrast.estimation.id, model_fitting.mask_map.id + ) + analysis_masks[contrast.estimation.id] = ( model_fitting.mask_map.id - self.bundle.used(contrast.estimation.id, - contrast.weights.id) - self.bundle.used(contrast.estimation.id, - model_fitting.design_matrix.id) + ) + self.bundle.used( + contrast.estimation.id, contrast.weights.id + ) + self.bundle.used( + contrast.estimation.id, model_fitting.design_matrix.id + ) # contrast.estimation.wasAssociatedWith(self.software) - self.bundle.wasAssociatedWith(contrast.estimation.id, - self.software.id) + self.bundle.wasAssociatedWith( + contrast.estimation.id, self.software.id + ) for pe_id in pe_ids: # contrast.estimation.used(pe_id) @@ -328,8 +357,9 @@ def export(self): if contrast.contrast_map is not None: # Create contrast Map # contrast.contrast_map.wasGeneratedBy(contrast.estimation) - self.bundle.wasGeneratedBy(contrast.contrast_map.id, - contrast.estimation.id) + self.bundle.wasGeneratedBy( + contrast.contrast_map.id, contrast.estimation.id + ) self.add_object(contrast.contrast_map) self.add_object(contrast.contrast_map.coord_space) # Copy contrast map in export directory @@ -338,46 +368,52 @@ def export(self): if contrast.contrast_map.derfrom is not None: self.bundle.wasDerivedFrom( contrast.contrast_map.id, - contrast.contrast_map.derfrom.id) + contrast.contrast_map.derfrom.id, + ) self.add_object(contrast.contrast_map.derfrom) - self.add_object(contrast.contrast_map.derfrom.file, - export_file=False) + self.add_object( + contrast.contrast_map.derfrom.file, + export_file=False, + ) # Create Std Err. Map (T-tests) or Explained Mean Sq. Map # (F-tests) # contrast.stderr_or_expl_mean_sq_map.wasGeneratedBy # (contrast.estimation) - stderr_explmeansq_map = ( - contrast.stderr_or_expl_mean_sq_map) + stderr_explmeansq_map = contrast.stderr_or_expl_mean_sq_map self.bundle.wasGeneratedBy( - stderr_explmeansq_map.id, - contrast.estimation.id) + stderr_explmeansq_map.id, contrast.estimation.id + ) self.add_object(stderr_explmeansq_map) - self.add_object( - stderr_explmeansq_map.coord_space) - if isinstance(stderr_explmeansq_map, - ContrastStdErrMap) and \ - stderr_explmeansq_map.contrast_var: - self.add_object( - stderr_explmeansq_map.contrast_var) + self.add_object(stderr_explmeansq_map.coord_space) + if ( + isinstance(stderr_explmeansq_map, ContrastStdErrMap) + and stderr_explmeansq_map.contrast_var + ): + self.add_object(stderr_explmeansq_map.contrast_var) if stderr_explmeansq_map.var_coord_space: self.add_object( - stderr_explmeansq_map.var_coord_space) + stderr_explmeansq_map.var_coord_space + ) if stderr_explmeansq_map.contrast_var.coord_space: self.add_object( - stderr_explmeansq_map.contrast_var.coord_space) + stderr_explmeansq_map.contrast_var.coord_space + ) self.add_object( stderr_explmeansq_map.contrast_var.file, - export_file=False) + export_file=False, + ) self.bundle.wasDerivedFrom( stderr_explmeansq_map.id, - stderr_explmeansq_map.contrast_var.id) + stderr_explmeansq_map.contrast_var.id, + ) self.add_object(stderr_explmeansq_map.file) # Create Statistic Map # contrast.stat_map.wasGeneratedBy(contrast.estimation) - self.bundle.wasGeneratedBy(contrast.stat_map.id, - contrast.estimation.id) + self.bundle.wasGeneratedBy( + contrast.stat_map.id, contrast.estimation.id + ) self.add_object(contrast.stat_map) self.add_object(contrast.stat_map.coord_space) # Copy Statistical map in export directory @@ -385,17 +421,19 @@ def export(self): if contrast.stat_map.derfrom is not None: self.bundle.wasDerivedFrom( - contrast.stat_map.id, - contrast.stat_map.derfrom.id) + contrast.stat_map.id, contrast.stat_map.derfrom.id + ) self.add_object(contrast.stat_map.derfrom) - self.add_object(contrast.stat_map.derfrom.file, - export_file=False) + self.add_object( + contrast.stat_map.derfrom.file, export_file=False + ) # Create Z Statistic Map if contrast.z_stat_map: # contrast.z_stat_map.wasGeneratedBy(contrast.estimation) - self.bundle.wasGeneratedBy(contrast.z_stat_map.id, - contrast.estimation.id) + self.bundle.wasGeneratedBy( + contrast.z_stat_map.id, contrast.estimation.id + ) self.add_object(contrast.z_stat_map) self.add_object(contrast.z_stat_map.coord_space) # Copy Statistical map in export directory @@ -415,14 +453,16 @@ def export(self): # inference.inference_act.used(used_id) self.bundle.used(inference.inference_act.id, used_id) # inference.inference_act.wasAssociatedWith(self.software) - self.bundle.wasAssociatedWith(inference.inference_act.id, - self.software.id) + self.bundle.wasAssociatedWith( + inference.inference_act.id, self.software.id + ) # self.add_object(inference) # Excursion set # inference.excursion_set.wasGeneratedBy(inference.inference_act) - self.bundle.wasGeneratedBy(inference.excursion_set.id, - inference.inference_act.id) + self.bundle.wasGeneratedBy( + inference.excursion_set.id, inference.inference_act.id + ) self.add_object(inference.excursion_set) self.add_object(inference.excursion_set.coord_space) if inference.excursion_set.visu is not None: @@ -435,7 +475,8 @@ def export(self): self.add_object(inference.excursion_set.clust_map) self.add_object(inference.excursion_set.clust_map.file) self.add_object( - inference.excursion_set.clust_map.coord_space) + inference.excursion_set.clust_map.coord_space + ) if inference.excursion_set.mip is not None: self.add_object(inference.excursion_set.mip) @@ -457,8 +498,9 @@ def export(self): if inference.disp_mask: for mask in inference.disp_mask: # inference.inference_act.used(mask) - self.bundle.used(inference.inference_act.id, - mask.id) + self.bundle.used( + inference.inference_act.id, mask.id + ) self.add_object(mask) # Create coordinate space entity self.add_object(mask.coord_space) @@ -466,15 +508,18 @@ def export(self): self.add_object(mask.file) if mask.derfrom is not None: - self.bundle.wasDerivedFrom(mask.id, - mask.derfrom.id) + self.bundle.wasDerivedFrom( + mask.id, mask.derfrom.id + ) self.add_object(mask.derfrom) - self.add_object(mask.derfrom.file, - export_file=False) + self.add_object( + mask.derfrom.file, export_file=False + ) # Search Space - self.bundle.wasGeneratedBy(inference.search_space.id, - inference.inference_act.id) + self.bundle.wasGeneratedBy( + inference.search_space.id, inference.inference_act.id + ) # inference.search_space.wasGeneratedBy(inference.inference_act) self.add_object(inference.search_space) self.add_object(inference.search_space.coord_space) @@ -484,15 +529,19 @@ def export(self): # Peak Definition if inference.peak_criteria: # inference.inference_act.used(inference.peak_criteria) - self.bundle.used(inference.inference_act.id, - inference.peak_criteria.id) + self.bundle.used( + inference.inference_act.id, + inference.peak_criteria.id, + ) self.add_object(inference.peak_criteria) # Cluster Definition if inference.cluster_criteria: # inference.inference_act.used(inference.cluster_criteria) - self.bundle.used(inference.inference_act.id, - inference.cluster_criteria.id) + self.bundle.used( + inference.inference_act.id, + inference.cluster_criteria.id, + ) self.add_object(inference.cluster_criteria) if inference.clusters: @@ -500,7 +549,8 @@ def export(self): for cluster in inference.clusters: # cluster.wasDerivedFrom(inference.excursion_set) self.bundle.wasDerivedFrom( - cluster.id, inference.excursion_set.id) + cluster.id, inference.excursion_set.id + ) self.add_object(cluster) for peak in cluster.peaks: self.bundle.wasDerivedFrom(peak.id, cluster.id) @@ -508,21 +558,26 @@ def export(self): self.add_object(peak.coordinate) if cluster.cog is not None: - self.bundle.wasDerivedFrom(cluster.cog.id, - cluster.id) + self.bundle.wasDerivedFrom( + cluster.cog.id, cluster.id + ) self.add_object(cluster.cog) self.add_object(cluster.cog.coordinate) # Inference activity # inference.inference_act.wasAssociatedWith(inference.software_id) # inference.inference_act.used(inference.height_thresh) - self.bundle.used(inference.inference_act.id, - inference.height_thresh.id) + self.bundle.used( + inference.inference_act.id, inference.height_thresh.id + ) # inference.inference_act.used(inference.extent_thresh) - self.bundle.used(inference.inference_act.id, - inference.extent_thresh.id) - self.bundle.used(inference.inference_act.id, - analysis_masks[contrast.estimation.id]) + self.bundle.used( + inference.inference_act.id, inference.extent_thresh.id + ) + self.bundle.used( + inference.inference_act.id, + analysis_masks[contrast.estimation.id], + ) self.add_object(inference.inference_act) # Write-out prov file @@ -534,33 +589,31 @@ def export(self): raise def _get_model_fitting(self, mf_id): - """ - Retrieve model fitting with identifier 'mf_id' from the list of model - fitting objects stored in self.model_fitting - """ + """Retrieve model fitting with identifier 'mf_id' \ + from the list of model fitting objects stored \ + in self.model_fitting.""" for model_fitting in self.model_fittings: if model_fitting.activity.id == mf_id: return model_fitting - raise Exception("Model fitting activity with id: " + str(mf_id) + - " not found.") + raise Exception( + "Model fitting activity with id: " + str(mf_id) + " not found." + ) def _get_contrast(self, con_id): - """ - Retrieve contrast with identifier 'con_id' from the list of contrast - objects stored in self.contrasts - """ + """Retrieve contrast with identifier 'con_id' \ + from the list of contrast objects stored \ + in self.contrasts.""" for contrasts in list(self.contrasts.values()): for contrast in contrasts: if contrast.estimation.id == con_id: return contrast - raise Exception("Contrast activity with id: " + str(con_id) + - " not found.") + raise Exception( + "Contrast activity with id: " + str(con_id) + " not found." + ) def _add_namespaces(self): - """ - Add namespaces to NIDM document. - """ + """Add namespaces to NIDM document.""" self.doc.add_namespace(NIDM) self.doc.add_namespace(NIIRI) self.doc.add_namespace(CRYPTO) @@ -572,12 +625,10 @@ def _add_namespaces(self): self.doc.add_namespace(NIF) def _create_bundle(self, version): - """ - Initialise NIDM-Results bundle. - """ + """Initialise NIDM-Results bundle.""" # *** Bundle entity - if not hasattr(self, 'bundle_ent'): - self.bundle_ent = NIDMResultsBundle(nidm_version=version['num']) + if not hasattr(self, "bundle_ent"): + self.bundle_ent = NIDMResultsBundle(nidm_version=version["num"]) self.bundle = ProvBundle(identifier=self.bundle_ent.id) @@ -586,46 +637,52 @@ def _create_bundle(self, version): # # provn export # self.bundle = ProvBundle(identifier=bundle_id) - self.doc.entity(self.bundle_ent.id, - other_attributes=self.bundle_ent.attributes) + self.doc.entity( + self.bundle_ent.id, other_attributes=self.bundle_ent.attributes + ) # *** NIDM-Results Export Activity - if version['num'] not in ["1.0.0", "1.1.0"]: - if not hasattr(self, 'export_act'): + if version["num"] not in ["1.0.0", "1.1.0"]: + if not hasattr(self, "export_act"): self.export_act = NIDMResultsExport() self.export_act.export(self.version, self.export_dir) # self.doc.update(self.export_act.p) - self.doc.activity(self.export_act.id, - other_attributes=self.export_act.attributes) + self.doc.activity( + self.export_act.id, other_attributes=self.export_act.attributes + ) # *** bundle was Generated by NIDM-Results Export Activity - if not hasattr(self, 'export_time'): + if not hasattr(self, "export_time"): self.export_time = str(datetime.datetime.now().time()) - if version['num'] in ["1.0.0", "1.1.0"]: - self.doc.wasGeneratedBy(entity=self.bundle_ent.id, - time=self.export_time) + if version["num"] in ["1.0.0", "1.1.0"]: + self.doc.wasGeneratedBy( + entity=self.bundle_ent.id, time=self.export_time + ) else: # provn self.doc.wasGeneratedBy( - entity=self.bundle_ent.id, activity=self.export_act.id, - time=self.export_time) + entity=self.bundle_ent.id, + activity=self.export_act.id, + time=self.export_time, + ) # *** NIDM-Results Exporter (Software Agent) - if version['num'] not in ["1.0.0", "1.1.0"]: - if not hasattr(self, 'exporter'): + if version["num"] not in ["1.0.0", "1.1.0"]: + if not hasattr(self, "exporter"): self.exporter = self._get_exporter() self.exporter.export(self.version, self.export_dir) # self.doc.update(self.exporter.p) - self.doc.agent(self.exporter.id, - other_attributes=self.exporter.attributes) + self.doc.agent( + self.exporter.id, other_attributes=self.exporter.attributes + ) self.doc.wasAssociatedWith(self.export_act.id, self.exporter.id) def _get_model_parameters_estimations(self, error_model): - """ - Infer model estimation method from the 'error_model'. Return an object - of type ModelParametersEstimation. + """Infer model estimation method from the 'error_model'. + + Return an object of type ModelParametersEstimation. """ if error_model.dependence == NIDM_INDEPEDENT_ERROR: if error_model.variance_homo: @@ -640,7 +697,7 @@ def _get_model_parameters_estimations(self, error_model): return mpe def use_prefixes(self, ttl): - prefix_file = os.path.join(os.path.dirname(__file__), 'prefixes.csv') + prefix_file = os.path.join(os.path.dirname(__file__), "prefixes.csv") context = dict() with open(prefix_file, encoding="ascii") as csvfile: reader = csv.reader(csvfile) @@ -659,9 +716,7 @@ def use_prefixes(self, ttl): return (ttl, context) def save_prov_to_files(self, showattributes=False): - """ - Write-out provn serialisation to nidm.provn. - """ + """Write-out provn serialisation to nidm.provn.""" self.doc.add_bundle(self.bundle) # provn_file = os.path.join(self.export_dir, 'nidm.provn') # provn_fid = open(provn_file, 'w') @@ -669,41 +724,46 @@ def save_prov_to_files(self, showattributes=False): # # provn_fid.write(self.doc.get_provn(4).replace("None", "-")) # provn_fid.close() - ttl_file = os.path.join(self.export_dir, 'nidm.ttl') - ttl_txt = self.doc.serialize(format='rdf', rdf_format='turtle') + ttl_file = os.path.join(self.export_dir, "nidm.ttl") + ttl_txt = self.doc.serialize(format="rdf", rdf_format="turtle") ttl_txt, json_context = self.use_prefixes(ttl_txt) # Add namespaces to json-ld context for namespace in self.doc._namespaces.get_registered_namespaces(): json_context[namespace._prefix] = namespace._uri - for namespace in \ - list(self.doc._namespaces._default_namespaces.values()): + for namespace in list( + self.doc._namespaces._default_namespaces.values() + ): json_context[namespace._prefix] = namespace._uri json_context["xsd"] = "http://www.w3.org/2000/01/rdf-schema#" # Work-around to issue with INF value in rdflib (reported in # https://github.com/RDFLib/rdflib/pull/655) - ttl_txt = ttl_txt.replace(' inf ', ' "INF"^^xsd:float ') - with open(ttl_file, 'w') as ttl_fid: + ttl_txt = ttl_txt.replace(" inf ", ' "INF"^^xsd:float ') + with open(ttl_file, "w") as ttl_fid: ttl_fid.write(ttl_txt) # JSON-LD (deprecated kept for background compatibility w/ viewers) - jsonld_file = os.path.join(self.export_dir, 'nidm_deprecated.json') - jsonld_txt = self.doc.serialize(format='rdf', rdf_format='json-ld', - context=json_context) - with open(jsonld_file, 'w') as jsonld_fid: + jsonld_file = os.path.join(self.export_dir, "nidm_deprecated.json") + jsonld_txt = self.doc.serialize( + format="rdf", rdf_format="json-ld", context=json_context + ) + with open(jsonld_file, "w") as jsonld_fid: jsonld_fid.write(jsonld_txt) # JSON-LD using specification 1.1 (a.k.a "nice" JSON-LD) - jsonld_11 = json.dumps(ld.jsonld.compact( - json.loads(jsonld_txt), "http://purl.org/nidash/context")) + jsonld_11 = json.dumps( + ld.jsonld.compact( + json.loads(jsonld_txt), "http://purl.org/nidash/context" + ) + ) # If python 2 convert string to unicode to avoid # 'must be unicode not str' error - if (sys.version_info < (3, 0)): + if sys.version_info < (3, 0): jsonld_11 = unicode(jsonld_11) - jsonld_11_file = os.path.join(self.export_dir, 'nidm.json') + jsonld_11_file = os.path.join(self.export_dir, "nidm.json") with open(jsonld_11_file, "w") as fid: fid.write(jsonld_11) @@ -725,7 +785,7 @@ def save_prov_to_files(self, showattributes=False): else: # Create a zip file that contains the content of the temp directory os.chdir(self.export_dir) - zf = zipfile.ZipFile(os.path.join("..", self.out_dir), mode='w') + zf = zipfile.ZipFile(os.path.join("..", self.out_dir), mode="w") try: for root, dirnames, filenames in os.walk("."): for filename in filenames: @@ -742,7 +802,7 @@ def save_prov_to_files(self, showattributes=False): # graph.parse(data=self.doc.serialize(format='rdf'), format="xml") # ttl_fid.write(graph.serialize(format="turtle")) # ttl_fid.write(self.doc.serialize(format='rdf'). - # replace("inf", '"INF"')) + # replace("inf", '"INF"')) # ttl_fid.close() # print("provconvert -infile " + provn_file + " -outfile " + ttl_file) # check_call("provconvert -infile " + provn_file + diff --git a/nidmresults/graph.py b/nidmresults/graph.py index 23327b8..cb8f4a9 100644 --- a/nidmresults/graph.py +++ b/nidmresults/graph.py @@ -1,5 +1,4 @@ -""" -Export neuroimaging results created by neuroimaging software packages +"""Export neuroimaging results created by neuroimaging software packages \ (FSL, AFNI, ...) following NIDM-Results specification. Specification: http://nidm.nidash.org/specs/nidm-results.html @@ -7,34 +6,36 @@ @author: Camille Maumet @copyright: University of Warwick 2013-2014 """ + +import collections +import csv +import warnings +import zipfile + +import rdflib +from rdflib.plugins.parsers.notation3 import BadSyntax + +from nidmresults.exporter import NIDMExporter from nidmresults.objects.constants_rdflib import * -from nidmresults.objects.modelfitting import * from nidmresults.objects.contrast import * from nidmresults.objects.inference import * -from nidmresults.exporter import NIDMExporter -import collections -# from rdflib.term import Literal +from nidmresults.objects.modelfitting import * -from rdflib.plugins.parsers.notation3 import BadSyntax -import rdflib -import zipfile -import csv -import warnings +# from rdflib.term import Literal -class NIDMResults(): - """ - NIDM-result object containing all metadata and link to image files. - """ +class NIDMResults: + """NIDM-result object containing all metadata and link to image files.""" - def __init__(self, nidm_zip=None, rdf_file=None, workaround=False, - to_replace=dict()): + def __init__( + self, nidm_zip=None, rdf_file=None, workaround=False, to_replace=dict() + ): self.study_name = os.path.basename(nidm_zip).replace(".nidm.zip", "") self.zip_path = nidm_zip # Load the turtle file - with zipfile.ZipFile(self.zip_path, 'r') as z: - rdf_data = z.read('nidm.ttl') + with zipfile.ZipFile(self.zip_path, "r") as z: + rdf_data = z.read("nidm.ttl") rdf_data = rdf_data.decode() # Exporter-version-specific fixes in the RDF @@ -48,18 +49,19 @@ def __init__(self, nidm_zip=None, rdf_file=None, workaround=False, # Query the RDF document and create the objects self.software = self.load_software() - (self.bundle, self.exporter, self.export_act, self.export_time) = \ + (self.bundle, self.exporter, self.export_act, self.export_time) = ( self.load_bundle_export() + ) self.model_fittings = self.load_modelfitting() self.contrasts = self.load_contrasts(workaround=workaround) self.inferences = self.load_inferences() def fix_for_specific_versions(self, rdf_data, to_replace): - """ - Fixes of the RDF before loading the graph. All of these are workaround + """Fix of the RDF before loading the graph. + + All of these are workaround to circumvent known issues of the SPM and FSL exporters. """ - # Load the graph as is so that we can query g = self.parse(rdf_data) @@ -85,29 +87,44 @@ def fix_for_specific_versions(self, rdf_data, to_replace): if sd: for row in sd: argums = row.asdict() - if (argums['type'] == NIDM_SPM_RESULTS_NIDM and - (argums['version'].eq('12.6903') or - argums['version'].eq('12.575ac2c'))): - warnings.warn('Applying fixes for SPM exporter ' + - str(argums['version'])) + if argums["type"] == NIDM_SPM_RESULTS_NIDM and ( + argums["version"].eq("12.6903") + or argums["version"].eq("12.575ac2c") + ): + warnings.warn( + "Applying fixes for SPM exporter " + + str(argums["version"]) + ) # crypto namespace inconsistent with NIDM-Results spec - to_replace[('http://id.loc.gov/vocabulary/preservation/' + - 'cryptographicHashFunctions/')] = ( - 'http://id.loc.gov/vocabulary/preservation/' + - 'cryptographicHashFunctions#') + to_replace[ + ( + "http://id.loc.gov/vocabulary/preservation/" + + "cryptographicHashFunctions/" + ) + ] = ( + "http://id.loc.gov/vocabulary/preservation/" + + "cryptographicHashFunctions#" + ) # Missing 'activity' attribute in qualified Generation - to_replace['a prov:Generation .'] = ( - 'a prov:Generation ; prov:activity <' + - str(argums['exp_act']) + '> .') + to_replace["a prov:Generation ."] = ( + "a prov:Generation ; prov:activity <" + + str(argums["exp_act"]) + + "> ." + ) # Avoid confusion between attribute and # class uncorrected p-value # cf. https://github.com/incf-nidash/nidm/issues/421 - to_replace[('@prefix nidm_PValueUncorrected: ' + - '')] = ( - '@prefix nidm_UncorrectedPValue: ' + - '') - to_replace['nidm_PValueUncorrected'] = 'nidm_UncorrectedPValue' + to_replace[ + ( + "@prefix nidm_PValueUncorrected: " + + "" + ) + ] = ( + "@prefix nidm_UncorrectedPValue: " + + "" + ) + to_replace["nidm_PValueUncorrected"] = "nidm_UncorrectedPValue" if to_replace is not None: for to_rep, replacement in to_replace.items(): @@ -117,8 +134,9 @@ def fix_for_specific_versions(self, rdf_data, to_replace): @classmethod def load_from_pack(klass, nidm_zip, workaround=False, to_replace=dict()): - nidmr = NIDMResults(nidm_zip=nidm_zip, workaround=workaround, - to_replace=to_replace) + nidmr = NIDMResults( + nidm_zip=nidm_zip, workaround=workaround, to_replace=to_replace + ) return nidmr def get_info(self): @@ -129,220 +147,286 @@ def get_info(self): # nidm-results pack, this should # be stated explicitly in the spec? if len(self.model_fittings) > 1: - raise Exception("Can't handle NIDM-Results packs with \ - multiple model parameter estimation activities") + raise Exception( + "Can't handle NIDM-Results packs with \ + multiple model parameter estimation activities" + ) - self.info['NeuroimagingAnalysisSoftware_type'] = self.software.name - self.info['NeuroimagingAnalysisSoftware_softwareVersion'] = \ + self.info["NeuroimagingAnalysisSoftware_type"] = self.software.name + self.info["NeuroimagingAnalysisSoftware_softwareVersion"] = ( self.software.version - self.info['Data_grandMeanScaling'] = \ - self.model_fittings[0].data.grand_mean_sc - self.info['Data_targetIntensity'] = \ - self.model_fittings[0].data.target_intensity - self.info['DesignMatrix_atLocation'] = \ - self.model_fittings[0].design_matrix.csv_file - self.info['DesignMatrix_regressorNames'] = \ - self.model_fittings[0].design_matrix.regressors - self.info['ErrorModel_hasErrorDistribution'] = \ - str(self.model_fittings[0].error_model.error_distribution) - self.info['ErrorModel_errorVarianceHomogeneous'] = \ + ) + self.info["Data_grandMeanScaling"] = self.model_fittings[ + 0 + ].data.grand_mean_sc + self.info["Data_targetIntensity"] = self.model_fittings[ + 0 + ].data.target_intensity + self.info["DesignMatrix_atLocation"] = self.model_fittings[ + 0 + ].design_matrix.csv_file + self.info["DesignMatrix_regressorNames"] = self.model_fittings[ + 0 + ].design_matrix.regressors + self.info["ErrorModel_hasErrorDistribution"] = str( + self.model_fittings[0].error_model.error_distribution + ) + self.info["ErrorModel_errorVarianceHomogeneous"] = ( self.model_fittings[0].error_model.variance_homo + ) # TODO: replace IRIs by preferred prefixes for readability - self.info['ErrorModel_varianceMapWiseDependence'] = \ - str(self.model_fittings[0].error_model.variance_spatial) - self.info['ErrorModel_hasErrorDependence'] = \ - str(self.model_fittings[0].error_model.dependence) - self.info['ErrorModel_dependenceMapWiseDependence'] = \ - str(self.model_fittings[0].error_model.dependance_spatial) - self.info['ModelParameterEstimation_withEstimationMethod'] = \ - str(self.model_fittings[0].activity.estimation_method) - self.info['ResidualMeanSquaresMap_atLocation'] = \ + self.info["ErrorModel_varianceMapWiseDependence"] = str( + self.model_fittings[0].error_model.variance_spatial + ) + self.info["ErrorModel_hasErrorDependence"] = str( + self.model_fittings[0].error_model.dependence + ) + self.info["ErrorModel_dependenceMapWiseDependence"] = str( + self.model_fittings[0].error_model.dependance_spatial + ) + self.info["ModelParameterEstimation_withEstimationMethod"] = str( + self.model_fittings[0].activity.estimation_method + ) + self.info["ResidualMeanSquaresMap_atLocation"] = ( self.model_fittings[0].rms_map.file.filename - self.info['ResidualMeanSquaresMap_inWorldCoordinateSystem'] = str( - self.model_fittings[0].rms_map.coord_space.coordinate_system) + ) + self.info["ResidualMeanSquaresMap_inWorldCoordinateSystem"] = str( + self.model_fittings[0].rms_map.coord_space.coordinate_system + ) gm_map = self.model_fittings[0].grand_mean_map - self.info['GrandMeanMap_atLocation'] = \ - gm_map.file.filename - self.info['GrandMeanMap_inWorldCoordinateSystem'] = \ - str(gm_map.coord_space.coordinate_system) - self.info['MaskMap_atLocation'] = \ - self.model_fittings[0].mask_map.file.filename - self.info['MaskMap_inWorldCoordinateSystem'] = str( - self.model_fittings[0].mask_map.coord_space.coordinate_system) - - self.info['ParameterEstimateMaps'] = list() + self.info["GrandMeanMap_atLocation"] = gm_map.file.filename + self.info["GrandMeanMap_inWorldCoordinateSystem"] = str( + gm_map.coord_space.coordinate_system + ) + self.info["MaskMap_atLocation"] = self.model_fittings[ + 0 + ].mask_map.file.filename + self.info["MaskMap_inWorldCoordinateSystem"] = str( + self.model_fittings[0].mask_map.coord_space.coordinate_system + ) + + self.info["ParameterEstimateMaps"] = list() # TODO the order of the pe maps matters!! for pe in self.model_fittings[0].param_estimates: - self.info['ParameterEstimateMaps'].append(pe.file.filename) + self.info["ParameterEstimateMaps"].append(pe.file.filename) - self.info['Contrasts'] = list() + self.info["Contrasts"] = list() for contrasts in self.contrasts.values(): for contrast in contrasts: - self.info['Contrasts'].append(collections.OrderedDict()) - self.info['Contrasts'][-1]['StatisticMap_contrastName'] = \ - contrast.stat_map.contrast_name - self.info['Contrasts'][-1]['ContrastWeightMatrix_value'] =\ - contrast.weights.contrast_weights - self.info['Contrasts'][-1]['StatisticMap_statisticType'] =\ - str(contrast.stat_map.stat_type) - dof = 'StatisticMap_errorDegreesOfFreedom' - self.info['Contrasts'][-1][dof] = contrast.stat_map.dof + self.info["Contrasts"].append(collections.OrderedDict()) + self.info["Contrasts"][-1][ + "StatisticMap_contrastName" + ] = contrast.stat_map.contrast_name + self.info["Contrasts"][-1][ + "ContrastWeightMatrix_value" + ] = contrast.weights.contrast_weights + self.info["Contrasts"][-1][ + "StatisticMap_statisticType" + ] = str(contrast.stat_map.stat_type) + dof = "StatisticMap_errorDegreesOfFreedom" + self.info["Contrasts"][-1][dof] = contrast.stat_map.dof if contrast.stat_map.effdof: - edof = 'StatisticMap_effectDegreesOfFreedom' - self.info['Contrasts'][-1][edof] = ( - contrast.stat_map.effdof) - self.info['Contrasts'][-1]['StatisticMap_atLocation'] \ - = contrast.stat_map.file.filename - st_world = 'StatisticMap_inWorldCoordinateSystem' - self.info['Contrasts'][-1][st_world] = str( - contrast.stat_map.coord_space.coordinate_system) + edof = "StatisticMap_effectDegreesOfFreedom" + self.info["Contrasts"][-1][ + edof + ] = contrast.stat_map.effdof + self.info["Contrasts"][-1][ + "StatisticMap_atLocation" + ] = contrast.stat_map.file.filename + st_world = "StatisticMap_inWorldCoordinateSystem" + self.info["Contrasts"][-1][st_world] = str( + contrast.stat_map.coord_space.coordinate_system + ) if contrast.z_stat_map is not None: - self.info['Contrasts'][-1]['ZStatisticMap_atLocation']\ - = contrast.z_stat_map.file.filename - zst_world = 'ZStatisticMap_inWorldCoordinateSystem' - self.info['Contrasts'][-1][zst_world] = str( - contrast.z_stat_map.coord_space.coordinate_system) + self.info["Contrasts"][-1][ + "ZStatisticMap_atLocation" + ] = contrast.z_stat_map.file.filename + zst_world = "ZStatisticMap_inWorldCoordinateSystem" + self.info["Contrasts"][-1][zst_world] = str( + contrast.z_stat_map.coord_space.coordinate_system + ) if contrast.contrast_map: - self.info['Contrasts'][-1]['ContrastMap_atLocation'] =\ - contrast.contrast_map.file.filename - c_world = 'ContrastMap_inWorldCoordinateSystem' - self.info['Contrasts'][-1][c_world] = str( - contrast.contrast_map.coord_space.coordinate_system) + self.info["Contrasts"][-1][ + "ContrastMap_atLocation" + ] = contrast.contrast_map.file.filename + c_world = "ContrastMap_inWorldCoordinateSystem" + self.info["Contrasts"][-1][c_world] = str( + contrast.contrast_map.coord_space.coordinate_system + ) # TODO: deal when this is not created yet... - stderr_loc = 'ContrastStandardErrorMap_atLocation' + stderr_loc = "ContrastStandardErrorMap_atLocation" stderr_sys = ( - 'ContrastStandardErrorMap_inWorldCoordinateSystem') + "ContrastStandardErrorMap_inWorldCoordinateSystem" + ) sderr_explmeansq_map = ( - contrast.stderr_or_expl_mean_sq_map) - self.info['Contrasts'][-1][stderr_loc] = ( - sderr_explmeansq_map.file.filename) - self.info['Contrasts'][-1][stderr_sys] = str( - sderr_explmeansq_map.coord_space.coordinate_system) - - self.info['Inferences'] = list() + contrast.stderr_or_expl_mean_sq_map + ) + self.info["Contrasts"][-1][ + stderr_loc + ] = sderr_explmeansq_map.file.filename + self.info["Contrasts"][-1][stderr_sys] = str( + sderr_explmeansq_map.coord_space.coordinate_system + ) + + self.info["Inferences"] = list() for con_est_id, inferences in self.inferences.items(): for inference in inferences: clustdef = ( - 'ClusterDefinitionCriteria_hasConnectivityCriterion') + "ClusterDefinitionCriteria_hasConnectivityCriterion" + ) peakdef_mindist = ( - 'PeakDefinitionCriteria_minDistanceBetweenPeaks') - peakdef_maxpeak = \ - 'PeakDefinitionCriteria_maxNumberOfPeaksPerCluster' + "PeakDefinitionCriteria_minDistanceBetweenPeaks" + ) + peakdef_maxpeak = ( + "PeakDefinitionCriteria_maxNumberOfPeaksPerCluster" + ) if clustdef not in self.info: # Assume that all inference have the same cluster def # and peak def > should be stated explicitly in JSON # spec and tested - self.info[clustdef] = ( - str(inference.cluster_criteria.connectivity)) + self.info[clustdef] = str( + inference.cluster_criteria.connectivity + ) self.info[peakdef_mindist] = ( - inference.peak_criteria.peak_dist) + inference.peak_criteria.peak_dist + ) self.info[peakdef_maxpeak] = ( - inference.peak_criteria.num_peak) + inference.peak_criteria.num_peak + ) else: - if (not str(inference.cluster_criteria.connectivity) == - str(self.info[clustdef])): + if not str( + inference.cluster_criteria.connectivity + ) == str(self.info[clustdef]): raise Exception( - 'Inferences using multiple connectivity' + - ' criteria ' + - str(inference.cluster_criteria.connectivity) + - str(self.info[clustdef]) + - ' not handled yet.') - if not (inference.peak_criteria.peak_dist == - self.info[peakdef_mindist]): + "Inferences using multiple connectivity" + + " criteria " + + str(inference.cluster_criteria.connectivity) + + str(self.info[clustdef]) + + " not handled yet." + ) + if not ( + inference.peak_criteria.peak_dist + == self.info[peakdef_mindist] + ): raise Exception( - 'Inferences using multiple distance between ' + - 'peaks criteria ' + - str(inference.peak_criteria.peak_dist) + - str(self.info[peakdef_mindist]) + - ' not handled yet.') - if (not inference.peak_criteria.num_peak == - self.info[peakdef_maxpeak]): + "Inferences using multiple distance between " + + "peaks criteria " + + str(inference.peak_criteria.peak_dist) + + str(self.info[peakdef_mindist]) + + " not handled yet." + ) + if ( + not inference.peak_criteria.num_peak + == self.info[peakdef_maxpeak] + ): raise Exception( - 'Inferences using multiple number of peak ' + - 'per cluster criteria ' + - str(inference.peak_criteria.num_peak) + - str(self.info[peakdef_maxpeak]) + - ' not handled yet.') + "Inferences using multiple number of peak " + + "per cluster criteria " + + str(inference.peak_criteria.num_peak) + + str(self.info[peakdef_maxpeak]) + + " not handled yet." + ) contrast = self._get_contrast(con_est_id) # (model_fitting, pe_map_ids) = # self._get_model_fitting(con_est_id) - self.info['Inferences'].append(collections.OrderedDict()) - self.info['Inferences'][-1]['StatisticMap_contrastName'] =\ - contrast.stat_map.contrast_name - self.info['Inferences'][-1]['HeightThreshold_type'] = ( - str(inference.height_thresh.threshold_type)) - self.info['Inferences'][-1]['HeightThreshold_value'] = ( - inference.height_thresh.value) - self.info['Inferences'][-1]['ExtentThreshold_type'] = ( - str(inference.extent_thresh.threshold_type)) - clustsize_vox = 'ExtentThreshold_clusterSizeInVoxels' - self.info['Inferences'][-1][clustsize_vox] = ( - inference.extent_thresh.extent) - althyp = 'Inference_hasAlternativeHypothesis' - self.info['Inferences'][-1][althyp] = str( - inference.inference_act.tail) - search_loc = 'SearchSpaceMaskMap_atLocation' - self.info['Inferences'][-1][search_loc] = ( - inference.search_space.file.filename) - search_sys = 'SearchSpaceMaskMap_inWorldCoordinateSystem' - self.info['Inferences'][-1][search_sys] = str( - inference.search_space.coord_space.coordinate_system) - search_vol_vox = 'SearchSpaceMaskMap_searchVolumeInVoxels' - self.info['Inferences'][-1][search_vol_vox] = ( - inference.search_space.search_volume_in_voxels) - search_vol_units = 'SearchSpaceMaskMap_searchVolumeInUnits' - self.info['Inferences'][-1][search_vol_units] = ( - inference.search_space.search_volume_in_units) - exc_loc = 'ExcursionSetMap_atLocation' - self.info['Inferences'][-1][exc_loc] = ( - inference.excursion_set.file.filename) - exc_sys = 'ExcursionSetMap_inWorldCoordinateSystem' - self.info['Inferences'][-1][exc_sys] = str( - inference.excursion_set.coord_space.coordinate_system) - self.info['Inferences'][-1]['Clusters'] = list() - clus = 'Clusters' - pk = 'Peaks' - cl_size_vox = 'SupraThresholdCluster_clusterSizeInVoxels' - cl_punc = 'SupraThresholdCluster_pValueUncorrected' - cl_pfwe = 'SupraThresholdCluster_pValueFWER' - cl_pfdr = 'SupraThresholdCluster_qValueFDR' + self.info["Inferences"].append(collections.OrderedDict()) + self.info["Inferences"][-1][ + "StatisticMap_contrastName" + ] = contrast.stat_map.contrast_name + self.info["Inferences"][-1]["HeightThreshold_type"] = str( + inference.height_thresh.threshold_type + ) + self.info["Inferences"][-1][ + "HeightThreshold_value" + ] = inference.height_thresh.value + self.info["Inferences"][-1]["ExtentThreshold_type"] = str( + inference.extent_thresh.threshold_type + ) + clustsize_vox = "ExtentThreshold_clusterSizeInVoxels" + self.info["Inferences"][-1][ + clustsize_vox + ] = inference.extent_thresh.extent + althyp = "Inference_hasAlternativeHypothesis" + self.info["Inferences"][-1][althyp] = str( + inference.inference_act.tail + ) + search_loc = "SearchSpaceMaskMap_atLocation" + self.info["Inferences"][-1][ + search_loc + ] = inference.search_space.file.filename + search_sys = "SearchSpaceMaskMap_inWorldCoordinateSystem" + self.info["Inferences"][-1][search_sys] = str( + inference.search_space.coord_space.coordinate_system + ) + search_vol_vox = "SearchSpaceMaskMap_searchVolumeInVoxels" + self.info["Inferences"][-1][ + search_vol_vox + ] = inference.search_space.search_volume_in_voxels + search_vol_units = "SearchSpaceMaskMap_searchVolumeInUnits" + self.info["Inferences"][-1][ + search_vol_units + ] = inference.search_space.search_volume_in_units + exc_loc = "ExcursionSetMap_atLocation" + self.info["Inferences"][-1][ + exc_loc + ] = inference.excursion_set.file.filename + exc_sys = "ExcursionSetMap_inWorldCoordinateSystem" + self.info["Inferences"][-1][exc_sys] = str( + inference.excursion_set.coord_space.coordinate_system + ) + self.info["Inferences"][-1]["Clusters"] = list() + clus = "Clusters" + pk = "Peaks" + cl_size_vox = "SupraThresholdCluster_clusterSizeInVoxels" + cl_punc = "SupraThresholdCluster_pValueUncorrected" + cl_pfwe = "SupraThresholdCluster_pValueFWER" + cl_pfdr = "SupraThresholdCluster_qValueFDR" for cluster in inference.clusters: - self.info['Inferences'][-1][clus].append( - collections.OrderedDict()) - self.info['Inferences'][-1][clus][-1][cl_size_vox] =\ - cluster.size + self.info["Inferences"][-1][clus].append( + collections.OrderedDict() + ) + self.info["Inferences"][-1][clus][-1][ + cl_size_vox + ] = cluster.size if cluster.punc is not None: - self.info['Inferences'][-1][clus][-1][cl_punc] = ( - cluster.punc) + self.info["Inferences"][-1][clus][-1][ + cl_punc + ] = cluster.punc if cluster.pFWER is not None: - self.info['Inferences'][-1][clus][-1][cl_pfwe] = ( - cluster.pFWER) + self.info["Inferences"][-1][clus][-1][ + cl_pfwe + ] = cluster.pFWER if cluster.pFDR is not None: - self.info['Inferences'][-1][clus][-1][cl_pfdr] = ( - cluster.pFDR) - self.info['Inferences'][-1][clus][-1][pk] = list() + self.info["Inferences"][-1][clus][-1][ + cl_pfdr + ] = cluster.pFDR + self.info["Inferences"][-1][clus][-1][pk] = list() peaks = list() for peak in cluster.peaks: peaks.append(collections.OrderedDict()) if peak.value is not None: - peaks[-1]['Peak_value'] = peak.value - peaks[-1]['Coordinate_coordinateVector'] = ( - peak.coordinate.coord_vector_std) + peaks[-1]["Peak_value"] = peak.value + peaks[-1][ + "Coordinate_coordinateVector" + ] = peak.coordinate.coord_vector_std if peak.p_unc is not None: - peaks[-1]['Peak_pValueUncorrected'] = ( - peak.p_unc) + peaks[-1][ + "Peak_pValueUncorrected" + ] = peak.p_unc if peak.p_fwer is not None: - peaks[-1]['Peak_pValueFWER'] = peak.p_fwer + peaks[-1]["Peak_pValueFWER"] = peak.p_fwer if peak.p_fdr is not None: - peaks[-1]['Peak_qValueFDR'] = peak.p_fdr + peaks[-1]["Peak_qValueFDR"] = peak.p_fdr if peak.equiv_z is not None: - peaks[-1]['Peak_equivalentZStatistic'] = ( - peak.equiv_z) - self.info['Inferences'][-1][clus][-1][pk].append( - peaks) + peaks[-1][ + "Peak_equivalentZStatistic" + ] = peak.equiv_z + self.info["Inferences"][-1][clus][-1][pk].append( + peaks + ) # TODO: if all world coord system are identical then use # self.info['CoordinateSpace_inWorldCoordinateSystem'] = '' @@ -354,11 +438,10 @@ def get_metadata(self): return self.objects def _get_model_fitting(self, con_est_id): - """ - Retrieve model fitting that corresponds to contrast with identifier - 'con_id' - from the list of model fitting objects stored in self.model_fittings - """ + """Retrieve model fitting that corresponds \ + to contrast with identifier 'con_id' \ + from the list of model fitting objects \ + stored in self.model_fittings.""" for (mpe_id, pe_ids), contrasts in self.contrasts.items(): for contrast in contrasts: if contrast.estimation.id == con_est_id: @@ -370,20 +453,20 @@ def _get_model_fitting(self, con_est_id): if model_fitting.activity.id == model_fitting_id: return (model_fitting, pe_map_ids) - raise Exception("Model fitting of contrast : " + str(con_est_id) + - " not found.") + raise Exception( + "Model fitting of contrast : " + str(con_est_id) + " not found." + ) def _get_contrast(self, con_id): - """ - Retrieve contrast with identifier 'con_id' from the list of contrast - objects stored in self.contrasts - """ + """Retrieve contrast with identifier 'con_id' \ + from the list of contrast objects stored in self.contrasts.""" for contrasts in list(self.contrasts.values()): for contrast in contrasts: if contrast.estimation.id == con_id: return contrast - raise Exception("Contrast activity with id: " + str(con_id) + - " not found.") + raise Exception( + "Contrast activity with id: " + str(con_id) + " not found." + ) def parse(self, rdf_data, fmt="turtle"): g = rdflib.Graph() @@ -391,14 +474,15 @@ def parse(self, rdf_data, fmt="turtle"): g.parse(data=rdf_data, format=fmt) except BadSyntax: raise self.ParseException( - "RDFLib was unable to parse the RDF file.") + "RDFLib was unable to parse the RDF file." + ) return g def get_object(self, klass, oid=None, err_if_none=True, **kwargs): if oid is not None: if oid in self.objects: - return(self.objects[oid]) + return self.objects[oid] query = klass.get_query(oid) sd = self.graph.query(query) @@ -412,9 +496,14 @@ def get_object(self, klass, oid=None, err_if_none=True, **kwargs): argums = {k: v.toPython() for k, v in argums.items()} # Convert URIs to qnames argums = { - k: namespace_manager.valid_qualified_name(v) if - namespace_manager.valid_qualified_name(v) is not None - else v for k, v in argums.items()} + k: ( + namespace_manager.valid_qualified_name(v) + if namespace_manager.valid_qualified_name(v) + is not None + else v + ) + for k, v in argums.items() + } # for k,v in argums.items(): # if not isinstance(drift_type, QualifiedName): @@ -435,9 +524,9 @@ def get_object(self, klass, oid=None, err_if_none=True, **kwargs): to_return = objects if err_if_none and (to_return is None): - raise Exception('No results found for query:' + query) + raise Exception("No results found for query:" + query) - return(to_return) + return to_return def load_software(self): query = """ @@ -458,11 +547,12 @@ def load_software(self): if sd: for row in sd: args = row.asdict() - software = self.get_object(NeuroimagingSoftware, - args['ni_software_id']) + software = self.get_object( + NeuroimagingSoftware, args["ni_software_id"] + ) if software is None: - raise Exception('No results found for query:' + query) + raise Exception("No results found for query:" + query) return software @@ -518,12 +608,13 @@ def load_bundle_export(self): for row in sd: args = row.asdict() exporter = self.get_object( - ExporterSoftware, args['exporter_id']) - export = self.get_object(NIDMResultsExport, args['export_id']) - bundle = self.get_object(NIDMResultsBundle, args['bundle_id']) - export_time = args['export_time'].toPython() + ExporterSoftware, args["exporter_id"] + ) + export = self.get_object(NIDMResultsExport, args["export_id"]) + bundle = self.get_object(NIDMResultsBundle, args["bundle_id"]) + export_time = args["export_time"].toPython() else: - raise Exception('No results found for query:' + query) + raise Exception("No results found for query:" + query) return (bundle, exporter, export, export_time) @@ -603,17 +694,22 @@ def load_modelfitting(self): # TODO: should software_id really be an input? activity = self.get_object( - ModelParametersEstimation, args['mpe_id']) + ModelParametersEstimation, args["mpe_id"] + ) # Find list of HRF basis - query_hrf_bases = """ + query_hrf_bases = ( + """ prefix nidm_DesignMatrix: prefix nidm_hasHRFBasis: SELECT DISTINCT * WHERE { - <""" + args['design_id'] + """> nidm_hasHRFBasis: ?hrf_basis . + <""" + + args["design_id"] + + """> nidm_hasHRFBasis: ?hrf_basis . } """ + ) hrf_models = None sd_hrf = self.graph.query(query_hrf_bases) if sd_hrf: @@ -623,85 +719,118 @@ def load_modelfitting(self): args_hrf = row_hrf.asdict() hrf_models.append( namespace_manager.valid_qualified_name( - args_hrf['hrf_basis'])) + args_hrf["hrf_basis"] + ) + ) - if 'png_id' in args: - design_matrix_png = self.get_object(Image, args['png_id']) + if "png_id" in args: + design_matrix_png = self.get_object(Image, args["png_id"]) else: design_matrix_png = None - if 'drift_model_id' in args: + if "drift_model_id" in args: drift_model = self.get_object( - DriftModel, args['drift_model_id']) + DriftModel, args["drift_model_id"] + ) else: drift_model = None design_matrix = self.get_object( - DesignMatrix, args['design_id'], matrix=None, - image_file=design_matrix_png, drift_model=drift_model, - hrf_models=hrf_models) - data = self.get_object(Data, args['data_id']) - error_model = self.get_object(ErrorModel, args['error_id']) + DesignMatrix, + args["design_id"], + matrix=None, + image_file=design_matrix_png, + drift_model=drift_model, + hrf_models=hrf_models, + ) + data = self.get_object(Data, args["data_id"]) + error_model = self.get_object(ErrorModel, args["error_id"]) # Find list of model parameter estimate maps - query_pe_maps = """ + query_pe_maps = ( + """ prefix nidm_ParameterEstimateMap: prefix nidm_inCoordinateSpace: SELECT DISTINCT * WHERE { ?pe_id a nidm_ParameterEstimateMap: ; nidm_inCoordinateSpace: ?pe_coordspace_id ; - prov:wasGeneratedBy <""" + str(args['mpe_id']) + """> . + prov:wasGeneratedBy <""" + + str(args["mpe_id"]) + + """> . } """ + ) param_estimates = list() sd_pe_maps = self.graph.query(query_pe_maps) if sd_pe_maps: for row_pe in sd_pe_maps: args_pe = row_pe.asdict() pe_map_coordspace = self.get_object( - CoordinateSpace, args_pe['pe_coordspace_id']) - - param_estimates.append(self.get_object( - ParameterEstimateMap, args_pe['pe_id'], - coord_space=pe_map_coordspace, pe_num=None)) + CoordinateSpace, args_pe["pe_coordspace_id"] + ) + + param_estimates.append( + self.get_object( + ParameterEstimateMap, + args_pe["pe_id"], + coord_space=pe_map_coordspace, + pe_num=None, + ) + ) rms_coord_space = self.get_object( - CoordinateSpace, args['rms_coordspace_id']) + CoordinateSpace, args["rms_coordspace_id"] + ) rms_map = self.get_object( - ResidualMeanSquares, args['rms_id'], - coord_space=rms_coord_space) + ResidualMeanSquares, + args["rms_id"], + coord_space=rms_coord_space, + ) mask_coord_space = self.get_object( - CoordinateSpace, args['mask_coordspace_id']) + CoordinateSpace, args["mask_coordspace_id"] + ) mask_map = self.get_object( - MaskMap, args['mask_id'], coord_space=mask_coord_space) + MaskMap, args["mask_id"], coord_space=mask_coord_space + ) gm_coord_space = self.get_object( - CoordinateSpace, args['gm_coordspace_id']) + CoordinateSpace, args["gm_coordspace_id"] + ) grand_mean_map = self.get_object( - GrandMeanMap, args['gm_id'], coord_space=mask_coord_space, - mask_file=None) + GrandMeanMap, + args["gm_id"], + coord_space=mask_coord_space, + mask_file=None, + ) - if 'rpv_coordspace_id' in args: + if "rpv_coordspace_id" in args: rpv_coord_space = self.get_object( - CoordinateSpace, args['rpv_coordspace_id']) + CoordinateSpace, args["rpv_coordspace_id"] + ) rpv_map = self.get_object( - ReselsPerVoxelMap, args['rpv_id'], - coord_space=mask_coord_space) + ReselsPerVoxelMap, + args["rpv_id"], + coord_space=mask_coord_space, + ) else: rpv_map = None machine = self.get_object( - ImagingInstrument, args['machine_id']) + ImagingInstrument, args["machine_id"] + ) # Find subject or group(s) - query_subjects = """ + query_subjects = ( + """ prefix nidm_Data: prefix obo_studygrouppopulation: SELECT DISTINCT * WHERE { - <""" + str(args['data_id']) + """> a nidm_Data: ; + <""" + + str(args["data_id"]) + + """> a nidm_Data: ; prov:wasAttributedTo ?person_or_group_id . {?person_or_group_id a prov:Person .} UNION @@ -709,6 +838,7 @@ def load_modelfitting(self): } """ + ) sd_subjects = self.graph.query(query_subjects) subjects = None @@ -718,39 +848,56 @@ def load_modelfitting(self): for row_sub in sd_subjects: args_sub = row_sub.asdict() group = self.get_object( - Group, args_sub['person_or_group_id'], - err_if_none=False) + Group, + args_sub["person_or_group_id"], + err_if_none=False, + ) if group is None: # Try loading as a single subject subject = self.get_object( - Person, args_sub['person_or_group_id']) + Person, args_sub["person_or_group_id"] + ) subjects.append(subject) else: subjects.append(group) - model_fittings.append(ModelFitting( - activity, design_matrix, data, error_model, - param_estimates, rms_map, mask_map, grand_mean_map, - machine, subjects, rpv_map)) + model_fittings.append( + ModelFitting( + activity, + design_matrix, + data, + error_model, + param_estimates, + rms_map, + mask_map, + grand_mean_map, + machine, + subjects, + rpv_map, + ) + ) con_num = row_num + 1 else: - raise Exception('No model fitting found') + raise Exception("No model fitting found") return model_fittings def load_contrasts(self, workaround=False): if workaround: - warnings.warn('Using workaround: links between contrast weights' + - 'and contrast estimations are not assessed') + warnings.warn( + "Using workaround: links between contrast weights" + + "and contrast estimations are not assessed" + ) con_est_att = "." else: con_est_att = """; prov:used ?conw_id ; prov:used ?design_id .""" - query = """ + query = ( + """ prefix nidm_DesignMatrix: prefix nidm_ModelParameterEstimation: @@ -775,7 +922,9 @@ def load_contrasts(self, workaround=False): ?conw_id a obo_contrastweightmatrix: . - ?conest_id a nidm_ContrastEstimation: """ + con_est_att + """ + ?conest_id a nidm_ContrastEstimation: """ + + con_est_att + + """ ?mpe_id a nidm_ModelParameterEstimation: ; prov:used ?design_id . @@ -818,6 +967,7 @@ def load_contrasts(self, workaround=False): } """ + ) sd = self.graph.query(query) @@ -827,87 +977,120 @@ def load_contrasts(self, workaround=False): for row in sd: args = row.asdict() contrast_num = str(con_num) - contrast_name = args['contrast_name'] + contrast_name = args["contrast_name"] weights = self.get_object( - ContrastWeights, args['conw_id'], - contrast_num=contrast_num) + ContrastWeights, args["conw_id"], contrast_num=contrast_num + ) estimation = self.get_object( - ContrastEstimation, args['conest_id'], - contrast_num=contrast_num) + ContrastEstimation, + args["conest_id"], + contrast_num=contrast_num, + ) contraststd_map_coordspace = self.get_object( - CoordinateSpace, args['constdm_coordspace_id']) + CoordinateSpace, args["constdm_coordspace_id"] + ) - if 'conm_id' in args: + if "conm_id" in args: # T-contrast contrast_map_coordspace = self.get_object( - CoordinateSpace, args['conm_coordspace_id']) + CoordinateSpace, args["conm_coordspace_id"] + ) contrast_map = self.get_object( - ContrastMap, args['conm_id'], + ContrastMap, + args["conm_id"], coord_space=contrast_map_coordspace, - contrast_num=contrast_num) + contrast_num=contrast_num, + ) stderr_or_expl_mean_sq_map = self.get_object( - ContrastStdErrMap, args['constdm_id'], + ContrastStdErrMap, + args["constdm_id"], coord_space=contraststd_map_coordspace, - contrast_num=contrast_num, is_variance=False, - var_coord_space=None, filepath=None) + contrast_num=contrast_num, + is_variance=False, + var_coord_space=None, + filepath=None, + ) else: # F-contrast contrast_map = None stderr_or_expl_mean_sq_map = self.get_object( - ContrastExplainedMeanSquareMap, args['constdm_id'], + ContrastExplainedMeanSquareMap, + args["constdm_id"], coord_space=contraststd_map_coordspace, - contrast_num=contrast_num, stat_file=None, - sigma_sq_file=None) + contrast_num=contrast_num, + stat_file=None, + sigma_sq_file=None, + ) stat_map_coordspace = self.get_object( - CoordinateSpace, args['statm_coordspace_id']) + CoordinateSpace, args["statm_coordspace_id"] + ) stat_map = self.get_object( - StatisticMap, args['statm_id'], - coord_space=stat_map_coordspace) + StatisticMap, + args["statm_id"], + coord_space=stat_map_coordspace, + ) zstat_exist = False - if 'otherstatm_id' in args: + if "otherstatm_id" in args: zstat_exist = True otherstat_map_coordspace = self.get_object( - CoordinateSpace, args['otherstatm_coordspace_id']) + CoordinateSpace, args["otherstatm_coordspace_id"] + ) otherstat_map = self.get_object( - StatisticMap, args['otherstatm_id'], - coord_space=stat_map_coordspace) + StatisticMap, + args["otherstatm_id"], + coord_space=stat_map_coordspace, + ) if zstat_exist: con = Contrast( - contrast_num, args['contrast_name'], weights, - estimation, contrast_map, - stderr_or_expl_mean_sq_map, stat_map=otherstat_map, - z_stat_map=stat_map) + contrast_num, + args["contrast_name"], + weights, + estimation, + contrast_map, + stderr_or_expl_mean_sq_map, + stat_map=otherstat_map, + z_stat_map=stat_map, + ) else: con = Contrast( - contrast_num, args['contrast_name'], - weights, estimation, contrast_map, - stderr_or_expl_mean_sq_map, stat_map=stat_map) + contrast_num, + args["contrast_name"], + weights, + estimation, + contrast_map, + stderr_or_expl_mean_sq_map, + stat_map=stat_map, + ) # Find list of model parameter estimate maps - query_pe_maps = """ + query_pe_maps = ( + """ prefix nidm_ParameterEstimateMap: SELECT DISTINCT * WHERE { - <""" + str(args['conest_id']) + """> prov:used ?pe_id . + <""" + + str(args["conest_id"]) + + """> prov:used ?pe_id . ?pe_id a nidm_ParameterEstimateMap: . } """ + ) pe_ids = () sd_pe_maps = self.graph.query(query_pe_maps) if sd_pe_maps: for row_pe in sd_pe_maps: args_pe = row_pe.asdict() - pe_ids = pe_ids + (NIIRI.qname(str(args_pe['pe_id'])),) + pe_ids = pe_ids + (NIIRI.qname(str(args_pe["pe_id"])),) - mpe_id = NIIRI.qname(str(args['mpe_id'])) - if not (mpe_id, pe_ids) in contrasts: + mpe_id = NIIRI.qname(str(args["mpe_id"])) + if (mpe_id, pe_ids) not in contrasts: contrasts[(mpe_id, pe_ids)] = [con] else: contrasts[(mpe_id, pe_ids)].append(con) @@ -915,7 +1098,7 @@ def load_contrasts(self, workaround=False): con_num = con_num + 1 if not contrasts: - raise Exception('No contrast found') + raise Exception("No contrast found") return contrasts @@ -989,105 +1172,147 @@ def load_inferences(self): for row in sd: args = row.asdict() inference = self.get_object( - InferenceActivity, args['inference_id'], err_if_none=False) + InferenceActivity, args["inference_id"], err_if_none=False + ) # Find list of equivalent height thresholds - query_equiv_threshs = """ + query_equiv_threshs = ( + """ prefix nidm_equivalentThreshold: SELECT DISTINCT * WHERE { - <""" + str(args['height_thresh_id']) + """> nidm_equivalentThreshold: ?equiv_h_thresh_id . + <""" + + str(args["height_thresh_id"]) + + """> nidm_equivalentThreshold: ?equiv_h_thresh_id . } """ + ) equiv_h_threshs = list() sd_equiv_h_threshs = self.graph.query(query_equiv_threshs) if sd_equiv_h_threshs: for row_equiv_h in sd_equiv_h_threshs: args_hequiv = row_equiv_h.asdict() - equiv_h_threshs.append(self.get_object( - HeightThreshold, - args_hequiv['equiv_h_thresh_id'])) + equiv_h_threshs.append( + self.get_object( + HeightThreshold, + args_hequiv["equiv_h_thresh_id"], + ) + ) height_thresh = self.get_object( - HeightThreshold, args['height_thresh_id'], - equiv_thresh=equiv_h_threshs) + HeightThreshold, + args["height_thresh_id"], + equiv_thresh=equiv_h_threshs, + ) # Find list of equivalent extent thresholds - query_equiv_threshs = """ + query_equiv_threshs = ( + """ prefix nidm_equivalentThreshold: SELECT DISTINCT * WHERE { - <""" + str(args['extent_thresh_id']) + """> nidm_equivalentThreshold: ?equiv_e_thresh_id . + <""" + + str(args["extent_thresh_id"]) + + """> nidm_equivalentThreshold: ?equiv_e_thresh_id . } """ + ) equiv_e_threshs = list() sd_equiv_e_threshs = self.graph.query(query_equiv_threshs) if sd_equiv_e_threshs: for row_equiv_e in sd_equiv_e_threshs: args_eequiv = row_equiv_e.asdict() - equiv_e_threshs.append(self.get_object( - ExtentThreshold, args_eequiv['equiv_e_thresh_id'])) + equiv_e_threshs.append( + self.get_object( + ExtentThreshold, + args_eequiv["equiv_e_thresh_id"], + ) + ) extent_thresh = self.get_object( - ExtentThreshold, args['extent_thresh_id'], - equiv_thresh=equiv_e_threshs) + ExtentThreshold, + args["extent_thresh_id"], + equiv_thresh=equiv_e_threshs, + ) peak_criteria = self.get_object( - PeakCriteria, args['peak_criteria_id'], contrast_num=None) + PeakCriteria, args["peak_criteria_id"], contrast_num=None + ) cluster_criteria = self.get_object( - ClusterCriteria, args['cluster_criteria_id'], - contrast_num=None) + ClusterCriteria, + args["cluster_criteria_id"], + contrast_num=None, + ) - if 'display_mask_id' in args: + if "display_mask_id" in args: disp_coordspace = self.get_object( - CoordinateSpace, args['disp_coord_space_id']) + CoordinateSpace, args["disp_coord_space_id"] + ) # TODO we need to deal with more than 1 DisplayMaskMap - disp_mask = [self.get_object( - DisplayMaskMap, args['display_mask_id'], - contrast_num=None, coord_space=disp_coordspace, - mask_num=None)] + disp_mask = [ + self.get_object( + DisplayMaskMap, + args["display_mask_id"], + contrast_num=None, + coord_space=disp_coordspace, + mask_num=None, + ) + ] else: disp_mask = None - if 'excset_visu_id' in args: + if "excset_visu_id" in args: excset_visu = self.get_object( - Image, args['excset_visu_id']) + Image, args["excset_visu_id"] + ) else: excset_visu = None - if 'cluster_map_id' in args: + if "cluster_map_id" in args: clustermap_coordspace = self.get_object( - CoordinateSpace, args['cluster_map_coord_space_id']) + CoordinateSpace, args["cluster_map_coord_space_id"] + ) cluster_map = self.get_object( - ClusterLabelsMap, args['cluster_map_id'], - coord_space=clustermap_coordspace) + ClusterLabelsMap, + args["cluster_map_id"], + coord_space=clustermap_coordspace, + ) else: cluster_map = None - if 'mip_id' in args: - mip = self.get_object(Image, args['mip_id']) + if "mip_id" in args: + mip = self.get_object(Image, args["mip_id"]) else: mip = None excset_coordspace = self.get_object( - CoordinateSpace, args['excset_coord_space_id']) + CoordinateSpace, args["excset_coord_space_id"] + ) excursion_set = self.get_object( - ExcursionSet, args['exc_set_id'], - coord_space=excset_coordspace, visu=excset_visu, - clust_map=cluster_map, mip=mip) + ExcursionSet, + args["exc_set_id"], + coord_space=excset_coordspace, + visu=excset_visu, + clust_map=cluster_map, + mip=mip, + ) searchspace_coordspace = self.get_object( - CoordinateSpace, args['search_space_coord_space_id']) + CoordinateSpace, args["search_space_coord_space_id"] + ) search_space = self.get_object( - SearchSpace, args['search_space_id'], - coord_space=searchspace_coordspace) + SearchSpace, + args["search_space_id"], + coord_space=searchspace_coordspace, + ) # TODO software_id = self.software.id # Find list of clusters - query_clusters = """ + query_clusters = ( + """ prefix nidm_SupraThresholdCluster: prefix nidm_ClusterCenterOfGravity: prefix nidm_clusterLabelId: @@ -1095,7 +1320,9 @@ def load_inferences(self): SELECT DISTINCT * WHERE { ?cluster_id a nidm_SupraThresholdCluster: ; nidm_clusterLabelId: ?cluster_num ; - prov:wasDerivedFrom <""" + str(args['exc_set_id']) + """> . + prov:wasDerivedFrom <""" + + str(args["exc_set_id"]) + + """> . OPTIONAL { ?cog_id a nidm_ClusterCenterOfGravity: ; @@ -1103,61 +1330,84 @@ def load_inferences(self): } } """ + ) clusters = list() sd_clusters = self.graph.query(query_clusters) if sd_clusters: for row_cluster in sd_clusters: args_cl = row_cluster.asdict() - if 'cog_id' in args_cl: + if "cog_id" in args_cl: cog = self.get_object( - CenterOfGravity, args_cl['cog_id'], - cluster_num=args_cl['cluster_num'].toPython()) + CenterOfGravity, + args_cl["cog_id"], + cluster_num=args_cl["cluster_num"].toPython(), + ) else: cog = None # Find list of peaks - query_peaks = """ + query_peaks = ( + """ prefix nidm_Peak: SELECT DISTINCT * WHERE { ?peak_id a nidm_Peak: ; - prov:wasDerivedFrom <""" + str(args_cl['cluster_id']) + """> . + prov:wasDerivedFrom <""" + + str(args_cl["cluster_id"]) + + """> . } """ + ) peaks = list() sd_peaks = self.graph.query(query_peaks) if sd_peaks: for row_peak in sd_peaks: args_peak = row_peak.asdict() - peaks.append(self.get_object( - Peak, args_peak['peak_id'])) + peaks.append( + self.get_object(Peak, args_peak["peak_id"]) + ) - clusters.append(self.get_object( - Cluster, args_cl['cluster_id'], peaks=peaks, - cog=cog)) + clusters.append( + self.get_object( + Cluster, + args_cl["cluster_id"], + peaks=peaks, + cog=cog, + ) + ) # Dictionary of (key, value) pairs where key is the identifier # of a ContrastEstimation object and value is an object of type # Inference describing the inference step in NIDM-Results (main # activity: Inference) # TODO: if key exist we need to append! - inferences[NIIRI.qname(args['con_est_id'])] = [ + inferences[NIIRI.qname(args["con_est_id"])] = [ Inference( - inference, height_thresh, extent_thresh, - peak_criteria, cluster_criteria, disp_mask, - excursion_set, clusters, search_space, software_id)] + inference, + height_thresh, + extent_thresh, + peak_criteria, + cluster_criteria, + disp_mask, + excursion_set, + clusters, + search_space, + software_id, + ) + ] return inferences - def serialize(self, destination, fmt="nidm", overwrite=False, - last_used_con_id=0): + def serialize( + self, destination, fmt="nidm", overwrite=False, last_used_con_id=0 + ): if fmt == "nidm": - exporter = NIDMExporter(version="1.3.0", - out_dir=destination.replace( - '.nidm.zip', '')) + exporter = NIDMExporter( + version="1.3.0", out_dir=destination.replace(".nidm.zip", "") + ) exporter.model_fittings = self.model_fittings exporter.contrasts = self.contrasts exporter.inferences = self.inferences @@ -1179,19 +1429,40 @@ def serialize(self, destination, fmt="nidm", overwrite=False, if overwrite: add_header = True - open_mode = 'wb' + open_mode = "wb" else: add_header = False - open_mode = 'ab' + open_mode = "ab" with open(csvfile, open_mode) as fid: - writer = csv.writer(fid, delimiter='\t') + writer = csv.writer(fid, delimiter="\t") if add_header: - writer.writerow(["9", "NaN", "NaN", "NaN", "NaN", "NaN", - "NaN", "NaN", "NaN"]) writer.writerow( - ["x", "y", "z", "Study", "Contrast", "N", - "FixedRandom", "CoordSys", "Name"]) + [ + "9", + "NaN", + "NaN", + "NaN", + "NaN", + "NaN", + "NaN", + "NaN", + "NaN", + ] + ) + writer.writerow( + [ + "x", + "y", + "z", + "Study", + "Contrast", + "N", + "FixedRandom", + "CoordSys", + "Name", + ] + ) # Assumed random effects self.FixedRandom = "random" @@ -1209,17 +1480,20 @@ def serialize(self, destination, fmt="nidm", overwrite=False, space = "T88" else: raise Exception( - "Unrecognised space for " + - str(exc_set.coord_space.coordinate_system)) + "Unrecognised space for " + + str(exc_set.coord_space.coordinate_system) + ) stat_map = exc_set.inference.stat_map con_name = stat_map.contrast_name.replace( - " ", "_").replace(":", "") + " ", "_" + ).replace(":", "") # FIXME: need to deal with more than one group - self.N = stat_map.contrast_estimation.param_estimate.\ - model_param_estimation.data.group_or_sub.num_subjects + self.N = ( + stat_map.contrast_estimation.param_estimate.model_param_estimation.data.group_or_sub.num_subjects # noqa + ) if con_name in con_ids: con_id = con_ids[con_name] @@ -1227,12 +1501,18 @@ def serialize(self, destination, fmt="nidm", overwrite=False, con_id = max(con_ids.values()) + 1 con_ids[con_name] = con_id - writer.writerow([ - peak.coordinate.coord_vector[0], - peak.coordinate.coord_vector[1], - peak.coordinate.coord_vector[2], self.study_name, - con_id, - self.N, self.FixedRandom, - space, con_name]) + writer.writerow( + [ + peak.coordinate.coord_vector[0], + peak.coordinate.coord_vector[1], + peak.coordinate.coord_vector[2], + self.study_name, + con_id, + self.N, + self.FixedRandom, + space, + con_name, + ] + ) return con_ids diff --git a/nidmresults/load.py b/nidmresults/load.py index 4551457..b013521 100644 --- a/nidmresults/load.py +++ b/nidmresults/load.py @@ -1,12 +1,14 @@ -""" Load and save NIDM-Results objects """ -from nidmresults.graph import NIDMResults +"""Load and save NIDM-Results objects.""" import os +from nidmresults.graph import NIDMResults + def load(filename, to_replace=dict()): - ''' Load NIDM-Results file given filename, guessing if it is a - NIDM-Results pack or a JSON file + """Load NIDM-Results file given filename. + + Guessing if it is a NIDM-Results pack or a JSON file. Parameters ---------- @@ -16,15 +18,15 @@ def load(filename, to_replace=dict()): ------- nidmres : ``NIDMResults`` NIDM-Results object - ''' + """ if not os.path.exists(filename): - raise IOException('File does not exist: %s' % filename) + raise OSError("File does not exist: %s" % filename) - if filename.endswith('.json'): - raise Exception('Minimal json file: not handled yet') - elif filename.endswith('.nidm.zip'): + if filename.endswith(".json"): + raise Exception("Minimal json file: not handled yet") + elif filename.endswith(".nidm.zip"): nidm = NIDMResults.load_from_pack(filename, to_replace=to_replace) else: - raise Exception('Unhandled format ' + filename) + raise Exception("Unhandled format " + filename) return nidm diff --git a/nidmresults/objects/constants.py b/nidmresults/objects/constants.py index ba7abb1..16a3cd5 100644 --- a/nidmresults/objects/constants.py +++ b/nidmresults/objects/constants.py @@ -7,11 +7,12 @@ from prov.model import PROV, Namespace, NamespaceManager -NIDM = Namespace('nidm', "http://purl.org/nidash/nidm#") +NIDM = Namespace("nidm", "http://purl.org/nidash/nidm#") NIIRI = Namespace("niiri", "http://iri.nidash.org/") CRYPTO = Namespace( "crypto", - "http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#") + "http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#", +) FSL = Namespace("fsl", "http://purl.org/nidash/fsl#") SPM = Namespace("spm", "http://purl.org/nidash/spm#") AFNI = Namespace("afni", "http://purl.org/nidash/afni#") @@ -21,249 +22,267 @@ NLX_OLD = Namespace("nlx_old", "http://neurolex.org/wiki/") DC = Namespace("dc", "http://purl.org/dc/elements/1.1/") NFO = Namespace( - "nfo", "http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#") + "nfo", "http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#" +) SCR = Namespace("scr", "http://scicrunch.org/resolver/") NIF = Namespace("nif", "http://uri.neuinfo.org/nif/nifstd/") -namespaces = (PROV, NIDM, NIIRI, CRYPTO, FSL, SPM, AFNI, DCT, OBO, - DCTYPE, DC, NFO, SCR, NIF) +namespaces = ( + PROV, + NIDM, + NIIRI, + CRYPTO, + FSL, + SPM, + AFNI, + DCT, + OBO, + DCTYPE, + DC, + NFO, + SCR, + NIF, +) namespace_manager = NamespaceManager(namespaces) # Sciencrunch constants -SCR_FSL = SCR['SCR_002823'] -SCR_SPM = SCR['SCR_007037'] +SCR_FSL = SCR["SCR_002823"] +SCR_SPM = SCR["SCR_007037"] # NeuroLex constants -NLX_OLD_FSL = NLX_OLD['birnlex_2067'] -NIDM_FSL = NIDM['NIDM_0000167'] +NLX_OLD_FSL = NLX_OLD["birnlex_2067"] +NIDM_FSL = NIDM["NIDM_0000167"] # NIFSTD constants -NIF_MRI = NIF['birnlex_2100'] -NIF_EEG = NIF['ixl_0050003'] -NIF_MEG = NIF['ixl_0050002'] -NIF_PET = NIF['ixl_0050000'] -NIF_SPECT = NIF['ixl_0050001'] -NLX_FMRI_PROTOCOL = NIF['birnlex_2250'] -NLX_IMAGING_INSTRUMENT = NIF['birnlex_2094'] +NIF_MRI = NIF["birnlex_2100"] +NIF_EEG = NIF["ixl_0050003"] +NIF_MEG = NIF["ixl_0050002"] +NIF_PET = NIF["ixl_0050000"] +NIF_SPECT = NIF["ixl_0050001"] +NLX_FMRI_PROTOCOL = NIF["birnlex_2250"] +NLX_IMAGING_INSTRUMENT = NIF["birnlex_2094"] # SPM constants -SPM_DCT_DRIFT_MODEL = SPM['SPM_0000002'] -SPM_SPMS_DRIFT_CUT_OFF_PERIOD = SPM['SPM_0000001'] -SPM_SEARCH_VOLUME_RESELS_GEOMETRY = SPM['SPM_0000010'] -SPM_SMALLEST_SIGNIFICANT_CLUSTER_SIZE_IN_VOXELS_FDR05 = SPM['SPM_0000013'] -SPM_SMALLEST_SIGNIFICANT_CLUSTER_SIZE_IN_VOXELS_FWE05 = SPM['SPM_0000014'] +SPM_DCT_DRIFT_MODEL = SPM["SPM_0000002"] +SPM_SPMS_DRIFT_CUT_OFF_PERIOD = SPM["SPM_0000001"] +SPM_SEARCH_VOLUME_RESELS_GEOMETRY = SPM["SPM_0000010"] +SPM_SMALLEST_SIGNIFICANT_CLUSTER_SIZE_IN_VOXELS_FDR05 = SPM["SPM_0000013"] +SPM_SMALLEST_SIGNIFICANT_CLUSTER_SIZE_IN_VOXELS_FWE05 = SPM["SPM_0000014"] # NIDM constants -FSL_FSLS_GAMMA_HRF = FSL['FSL_0000006'] -NIDM_HAS_MRI_PROTOCOL = NIDM['NIDM_0000172'] -NIDM_NUMBER_OF_SUBJECTS = NIDM['NIDM_0000171'] -NIDM_GROUP_NAME = NIDM['NIDM_0000170'] -NIDM_DATA = NIDM['NIDM_0000169'] -NIDM_NIDM_RESULTS_EXPORT = NIDM['NIDM_0000166'] -FSL_FEAT_VERSION = FSL['FSL_0000005'] -FSL_DRIFT_CUTOFF_PERIOD = FSL['FSL_0000004'] -FSL_TEMPORAL_DERIVATIVE = FSL['FSL_0000003'] -FSL_GAUSSIAN_RUNNING_LINE_DRIFT_MODEL = FSL['FSL_0000002'] -FSL_FSLS_GAMMA_DIFFERENCE_HRF = FSL['FSL_0000001'] -NIDM_CONTRAST_EXPLAINED_MEAN_SQUARE_MAP = NIDM['NIDM_0000163'] -NIDM_THRESHOLD = NIDM['NIDM_0000162'] -NIDM_EQUIVALENT_THRESHOLD = NIDM['NIDM_0000161'] -NIDM_P_VALUE_UNCORRECTED_CLASS = NIDM['NIDM_0000160'] -NIDM_NOISE_FWHM_IN_VOXELS = NIDM['NIDM_0000159'] -NIDM_NOISE_FWHM_IN_VERTICES = NIDM['NIDM_0000158'] -NIDM_NOISE_FWHM_IN_UNITS = NIDM['NIDM_0000157'] -NIDM_CLUSTER_SIZE_IN_RESELS = NIDM['NIDM_0000156'] -NIDM_F_MRI_DESIGN = NIDM['NIDM_0000155'] -NIDM_MIXED_DESIGN = NIDM['NIDM_0000154'] -NIDM_EVENT_RELATED_DESIGN = NIDM['NIDM_0000153'] -NIDM_BLOCK_BASED_DESIGN = NIDM['NIDM_0000152'] -NIDM_SINE_BASIS_SET = NIDM['NIDM_0000151'] -NIDM_LINEAR_SPLINE_BASIS_SET = NIDM['NIDM_0000150'] -NIDM_SEARCH_VOLUME_IN_RESELS = NIDM['NIDM_0000149'] -NIDM_RESEL_SIZE_IN_VOXELS = NIDM['NIDM_0000148'] -NIDM_HEIGHT_CRITICAL_THRESHOLD_FWE_05 = NIDM['NIDM_0000147'] -NIDM_HEIGHT_CRITICAL_THRESHOLD_FDR_05 = NIDM['NIDM_0000146'] -NIDM_NOISE_ROUGHNESS_IN_VOXELS = NIDM['NIDM_0000145'] -NIDM_RESELS_PER_VOXEL_MAP = NIDM['NIDM_0000144'] -NIDM_EXPECTED_NUMBER_OF_VOXELS_PER_CLUSTER = NIDM['NIDM_0000143'] -NIDM_EXPECTED_NUMBER_OF_VERTICES_PER_CLUSTER = NIDM['NIDM_0000142'] -NIDM_EXPECTED_NUMBER_OF_CLUSTERS = NIDM['NIDM_0000141'] -NIDM_CLUSTER_CENTER_OF_GRAVITY = NIDM['NIDM_0000140'] -NIDM_COORDINATE_VECTOR_IN_VOXELS = NIDM['NIDM_0000139'] -NIDM_HAS_MAXIMUM_INTENSITY_PROJECTION = NIDM['NIDM_0000138'] -NIDM_SEARCH_VOLUME_IN_VERTICES = NIDM['NIDM_0000137'] -NIDM_SEARCH_VOLUME_IN_UNITS = NIDM['NIDM_0000136'] -NIDM_CONTRAST_VARIANCE_MAP = NIDM['NIDM_0000135'] -NIDM_WITH_ESTIMATION_METHOD = NIDM['NIDM_0000134'] -NIDM_VOXEL_UNITS = NIDM['NIDM_0000133'] -NIDM_VOXEL_TO_WORLD_MAPPING = NIDM['NIDM_0000132'] -NIDM_VOXEL_SIZE = NIDM['NIDM_0000131'] -NIDM_VOXEL6CONNECTED = NIDM['NIDM_0000130'] -NIDM_VOXEL26CONNECTED = NIDM['NIDM_0000129'] -NIDM_VOXEL18CONNECTED = NIDM['NIDM_0000128'] -NIDM_VERSION = NIDM['NIDM_0000127'] -NIDM_VARIANCE_SPATIAL_MODEL = NIDM['NIDM_0000126'] -NIDM_USER_SPECIFIED_THRESHOLD_TYPE = NIDM['NIDM_0000125'] -NIDM_TARGET_INTENSITY = NIDM['NIDM_0000124'] -NIDM_STATISTIC_TYPE = NIDM['NIDM_0000123'] -NIDM_SOFTWARE_VERSION = NIDM['NIDM_0000122'] -NIDM_SEARCH_VOLUME_IN_VOXELS = NIDM['NIDM_0000121'] -NIDM_RANDOM_FIELD_STATIONARITY = NIDM['NIDM_0000120'] -NIDM_Q_VALUE_FDR = NIDM['NIDM_0000119'] -NIDM_PIXEL8CONNECTED = NIDM['NIDM_0000118'] -NIDM_PIXEL4CONNECTED = NIDM['NIDM_0000117'] -NIDM_P_VALUE_UNCORRECTED = NIDM['NIDM_0000116'] -NIDM_P_VALUE_FWER = NIDM['NIDM_0000115'] -NIDM_P_VALUE = NIDM['NIDM_0000114'] -NIDM_OBJECT_MODEL = NIDM['NIDM_0000113'] -NIDM_NUMBER_OF_DIMENSIONS = NIDM['NIDM_0000112'] -NIDM_NUMBER_OF_CLUSTERS = NIDM['NIDM_0000111'] -NIDM_GAUSSIAN_HRF = NIDM['NIDM_0000110'] -NIDM_MIN_DISTANCE_BETWEEN_PEAKS = NIDM['NIDM_0000109'] -NIDM_MAX_NUMBER_OF_PEAKS_PER_CLUSTER = NIDM['NIDM_0000108'] -NIDM_MASKED_MEDIAN = NIDM['NIDM_0000107'] -NIDM_IS_USER_DEFINED = NIDM['NIDM_0000106'] -NIDM_IN_WORLD_COORDINATE_SYSTEM = NIDM['NIDM_0000105'] -NIDM_IN_COORDINATE_SPACE = NIDM['NIDM_0000104'] -NIDM_HAS_MAP_HEADER = NIDM['NIDM_0000103'] -NIDM_HAS_HRF_BASIS = NIDM['NIDM_0000102'] -NIDM_HAS_ERROR_DISTRIBUTION = NIDM['NIDM_0000101'] -NIDM_HAS_ERROR_DEPENDENCE = NIDM['NIDM_0000100'] -NIDM_HAS_CONNECTIVITY_CRITERION = NIDM['NIDM_0000099'] -NIDM_HAS_CLUSTER_LABELS_MAP = NIDM['NIDM_0000098'] -NIDM_HAS_ALTERNATIVE_HYPOTHESIS = NIDM['NIDM_0000097'] -NIDM_GRAND_MEAN_SCALING = NIDM['NIDM_0000096'] -NIDM_GLOBAL_NULL_DEGREE = NIDM['NIDM_0000095'] -NIDM_ERROR_VARIANCE_HOMOGENEOUS = NIDM['NIDM_0000094'] -NIDM_ERROR_DEGREES_OF_FREEDOM = NIDM['NIDM_0000093'] -NIDM_EQUIVALENT_ZSTATISTIC = NIDM['NIDM_0000092'] -NIDM_EFFECT_DEGREES_OF_FREEDOM = NIDM['NIDM_0000091'] -NIDM_DIMENSIONS_IN_VOXELS = NIDM['NIDM_0000090'] -NIDM_DEPENDENCE_SPATIAL_MODEL = NIDM['NIDM_0000089'] -NIDM_HAS_DRIFT_MODEL = NIDM['NIDM_0000088'] -NIDM_DRIFT_MODEL = NIDM['NIDM_0000087'] -NIDM_COORDINATE_VECTOR = NIDM['NIDM_0000086'] -NIDM_CONTRAST_NAME = NIDM['NIDM_0000085'] -NIDM_CLUSTER_SIZE_IN_VOXELS = NIDM['NIDM_0000084'] -NIDM_CLUSTER_SIZE_IN_VERTICES = NIDM['NIDM_0000083'] -NIDM_CLUSTER_LABEL_ID = NIDM['NIDM_0000082'] -NIDM_WORLD_COORDINATE_SYSTEM = NIDM['NIDM_0000081'] -NIDM_VOXEL_CONNECTIVITY_CRITERION = NIDM['NIDM_0000080'] -NIDM_TWO_TAILED_TEST = NIDM['NIDM_0000079'] -NIDM_TALAIRACH_COORDINATE_SYSTEM = NIDM['NIDM_0000078'] -NIDM_SUBJECT_COORDINATE_SYSTEM = NIDM['NIDM_0000077'] -NIDM_STATISTIC_MAP = NIDM['NIDM_0000076'] -NIDM_STANDARDIZED_COORDINATE_SYSTEM = NIDM['NIDM_0000075'] -NIDM_SPATIALLY_REGULARIZED_MODEL = NIDM['NIDM_0000074'] -NIDM_SPATIALLY_LOCAL_MODEL = NIDM['NIDM_0000073'] -NIDM_SPATIALLY_GLOBAL_MODEL = NIDM['NIDM_0000072'] -NIDM_SPATIAL_MODEL = NIDM['NIDM_0000071'] -NIDM_SIGNIFICANT_CLUSTER = NIDM['NIDM_0000070'] -NIDM_FOURIER_BASIS_SET = NIDM['NIDM_0000069'] -NIDM_SEARCH_SPACE_MASK_MAP = NIDM['NIDM_0000068'] -NIDM_CUSTOM_BASIS_SET = NIDM['NIDM_0000067'] -NIDM_RESIDUAL_MEAN_SQUARES_MAP = NIDM['NIDM_0000066'] -NIDM_POISSON_DISTRIBUTION = NIDM['NIDM_0000065'] -NIDM_PIXEL_CONNECTIVITY_CRITERION = NIDM['NIDM_0000064'] -NIDM_PEAK_DEFINITION_CRITERIA = NIDM['NIDM_0000063'] -NIDM_PEAK = NIDM['NIDM_0000062'] -NIDM_PARAMETER_ESTIMATE_MAP = NIDM['NIDM_0000061'] -NIDM_ONE_TAILED_TEST = NIDM['NIDM_0000060'] -NIDM_NON_PARAMETRIC_SYMMETRIC_DISTRIBUTION = NIDM['NIDM_0000059'] -NIDM_NON_PARAMETRIC_DISTRIBUTION = NIDM['NIDM_0000058'] -NIDM['NIDM_OBJECT_MODEL = NIDM_NIDM_0000057'] -NIDM_MODEL_PARAMETERS_ESTIMATION = NIDM['NIDM_0000056'] -NIDM_MNI305_COORDINATE_SYSTEM = NIDM['NIDM_0000055'] -NIDM_MASK_MAP = NIDM['NIDM_0000054'] -NIDM_MAP_HEADER = NIDM['NIDM_0000053'] -NIDM_MAP = NIDM['NIDM_0000052'] -NIDM_MNI_COORDINATE_SYSTEM = NIDM['NIDM_0000051'] -NIDM_IXI549_COORDINATE_SYSTEM = NIDM['NIDM_0000050'] -NIDM_INFERENCE = NIDM['NIDM_0000049'] -NIDM_INDEPENDENT_ERROR = NIDM['NIDM_0000048'] -NIDM_ICBM_MNI152_NON_LINEAR6TH_GENERATION_COORDINATE_SYSTEM = \ - NIDM['NIDM_0000047'] -NIDM_ICBM_MNI152_NON_LINEAR2009C_SYMMETRIC_COORDINATE_SYSTEM = \ - NIDM['NIDM_0000046'] -NIDM_ICBM_MNI152_NON_LINEAR2009C_ASYMMETRIC_COORDINATE_SYSTEM = \ - NIDM['NIDM_0000045'] -NIDM_ICBM_MNI152_NON_LINEAR2009B_SYMMETRIC_COORDINATE_SYSTEM = \ - NIDM['NIDM_0000044'] -NIDM_ICBM_MNI152_NON_LINEAR2009B_ASYMMETRIC_COORDINATE_SYSTEM = \ - NIDM['NIDM_0000043'] -NIDM_ICBM_MNI152_NON_LINEAR2009A_SYMMETRIC_COORDINATE_SYSTEM = \ - NIDM['NIDM_0000042'] -NIDM_ICBM_MNI152_NON_LINEAR2009A_ASYMMETRIC_COORDINATE_SYSTEM = \ - NIDM['NIDM_0000041'] -NIDM_ICBM_MNI152_LINEAR_COORDINATE_SYSTEM = NIDM['NIDM_0000040'] -NIDM_ICBM452_WARP5_COORDINATE_SYSTEM = NIDM['NIDM_0000039'] -NIDM_ICBM452_AIR_COORDINATE_SYSTEM = NIDM['NIDM_0000038'] -NIDM_HEMODYNAMIC_RESPONSE_FUNCTION_DERIVATIVE = NIDM['NIDM_0000037'] -NIDM_HEMODYNAMIC_RESPONSE_FUNCTION_BASIS = NIDM['NIDM_0000036'] -NIDM_HEMODYNAMIC_RESPONSE_FUNCTION = NIDM['NIDM_0000035'] -NIDM_HEIGHT_THRESHOLD = NIDM['NIDM_0000034'] -NIDM_GRAND_MEAN_MAP = NIDM['NIDM_0000033'] -NIDM_GAUSSIAN_DISTRIBUTION = NIDM['NIDM_0000032'] -NIDM_GAMMA_HRF = NIDM['NIDM_0000031'] -NIDM_GAMMA_HRB = NIDM['NIDM_0000030'] -NIDM_GAMMA_DIFFERENCE_HRF = NIDM['NIDM_0000029'] -NIDM_FINITE_IMPULSE_RESPONSE_HRB = NIDM['NIDM_0000028'] -NIDM_RESULTS = NIDM['NIDM_0000027'] -NIDM_EXTENT_THRESHOLD = NIDM['NIDM_0000026'] -NIDM_EXCURSION_SET_MAP = NIDM['NIDM_0000025'] -NIDM_EXCHANGEABLE_ERROR = NIDM['NIDM_0000024'] -NIDM_ERROR_MODEL = NIDM['NIDM_0000023'] -NIDM_ERROR_DISTRIBUTION = NIDM['NIDM_0000022'] -NIDM_REGRESSOR_NAMES = NIDM['NIDM_0000021'] -NIDM_DISPLAY_MASK_MAP = NIDM['NIDM_0000020'] -NIDM_DESIGN_MATRIX = NIDM['NIDM_0000019'] -NIDM_DATA_SCALING = NIDM['NIDM_0000018'] -NIDM_CUSTOM_COORDINATE_SYSTEM = NIDM['NIDM_0000017'] -NIDM_COORDINATE_SPACE = NIDM['NIDM_0000016'] -NIDM_COORDINATE = NIDM['NIDM_0000015'] -NIDM_LEGENDRE_POLYNOMIAL_ORDER = NIDM['NIDM_0000014'] -NIDM_CONTRAST_STANDARD_ERROR_MAP = NIDM['NIDM_0000013'] -NIDM_CONNECTIVITY_CRITERION = NIDM['NIDM_0000012'] -NIDM_CONJUNCTION_INFERENCE = NIDM['NIDM_0000011'] -SPM_PARTIAL_CONJUNCTION_DEGREE = SPM['SPM_0000015'] -SPM_KCONJUNCTION_INFERENCE = SPM['SPM_0000005'] -NIDM_HAS_FMRI_DESIGN = NIDM['NIDM_0000010'] -NIDM_COLIN27_COORDINATE_SYSTEM = NIDM['NIDM_0000009'] -NIDM_CLUSTER_LABELS_MAP = NIDM['NIDM_0000008'] -NIDM_CLUSTER_DEFINITION_CRITERIA = NIDM['NIDM_0000007'] -NIDM_CLUSTER = NIDM['NIDM_0000006'] -NIDM_BINOMIAL_DISTRIBUTION = NIDM['NIDM_0000005'] -NIDM_BINARY_MAP = NIDM['NIDM_0000004'] -NIDM_ARBITRARILY_CORRELATED_ERROR = NIDM['NIDM_0000003'] -NIDM_CONTRAST_ESTIMATION = NIDM['NIDM_0000001'] -NIDM_CONTRAST_MAP = NIDM['NIDM_0000002'] +FSL_FSLS_GAMMA_HRF = FSL["FSL_0000006"] +NIDM_HAS_MRI_PROTOCOL = NIDM["NIDM_0000172"] +NIDM_NUMBER_OF_SUBJECTS = NIDM["NIDM_0000171"] +NIDM_GROUP_NAME = NIDM["NIDM_0000170"] +NIDM_DATA = NIDM["NIDM_0000169"] +NIDM_NIDM_RESULTS_EXPORT = NIDM["NIDM_0000166"] +FSL_FEAT_VERSION = FSL["FSL_0000005"] +FSL_DRIFT_CUTOFF_PERIOD = FSL["FSL_0000004"] +FSL_TEMPORAL_DERIVATIVE = FSL["FSL_0000003"] +FSL_GAUSSIAN_RUNNING_LINE_DRIFT_MODEL = FSL["FSL_0000002"] +FSL_FSLS_GAMMA_DIFFERENCE_HRF = FSL["FSL_0000001"] +NIDM_CONTRAST_EXPLAINED_MEAN_SQUARE_MAP = NIDM["NIDM_0000163"] +NIDM_THRESHOLD = NIDM["NIDM_0000162"] +NIDM_EQUIVALENT_THRESHOLD = NIDM["NIDM_0000161"] +NIDM_P_VALUE_UNCORRECTED_CLASS = NIDM["NIDM_0000160"] +NIDM_NOISE_FWHM_IN_VOXELS = NIDM["NIDM_0000159"] +NIDM_NOISE_FWHM_IN_VERTICES = NIDM["NIDM_0000158"] +NIDM_NOISE_FWHM_IN_UNITS = NIDM["NIDM_0000157"] +NIDM_CLUSTER_SIZE_IN_RESELS = NIDM["NIDM_0000156"] +NIDM_F_MRI_DESIGN = NIDM["NIDM_0000155"] +NIDM_MIXED_DESIGN = NIDM["NIDM_0000154"] +NIDM_EVENT_RELATED_DESIGN = NIDM["NIDM_0000153"] +NIDM_BLOCK_BASED_DESIGN = NIDM["NIDM_0000152"] +NIDM_SINE_BASIS_SET = NIDM["NIDM_0000151"] +NIDM_LINEAR_SPLINE_BASIS_SET = NIDM["NIDM_0000150"] +NIDM_SEARCH_VOLUME_IN_RESELS = NIDM["NIDM_0000149"] +NIDM_RESEL_SIZE_IN_VOXELS = NIDM["NIDM_0000148"] +NIDM_HEIGHT_CRITICAL_THRESHOLD_FWE_05 = NIDM["NIDM_0000147"] +NIDM_HEIGHT_CRITICAL_THRESHOLD_FDR_05 = NIDM["NIDM_0000146"] +NIDM_NOISE_ROUGHNESS_IN_VOXELS = NIDM["NIDM_0000145"] +NIDM_RESELS_PER_VOXEL_MAP = NIDM["NIDM_0000144"] +NIDM_EXPECTED_NUMBER_OF_VOXELS_PER_CLUSTER = NIDM["NIDM_0000143"] +NIDM_EXPECTED_NUMBER_OF_VERTICES_PER_CLUSTER = NIDM["NIDM_0000142"] +NIDM_EXPECTED_NUMBER_OF_CLUSTERS = NIDM["NIDM_0000141"] +NIDM_CLUSTER_CENTER_OF_GRAVITY = NIDM["NIDM_0000140"] +NIDM_COORDINATE_VECTOR_IN_VOXELS = NIDM["NIDM_0000139"] +NIDM_HAS_MAXIMUM_INTENSITY_PROJECTION = NIDM["NIDM_0000138"] +NIDM_SEARCH_VOLUME_IN_VERTICES = NIDM["NIDM_0000137"] +NIDM_SEARCH_VOLUME_IN_UNITS = NIDM["NIDM_0000136"] +NIDM_CONTRAST_VARIANCE_MAP = NIDM["NIDM_0000135"] +NIDM_WITH_ESTIMATION_METHOD = NIDM["NIDM_0000134"] +NIDM_VOXEL_UNITS = NIDM["NIDM_0000133"] +NIDM_VOXEL_TO_WORLD_MAPPING = NIDM["NIDM_0000132"] +NIDM_VOXEL_SIZE = NIDM["NIDM_0000131"] +NIDM_VOXEL6CONNECTED = NIDM["NIDM_0000130"] +NIDM_VOXEL26CONNECTED = NIDM["NIDM_0000129"] +NIDM_VOXEL18CONNECTED = NIDM["NIDM_0000128"] +NIDM_VERSION = NIDM["NIDM_0000127"] +NIDM_VARIANCE_SPATIAL_MODEL = NIDM["NIDM_0000126"] +NIDM_USER_SPECIFIED_THRESHOLD_TYPE = NIDM["NIDM_0000125"] +NIDM_TARGET_INTENSITY = NIDM["NIDM_0000124"] +NIDM_STATISTIC_TYPE = NIDM["NIDM_0000123"] +NIDM_SOFTWARE_VERSION = NIDM["NIDM_0000122"] +NIDM_SEARCH_VOLUME_IN_VOXELS = NIDM["NIDM_0000121"] +NIDM_RANDOM_FIELD_STATIONARITY = NIDM["NIDM_0000120"] +NIDM_Q_VALUE_FDR = NIDM["NIDM_0000119"] +NIDM_PIXEL8CONNECTED = NIDM["NIDM_0000118"] +NIDM_PIXEL4CONNECTED = NIDM["NIDM_0000117"] +NIDM_P_VALUE_UNCORRECTED = NIDM["NIDM_0000116"] +NIDM_P_VALUE_FWER = NIDM["NIDM_0000115"] +NIDM_P_VALUE = NIDM["NIDM_0000114"] +NIDM_OBJECT_MODEL = NIDM["NIDM_0000113"] +NIDM_NUMBER_OF_DIMENSIONS = NIDM["NIDM_0000112"] +NIDM_NUMBER_OF_CLUSTERS = NIDM["NIDM_0000111"] +NIDM_GAUSSIAN_HRF = NIDM["NIDM_0000110"] +NIDM_MIN_DISTANCE_BETWEEN_PEAKS = NIDM["NIDM_0000109"] +NIDM_MAX_NUMBER_OF_PEAKS_PER_CLUSTER = NIDM["NIDM_0000108"] +NIDM_MASKED_MEDIAN = NIDM["NIDM_0000107"] +NIDM_IS_USER_DEFINED = NIDM["NIDM_0000106"] +NIDM_IN_WORLD_COORDINATE_SYSTEM = NIDM["NIDM_0000105"] +NIDM_IN_COORDINATE_SPACE = NIDM["NIDM_0000104"] +NIDM_HAS_MAP_HEADER = NIDM["NIDM_0000103"] +NIDM_HAS_HRF_BASIS = NIDM["NIDM_0000102"] +NIDM_HAS_ERROR_DISTRIBUTION = NIDM["NIDM_0000101"] +NIDM_HAS_ERROR_DEPENDENCE = NIDM["NIDM_0000100"] +NIDM_HAS_CONNECTIVITY_CRITERION = NIDM["NIDM_0000099"] +NIDM_HAS_CLUSTER_LABELS_MAP = NIDM["NIDM_0000098"] +NIDM_HAS_ALTERNATIVE_HYPOTHESIS = NIDM["NIDM_0000097"] +NIDM_GRAND_MEAN_SCALING = NIDM["NIDM_0000096"] +NIDM_GLOBAL_NULL_DEGREE = NIDM["NIDM_0000095"] +NIDM_ERROR_VARIANCE_HOMOGENEOUS = NIDM["NIDM_0000094"] +NIDM_ERROR_DEGREES_OF_FREEDOM = NIDM["NIDM_0000093"] +NIDM_EQUIVALENT_ZSTATISTIC = NIDM["NIDM_0000092"] +NIDM_EFFECT_DEGREES_OF_FREEDOM = NIDM["NIDM_0000091"] +NIDM_DIMENSIONS_IN_VOXELS = NIDM["NIDM_0000090"] +NIDM_DEPENDENCE_SPATIAL_MODEL = NIDM["NIDM_0000089"] +NIDM_HAS_DRIFT_MODEL = NIDM["NIDM_0000088"] +NIDM_DRIFT_MODEL = NIDM["NIDM_0000087"] +NIDM_COORDINATE_VECTOR = NIDM["NIDM_0000086"] +NIDM_CONTRAST_NAME = NIDM["NIDM_0000085"] +NIDM_CLUSTER_SIZE_IN_VOXELS = NIDM["NIDM_0000084"] +NIDM_CLUSTER_SIZE_IN_VERTICES = NIDM["NIDM_0000083"] +NIDM_CLUSTER_LABEL_ID = NIDM["NIDM_0000082"] +NIDM_WORLD_COORDINATE_SYSTEM = NIDM["NIDM_0000081"] +NIDM_VOXEL_CONNECTIVITY_CRITERION = NIDM["NIDM_0000080"] +NIDM_TWO_TAILED_TEST = NIDM["NIDM_0000079"] +NIDM_TALAIRACH_COORDINATE_SYSTEM = NIDM["NIDM_0000078"] +NIDM_SUBJECT_COORDINATE_SYSTEM = NIDM["NIDM_0000077"] +NIDM_STATISTIC_MAP = NIDM["NIDM_0000076"] +NIDM_STANDARDIZED_COORDINATE_SYSTEM = NIDM["NIDM_0000075"] +NIDM_SPATIALLY_REGULARIZED_MODEL = NIDM["NIDM_0000074"] +NIDM_SPATIALLY_LOCAL_MODEL = NIDM["NIDM_0000073"] +NIDM_SPATIALLY_GLOBAL_MODEL = NIDM["NIDM_0000072"] +NIDM_SPATIAL_MODEL = NIDM["NIDM_0000071"] +NIDM_SIGNIFICANT_CLUSTER = NIDM["NIDM_0000070"] +NIDM_FOURIER_BASIS_SET = NIDM["NIDM_0000069"] +NIDM_SEARCH_SPACE_MASK_MAP = NIDM["NIDM_0000068"] +NIDM_CUSTOM_BASIS_SET = NIDM["NIDM_0000067"] +NIDM_RESIDUAL_MEAN_SQUARES_MAP = NIDM["NIDM_0000066"] +NIDM_POISSON_DISTRIBUTION = NIDM["NIDM_0000065"] +NIDM_PIXEL_CONNECTIVITY_CRITERION = NIDM["NIDM_0000064"] +NIDM_PEAK_DEFINITION_CRITERIA = NIDM["NIDM_0000063"] +NIDM_PEAK = NIDM["NIDM_0000062"] +NIDM_PARAMETER_ESTIMATE_MAP = NIDM["NIDM_0000061"] +NIDM_ONE_TAILED_TEST = NIDM["NIDM_0000060"] +NIDM_NON_PARAMETRIC_SYMMETRIC_DISTRIBUTION = NIDM["NIDM_0000059"] +NIDM_NON_PARAMETRIC_DISTRIBUTION = NIDM["NIDM_0000058"] +NIDM["NIDM_OBJECT_MODEL = NIDM_NIDM_0000057"] +NIDM_MODEL_PARAMETERS_ESTIMATION = NIDM["NIDM_0000056"] +NIDM_MNI305_COORDINATE_SYSTEM = NIDM["NIDM_0000055"] +NIDM_MASK_MAP = NIDM["NIDM_0000054"] +NIDM_MAP_HEADER = NIDM["NIDM_0000053"] +NIDM_MAP = NIDM["NIDM_0000052"] +NIDM_MNI_COORDINATE_SYSTEM = NIDM["NIDM_0000051"] +NIDM_IXI549_COORDINATE_SYSTEM = NIDM["NIDM_0000050"] +NIDM_INFERENCE = NIDM["NIDM_0000049"] +NIDM_INDEPENDENT_ERROR = NIDM["NIDM_0000048"] +NIDM_ICBM_MNI152_NON_LINEAR6TH_GENERATION_COORDINATE_SYSTEM = NIDM[ + "NIDM_0000047" +] +NIDM_ICBM_MNI152_NON_LINEAR2009C_SYMMETRIC_COORDINATE_SYSTEM = NIDM[ + "NIDM_0000046" +] +NIDM_ICBM_MNI152_NON_LINEAR2009C_ASYMMETRIC_COORDINATE_SYSTEM = NIDM[ + "NIDM_0000045" +] +NIDM_ICBM_MNI152_NON_LINEAR2009B_SYMMETRIC_COORDINATE_SYSTEM = NIDM[ + "NIDM_0000044" +] +NIDM_ICBM_MNI152_NON_LINEAR2009B_ASYMMETRIC_COORDINATE_SYSTEM = NIDM[ + "NIDM_0000043" +] +NIDM_ICBM_MNI152_NON_LINEAR2009A_SYMMETRIC_COORDINATE_SYSTEM = NIDM[ + "NIDM_0000042" +] +NIDM_ICBM_MNI152_NON_LINEAR2009A_ASYMMETRIC_COORDINATE_SYSTEM = NIDM[ + "NIDM_0000041" +] +NIDM_ICBM_MNI152_LINEAR_COORDINATE_SYSTEM = NIDM["NIDM_0000040"] +NIDM_ICBM452_WARP5_COORDINATE_SYSTEM = NIDM["NIDM_0000039"] +NIDM_ICBM452_AIR_COORDINATE_SYSTEM = NIDM["NIDM_0000038"] +NIDM_HEMODYNAMIC_RESPONSE_FUNCTION_DERIVATIVE = NIDM["NIDM_0000037"] +NIDM_HEMODYNAMIC_RESPONSE_FUNCTION_BASIS = NIDM["NIDM_0000036"] +NIDM_HEMODYNAMIC_RESPONSE_FUNCTION = NIDM["NIDM_0000035"] +NIDM_HEIGHT_THRESHOLD = NIDM["NIDM_0000034"] +NIDM_GRAND_MEAN_MAP = NIDM["NIDM_0000033"] +NIDM_GAUSSIAN_DISTRIBUTION = NIDM["NIDM_0000032"] +NIDM_GAMMA_HRF = NIDM["NIDM_0000031"] +NIDM_GAMMA_HRB = NIDM["NIDM_0000030"] +NIDM_GAMMA_DIFFERENCE_HRF = NIDM["NIDM_0000029"] +NIDM_FINITE_IMPULSE_RESPONSE_HRB = NIDM["NIDM_0000028"] +NIDM_RESULTS = NIDM["NIDM_0000027"] +NIDM_EXTENT_THRESHOLD = NIDM["NIDM_0000026"] +NIDM_EXCURSION_SET_MAP = NIDM["NIDM_0000025"] +NIDM_EXCHANGEABLE_ERROR = NIDM["NIDM_0000024"] +NIDM_ERROR_MODEL = NIDM["NIDM_0000023"] +NIDM_ERROR_DISTRIBUTION = NIDM["NIDM_0000022"] +NIDM_REGRESSOR_NAMES = NIDM["NIDM_0000021"] +NIDM_DISPLAY_MASK_MAP = NIDM["NIDM_0000020"] +NIDM_DESIGN_MATRIX = NIDM["NIDM_0000019"] +NIDM_DATA_SCALING = NIDM["NIDM_0000018"] +NIDM_CUSTOM_COORDINATE_SYSTEM = NIDM["NIDM_0000017"] +NIDM_COORDINATE_SPACE = NIDM["NIDM_0000016"] +NIDM_COORDINATE = NIDM["NIDM_0000015"] +NIDM_LEGENDRE_POLYNOMIAL_ORDER = NIDM["NIDM_0000014"] +NIDM_CONTRAST_STANDARD_ERROR_MAP = NIDM["NIDM_0000013"] +NIDM_CONNECTIVITY_CRITERION = NIDM["NIDM_0000012"] +NIDM_CONJUNCTION_INFERENCE = NIDM["NIDM_0000011"] +SPM_PARTIAL_CONJUNCTION_DEGREE = SPM["SPM_0000015"] +SPM_KCONJUNCTION_INFERENCE = SPM["SPM_0000005"] +NIDM_HAS_FMRI_DESIGN = NIDM["NIDM_0000010"] +NIDM_COLIN27_COORDINATE_SYSTEM = NIDM["NIDM_0000009"] +NIDM_CLUSTER_LABELS_MAP = NIDM["NIDM_0000008"] +NIDM_CLUSTER_DEFINITION_CRITERIA = NIDM["NIDM_0000007"] +NIDM_CLUSTER = NIDM["NIDM_0000006"] +NIDM_BINOMIAL_DISTRIBUTION = NIDM["NIDM_0000005"] +NIDM_BINARY_MAP = NIDM["NIDM_0000004"] +NIDM_ARBITRARILY_CORRELATED_ERROR = NIDM["NIDM_0000003"] +NIDM_CONTRAST_ESTIMATION = NIDM["NIDM_0000001"] +NIDM_CONTRAST_MAP = NIDM["NIDM_0000002"] -STATO_OLS = OBO['STATO_0000370'] -STATO_WLS = OBO['STATO_0000371'] -STATO_GLS = OBO['STATO_0000372'] -STATO_TSTATISTIC = OBO['STATO_0000176'] -STATO_ZSTATISTIC = OBO['STATO_0000376'] -STATO_FSTATISTIC = OBO['STATO_0000282'] -STATO_CONTRAST_WEIGHT_MATRIX = OBO['STATO_0000323'] -STATO_NORMAL_DISTRIBUTION = OBO['STATO_0000227'] -STATO_GROUP = OBO['STATO_0000193'] +STATO_OLS = OBO["STATO_0000370"] +STATO_WLS = OBO["STATO_0000371"] +STATO_GLS = OBO["STATO_0000372"] +STATO_TSTATISTIC = OBO["STATO_0000176"] +STATO_ZSTATISTIC = OBO["STATO_0000376"] +STATO_FSTATISTIC = OBO["STATO_0000282"] +STATO_CONTRAST_WEIGHT_MATRIX = OBO["STATO_0000323"] +STATO_NORMAL_DISTRIBUTION = OBO["STATO_0000227"] +STATO_GROUP = OBO["STATO_0000193"] -OBO_STATISTIC = OBO['STATO_0000039'] -OBO_P_VALUE_FWER = OBO['OBI_0001265'] -OBO_Q_VALUE_FDR = OBO['OBI_0001442'] +OBO_STATISTIC = OBO["STATO_0000039"] +OBO_P_VALUE_FWER = OBO["OBI_0001265"] +OBO_Q_VALUE_FDR = OBO["OBI_0001442"] -NIDM_INDEPEDENT_ERROR = NIDM['NIDM_0000048'] -OBO_SERIALLY_CORR_COV = OBO['STATO_0000357'] -OBO_COMPOUND_SYMMETRY_COV = OBO['STATO_0000362'] -OBO_UNSTRUCTURED_COV = OBO['STATO_0000405'] +NIDM_INDEPEDENT_ERROR = NIDM["NIDM_0000048"] +OBO_SERIALLY_CORR_COV = OBO["STATO_0000357"] +OBO_COMPOUND_SYMMETRY_COV = OBO["STATO_0000362"] +OBO_UNSTRUCTURED_COV = OBO["STATO_0000405"] SPATIALLY_GLOBAL = NIDM_SPATIALLY_GLOBAL_MODEL SPATIALLY_LOCAL = NIDM_SPATIALLY_LOCAL_MODEL SPATIALLY_REGUL = NIDM_SPATIALLY_REGULARIZED_MODEL -SPATIAL_DEPENDENCY_ENUM = ( - SPATIALLY_GLOBAL, - SPATIALLY_LOCAL, - SPATIALLY_REGUL -) +SPATIAL_DEPENDENCY_ENUM = (SPATIALLY_GLOBAL, SPATIALLY_LOCAL, SPATIALLY_REGUL) diff --git a/nidmresults/objects/constants_rdflib.py b/nidmresults/objects/constants_rdflib.py index 5836699..88e98ea 100644 --- a/nidmresults/objects/constants_rdflib.py +++ b/nidmresults/objects/constants_rdflib.py @@ -1,32 +1,34 @@ #!/usr/bin/env python -''' Definition of constants +"""Definition of constants. @author: Camille Maumet @copyright: University of Warwick 2014 -''' +""" -from rdflib import Namespace, Graph +from rdflib import Graph, Namespace -PROV = Namespace('http://www.w3.org/ns/prov#') -NIDM_URL = 'http://purl.org/nidash/nidm#' +PROV = Namespace("http://www.w3.org/ns/prov#") +NIDM_URL = "http://purl.org/nidash/nidm#" NIDM = Namespace(NIDM_URL) -NIIRI = Namespace('http://iri.nidash.org/') -AFNI = Namespace('http://purl.org/nidash/afni#') -SPM = Namespace('http://purl.org/nidash/spm#') -FSL = Namespace('http://purl.org/nidash/fsl#') -RDFS = Namespace('http://www.w3.org/2000/01/rdf-schema#') -CRYPTO = Namespace('http://id.loc.gov/vocabulary/preservation/\ -cryptographicHashFunctions#') -DC = Namespace('http://purl.org/dc/elements/1.1/') -DCT = Namespace('http://purl.org/dc/terms/') -OWL = Namespace('http://www.w3.org/2002/07/owl#') -XSD = Namespace('http://www.w3.org/2001/XMLSchema#') +NIIRI = Namespace("http://iri.nidash.org/") +AFNI = Namespace("http://purl.org/nidash/afni#") +SPM = Namespace("http://purl.org/nidash/spm#") +FSL = Namespace("http://purl.org/nidash/fsl#") +RDFS = Namespace("http://www.w3.org/2000/01/rdf-schema#") +CRYPTO = Namespace( + "http://id.loc.gov/vocabulary/preservation/\ +cryptographicHashFunctions#" +) +DC = Namespace("http://purl.org/dc/elements/1.1/") +DCT = Namespace("http://purl.org/dc/terms/") +OWL = Namespace("http://www.w3.org/2002/07/owl#") +XSD = Namespace("http://www.w3.org/2001/XMLSchema#") OBO_URL = "http://purl.obolibrary.org/obo/" OBO = Namespace(OBO_URL) -NFO = Namespace('http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#') +NFO = Namespace("http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#") SCR = Namespace("http://scicrunch.org/resolver/") NLX = Namespace("http://uri.neuinfo.org/nif/nifstd/") SKOS = Namespace("http://www.w3.org/2004/02/skos/core#") @@ -45,8 +47,8 @@ "nfo": NFO, "dc": DC, "nlx": NLX, - "scr": SCR - } + "scr": SCR, +} # Empty graph used to compute qnames q_graph = Graph() @@ -54,252 +56,261 @@ q_graph.bind(name, namespace) # NIDM constants -FSL_GAMMAHRF = FSL['FSL_0000007'] -FSL_FSLS_GAMMA_HRF = FSL['FSL_0000006'] -NIDM_HAS_MRI_PROTOCOL = NIDM['NIDM_0000172'] -NIDM_NUMBER_OF_SUBJECTS = NIDM['NIDM_0000171'] -NIDM_GROUP_NAME = NIDM['NIDM_0000170'] -NIDM_DATA = NIDM['NIDM_0000169'] -NIDM_SPM_RESULTS_NIDM = NIDM['NIDM_0000168'] -NIDM_NIDMFSL = NIDM['NIDM_0000167'] -NIDM_NIDM_RESULTS_EXPORT = NIDM['NIDM_0000166'] -NIDM_NIDM_RESULTS_EXPORTER = NIDM['NIDM_0000165'] -NIDM_NEUROIMAGING_ANALYSIS_SOFTWARE = NIDM['NIDM_0000164'] -NIDM_CONTRAST_EXPLAINED_MEAN_SQUARE_MAP = NIDM['NIDM_0000163'] -NIDM_THRESHOLD = NIDM['NIDM_0000162'] -NIDM_EQUIVALENT_THRESHOLD = NIDM['NIDM_0000161'] -NIDM_P_VALUE_UNCORRECTED_CLASS = NIDM['NIDM_0000160'] +FSL_GAMMAHRF = FSL["FSL_0000007"] +FSL_FSLS_GAMMA_HRF = FSL["FSL_0000006"] +NIDM_HAS_MRI_PROTOCOL = NIDM["NIDM_0000172"] +NIDM_NUMBER_OF_SUBJECTS = NIDM["NIDM_0000171"] +NIDM_GROUP_NAME = NIDM["NIDM_0000170"] +NIDM_DATA = NIDM["NIDM_0000169"] +NIDM_SPM_RESULTS_NIDM = NIDM["NIDM_0000168"] +NIDM_NIDMFSL = NIDM["NIDM_0000167"] +NIDM_NIDM_RESULTS_EXPORT = NIDM["NIDM_0000166"] +NIDM_NIDM_RESULTS_EXPORTER = NIDM["NIDM_0000165"] +NIDM_NEUROIMAGING_ANALYSIS_SOFTWARE = NIDM["NIDM_0000164"] +NIDM_CONTRAST_EXPLAINED_MEAN_SQUARE_MAP = NIDM["NIDM_0000163"] +NIDM_THRESHOLD = NIDM["NIDM_0000162"] +NIDM_EQUIVALENT_THRESHOLD = NIDM["NIDM_0000161"] +NIDM_P_VALUE_UNCORRECTED_CLASS = NIDM["NIDM_0000160"] NIDM_P_VALUE_UNCORRECTED_QNAME = q_graph.qname(NIDM_P_VALUE_UNCORRECTED_CLASS) -NIDM_NOISE_FWHM_IN_VOXELS = NIDM['NIDM_0000159'] -NIDM_NOISE_FWHM_IN_VERTICES = NIDM['NIDM_0000158'] -NIDM_NOISE_FWHM_IN_UNITS = NIDM['NIDM_0000157'] -FSL_FEAT_VERSION = FSL['FSL_0000005'] -FSL_DRIFT_CUTOFF_PERIOD = FSL['FSL_0000004'] -FSL_TEMPORAL_DERIVATIVE = FSL['FSL_0000003'] -FSL_GAUSSIAN_RUNNING_LINE_DRIFT_MODEL = FSL['FSL_0000002'] -FSL_FSLS_GAMMA_DIFFERENCE_HRF = FSL['FSL_0000001'] -SPM_PARTIAL_CONJUNCTION_DEGREE = SPM['SPM_0000015'] -SPM_SMALLEST_SUPRA_THRESHOLD_CLUSTER_SIZE_IN_VOXELS_FWE05 = SPM['SPM_0000014'] -SPM_SMALLEST_SUPRA_THRESHOLD_CLUSTER_SIZE_IN_VOXELS_FDR05 = SPM['SPM_0000013'] -SPM_SMALLEST_SUPRA_THRESHOLD_CLUSTER_SIZE_IN_VERTICES_FWE05 = ( - SPM['SPM_0000012']) -SPM_SMALLEST_SUPRA_THRESHOLD_CLUSTER_SIZE_IN_VERTICES_FDR05 = ( - SPM['SPM_0000011']) -SPM_SEARCH_VOLUME_RESELS_GEOMETRY = SPM['SPM_0000010'] -SPM_TEMPORAL_DERIVATIVE = SPM['SPM_0000006'] -SPM_KCONJUNCTION_INFERENCE = SPM['SPM_0000005'] -SPM_CANONICAL_HRF = SPM['SPM_0000004'] -SPM_DISPERSION_DERIVATIVE = SPM['SPM_0000003'] -SPM_DCT_DRIFT_MODEL = SPM['SPM_0000002'] -SPM_SPMS_DRIFT_CUT_OFF_PERIOD = SPM['SPM_0000001'] -NIDM_CLUSTER_SIZE_IN_RESELS = NIDM['NIDM_0000156'] -NIDM_F_MRI_DESIGN = NIDM['NIDM_0000155'] -NIDM_MIXED_DESIGN = NIDM['NIDM_0000154'] -NIDM_EVENT_RELATED_DESIGN = NIDM['NIDM_0000153'] -NIDM_BLOCK_BASED_DESIGN = NIDM['NIDM_0000152'] -NIDM_SINE_BASIS_SET = NIDM['NIDM_0000151'] -NIDM_LINEAR_SPLINE_BASIS_SET = NIDM['NIDM_0000150'] -NIDM_SEARCH_VOLUME_IN_RESELS = NIDM['NIDM_0000149'] -NIDM_RESEL_SIZE_IN_VOXELS = NIDM['NIDM_0000148'] -NIDM_HEIGHT_CRITICAL_THRESHOLD_FWE_05 = NIDM['NIDM_0000147'] -NIDM_HEIGHT_CRITICAL_THRESHOLD_FDR_05 = NIDM['NIDM_0000146'] -NIDM_NOISE_ROUGHNESS_IN_VOXELS = NIDM['NIDM_0000145'] -NIDM_RESELS_PER_VOXEL_MAP = NIDM['NIDM_0000144'] -NIDM_EXPECTED_NUMBER_OF_VOXELS_PER_CLUSTER = NIDM['NIDM_0000143'] -NIDM_EXPECTED_NUMBER_OF_VERTICES_PER_CLUSTER = NIDM['NIDM_0000142'] -NIDM_EXPECTED_NUMBER_OF_CLUSTERS = NIDM['NIDM_0000141'] -NIDM_CLUSTER_CENTER_OF_GRAVITY = NIDM['NIDM_0000140'] -NIDM_COORDINATE_VECTOR_IN_VOXELS = NIDM['NIDM_0000139'] -NIDM_HAS_MAXIMUM_INTENSITY_PROJECTION = NIDM['NIDM_0000138'] -NIDM_SEARCH_VOLUME_IN_VERTICES = NIDM['NIDM_0000137'] -NIDM_SEARCH_VOLUME_IN_UNITS = NIDM['NIDM_0000136'] -NIDM_CONTRAST_VARIANCE_MAP = NIDM['NIDM_0000135'] -NIDM_WITH_ESTIMATION_METHOD = NIDM['NIDM_0000134'] -NIDM_VOXEL_UNITS = NIDM['NIDM_0000133'] -NIDM_VOXEL_TO_WORLD_MAPPING = NIDM['NIDM_0000132'] -NIDM_VOXEL_SIZE = NIDM['NIDM_0000131'] -NIDM_VOXEL6CONNECTED = NIDM['NIDM_0000130'] -NIDM_VOXEL26CONNECTED = NIDM['NIDM_0000129'] -NIDM_VOXEL18CONNECTED = NIDM['NIDM_0000128'] -NIDM_VERSION = NIDM['NIDM_0000127'] -NIDM_VARIANCE_SPATIAL_MODEL = NIDM['NIDM_0000126'] -NIDM_USER_SPECIFIED_THRESHOLD_TYPE = NIDM['NIDM_0000125'] -NIDM_TARGET_INTENSITY = NIDM['NIDM_0000124'] -NIDM_STATISTIC_TYPE = NIDM['NIDM_0000123'] -NIDM_SOFTWARE_VERSION = NIDM['NIDM_0000122'] -NIDM_SEARCH_VOLUME_IN_VOXELS = NIDM['NIDM_0000121'] -NIDM_RANDOM_FIELD_STATIONARITY = NIDM['NIDM_0000120'] -NIDM_Q_VALUE_FDR = NIDM['NIDM_0000119'] -NIDM_PIXEL8CONNECTED = NIDM['NIDM_0000118'] -NIDM_PIXEL4CONNECTED = NIDM['NIDM_0000117'] -NIDM_P_VALUE_UNCORRECTED = NIDM['NIDM_0000116'] -NIDM_P_VALUE_FWER = NIDM['NIDM_0000115'] -NIDM_P_VALUE = NIDM['NIDM_0000114'] -NIDM_OBJECT_MODEL = NIDM['NIDM_0000113'] -NIDM_NUMBER_OF_DIMENSIONS = NIDM['NIDM_0000112'] -NIDM_NUMBER_OF_CLUSTERS = NIDM['NIDM_0000111'] -NIDM_GAUSSIAN_HRF = NIDM['NIDM_0000110'] -NIDM_MIN_DISTANCE_BETWEEN_PEAKS = NIDM['NIDM_0000109'] -NIDM_MAX_NUMBER_OF_PEAKS_PER_CLUSTER = NIDM['NIDM_0000108'] -NIDM_MASKED_MEDIAN = NIDM['NIDM_0000107'] -NIDM_IS_USER_DEFINED = NIDM['NIDM_0000106'] -NIDM_IN_WORLD_COORDINATE_SYSTEM = NIDM['NIDM_0000105'] -NIDM_IN_COORDINATE_SPACE = NIDM['NIDM_0000104'] -NIDM_HAS_MAP_HEADER = NIDM['NIDM_0000103'] -NIDM_HAS_HRF_BASIS = NIDM['NIDM_0000102'] -NIDM_HAS_ERROR_DISTRIBUTION = NIDM['NIDM_0000101'] -NIDM_HAS_ERROR_DEPENDENCE = NIDM['NIDM_0000100'] -NIDM_HAS_CONNECTIVITY_CRITERION = NIDM['NIDM_0000099'] -NIDM_HAS_CLUSTER_LABELS_MAP = NIDM['NIDM_0000098'] -NIDM_HAS_ALTERNATIVE_HYPOTHESIS = NIDM['NIDM_0000097'] -NIDM_GRAND_MEAN_SCALING = NIDM['NIDM_0000096'] -NIDM_ERROR_VARIANCE_HOMOGENEOUS = NIDM['NIDM_0000094'] -NIDM_ERROR_DEGREES_OF_FREEDOM = NIDM['NIDM_0000093'] -NIDM_EQUIVALENT_ZSTATISTIC = NIDM['NIDM_0000092'] -NIDM_EFFECT_DEGREES_OF_FREEDOM = NIDM['NIDM_0000091'] -NIDM_DIMENSIONS_IN_VOXELS = NIDM['NIDM_0000090'] -NIDM_DEPENDENCE_SPATIAL_MODEL = NIDM['NIDM_0000089'] -NIDM_HAS_DRIFT_MODEL = NIDM['NIDM_0000088'] -NIDM_DRIFT_MODEL = NIDM['NIDM_0000087'] -NIDM_COORDINATE_VECTOR = NIDM['NIDM_0000086'] -NIDM_CONTRAST_NAME = NIDM['NIDM_0000085'] -NIDM_CLUSTER_SIZE_IN_VOXELS = NIDM['NIDM_0000084'] -NIDM_CLUSTER_SIZE_IN_VERTICES = NIDM['NIDM_0000083'] -NIDM_CLUSTER_LABEL_ID = NIDM['NIDM_0000082'] -NIDM_WORLD_COORDINATE_SYSTEM = NIDM['NIDM_0000081'] -NIDM_VOXEL_CONNECTIVITY_CRITERION = NIDM['NIDM_0000080'] -NIDM_TWO_TAILED_TEST = NIDM['NIDM_0000079'] -NIDM_TALAIRACH_COORDINATE_SYSTEM = NIDM['NIDM_0000078'] -NIDM_SUBJECT_COORDINATE_SYSTEM = NIDM['NIDM_0000077'] -NIDM_STATISTIC_MAP = NIDM['NIDM_0000076'] -NIDM_STANDARDIZED_COORDINATE_SYSTEM = NIDM['NIDM_0000075'] -NIDM_SPATIALLY_REGULARIZED_MODEL = NIDM['NIDM_0000074'] -NIDM_SPATIALLY_LOCAL_MODEL = NIDM['NIDM_0000073'] -NIDM_SPATIALLY_GLOBAL_MODEL = NIDM['NIDM_0000072'] -NIDM_SPATIAL_MODEL = NIDM['NIDM_0000071'] -NIDM_SUPRA_THRESHOLD_CLUSTER = NIDM['NIDM_0000070'] -NIDM_FOURIER_BASIS_SET = NIDM['NIDM_0000069'] -NIDM_SEARCH_SPACE_MASK_MAP = NIDM['NIDM_0000068'] -NIDM_CUSTOM_BASIS_SET = NIDM['NIDM_0000067'] -NIDM_RESIDUAL_MEAN_SQUARES_MAP = NIDM['NIDM_0000066'] -NIDM_POISSON_DISTRIBUTION = NIDM['NIDM_0000065'] -NIDM_PIXEL_CONNECTIVITY_CRITERION = NIDM['NIDM_0000064'] -NIDM_PEAK_DEFINITION_CRITERIA = NIDM['NIDM_0000063'] -NIDM_PEAK = NIDM['NIDM_0000062'] -NIDM_PARAMETER_ESTIMATE_MAP = NIDM['NIDM_0000061'] -NIDM_ONE_TAILED_TEST = NIDM['NIDM_0000060'] -NIDM_NON_PARAMETRIC_SYMMETRIC_DISTRIBUTION = NIDM['NIDM_0000059'] -NIDM_NON_PARAMETRIC_DISTRIBUTION = NIDM['NIDM_0000058'] -NIDM_NIDM_OBJECT_MODEL = NIDM['NIDM_0000057'] -NIDM_MODEL_PARAMETERS_ESTIMATION = NIDM['NIDM_0000056'] -NIDM_MNI305_COORDINATE_SYSTEM = NIDM['NIDM_0000055'] -NIDM_MASK_MAP = NIDM['NIDM_0000054'] -NIDM_MAP_HEADER = NIDM['NIDM_0000053'] -NIDM_MAP = NIDM['NIDM_0000052'] -NIDM_MNI_COORDINATE_SYSTEM = NIDM['NIDM_0000051'] -NIDM_IXI549_COORDINATE_SYSTEM = NIDM['NIDM_0000050'] -NIDM_INFERENCE = NIDM['NIDM_0000049'] -NIDM_INDEPENDENT_ERROR = NIDM['NIDM_0000048'] -NIDM_ICBM_MNI152_NON_LINEAR6TH_GENERATION_COORDINATE_SYSTEM = ( - NIDM['NIDM_0000047']) -NIDM_ICBM_MNI152_NON_LINEAR2009C_SYMMETRIC_COORDINATE_SYSTEM = ( - NIDM['NIDM_0000046']) -NIDM_ICBM_MNI152_NON_LINEAR2009C_ASYMMETRIC_COORDINATE_SYSTEM = ( - NIDM['NIDM_0000045']) -NIDM_ICBM_MNI152_NON_LINEAR2009B_SYMMETRIC_COORDINATE_SYSTEM = ( - NIDM['NIDM_0000044']) -NIDM_ICBM_MNI152_NON_LINEAR2009B_ASYMMETRIC_COORDINATE_SYSTEM = ( - NIDM['NIDM_0000043']) -NIDM_ICBM_MNI152_NON_LINEAR2009A_SYMMETRIC_COORDINATE_SYSTEM = ( - NIDM['NIDM_0000042']) -NIDM_ICBM_MNI152_NON_LINEAR2009A_ASYMMETRIC_COORDINATE_SYSTEM = ( - NIDM['NIDM_0000041']) -NIDM_ICBM_MNI152_LINEAR_COORDINATE_SYSTEM = NIDM['NIDM_0000040'] -NIDM_ICBM452_WARP5_COORDINATE_SYSTEM = NIDM['NIDM_0000039'] -NIDM_ICBM452_AIR_COORDINATE_SYSTEM = NIDM['NIDM_0000038'] -NIDM_HEMODYNAMIC_RESPONSE_FUNCTION_DERIVATIVE = NIDM['NIDM_0000037'] -NIDM_HEMODYNAMIC_RESPONSE_FUNCTION_BASIS = NIDM['NIDM_0000036'] -NIDM_HEMODYNAMIC_RESPONSE_FUNCTION = NIDM['NIDM_0000035'] -NIDM_HEIGHT_THRESHOLD = NIDM['NIDM_0000034'] -NIDM_GRAND_MEAN_MAP = NIDM['NIDM_0000033'] -NIDM_GAMMA_HRF = NIDM['NIDM_0000031'] -NIDM_GAMMA_HRB = NIDM['NIDM_0000030'] -NIDM_GAMMA_DIFFERENCE_HRF = NIDM['NIDM_0000029'] -NIDM_FINITE_IMPULSE_RESPONSE_HRB = NIDM['NIDM_0000028'] -NIDM_RESULTS = NIDM['NIDM_0000027'] -NIDM_EXTENT_THRESHOLD = NIDM['NIDM_0000026'] -NIDM_EXCURSION_SET_MAP = NIDM['NIDM_0000025'] -NIDM_EXCHANGEABLE_ERROR = NIDM['NIDM_0000024'] -NIDM_ERROR_MODEL = NIDM['NIDM_0000023'] -NIDM_ERROR_DISTRIBUTION = NIDM['NIDM_0000022'] -NIDM_REGRESSOR_NAMES = NIDM['NIDM_0000021'] -NIDM_DISPLAY_MASK_MAP = NIDM['NIDM_0000020'] -NIDM_DESIGN_MATRIX = NIDM['NIDM_0000019'] -NIDM_CUSTOM_COORDINATE_SYSTEM = NIDM['NIDM_0000017'] -NIDM_COORDINATE_SPACE = NIDM['NIDM_0000016'] -NIDM_COORDINATE = NIDM['NIDM_0000015'] -NIDM_LEGENDRE_POLYNOMIAL_ORDER = NIDM['NIDM_0000014'] -NIDM_CONTRAST_STANDARD_ERROR_MAP = NIDM['NIDM_0000013'] -NIDM_CONNECTIVITY_CRITERION = NIDM['NIDM_0000012'] -NIDM_CONJUNCTION_INFERENCE = NIDM['NIDM_0000011'] -NIDM_HAS_FMRI_DESIGN = NIDM['NIDM_0000010'] -NIDM_COLIN27_COORDINATE_SYSTEM = NIDM['NIDM_0000009'] -NIDM_CLUSTER_LABELS_MAP = NIDM['NIDM_0000008'] -NIDM_CLUSTER_DEFINITION_CRITERIA = NIDM['NIDM_0000007'] -NIDM_CLUSTER = NIDM['NIDM_0000006'] -NIDM_BINOMIAL_DISTRIBUTION = NIDM['NIDM_0000005'] -NIDM_BINARY_MAP = NIDM['NIDM_0000004'] -NIDM_CONTRAST_ESTIMATION = NIDM['NIDM_0000001'] -NIDM_CONTRAST_MAP = NIDM['NIDM_0000002'] +NIDM_NOISE_FWHM_IN_VOXELS = NIDM["NIDM_0000159"] +NIDM_NOISE_FWHM_IN_VERTICES = NIDM["NIDM_0000158"] +NIDM_NOISE_FWHM_IN_UNITS = NIDM["NIDM_0000157"] +FSL_FEAT_VERSION = FSL["FSL_0000005"] +FSL_DRIFT_CUTOFF_PERIOD = FSL["FSL_0000004"] +FSL_TEMPORAL_DERIVATIVE = FSL["FSL_0000003"] +FSL_GAUSSIAN_RUNNING_LINE_DRIFT_MODEL = FSL["FSL_0000002"] +FSL_FSLS_GAMMA_DIFFERENCE_HRF = FSL["FSL_0000001"] +SPM_PARTIAL_CONJUNCTION_DEGREE = SPM["SPM_0000015"] +SPM_SMALLEST_SUPRA_THRESHOLD_CLUSTER_SIZE_IN_VOXELS_FWE05 = SPM["SPM_0000014"] +SPM_SMALLEST_SUPRA_THRESHOLD_CLUSTER_SIZE_IN_VOXELS_FDR05 = SPM["SPM_0000013"] +SPM_SMALLEST_SUPRA_THRESHOLD_CLUSTER_SIZE_IN_VERTICES_FWE05 = SPM[ + "SPM_0000012" +] +SPM_SMALLEST_SUPRA_THRESHOLD_CLUSTER_SIZE_IN_VERTICES_FDR05 = SPM[ + "SPM_0000011" +] +SPM_SEARCH_VOLUME_RESELS_GEOMETRY = SPM["SPM_0000010"] +SPM_TEMPORAL_DERIVATIVE = SPM["SPM_0000006"] +SPM_KCONJUNCTION_INFERENCE = SPM["SPM_0000005"] +SPM_CANONICAL_HRF = SPM["SPM_0000004"] +SPM_DISPERSION_DERIVATIVE = SPM["SPM_0000003"] +SPM_DCT_DRIFT_MODEL = SPM["SPM_0000002"] +SPM_SPMS_DRIFT_CUT_OFF_PERIOD = SPM["SPM_0000001"] +NIDM_CLUSTER_SIZE_IN_RESELS = NIDM["NIDM_0000156"] +NIDM_F_MRI_DESIGN = NIDM["NIDM_0000155"] +NIDM_MIXED_DESIGN = NIDM["NIDM_0000154"] +NIDM_EVENT_RELATED_DESIGN = NIDM["NIDM_0000153"] +NIDM_BLOCK_BASED_DESIGN = NIDM["NIDM_0000152"] +NIDM_SINE_BASIS_SET = NIDM["NIDM_0000151"] +NIDM_LINEAR_SPLINE_BASIS_SET = NIDM["NIDM_0000150"] +NIDM_SEARCH_VOLUME_IN_RESELS = NIDM["NIDM_0000149"] +NIDM_RESEL_SIZE_IN_VOXELS = NIDM["NIDM_0000148"] +NIDM_HEIGHT_CRITICAL_THRESHOLD_FWE_05 = NIDM["NIDM_0000147"] +NIDM_HEIGHT_CRITICAL_THRESHOLD_FDR_05 = NIDM["NIDM_0000146"] +NIDM_NOISE_ROUGHNESS_IN_VOXELS = NIDM["NIDM_0000145"] +NIDM_RESELS_PER_VOXEL_MAP = NIDM["NIDM_0000144"] +NIDM_EXPECTED_NUMBER_OF_VOXELS_PER_CLUSTER = NIDM["NIDM_0000143"] +NIDM_EXPECTED_NUMBER_OF_VERTICES_PER_CLUSTER = NIDM["NIDM_0000142"] +NIDM_EXPECTED_NUMBER_OF_CLUSTERS = NIDM["NIDM_0000141"] +NIDM_CLUSTER_CENTER_OF_GRAVITY = NIDM["NIDM_0000140"] +NIDM_COORDINATE_VECTOR_IN_VOXELS = NIDM["NIDM_0000139"] +NIDM_HAS_MAXIMUM_INTENSITY_PROJECTION = NIDM["NIDM_0000138"] +NIDM_SEARCH_VOLUME_IN_VERTICES = NIDM["NIDM_0000137"] +NIDM_SEARCH_VOLUME_IN_UNITS = NIDM["NIDM_0000136"] +NIDM_CONTRAST_VARIANCE_MAP = NIDM["NIDM_0000135"] +NIDM_WITH_ESTIMATION_METHOD = NIDM["NIDM_0000134"] +NIDM_VOXEL_UNITS = NIDM["NIDM_0000133"] +NIDM_VOXEL_TO_WORLD_MAPPING = NIDM["NIDM_0000132"] +NIDM_VOXEL_SIZE = NIDM["NIDM_0000131"] +NIDM_VOXEL6CONNECTED = NIDM["NIDM_0000130"] +NIDM_VOXEL26CONNECTED = NIDM["NIDM_0000129"] +NIDM_VOXEL18CONNECTED = NIDM["NIDM_0000128"] +NIDM_VERSION = NIDM["NIDM_0000127"] +NIDM_VARIANCE_SPATIAL_MODEL = NIDM["NIDM_0000126"] +NIDM_USER_SPECIFIED_THRESHOLD_TYPE = NIDM["NIDM_0000125"] +NIDM_TARGET_INTENSITY = NIDM["NIDM_0000124"] +NIDM_STATISTIC_TYPE = NIDM["NIDM_0000123"] +NIDM_SOFTWARE_VERSION = NIDM["NIDM_0000122"] +NIDM_SEARCH_VOLUME_IN_VOXELS = NIDM["NIDM_0000121"] +NIDM_RANDOM_FIELD_STATIONARITY = NIDM["NIDM_0000120"] +NIDM_Q_VALUE_FDR = NIDM["NIDM_0000119"] +NIDM_PIXEL8CONNECTED = NIDM["NIDM_0000118"] +NIDM_PIXEL4CONNECTED = NIDM["NIDM_0000117"] +NIDM_P_VALUE_UNCORRECTED = NIDM["NIDM_0000116"] +NIDM_P_VALUE_FWER = NIDM["NIDM_0000115"] +NIDM_P_VALUE = NIDM["NIDM_0000114"] +NIDM_OBJECT_MODEL = NIDM["NIDM_0000113"] +NIDM_NUMBER_OF_DIMENSIONS = NIDM["NIDM_0000112"] +NIDM_NUMBER_OF_CLUSTERS = NIDM["NIDM_0000111"] +NIDM_GAUSSIAN_HRF = NIDM["NIDM_0000110"] +NIDM_MIN_DISTANCE_BETWEEN_PEAKS = NIDM["NIDM_0000109"] +NIDM_MAX_NUMBER_OF_PEAKS_PER_CLUSTER = NIDM["NIDM_0000108"] +NIDM_MASKED_MEDIAN = NIDM["NIDM_0000107"] +NIDM_IS_USER_DEFINED = NIDM["NIDM_0000106"] +NIDM_IN_WORLD_COORDINATE_SYSTEM = NIDM["NIDM_0000105"] +NIDM_IN_COORDINATE_SPACE = NIDM["NIDM_0000104"] +NIDM_HAS_MAP_HEADER = NIDM["NIDM_0000103"] +NIDM_HAS_HRF_BASIS = NIDM["NIDM_0000102"] +NIDM_HAS_ERROR_DISTRIBUTION = NIDM["NIDM_0000101"] +NIDM_HAS_ERROR_DEPENDENCE = NIDM["NIDM_0000100"] +NIDM_HAS_CONNECTIVITY_CRITERION = NIDM["NIDM_0000099"] +NIDM_HAS_CLUSTER_LABELS_MAP = NIDM["NIDM_0000098"] +NIDM_HAS_ALTERNATIVE_HYPOTHESIS = NIDM["NIDM_0000097"] +NIDM_GRAND_MEAN_SCALING = NIDM["NIDM_0000096"] +NIDM_ERROR_VARIANCE_HOMOGENEOUS = NIDM["NIDM_0000094"] +NIDM_ERROR_DEGREES_OF_FREEDOM = NIDM["NIDM_0000093"] +NIDM_EQUIVALENT_ZSTATISTIC = NIDM["NIDM_0000092"] +NIDM_EFFECT_DEGREES_OF_FREEDOM = NIDM["NIDM_0000091"] +NIDM_DIMENSIONS_IN_VOXELS = NIDM["NIDM_0000090"] +NIDM_DEPENDENCE_SPATIAL_MODEL = NIDM["NIDM_0000089"] +NIDM_HAS_DRIFT_MODEL = NIDM["NIDM_0000088"] +NIDM_DRIFT_MODEL = NIDM["NIDM_0000087"] +NIDM_COORDINATE_VECTOR = NIDM["NIDM_0000086"] +NIDM_CONTRAST_NAME = NIDM["NIDM_0000085"] +NIDM_CLUSTER_SIZE_IN_VOXELS = NIDM["NIDM_0000084"] +NIDM_CLUSTER_SIZE_IN_VERTICES = NIDM["NIDM_0000083"] +NIDM_CLUSTER_LABEL_ID = NIDM["NIDM_0000082"] +NIDM_WORLD_COORDINATE_SYSTEM = NIDM["NIDM_0000081"] +NIDM_VOXEL_CONNECTIVITY_CRITERION = NIDM["NIDM_0000080"] +NIDM_TWO_TAILED_TEST = NIDM["NIDM_0000079"] +NIDM_TALAIRACH_COORDINATE_SYSTEM = NIDM["NIDM_0000078"] +NIDM_SUBJECT_COORDINATE_SYSTEM = NIDM["NIDM_0000077"] +NIDM_STATISTIC_MAP = NIDM["NIDM_0000076"] +NIDM_STANDARDIZED_COORDINATE_SYSTEM = NIDM["NIDM_0000075"] +NIDM_SPATIALLY_REGULARIZED_MODEL = NIDM["NIDM_0000074"] +NIDM_SPATIALLY_LOCAL_MODEL = NIDM["NIDM_0000073"] +NIDM_SPATIALLY_GLOBAL_MODEL = NIDM["NIDM_0000072"] +NIDM_SPATIAL_MODEL = NIDM["NIDM_0000071"] +NIDM_SUPRA_THRESHOLD_CLUSTER = NIDM["NIDM_0000070"] +NIDM_FOURIER_BASIS_SET = NIDM["NIDM_0000069"] +NIDM_SEARCH_SPACE_MASK_MAP = NIDM["NIDM_0000068"] +NIDM_CUSTOM_BASIS_SET = NIDM["NIDM_0000067"] +NIDM_RESIDUAL_MEAN_SQUARES_MAP = NIDM["NIDM_0000066"] +NIDM_POISSON_DISTRIBUTION = NIDM["NIDM_0000065"] +NIDM_PIXEL_CONNECTIVITY_CRITERION = NIDM["NIDM_0000064"] +NIDM_PEAK_DEFINITION_CRITERIA = NIDM["NIDM_0000063"] +NIDM_PEAK = NIDM["NIDM_0000062"] +NIDM_PARAMETER_ESTIMATE_MAP = NIDM["NIDM_0000061"] +NIDM_ONE_TAILED_TEST = NIDM["NIDM_0000060"] +NIDM_NON_PARAMETRIC_SYMMETRIC_DISTRIBUTION = NIDM["NIDM_0000059"] +NIDM_NON_PARAMETRIC_DISTRIBUTION = NIDM["NIDM_0000058"] +NIDM_NIDM_OBJECT_MODEL = NIDM["NIDM_0000057"] +NIDM_MODEL_PARAMETERS_ESTIMATION = NIDM["NIDM_0000056"] +NIDM_MNI305_COORDINATE_SYSTEM = NIDM["NIDM_0000055"] +NIDM_MASK_MAP = NIDM["NIDM_0000054"] +NIDM_MAP_HEADER = NIDM["NIDM_0000053"] +NIDM_MAP = NIDM["NIDM_0000052"] +NIDM_MNI_COORDINATE_SYSTEM = NIDM["NIDM_0000051"] +NIDM_IXI549_COORDINATE_SYSTEM = NIDM["NIDM_0000050"] +NIDM_INFERENCE = NIDM["NIDM_0000049"] +NIDM_INDEPENDENT_ERROR = NIDM["NIDM_0000048"] +NIDM_ICBM_MNI152_NON_LINEAR6TH_GENERATION_COORDINATE_SYSTEM = NIDM[ + "NIDM_0000047" +] +NIDM_ICBM_MNI152_NON_LINEAR2009C_SYMMETRIC_COORDINATE_SYSTEM = NIDM[ + "NIDM_0000046" +] +NIDM_ICBM_MNI152_NON_LINEAR2009C_ASYMMETRIC_COORDINATE_SYSTEM = NIDM[ + "NIDM_0000045" +] +NIDM_ICBM_MNI152_NON_LINEAR2009B_SYMMETRIC_COORDINATE_SYSTEM = NIDM[ + "NIDM_0000044" +] +NIDM_ICBM_MNI152_NON_LINEAR2009B_ASYMMETRIC_COORDINATE_SYSTEM = NIDM[ + "NIDM_0000043" +] +NIDM_ICBM_MNI152_NON_LINEAR2009A_SYMMETRIC_COORDINATE_SYSTEM = NIDM[ + "NIDM_0000042" +] +NIDM_ICBM_MNI152_NON_LINEAR2009A_ASYMMETRIC_COORDINATE_SYSTEM = NIDM[ + "NIDM_0000041" +] +NIDM_ICBM_MNI152_LINEAR_COORDINATE_SYSTEM = NIDM["NIDM_0000040"] +NIDM_ICBM452_WARP5_COORDINATE_SYSTEM = NIDM["NIDM_0000039"] +NIDM_ICBM452_AIR_COORDINATE_SYSTEM = NIDM["NIDM_0000038"] +NIDM_HEMODYNAMIC_RESPONSE_FUNCTION_DERIVATIVE = NIDM["NIDM_0000037"] +NIDM_HEMODYNAMIC_RESPONSE_FUNCTION_BASIS = NIDM["NIDM_0000036"] +NIDM_HEMODYNAMIC_RESPONSE_FUNCTION = NIDM["NIDM_0000035"] +NIDM_HEIGHT_THRESHOLD = NIDM["NIDM_0000034"] +NIDM_GRAND_MEAN_MAP = NIDM["NIDM_0000033"] +NIDM_GAMMA_HRF = NIDM["NIDM_0000031"] +NIDM_GAMMA_HRB = NIDM["NIDM_0000030"] +NIDM_GAMMA_DIFFERENCE_HRF = NIDM["NIDM_0000029"] +NIDM_FINITE_IMPULSE_RESPONSE_HRB = NIDM["NIDM_0000028"] +NIDM_RESULTS = NIDM["NIDM_0000027"] +NIDM_EXTENT_THRESHOLD = NIDM["NIDM_0000026"] +NIDM_EXCURSION_SET_MAP = NIDM["NIDM_0000025"] +NIDM_EXCHANGEABLE_ERROR = NIDM["NIDM_0000024"] +NIDM_ERROR_MODEL = NIDM["NIDM_0000023"] +NIDM_ERROR_DISTRIBUTION = NIDM["NIDM_0000022"] +NIDM_REGRESSOR_NAMES = NIDM["NIDM_0000021"] +NIDM_DISPLAY_MASK_MAP = NIDM["NIDM_0000020"] +NIDM_DESIGN_MATRIX = NIDM["NIDM_0000019"] +NIDM_CUSTOM_COORDINATE_SYSTEM = NIDM["NIDM_0000017"] +NIDM_COORDINATE_SPACE = NIDM["NIDM_0000016"] +NIDM_COORDINATE = NIDM["NIDM_0000015"] +NIDM_LEGENDRE_POLYNOMIAL_ORDER = NIDM["NIDM_0000014"] +NIDM_CONTRAST_STANDARD_ERROR_MAP = NIDM["NIDM_0000013"] +NIDM_CONNECTIVITY_CRITERION = NIDM["NIDM_0000012"] +NIDM_CONJUNCTION_INFERENCE = NIDM["NIDM_0000011"] +NIDM_HAS_FMRI_DESIGN = NIDM["NIDM_0000010"] +NIDM_COLIN27_COORDINATE_SYSTEM = NIDM["NIDM_0000009"] +NIDM_CLUSTER_LABELS_MAP = NIDM["NIDM_0000008"] +NIDM_CLUSTER_DEFINITION_CRITERIA = NIDM["NIDM_0000007"] +NIDM_CLUSTER = NIDM["NIDM_0000006"] +NIDM_BINOMIAL_DISTRIBUTION = NIDM["NIDM_0000005"] +NIDM_BINARY_MAP = NIDM["NIDM_0000004"] +NIDM_CONTRAST_ESTIMATION = NIDM["NIDM_0000001"] +NIDM_CONTRAST_MAP = NIDM["NIDM_0000002"] # OBO constants -OBO_EXAMPLE = OBO['IAO_0000112'] -OBO_TERM_EDITOR = OBO['IAO_0000117'] -OBO_EDITOR_NOTE = OBO['IAO_0000116'] +OBO_EXAMPLE = OBO["IAO_0000112"] +OBO_TERM_EDITOR = OBO["IAO_0000117"] +OBO_EDITOR_NOTE = OBO["IAO_0000116"] -OBO_PENDING_FINAL = OBO['IAO_0000125'] -OBO_METADATA_COMPLETE = OBO['IAO_0000120'] -OBO_METADATA_INCOMPLETE = OBO['IAO_0000123'] -OBO_REQUIRES_DISCUSSION = OBO['IAO_0000428'] -OBO_UNCURATED = OBO['IAO_0000124'] -OBO_TO_BE_REPLACED = OBO['IAO_0000423'] -OBO_READY = OBO['IAO_0000122'] -OBO_DEFINITION = OBO['IAO_0000115'] +OBO_PENDING_FINAL = OBO["IAO_0000125"] +OBO_METADATA_COMPLETE = OBO["IAO_0000120"] +OBO_METADATA_INCOMPLETE = OBO["IAO_0000123"] +OBO_REQUIRES_DISCUSSION = OBO["IAO_0000428"] +OBO_UNCURATED = OBO["IAO_0000124"] +OBO_TO_BE_REPLACED = OBO["IAO_0000423"] +OBO_READY = OBO["IAO_0000122"] +OBO_DEFINITION = OBO["IAO_0000115"] -OBO_STATISTIC = OBO['STATO_0000039'] +OBO_STATISTIC = OBO["STATO_0000039"] OBO_STATISTIC_QNAME = q_graph.qname(OBO_STATISTIC) -OBO_P_VALUE_FWER = OBO['OBI_0001265'] +OBO_P_VALUE_FWER = OBO["OBI_0001265"] OBO_P_VALUE_FWER_QNAME = q_graph.qname(OBO_P_VALUE_FWER) -OBO_Q_VALUE_FDR = OBO['OBI_0001442'] +OBO_Q_VALUE_FDR = OBO["OBI_0001442"] OBO_Q_VALUE_FDR_QNAME = q_graph.qname(OBO_Q_VALUE_FDR) -HAS_CURATION_STATUS = OBO['IAO_0000114'] +HAS_CURATION_STATUS = OBO["IAO_0000114"] -STATO_OLS = OBO['STATO_0000370'] +STATO_OLS = OBO["STATO_0000370"] STATO_OLS_STR = q_graph.qname(STATO_OLS) # TODO: labels should be grabbed automatically from the corresponding owl file STATO_OLS_LABEL = "obo:'ordinary least squares estimation'" -STATO_GLS = OBO['STATO_0000372'] +STATO_GLS = OBO["STATO_0000372"] STATO_GLS_STR = q_graph.qname(STATO_GLS) STATO_GLS_LABEL = "obo:'generalized least squares estimation'" -STATO_TSTATISTIC = OBO['STATO_0000176'] +STATO_TSTATISTIC = OBO["STATO_0000176"] STATO_TSTATISTIC_STR = q_graph.qname(STATO_TSTATISTIC) STATO_TSTATISTIC_LABEL = "obo:'t-statistic'" -STATO_ZSTATISTIC = OBO['STATO_0000376'] +STATO_ZSTATISTIC = OBO["STATO_0000376"] STATO_ZSTATISTIC_STR = q_graph.qname(STATO_ZSTATISTIC) STATO_ZSTATISTIC_LABEL = "obo:'Z-statistic'" -STATO_CONTRAST_WEIGHT_MATRIX = OBO['STATO_0000323'] -STATO_GAUSSIAN_DISTRIBUTION = OBO['STATO_0000227'] -STATO_UNSTRUCTURED_COVARIANCE = OBO['STATO_0000405'] -STATO_GROUP = OBO['STATO_0000193'] -STATO_SERIALLY_CORR_COV = OBO['STATO_0000357'] +STATO_CONTRAST_WEIGHT_MATRIX = OBO["STATO_0000323"] +STATO_GAUSSIAN_DISTRIBUTION = OBO["STATO_0000227"] +STATO_UNSTRUCTURED_COVARIANCE = OBO["STATO_0000405"] +STATO_GROUP = OBO["STATO_0000193"] +STATO_SERIALLY_CORR_COV = OBO["STATO_0000357"] -SPM_SOFTWARE = SCR['SCR_007037'] -FSL_SOFTWARE = SCR['SCR_002823'] +SPM_SOFTWARE = SCR["SCR_007037"] +FSL_SOFTWARE = SCR["SCR_002823"] -NLX_MRI_SCANNER = NLX['birnlex_2100'] -NLX_FMRI_PROTOCOL = NLX['birnlex_2250'] -NLX_IMAGING_INSTRUMENT = NLX['birnlex_2094'] +NLX_MRI_SCANNER = NLX["birnlex_2100"] +NLX_FMRI_PROTOCOL = NLX["birnlex_2250"] +NLX_IMAGING_INSTRUMENT = NLX["birnlex_2094"] -SKOS_DEFINITION = SKOS['definition'] +SKOS_DEFINITION = SKOS["definition"] diff --git a/nidmresults/objects/contrast.py b/nidmresults/objects/contrast.py index c0afb31..0110ff0 100644 --- a/nidmresults/objects/contrast.py +++ b/nidmresults/objects/contrast.py @@ -1,33 +1,41 @@ -""" -Objects describing the Contrast Estimation activity, its inputs and outputs as -specified in NIDM-Results. +"""Objects describing the Contrast Estimation activity, \ + its inputs and outputs as specified in NIDM-Results. Specification: http://nidm.nidash.org/specs/nidm-results.html @author: Camille Maumet @copyright: University of Warwick 2013-2014 """ -import numpy as np + import os -from nidmresults.objects.constants import * + import nibabel as nib -from nidmresults.objects.generic import * -import uuid -from prov.model import Identifier +import numpy as np from prov.identifier import QualifiedName +from prov.model import Identifier +from nidmresults.objects.constants import * +from nidmresults.objects.generic import * -class Contrast(object): - """ - Object representing a Contrast Estimation step: including a - ContrastEstimation activity, its inputs and outputs. +class Contrast: + """Object representing a Contrast Estimation step. + + Includes a ContrastEstimation activity, its inputs and outputs. """ - def __init__(self, contrast_num, contrast_name, weights, estimation, - contrast_map, stderr_or_expl_mean_sq_map, stat_map, - z_stat_map=None): - super(Contrast, self).__init__() + def __init__( + self, + contrast_num, + contrast_name, + weights, + estimation, + contrast_map, + stderr_or_expl_mean_sq_map, + stat_map, + z_stat_map=None, + ): + super().__init__() # FIXME: contrast_num might only be defined in FSL if this is not # generic the class should be overloaded in fsl_objects self.contrast_num = contrast_num @@ -41,22 +49,26 @@ def __init__(self, contrast_num, contrast_name, weights, estimation, class ContrastWeights(NIDMObject): - - """ - Object representing a ContrastWeight entity. - """ - - def __init__(self, contrast_num, contrast_name, contrast_weights, - stat_type, label=None, oid=None): - super(ContrastWeights, self).__init__(oid=oid) + """Object representing a ContrastWeight entity.""" + + def __init__( + self, + contrast_num, + contrast_name, + contrast_weights, + stat_type, + label=None, + oid=None, + ): + super().__init__(oid=oid) self.contrast_name = contrast_name - if not type(contrast_weights) is list: + if type(contrast_weights) is not list: contrast_weights = json.loads(contrast_weights) self.contrast_weights = contrast_weights self.contrast_num = contrast_num self.stat_type = stat_type self.type = STATO_CONTRAST_WEIGHT_MATRIX - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] if label is None: self.label = "Contrast Weights: " + self.contrast_name else: @@ -69,25 +81,27 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix obo_contrastweightmatrix: prefix nidm_statisticType: prefix nidm_contrastName: SELECT DISTINCT * WHERE { - """ + oid_var + """ a obo_contrastweightmatrix: ; + """ + + oid_var + + """ a obo_contrastweightmatrix: ; rdfs:label ?label ; prov:value ?contrast_weights ; nidm_statisticType: ?stat_type ; nidm_contrastName: ?contrast_name . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov graph. - """ + """Create prov graph.""" self.stat = None if isinstance(self.stat_type, QualifiedName): stat = self.stat_type @@ -98,38 +112,51 @@ def export(self, nidm_version, export_dir): stat = STATO_ZSTATISTIC elif self.stat_type.lower() == "f": stat = STATO_FSTATISTIC - elif self.stat_type.startswith('http'): + elif self.stat_type.startswith("http"): stat = Identifier(self.stat_type) - self.add_attributes(( - (PROV['type'], STATO_CONTRAST_WEIGHT_MATRIX), - (NIDM_STATISTIC_TYPE, stat), - (PROV['label'], self.label), - (NIDM_CONTRAST_NAME, self.contrast_name), - (PROV['value'], json.dumps(self.contrast_weights)))) + self.add_attributes( + ( + (PROV["type"], STATO_CONTRAST_WEIGHT_MATRIX), + (NIDM_STATISTIC_TYPE, stat), + (PROV["label"], self.label), + (NIDM_CONTRAST_NAME, self.contrast_name), + (PROV["value"], json.dumps(self.contrast_weights)), + ) + ) class ContrastMap(NIDMObject): - - """ - Object representing a ContrastMap entity. - """ - - def __init__(self, contrast_file, contrast_num, contrast_name, - coord_space, sha=None, fmt=None, - label=None, filename=None, oid=None, derfrom_id=None, - derfrom_filename=None, derfrom_fmt=None, - derfrom_sha=None, isderfrommap=False): - super(ContrastMap, self).__init__(oid=oid) + """Object representing a ContrastMap entity.""" + + def __init__( + self, + contrast_file, + contrast_num, + contrast_name, + coord_space, + sha=None, + fmt=None, + label=None, + filename=None, + oid=None, + derfrom_id=None, + derfrom_filename=None, + derfrom_fmt=None, + derfrom_sha=None, + isderfrommap=False, + ): + super().__init__(oid=oid) self.num = contrast_num self.name = contrast_name if filename is None: - filename = 'Contrast' + self.num + '.nii.gz' - self.file = NIDMFile(self.id, contrast_file, filename, sha=sha, - fmt=fmt) + filename = "Contrast" + self.num + ".nii.gz" + self.file = NIDMFile( + self.id, contrast_file, filename, sha=sha, fmt=fmt + ) self.coord_space = coord_space self.type = NIDM_CONTRAST_MAP - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] if label is None: if self.name: self.label = "Contrast Map: " + self.name @@ -140,10 +167,16 @@ def __init__(self, contrast_file, contrast_num, contrast_name, if derfrom_id is not None: self.derfrom = ContrastMap( - contrast_file=None, contrast_num=None, - contrast_name=None, oid=derfrom_id, coord_space=coord_space, - filename=derfrom_filename, sha=derfrom_sha, - fmt=derfrom_fmt, isderfrommap=True) + contrast_file=None, + contrast_num=None, + contrast_name=None, + oid=derfrom_id, + coord_space=coord_space, + filename=derfrom_filename, + sha=derfrom_sha, + fmt=derfrom_fmt, + isderfrommap=True, + ) else: self.derfrom = None self.isderfrommap = isderfrommap @@ -155,11 +188,14 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_ContrastMap: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_ContrastMap: ; + """ + + oid_var + + """ a nidm_ContrastMap: ; rdfs:label ?label ; prov:atLocation ?contrast_file ; dct:format ?fmt ; @@ -167,7 +203,9 @@ def get_query(klass, oid=None): nidm_contrastName: ?contrast_name ; crypto:sha512 ?sha . - OPTIONAL {""" + oid_var + """ prov:wasDerivedFrom ?derfrom_id . + OPTIONAL {""" + + oid_var + + """ prov:wasDerivedFrom ?derfrom_id . ?derfrom_id a nidm_ContrastMap: ; nfo:fileName ?derfrom_filename ; @@ -176,48 +214,53 @@ def get_query(klass, oid=None): } . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov graph. - """ + """Create prov graph.""" # Contrast Map entity atts = ( - (PROV['type'], NIDM_CONTRAST_MAP), - (NIDM_CONTRAST_NAME, self.name)) + (PROV["type"], NIDM_CONTRAST_MAP), + (NIDM_CONTRAST_NAME, self.name), + ) if not self.isderfrommap: - atts = atts + ( - (NIDM_IN_COORDINATE_SPACE, self.coord_space.id),) + atts = atts + ((NIDM_IN_COORDINATE_SPACE, self.coord_space.id),) if self.label is not None: - atts = atts + ( - (PROV['label'], self.label),) + atts = atts + ((PROV["label"], self.label),) if self.name is not None: - atts = atts + ( - (NIDM_CONTRAST_NAME, self.name),) + atts = atts + ((NIDM_CONTRAST_NAME, self.name),) # Parameter estimate entity self.add_attributes(atts) class ContrastExplainedMeanSquareMap(NIDMObject): - """ - Object representing a ContrastExplainedMeanSquareMap entity. - """ - def __init__(self, stat_file, sigma_sq_file, contrast_num, - coord_space, expl_mean_sq_file=None, - sha=None, fmt=None, filename=None, oid=None, - label="Contrast Explained Mean Square Map"): - super(ContrastExplainedMeanSquareMap, self).__init__(oid=oid) + """Object representing a ContrastExplainedMeanSquareMap entity.""" + + def __init__( + self, + stat_file, + sigma_sq_file, + contrast_num, + coord_space, + expl_mean_sq_file=None, + sha=None, + fmt=None, + filename=None, + oid=None, + label="Contrast Explained Mean Square Map", + ): + super().__init__(oid=oid) self.stat_file = stat_file self.sigma_sq_file = sigma_sq_file self.num = contrast_num self.coord_space = coord_space self.type = NIDM_CONTRAST_EXPLAINED_MEAN_SQUARE_MAP - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] self.expl_mean_sq_file = expl_mean_sq_file self.sha = sha self.filename = filename @@ -231,12 +274,15 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_ContrastExplainedMeanSquareMap: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_ContrastExplainedMeanSquareMap: ; + """ + + oid_var + + """ a nidm_ContrastExplainedMeanSquareMap: ; rdfs:label ?label ; prov:atLocation ?expl_mean_sq_file ; dct:format ?fmt ; @@ -244,12 +290,11 @@ def get_query(klass, oid=None): crypto:sha512 ?sha . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov graph. - """ + """Create prov graph.""" if self.expl_mean_sq_file is None: # Create Contrast Explained Mean Square Map as fstat.nii.gz # multiplied by sigmasquareds.nii.gz and save it in export_dir @@ -260,42 +305,56 @@ def export(self, nidm_version, export_dir): sigma_sq = sigma_sq_img.get_data() expl_mean_sq = nib.Nifti1Image( - fstat*sigma_sq, fstat_img.get_qform()) + fstat * sigma_sq, fstat_img.get_qform() + ) - self.filename = ("ContrastExplainedMeanSquareMap" + - self.num + ".nii.gz") - self.expl_mean_sq_file = os.path.join( - export_dir, self.filename) + self.filename = ( + "ContrastExplainedMeanSquareMap" + self.num + ".nii.gz" + ) + self.expl_mean_sq_file = os.path.join(export_dir, self.filename) nib.save(expl_mean_sq, self.expl_mean_sq_file) - self.file = NIDMFile(self.id, self.expl_mean_sq_file, - filename=self.filename, - sha=self.sha, fmt=self.fmt) + self.file = NIDMFile( + self.id, + self.expl_mean_sq_file, + filename=self.filename, + sha=self.sha, + fmt=self.fmt, + ) # Contrast Explained Mean Square Map entity path, filename = os.path.split(self.expl_mean_sq_file) - self.add_attributes(( - (PROV['type'], self.type), - (NIDM_IN_COORDINATE_SPACE, self.coord_space.id), - (PROV['label'], self.label))) + self.add_attributes( + ( + (PROV["type"], self.type), + (NIDM_IN_COORDINATE_SPACE, self.coord_space.id), + (PROV["label"], self.label), + ) + ) class ContrastStdErrMap(NIDMObject): - - """ - Object representing a ContrastStdErrMap entity. - """ -# stderr_or_expl_mean_sq_map = self.get_object( -# ContrastStdErrMap, args['constdm_id'], -# coord_space=contraststd_map_coordspace, -# contrast_num=contrast_num, is_variance=False, var_coord_space=None) - - def __init__(self, contrast_num, filepath, is_variance, coord_space, - var_coord_space, label=None, fmt=None, - sha=None, filename=None, oid=None, derfrom_id=None, - derfrom_filename=None, derfrom_sha=None, derfrom_fmt=None, - export_dir=None): - super(ContrastStdErrMap, self).__init__(oid=oid) + """Object representing a ContrastStdErrMap entity.""" + + def __init__( + self, + contrast_num, + filepath, + is_variance, + coord_space, + var_coord_space, + label=None, + fmt=None, + sha=None, + filename=None, + oid=None, + derfrom_id=None, + derfrom_filename=None, + derfrom_sha=None, + derfrom_fmt=None, + export_dir=None, + ): + super().__init__(oid=oid) self.file = filepath self.is_variance = is_variance self.num = contrast_num @@ -303,7 +362,7 @@ def __init__(self, contrast_num, filepath, is_variance, coord_space, if is_variance or derfrom_id: self.var_coord_space = var_coord_space self.type = NIDM_CONTRAST_STANDARD_ERROR_MAP - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] self.fmt = fmt self.sha = sha self.filename = filename @@ -313,33 +372,42 @@ def __init__(self, contrast_num, filepath, is_variance, coord_space, # Copy contrast variance map in export directory path, var_cope_filename = os.path.split(self.file) contrast_var = ContrastVariance( - coord_space=self.var_coord_space, var_file=self.file, - filename=var_cope_filename, fmt=self.fmt, sha=self.sha, - oid=derfrom_id) + coord_space=self.var_coord_space, + var_file=self.file, + filename=var_cope_filename, + fmt=self.fmt, + sha=self.sha, + oid=derfrom_id, + ) self.contrast_var = contrast_var # Create standard error map from contrast variance map var_cope_img = nib.load(self.file) contrast_variance = var_cope_img.get_data() - standard_error_img = nib.Nifti1Image(np.sqrt(contrast_variance), - var_cope_img.get_qform()) + standard_error_img = nib.Nifti1Image( + np.sqrt(contrast_variance), var_cope_img.get_qform() + ) stderr_file = os.path.join(export_dir, std_filename) nib.save(standard_error_img, stderr_file) - self.file = NIDMFile( - self.id, stderr_file, std_filename) + self.file = NIDMFile(self.id, stderr_file, std_filename) else: - self.file = NIDMFile(self.id, self.file, self.filename, - fmt=self.fmt, sha=self.sha) + self.file = NIDMFile( + self.id, self.file, self.filename, fmt=self.fmt, sha=self.sha + ) if derfrom_id is not None: # TODO: assuming same coordinate space for derived from self.contrast_var = ContrastVariance( - coord_space=self.coord_space, var_file=None, - filename=derfrom_filename, fmt=derfrom_fmt, - sha=derfrom_sha, oid=derfrom_id) + coord_space=self.coord_space, + var_file=None, + filename=derfrom_filename, + fmt=derfrom_fmt, + sha=derfrom_sha, + oid=derfrom_id, + ) else: self.contrast_var = None @@ -350,20 +418,25 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_ContrastStandardErrorMap: prefix nidm_ContrastVarianceMap: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_ContrastStandardErrorMap: ; + """ + + oid_var + + """ a nidm_ContrastStandardErrorMap: ; rdfs:label ?label ; prov:atLocation ?filepath ; nfo:fileName ?filename ; dct:format ?fmt ; crypto:sha512 ?sha . - OPTIONAL {""" + oid_var + """ prov:wasDerivedFrom ?derfrom_id . + OPTIONAL {""" + + oid_var + + """ prov:wasDerivedFrom ?derfrom_id . ?derfrom_id a nidm_ContrastVarianceMap: ; nfo:fileName ?derfrom_filename ; @@ -372,50 +445,69 @@ def get_query(klass, oid=None): } . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov graph. - """ - - self.add_attributes(( - (PROV['type'], self.type), - (DCT['format'], "image/nifti"), - (NIDM_IN_COORDINATE_SPACE, self.coord_space.id), - (PROV['label'], "Contrast Standard Error Map"))) + """Create prov graph.""" + self.add_attributes( + ( + (PROV["type"], self.type), + (DCT["format"], "image/nifti"), + (NIDM_IN_COORDINATE_SPACE, self.coord_space.id), + (PROV["label"], "Contrast Standard Error Map"), + ) + ) class ContrastVariance(NIDMObject): - def __init__(self, coord_space, var_file, filename, fmt=None, - sha=None, oid=None): - super(ContrastVariance, self).__init__(oid=oid) + def __init__( + self, coord_space, var_file, filename, fmt=None, sha=None, oid=None + ): + super().__init__(oid=oid) self.coord_space = coord_space self.type = NIDM_CONTRAST_VARIANCE_MAP self.filename = filename self.fmt = fmt self.sha = sha - self.file = NIDMFile(self.id, var_file, filename=self.filename, - fmt=self.fmt, sha=self.sha) - self.prov_type = PROV['Entity'] + self.file = NIDMFile( + self.id, + var_file, + filename=self.filename, + fmt=self.fmt, + sha=self.sha, + ) + self.prov_type = PROV["Entity"] def export(self, nidm_version, export_dir): - self.add_attributes([(PROV['type'], NIDM_CONTRAST_VARIANCE_MAP)]) + self.add_attributes([(PROV["type"], NIDM_CONTRAST_VARIANCE_MAP)]) class StatisticMap(NIDMObject): - - """ - Object representing a StatisticMap entity. - """ - - def __init__(self, location, stat_type, contrast_name, dof, coord_space, - contrast_num=None, label=None, oid=None, - fmt="image/nifti", effdof=None, filename=None, sha=None, - contrast_estimation=None, derfrom_id=None, - derfrom_filename=None, derfrom_fmt=None, - derfrom_sha=None, isderfrommap=False): - super(StatisticMap, self).__init__(oid=oid) + """Object representing a StatisticMap entity.""" + + def __init__( + self, + location, + stat_type, + contrast_name, + dof, + coord_space, + contrast_num=None, + label=None, + oid=None, + fmt="image/nifti", + effdof=None, + filename=None, + sha=None, + contrast_estimation=None, + derfrom_id=None, + derfrom_filename=None, + derfrom_fmt=None, + derfrom_sha=None, + isderfrommap=False, + ): + super().__init__(oid=oid) self.num = contrast_num self.contrast_name = contrast_name self.stat_type = stat_type @@ -430,32 +522,40 @@ def __init__(self, location, stat_type, contrast_name, dof, coord_space, self.stat = STATO_ZSTATISTIC elif self.stat_type.lower() == "f": self.stat = STATO_FSTATISTIC - elif self.stat_type.startswith('http'): + elif self.stat_type.startswith("http"): self.stat = Identifier(self.stat_type) else: raise Exception( - 'Unrecognised statistic: ' + str(self.stat_type)) + "Unrecognised statistic: " + str(self.stat_type) + ) if derfrom_id is not None: self.derfrom = StatisticMap( - None, None, None, None, - coord_space=None, oid=derfrom_id, - filename=derfrom_filename, sha=derfrom_sha, + None, + None, + None, + None, + coord_space=None, + oid=derfrom_id, + filename=derfrom_filename, + sha=derfrom_sha, fmt=derfrom_fmt, - isderfrommap=True) + isderfrommap=True, + ) else: self.derfrom = None # FIXME use new 'preferred mathematical notation from stato' if self.num is not None: - filename = self.stat_type.upper() + \ - 'Statistic' + self.num + '.nii.gz' + filename = ( + self.stat_type.upper() + "Statistic" + self.num + ".nii.gz" + ) self.file = NIDMFile(self.id, location, filename, sha=sha) self.coord_space = coord_space self.dof = dof self.type = NIDM_STATISTIC_MAP - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] self.label = label if label is not None: self.label = label @@ -463,13 +563,14 @@ def __init__(self, location, stat_type, contrast_name, dof, coord_space, if self.contrast_name: self.label = "Statistic Map: " + self.contrast_name # Include statistic type in the label - self.label = self.stat_type + '-' + self.label + self.label = self.stat_type + "-" + self.label self.fmt = fmt # Effect degrees of freedom for T-test is always 1 - if (effdof is None) and (self.stat in - [STATO_TSTATISTIC, STATO_ZSTATISTIC]): + if (effdof is None) and ( + self.stat in [STATO_TSTATISTIC, STATO_ZSTATISTIC] + ): effdof = 1.0 self.effdof = effdof @@ -480,7 +581,7 @@ def __init__(self, location, stat_type, contrast_name, dof, coord_space, self.isderfrommap = isderfrommap def __str__(self): - return '%s\t%s' % (self.label, self.file) + return f"{self.label}\t{self.file}" @classmethod def get_query(klass, oid=None): @@ -489,7 +590,8 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_StatisticMap: prefix nidm_statisticType: @@ -498,7 +600,9 @@ def get_query(klass, oid=None): prefix nidm_errorDegreesOfFreedom: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_StatisticMap: ; + """ + + oid_var + + """ a nidm_StatisticMap: ; rdfs:label ?label ; prov:atLocation ?location ; dct:format ?fmt ; @@ -509,7 +613,9 @@ def get_query(klass, oid=None): nidm_effectDegreesOfFreedom: ?effdof ; nidm_errorDegreesOfFreedom: ?dof . - OPTIONAL {""" + oid_var + """ prov:wasDerivedFrom ?derfrom_id . + OPTIONAL {""" + + oid_var + + """ prov:wasDerivedFrom ?derfrom_id . ?derfrom_id a nidm_StatisticMap: ; nfo:fileName ?derfrom_filename ; @@ -518,21 +624,23 @@ def get_query(klass, oid=None): } . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov graph. - """ - attributes = [(PROV['type'], NIDM_STATISTIC_MAP), - (DCT['format'], self.fmt)] + """Create prov graph.""" + attributes = [ + (PROV["type"], NIDM_STATISTIC_MAP), + (DCT["format"], self.fmt), + ] if not self.isderfrommap: - attributes.insert(0, ( - NIDM_IN_COORDINATE_SPACE, self.coord_space.id)) - attributes.insert(0, (PROV['label'], self.label)) + attributes.insert( + 0, (NIDM_IN_COORDINATE_SPACE, self.coord_space.id) + ) + attributes.insert(0, (PROV["label"], self.label)) - if not self.stat_type == 'Z': + if not self.stat_type == "Z": attributes.insert(0, (NIDM_ERROR_DEGREES_OF_FREEDOM, self.dof)) attributes.insert(0, (NIDM_EFFECT_DEGREES_OF_FREEDOM, self.effdof)) else: @@ -552,17 +660,20 @@ def export(self, nidm_version, export_dir): class ContrastEstimation(NIDMObject): - - """ - Object representing a ContrastEstimation entity. - """ - - def __init__(self, contrast_num, contrast_name=None, label=None, - param_estimate_id=None, oid=None): - super(ContrastEstimation, self).__init__(oid=oid) + """Object representing a ContrastEstimation entity.""" + + def __init__( + self, + contrast_num, + contrast_name=None, + label=None, + param_estimate_id=None, + oid=None, + ): + super().__init__(oid=oid) self.num = contrast_num self.type = NIDM_CONTRAST_ESTIMATION - self.prov_type = PROV['Activity'] + self.prov_type = PROV["Activity"] if label is not None: self.label = label else: @@ -577,23 +688,25 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_ContrastEstimation: prefix nidm_ParameterEstimateMap: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_ContrastEstimation: ; + """ + + oid_var + + """ a nidm_ContrastEstimation: ; rdfs:label ?label ; prov:used ?param_estimate_id . ?param_estimate_id a nidm_ParameterEstimateMap: . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov graph. - """ - self.add_attributes(( - (PROV['type'], self.type), - (PROV['label'], self.label))) + """Create prov graph.""" + self.add_attributes( + ((PROV["type"], self.type), (PROV["label"], self.label)) + ) diff --git a/nidmresults/objects/generic.py b/nidmresults/objects/generic.py index 491d687..df47363 100644 --- a/nidmresults/objects/generic.py +++ b/nidmresults/objects/generic.py @@ -6,34 +6,33 @@ @author: Camille Maumet @copyright: University of Warwick 2013-2014 """ -from prov.model import Identifier -from prov.identifier import QualifiedName -import numpy as np + +import hashlib +import json import os -from nidmresults.objects.constants import * -import nibabel as nib import shutil -import hashlib import uuid -import json -from prov.model import Literal -from prov.constants import XSD_STRING import warnings import zipfile +import nibabel as nib +import numpy as np +from prov.constants import XSD_STRING +from prov.identifier import QualifiedName +from prov.model import Identifier, Literal -class NIDMObject(object): +from nidmresults.objects.constants import * - """ - Generic class, parent of all objects describing a NIDM entity, activity - or agent - """ + +class NIDMObject: + """Generic class, parent of all objects describing a NIDM entity, \ + activity or agent.""" def __init__(self, oid=None): if oid is None: self.id = NIIRI[str(uuid.uuid4())] else: - if not type(oid) is QualifiedName: + if type(oid) is not QualifiedName: oid = NIIRI.qname(Identifier(oid)) self.id = oid @@ -45,7 +44,7 @@ def __init__(self, oid=None): # with a NIDMFile object @property def file(self): - return getattr(self, '_file', None) + return getattr(self, "_file", None) @file.setter def file(self, fileobj): @@ -58,21 +57,25 @@ def _map_fileid(self, fileobj): def __str__(self): value = "" - if hasattr(self, 'value'): + if hasattr(self, "value"): value = ": " + self.value location = "" - if hasattr(self, 'file'): - if hasattr(self.file, 'path'): + if hasattr(self, "file"): + if hasattr(self.file, "path"): location = " - " + self.file.path return '"' + self.label + '"' + value + location def __repr__(self): - return '<"' + self.label + '" ' + \ - str(self.id).replace("niiri:", "").replace(NIIRI._uri, "")[0:8]\ - + '>' + return ( + '<"' + + self.label + + '" ' + + str(self.id).replace("niiri:", "").replace(NIIRI._uri, "")[0:8] + + ">" + ) def add_attributes(self, attributes): - if hasattr(self, 'attributes'): + if hasattr(self, "attributes"): if isinstance(attributes, tuple): attributes = list(attributes) if isinstance(self.attributes, tuple): @@ -89,19 +92,17 @@ def add_attributes(self, attributes): class NIDMResultsBundle(NIDMObject): - """ - Object representing a NIDM-Results bundle entity. - """ + """Object representing a NIDM-Results bundle entity.""" def __init__(self, nidm_version=None, label=None, oid=None): - super(NIDMResultsBundle, self).__init__(oid=oid) + super().__init__(oid=oid) self.type = NIDM_RESULTS self.nidm_version = nidm_version if label is None: self.label = "NIDM-Results" else: self.label = label - self.prov_type = PROV['Bundle'] + self.prov_type = PROV["Bundle"] @classmethod def get_query(klass, oid=None): @@ -110,53 +111,68 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix dctype: SELECT * WHERE { - """ + oid_var + """ a nidm_NIDMResults: ; + """ + + oid_var + + """ a nidm_NIDMResults: ; rdfs:label ?label ; nidm_version: ?nidm_version . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entity. - """ - self.add_attributes([ - (PROV['type'], self.type), - (PROV['type'], PROV['Bundle']), - # Explicitly add bundle type - (PROV['label'], self.label), - (NIDM_VERSION, self.nidm_version), - ]) + """Create prov entity.""" + self.add_attributes( + [ + (PROV["type"], self.type), + (PROV["type"], PROV["Bundle"]), + # Explicitly add bundle type + (PROV["label"], self.label), + (NIDM_VERSION, self.nidm_version), + ] + ) class CoordinateSpace(NIDMObject): - """ - Object representing a CoordinateSpace entity. - """ + """Object representing a CoordinateSpace entity.""" + + def __init__( + self, + coordinate_system, + nifti_file=None, + vox_to_world=None, + vox_size=None, + dimensions=None, + numdim=None, + units=None, + oid=None, + label="Coordinate space", + ): + super().__init__(oid) - def __init__(self, coordinate_system, nifti_file=None, vox_to_world=None, - vox_size=None, dimensions=None, numdim=None, units=None, - oid=None, label="Coordinate space"): - super(CoordinateSpace, self).__init__(oid) - if not isinstance(coordinate_system, QualifiedName): coordinate_system = NIDM.qname(coordinate_system) self.coordinate_system = coordinate_system self.type = NIDM_COORDINATE_SPACE - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] self.label = label - if (vox_to_world is None) and (vox_size is None) and\ - (dimensions is None) and (numdim is None) and\ - (units is None) and \ - (nifti_file is not None): + if ( + (vox_to_world is None) + and (vox_size is None) + and (dimensions is None) + and (numdim is None) + and (units is None) + and (nifti_file is not None) + ): thresImg = nib.load(nifti_file) thresImgHdr = thresImg.get_header() @@ -164,14 +180,14 @@ def __init__(self, coordinate_system, nifti_file=None, vox_to_world=None, dimensions = np.asarray(thresImg.shape) # FIXME: is vox_to_world the qform? vox_to_world = thresImg.get_qform() - vox_size = thresImgHdr['pixdim'][1:(numdim + 1)] + vox_size = thresImgHdr["pixdim"][1 : (numdim + 1)] # FIXME: this gives mm, sec => what is wrong: FSL file, nibabel, # other? # units = str(thresImgHdr.get_xyzt_units()).strip('()') units = ["mm", "mm", "mm"] self.number_of_dimensions = numdim - if not type(vox_to_world) is np.ndarray: + if type(vox_to_world) is not np.ndarray: # This is useful if info was read from a NIDM pack vox_to_world = np.array(json.loads(vox_to_world)) dimensions = np.array(json.loads(dimensions)) @@ -197,7 +213,8 @@ def is_mni(self): NIDM_ICBM452_AIR_COORDINATE_SYSTEM.uri, NIDM_ICBM452_WARP5_COORDINATE_SYSTEM.uri, NIDM_IXI549_COORDINATE_SYSTEM.uri, - NIDM_MNI305_COORDINATE_SYSTEM.uri] + NIDM_MNI305_COORDINATE_SYSTEM.uri, + ] if str(self.coordinate_system) in mni_coords: return True @@ -205,8 +222,9 @@ def is_mni(self): return False def is_talairach(self): - if str(self.coordinate_system) in \ - [NIDM_TALAIRACH_COORDINATE_SYSTEM.uri]: + if str(self.coordinate_system) in [ + NIDM_TALAIRACH_COORDINATE_SYSTEM.uri + ]: return True else: return False @@ -218,7 +236,8 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_CoordinateSpace: prefix nidm_voxelToWorldMapping: prefix nidm_voxelUnits: @@ -233,7 +252,9 @@ def get_query(klass, oid=None): ?dimensions WHERE { - """ + oid_var + """ a nidm_CoordinateSpace: ; + """ + + oid_var + + """ a nidm_CoordinateSpace: ; rdfs:label ?label ; nidm_voxelToWorldMapping: ?vox_to_world ; nidm_voxelUnits: ?units ; @@ -243,32 +264,46 @@ def get_query(klass, oid=None): nidm_dimensionsInVoxels: ?dimensions . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ - self.add_attributes({ - PROV['type']: self.type, - NIDM_DIMENSIONS_IN_VOXELS: json.dumps(self.dimensions.tolist()), - NIDM_NUMBER_OF_DIMENSIONS: self.number_of_dimensions, - NIDM_VOXEL_TO_WORLD_MAPPING: - json.dumps(self.voxel_to_world.tolist()), - NIDM_IN_WORLD_COORDINATE_SYSTEM: self.coordinate_system, - NIDM_VOXEL_UNITS: json.dumps(self.units), - NIDM_VOXEL_SIZE: json.dumps(self.voxel_size.tolist()), - PROV['label']: self.label}) + """Create prov entities and activities.""" + self.add_attributes( + { + PROV["type"]: self.type, + NIDM_DIMENSIONS_IN_VOXELS: json.dumps( + self.dimensions.tolist() + ), + NIDM_NUMBER_OF_DIMENSIONS: self.number_of_dimensions, + NIDM_VOXEL_TO_WORLD_MAPPING: json.dumps( + self.voxel_to_world.tolist() + ), + NIDM_IN_WORLD_COORDINATE_SYSTEM: self.coordinate_system, + NIDM_VOXEL_UNITS: json.dumps(self.units), + NIDM_VOXEL_SIZE: json.dumps(self.voxel_size.tolist()), + PROV["label"]: self.label, + } + ) class NIDMFile(NIDMObject): + """Object representing a File. + + To be used as attribute of another class. """ - Object representing a File (to be used as attribute of another class) - """ - def __init__(self, rdf_id, location, filename=None, - sha=None, fmt=None, temporary=False): - super(NIDMFile, self).__init__() - self.prov_type = PROV['Entity'] + + def __init__( + self, + rdf_id, + location, + filename=None, + sha=None, + fmt=None, + temporary=False, + ): + super().__init__() + self.prov_type = PROV["Entity"] self.path = location if filename is None: # Keep same file name @@ -291,10 +326,12 @@ def is_nifti(self): else: name = self.filename - return name.endswith(".nii") or \ - name.endswith(".nii.gz") or \ - name.endswith(".img") or \ - name.endswith(".hrd") + return ( + name.endswith(".nii") + or name.endswith(".nii.gz") + or name.endswith(".img") + or name.endswith(".hrd") + ) def get_sha_sum(self, nifti_file): nifti_img = nib.load(nifti_file) @@ -306,15 +343,13 @@ def get_sha_sum(self, nifti_file): return hashlib.sha512(data).hexdigest() def export(self, nidm_version, export_dir, prepend_path): - """ - Copy file over of export_dir and create corresponding triples - """ + """Copy file over of export_dir and create corresponding triples.""" if self.path is not None: if export_dir is not None: # Copy file only if export_dir is not None new_file = os.path.join(export_dir, self.filename) if not self.path == new_file: - if prepend_path.endswith('.zip'): + if prepend_path.endswith(".zip"): with zipfile.ZipFile(prepend_path) as z: extracted = z.extract(str(self.path), export_dir) shutil.move(extracted, new_file) @@ -330,21 +365,20 @@ def export(self, nidm_version, export_dir, prepend_path): else: new_file = self.path - if nidm_version['num'] in ["1.0.0", "1.1.0"]: + if nidm_version["num"] in ["1.0.0", "1.1.0"]: loc = Identifier("file://./" + self.filename) else: loc = Identifier(self.filename) - self.add_attributes([(NFO['fileName'], self.filename)]) + self.add_attributes([(NFO["fileName"], self.filename)]) if export_dir: - self.add_attributes([(PROV['atLocation'], loc)]) + self.add_attributes([(PROV["atLocation"], loc)]) - if nidm_version['num'] in ("1.0.0", "1.1.0"): + if nidm_version["num"] in ("1.0.0", "1.1.0"): path, org_filename = os.path.split(self.path) - if (org_filename is not self.filename) \ - and (not self.temporary): - self.add_attributes([(NFO['fileName'], org_filename)]) + if (org_filename is not self.filename) and (not self.temporary): + self.add_attributes([(NFO["fileName"], org_filename)]) if self.is_nifti(): if self.sha is None: @@ -352,22 +386,18 @@ def export(self, nidm_version, export_dir, prepend_path): if self.fmt is None: self.fmt = "image/nifti" - self.add_attributes([ - (CRYPTO['sha512'], self.sha), - (DCT['format'], self.fmt) - ]) + self.add_attributes( + [(CRYPTO["sha512"], self.sha), (DCT["format"], self.fmt)] + ) class Image(NIDMObject): + """Object representing an Image entity.""" - """ - Object representing an Image entity. - """ - - def __init__(self, image_file, filename, fmt='png', oid=None): - super(Image, self).__init__(oid=oid) - self.type = DCTYPE['Image'] - self.prov_type = PROV['Entity'] + def __init__(self, image_file, filename, fmt="png", oid=None): + super().__init__(oid=oid) + self.type = DCTYPE["Image"] + self.prov_type = PROV["Entity"] self.file = NIDMFile(self.id, image_file, filename) self.label = "" # Enable printing @@ -378,50 +408,53 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix dctype: SELECT * WHERE { - """ + oid_var + """ a dctype:Image ; + """ + + oid_var + + """ a dctype:Image ; prov:atLocation ?image_file ; nfo:fileName ?filename ; dct:format ?fmt . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entity. - """ + """Create prov entity.""" if self.file is not None: - self.add_attributes([ - (PROV['type'], self.type), - (DCT['format'], "image/png"), - ]) + self.add_attributes( + [ + (PROV["type"], self.type), + (DCT["format"], "image/png"), + ] + ) class NeuroimagingSoftware(NIDMObject): - """ - Class representing a NeuroimagingSoftware Agent. - """ + """Class representing a NeuroimagingSoftware Agent.""" - def __init__(self, software_type, version, label=None, feat_version=None, - oid=None): - super(NeuroimagingSoftware, self).__init__(oid=oid) + def __init__( + self, software_type, version, label=None, feat_version=None, oid=None + ): + super().__init__(oid=oid) self.version = version if isinstance(software_type, QualifiedName): self.type = software_type else: - if software_type.startswith('http'): + if software_type.startswith("http"): self.type = Identifier(software_type) elif software_type.lower() == "fsl": self.type = SCR_FSL else: - warnings.warn('Unrecognised software: ' + str(software_type)) + warnings.warn("Unrecognised software: " + str(software_type)) self.name = str(software_type) self.type = None @@ -431,14 +464,14 @@ def __init__(self, software_type, version, label=None, feat_version=None, elif self.type == SCR_SPM: self.name = "SPM" else: - warnings.warn('Unrecognised software: ' + str(software_type)) + warnings.warn("Unrecognised software: " + str(software_type)) self.name = str(software_type) if not label: self.label = self.name else: self.label = label - self.prov_type = PROV['Agent'] + self.prov_type = PROV["Agent"] self.feat_version = feat_version @classmethod @@ -448,7 +481,8 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_softwareVersion: prefix fsl_featVersion: prefix nidm_ModelParametersEstimation: " - query = """ + query = ( + """ prefix nidm_softwareVersion: prefix nidm_NIDMResultsExport: SELECT DISTINCT * WHERE { - """ + oid_var + """ a prov:SoftwareAgent ; + """ + + oid_var + + """ a prov:SoftwareAgent ; rdfs:label ?label ; rdf:type ?software_type ; nidm_softwareVersion: ?version . @@ -531,28 +574,28 @@ def get_query(klass, oid=None): FILTER ( ?software_type NOT IN (prov:SoftwareAgent, prov:Agent) ) } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ - self.add_attributes(( - (PROV['type'], self.type), - (PROV['type'], PROV['SoftwareAgent']), - (PROV['label'], self.label), - (NIDM_SOFTWARE_VERSION, self.version)) + """Create prov entities and activities.""" + self.add_attributes( + ( + (PROV["type"], self.type), + (PROV["type"], PROV["SoftwareAgent"]), + (PROV["label"], self.label), + (NIDM_SOFTWARE_VERSION, self.version), + ) ) class NIDMResultsExport(NIDMObject): - """ - Class representing a NIDM-Results Export activity. - """ + """Class representing a NIDM-Results Export activity.""" + def __init__(self, oid=None, label=None): - super(NIDMResultsExport, self).__init__(oid=oid) + super().__init__(oid=oid) self.type = NIDM_NIDM_RESULTS_EXPORT - self.prov_type = PROV['Activity'] + self.prov_type = PROV["Activity"] if label is None: self.label = "NIDM-Results export" else: @@ -565,21 +608,23 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_NIDMResultsExport: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_NIDMResultsExport: ; + """ + + oid_var + + """ a nidm_NIDMResultsExport: ; rdfs:label ?label . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ - self.add_attributes([ - (PROV['label'], self.label), - (PROV['type'], self.type)]) + """Create prov entities and activities.""" + self.add_attributes( + [(PROV["label"], self.label), (PROV["type"], self.type)] + ) diff --git a/nidmresults/objects/inference.py b/nidmresults/objects/inference.py index dfd076a..5169a6a 100644 --- a/nidmresults/objects/inference.py +++ b/nidmresults/objects/inference.py @@ -1,34 +1,41 @@ -""" -Objects describing the Inference activity, its inputs and outputs as specified -in NIDM-Results. +"""Objects describing the Inference activity, \ + its inputs and outputs as specified in NIDM-Results. Specification: http://nidm.nidash.org/specs/nidm-results.html @author: Camille Maumet @copyright: University of Warwick 2013-2014 """ -from nidmresults.objects.constants import * -from nidmresults.objects.generic import * -import uuid + from math import erf, sqrt -import rdflib -from prov.model import Literal + from prov.constants import XSD_FLOAT -from prov.model import Identifier +from prov.model import Identifier, Literal +from nidmresults.objects.constants import * +from nidmresults.objects.generic import * -class Inference(object): - """ - Object representing an Inference step: including an Inference activity, its - inputs and outputs. +class Inference: + """Object representing an Inference step. + + Include an Inference activity, its inputs and outputs. """ def __init__( - self, inference, height_thresh, extent_thresh, - peak_criteria, cluster_criteria, disp_mask, excursion_set, - clusters, search_space, software_id): - super(Inference, self).__init__() + self, + inference, + height_thresh, + extent_thresh, + peak_criteria, + cluster_criteria, + disp_mask, + excursion_set, + clusters, + search_space, + software_id, + ): + super().__init__() self.excursion_set = excursion_set self.inference_act = inference self.height_thresh = height_thresh @@ -42,19 +49,23 @@ def __init__( class InferenceActivity(NIDMObject): + """Object representing an Inference activity.""" - """ - Object representing an Inference activity. - """ - - def __init__(self, oid=None, tail=None, label=None, contrast_name=None, - inference_type=None, partial_degree=None): - super(InferenceActivity, self).__init__(oid=oid) + def __init__( + self, + oid=None, + tail=None, + label=None, + contrast_name=None, + inference_type=None, + partial_degree=None, + ): + super().__init__(oid=oid) if inference_type is None: self.type = NIDM_INFERENCE else: self.type = inference_type - self.prov_type = PROV['Activity'] + self.prov_type = PROV["Activity"] if tail is None: tail = NIDM_ONE_TAILED_TEST self.tail = tail @@ -72,7 +83,8 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_Inference: prefix nidm_ConjunctionInference: prefix nidm_hasAlternativeHypothesis: " - query = """ + query = ( + """ prefix nidm_ExcursionSetMap: prefix nidm_hasClusterLabelsMap: prefix nidm_hasMaximumIntensityProjection: " - query = """ + query = ( + """ prefix nidm_ClusterLabelsMap: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_ClusterLabelsMap: ; + """ + + oid_var + + """ a nidm_ClusterLabelsMap: ; nfo:fileName ?filename ; crypto:sha512 ?sha ; prov:atLocation ?location ; dct:format ?fmt . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ + """Create prov entities and activities.""" # Create "Cluster Labels Map" entity - self.add_attributes(( - (PROV['type'], self.type), - (NIDM_IN_COORDINATE_SPACE, self.coord_space.id), - (PROV['label'], self.label) - )) + self.add_attributes( + ( + (PROV["type"], self.type), + (NIDM_IN_COORDINATE_SPACE, self.coord_space.id), + (PROV["label"], self.label), + ) + ) class HeightThreshold(NIDMObject): + """Object representing a HeightThreshold entity.""" - """ - Object representing a HeightThreshold entity. - """ - - def __init__(self, stat_threshold=None, p_corr_threshold=None, - p_uncorr_threshold=None, threshold_type=None, value=None, - label=None, version={'num': '1.3.0'}, oid=None, - equiv_thresh=None): - super(HeightThreshold, self).__init__(oid=oid) - if not stat_threshold and not p_corr_threshold and \ - not p_uncorr_threshold and not value: - raise Exception('No threshold defined') + def __init__( + self, + stat_threshold=None, + p_corr_threshold=None, + p_uncorr_threshold=None, + threshold_type=None, + value=None, + label=None, + version={"num": "1.3.0"}, + oid=None, + equiv_thresh=None, + ): + super().__init__(oid=oid) + if ( + not stat_threshold + and not p_corr_threshold + and not p_uncorr_threshold + and not value + ): + raise Exception("No threshold defined") if isinstance(threshold_type, str): threshold_type = Identifier(threshold_type) @@ -298,28 +352,27 @@ def __init__(self, stat_threshold=None, p_corr_threshold=None, thresh_desc = "" if stat_threshold is not None: thresh_desc = "Z>" + str(stat_threshold) - if version['num'] == "1.0.0": + if version["num"] == "1.0.0": user_threshold_type = "Z-Statistic" else: threshold_type = OBO_STATISTIC value = stat_threshold elif p_uncorr_threshold is not None: - thresh_desc = "p<" + \ - str(p_uncorr_threshold) + " (uncorrected)" - if version['num'] == "1.0.0": + thresh_desc = "p<" + str(p_uncorr_threshold) + " (uncorrected)" + if version["num"] == "1.0.0": user_threshold_type = "p-value uncorrected" else: threshold_type = NIDM_P_VALUE_UNCORRECTED_CLASS value = p_uncorr_threshold elif p_corr_threshold is not None: thresh_desc = "p<" + str(p_corr_threshold) + " (FWE)" - if version['num'] == "1.0.0": + if version["num"] == "1.0.0": user_threshold_type = "p-value FWE" else: threshold_type = OBO_P_VALUE_FWER value = p_corr_threshold - if version['num'] == "1.0.0": + if version["num"] == "1.0.0": self.user_threshold_type = user_threshold_type self.p_uncorr_threshold = p_uncorr_threshold self.p_corr_threshold = p_corr_threshold @@ -334,7 +387,7 @@ def __init__(self, stat_threshold=None, p_corr_threshold=None, self.label = label self.type = NIDM_HEIGHT_THRESHOLD - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] self.equiv_thresh = equiv_thresh @classmethod @@ -344,13 +397,16 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_HeightThreshold: prefix nidm_hasAlternativeHypothesis: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_HeightThreshold: ; + """ + + oid_var + + """ a nidm_HeightThreshold: ; a ?threshold_type ; rdfs:label ?label ; prov:value ?value . @@ -358,52 +414,55 @@ def get_query(klass, oid=None): FILTER ( ?threshold_type NOT IN (prov:Entity, nidm_HeightThreshold:) ) } """ + ) return query def export(self, version, export_dir): - """ - Create prov entities and activities. - """ - + """Create prov entities and activities.""" atts = [ - (PROV['type'], self.type), - (PROV['label'], self.label), + (PROV["type"], self.type), + (PROV["label"], self.label), ] - if version['num'] == "1.0.0": + if version["num"] == "1.0.0": atts += [ (NIDM_USER_SPECIFIED_THRESHOLD_TYPE, self.user_threshold_type), - (PROV['value'], self.stat_threshold), + (PROV["value"], self.stat_threshold), (NIDM_P_VALUE_UNCORRECTED, self.p_uncorr_threshold), - (NIDM_P_VALUE_FWER, self.p_corr_threshold) - ] + (NIDM_P_VALUE_FWER, self.p_corr_threshold), + ] else: atts += [ - (PROV['type'], self.threshold_type), - (PROV['value'], self.value) - ] + (PROV["type"], self.threshold_type), + (PROV["value"], self.value), + ] if self.equiv_thresh is not None: for equiv in self.equiv_thresh: - atts += [ - (NIDM_EQUIVALENT_THRESHOLD, equiv.id) - ] + atts += [(NIDM_EQUIVALENT_THRESHOLD, equiv.id)] self.add_attributes([(k, v) for k, v in atts if v is not None]) class ExtentThreshold(NIDMObject): + """Object representing an ExtentThreshold entity.""" - """ - Object representing an ExtentThreshold entity. - """ - - def __init__(self, extent=None, p_corr=None, p_uncorr=None, - extent_rsl=None, label=None, version={'num': '1.3.0'}, - value=None, oid=None, equiv_thresh=None, threshold_type=None): - super(ExtentThreshold, self).__init__(oid=oid) + def __init__( + self, + extent=None, + p_corr=None, + p_uncorr=None, + extent_rsl=None, + label=None, + version={"num": "1.3.0"}, + value=None, + oid=None, + equiv_thresh=None, + threshold_type=None, + ): + super().__init__(oid=oid) self.type = NIDM_EXTENT_THRESHOLD - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] thresh_desc = "" @@ -433,7 +492,7 @@ def __init__(self, extent=None, p_corr=None, p_uncorr=None, else: thresh_desc = "k>=0" extent = 0 - if version['num'] == "1.0.0": + if version["num"] == "1.0.0": p_uncorr = 1.0 p_corr = 1.0 user_threshold_type = None @@ -443,7 +502,7 @@ def __init__(self, extent=None, p_corr=None, p_uncorr=None, self.threshold_type = threshold_type self.value = value - if version['num'] == "1.0.0": + if version["num"] == "1.0.0": self.user_threshold_type = user_threshold_type self.p_uncorr = p_uncorr self.p_corr = p_corr @@ -467,35 +526,41 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_ExtentThreshold: prefix nidm_clusterSizeInVoxels: prefix nidm_clusterSizeInResels: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_ExtentThreshold: ; + """ + + oid_var + + """ a nidm_ExtentThreshold: ; a ?threshold_type ; rdfs:label ?label . - OPTIONAL {""" + oid_var + """ prov:value ?value .} . - OPTIONAL {""" + oid_var + """ nidm_clusterSizeInVoxels: ?extent .} . - OPTIONAL {""" + oid_var + """ nidm_clusterSizeInResels: ?extent_rsl .} . + OPTIONAL {""" + + oid_var + + """ prov:value ?value .} . + OPTIONAL {""" + + oid_var + + """ nidm_clusterSizeInVoxels: ?extent .} . + OPTIONAL {""" + + oid_var + + """ nidm_clusterSizeInResels: ?extent_rsl .} . FILTER ( ?threshold_type NOT IN (prov:Entity, nidm_ExtentThreshold:) ) } """ + ) return query def export(self, version, export_dir): - """ - Create prov entities and activities. - """ + """Create prov entities and activities.""" atts = [ - (PROV['type'], self.type), + (PROV["type"], self.type), ] - atts += [ - (PROV['label'], self.label) - ] + atts += [(PROV["label"], self.label)] if self.extent_rsl is not None: atts += [ @@ -507,56 +572,69 @@ def export(self, version, export_dir): (NIDM_CLUSTER_SIZE_IN_VOXELS, self.extent), ] - if version['num'] == "1.0.0": + if version["num"] == "1.0.0": atts += [ (NIDM_USER_SPECIFIED_THRESHOLD_TYPE, self.user_threshold_type), (NIDM_P_VALUE_UNCORRECTED, self.p_uncorr), - (NIDM_P_VALUE_FWER, self.p_corr) + (NIDM_P_VALUE_FWER, self.p_corr), ] else: - atts += [ - (PROV['type'], self.threshold_type) - ] + atts += [(PROV["type"], self.threshold_type)] if self.value is not None: - atts += [ - (PROV['value'], self.value) - ] + atts += [(PROV["value"], self.value)] if self.equiv_thresh is not None: for equiv in self.equiv_thresh: - atts += [ - (NIDM_EQUIVALENT_THRESHOLD, equiv.id) - ] + atts += [(NIDM_EQUIVALENT_THRESHOLD, equiv.id)] self.add_attributes([(k, v) for k, v in atts if v is not None]) class Cluster(NIDMObject): + """Object representing a Cluster entity.""" - """ - Object representing a Cluster entity. - """ - - def __init__(self, cluster_num, size, pFWER, peaks, - x=None, y=None, z=None, x_std=None, y_std=None, z_std=None, - suffix='', clust_size_resels=None, pFDR=None, punc=None, - label=None, oid=None, cog=None): - super(Cluster, self).__init__(oid=oid) + def __init__( + self, + cluster_num, + size, + pFWER, + peaks, + x=None, + y=None, + z=None, + x_std=None, + y_std=None, + z_std=None, + suffix="", + clust_size_resels=None, + pFDR=None, + punc=None, + label=None, + oid=None, + cog=None, + ): + super().__init__(oid=oid) self.num = cluster_num if cog is not None: self.cog = cog else: if x and y and z: self.cog = CenterOfGravity( - cluster_num, x=x, y=y, z=z, x_std=x_std, y_std=y_std, - z_std=z_std) + cluster_num, + x=x, + y=y, + z=z, + x_std=x_std, + y_std=y_std, + z_std=z_std, + ) else: self.cog = None self.peaks = peaks self.size = size self.pFWER = pFWER self.type = NIDM_SIGNIFICANT_CLUSTER - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] self.punc = punc self.pFDR = pFDR if not label: @@ -574,7 +652,8 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_SupraThresholdCluster: prefix nidm_clusterSizeInVoxels: prefix nidm_clusterLabelId: @@ -584,86 +663,112 @@ def get_query(klass, oid=None): prefix nidm_qValueFDR: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_SupraThresholdCluster: ; + """ + + oid_var + + """ a nidm_SupraThresholdCluster: ; rdfs:label ?label ; nidm_clusterSizeInVoxels: ?size ; nidm_clusterLabelId: ?cluster_num . - OPTIONAL {""" + oid_var + """ nidm_clusterSizeInResels: ?clust_size_resels .} . - OPTIONAL {""" + oid_var + """ nidm_pValueUncorrected: ?punc .} . - OPTIONAL {""" + oid_var + """ nidm_pValueFWER: ?pFWER .} . - OPTIONAL {""" + oid_var + """ nidm_qValueFDR: ?pFDR .} . + OPTIONAL {""" + + oid_var + + """ nidm_clusterSizeInResels: ?clust_size_resels .} . + OPTIONAL {""" + + oid_var + + """ nidm_pValueUncorrected: ?punc .} . + OPTIONAL {""" + + oid_var + + """ nidm_pValueFWER: ?pFWER .} . + OPTIONAL {""" + + oid_var + + """ nidm_qValueFDR: ?pFDR .} . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ - if nidm_version['num'] in ["1.0.0", "1.1.0"]: + """Create prov entities and activities.""" + if nidm_version["num"] in ["1.0.0", "1.1.0"]: self.label = self.label.replace("Supra-Threshold", "Significant") # FIXME deal with multiple contrasts atts = ( - (PROV['type'], NIDM_SIGNIFICANT_CLUSTER), - (PROV['label'], self.label), + (PROV["type"], NIDM_SIGNIFICANT_CLUSTER), + (PROV["label"], self.label), (NIDM_CLUSTER_LABEL_ID, self.num), - (NIDM_CLUSTER_SIZE_IN_VOXELS, self.size) - ) + (NIDM_CLUSTER_SIZE_IN_VOXELS, self.size), + ) if self.clust_size_resels is not None: atts = atts + ( (NIDM_CLUSTER_SIZE_IN_RESELS, self.clust_size_resels), - ) + ) if self.punc is not None: atts = atts + ( - (NIDM_P_VALUE_UNCORRECTED, - Literal(self.punc, datatype=XSD_FLOAT)), - ) + ( + NIDM_P_VALUE_UNCORRECTED, + Literal(self.punc, datatype=XSD_FLOAT), + ), + ) if self.pFDR is not None: atts = atts + ( (NIDM_Q_VALUE_FDR, Literal(self.pFDR, datatype=XSD_FLOAT)), - ) + ) if self.pFWER is not None: atts = atts + ( (NIDM_P_VALUE_FWER, Literal(self.pFWER, datatype=XSD_FLOAT)), - ) + ) self.add_attributes(atts) class DisplayMaskMap(NIDMObject): + """Object representing a DisplayMaskMap entity.""" - """ - Object representing a DisplayMaskMap entity. - """ - def __init__(self, contrast_num, mask_file, mask_num, coord_space, - sha=None, filename=None, fmt=None, label=None, oid=None, - derfrom_id=None, derfrom_filename=None, derfrom_fmt=None, - derfrom_sha=None, isderfrommap=False): - super(DisplayMaskMap, self).__init__(oid=oid) + def __init__( + self, + contrast_num, + mask_file, + mask_num, + coord_space, + sha=None, + filename=None, + fmt=None, + label=None, + oid=None, + derfrom_id=None, + derfrom_filename=None, + derfrom_fmt=None, + derfrom_sha=None, + isderfrommap=False, + ): + super().__init__(oid=oid) if not filename: - filename = 'DisplayMask' + str(mask_num) + '.nii.gz' - self.file = NIDMFile(self.id, mask_file, filename, - sha=sha, fmt=fmt) + filename = "DisplayMask" + str(mask_num) + ".nii.gz" + self.file = NIDMFile(self.id, mask_file, filename, sha=sha, fmt=fmt) self.coord_space = coord_space self.type = NIDM_DISPLAY_MASK_MAP - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] if not label: self.label = "Display Mask Map " + str(mask_num) else: self.label = label if derfrom_id is not None: self.derfrom = DisplayMaskMap( - None, None, None, - coord_space=None, oid=derfrom_id, - filename=derfrom_filename, sha=derfrom_sha, + None, + None, + None, + coord_space=None, + oid=derfrom_id, + filename=derfrom_filename, + sha=derfrom_sha, fmt=derfrom_fmt, - isderfrommap=True) + isderfrommap=True, + ) else: self.derfrom = None self.isderfrommap = isderfrommap @@ -675,18 +780,23 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_DisplayMaskMap: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_DisplayMaskMap: ; + """ + + oid_var + + """ a nidm_DisplayMaskMap: ; rdfs:label ?label ; nfo:fileName ?filename ; crypto:sha512 ?sha ; prov:atLocation ?mask_file ; dct:format ?fmt . - OPTIONAL {""" + oid_var + """ prov:wasDerivedFrom ?derfrom_id . + OPTIONAL {""" + + oid_var + + """ prov:wasDerivedFrom ?derfrom_id . ?derfrom_id a nidm_DisplayMaskMap: ; nfo:fileName ?derfrom_filename ; @@ -696,37 +806,33 @@ def get_query(klass, oid=None): } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ - atts = ( - (PROV['type'], self.type), - ) + """Create prov entities and activities.""" + atts = ((PROV["type"], self.type),) if not self.isderfrommap: atts = atts + ( (NIDM_IN_COORDINATE_SPACE, self.coord_space.id), - (PROV['label'], self.label)) + (PROV["label"], self.label), + ) self.add_attributes(atts) class PeakCriteria(NIDMObject): + """Object representing a PeakCriteria entity.""" - """ - Object representing a PeakCriteria entity. - """ - - def __init__(self, contrast_num, peak_dist, num_peak=None, label=None, - oid=None): - super(PeakCriteria, self).__init__(oid=oid) + def __init__( + self, contrast_num, peak_dist, num_peak=None, label=None, oid=None + ): + super().__init__(oid=oid) self.num_peak = num_peak self.peak_dist = peak_dist self.type = NIDM_PEAK_DEFINITION_CRITERIA - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] if not label: self.label = "Peak Definition Criteria" else: @@ -739,52 +845,57 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_PeakDefinitionCriteria: prefix nidm_minDistanceBetweenPeaks: prefix nidm_maxNumberOfPeaksPerCluster: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_PeakDefinitionCriteria: ; + """ + + oid_var + + """ a nidm_PeakDefinitionCriteria: ; rdfs:label ?label ; nidm_minDistanceBetweenPeaks: ?peak_dist . - OPTIONAL { """ + oid_var + """ nidm_maxNumberOfPeaksPerCluster: ?num_peak .} . + OPTIONAL { """ + + oid_var + + """ nidm_maxNumberOfPeaksPerCluster: ?num_peak .} . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ + """Create prov entities and activities.""" num_peak = () if self.num_peak: num_peak = ((NIDM_MAX_NUMBER_OF_PEAKS_PER_CLUSTER, self.num_peak),) # Create "Peak definition criteria" entity - self.add_attributes(( - (PROV['type'], self.type), - (PROV['label'], self.label), - (NIDM_MIN_DISTANCE_BETWEEN_PEAKS, self.peak_dist) - ) + num_peak) + self.add_attributes( + ( + (PROV["type"], self.type), + (PROV["label"], self.label), + (NIDM_MIN_DISTANCE_BETWEEN_PEAKS, self.peak_dist), + ) + + num_peak + ) class ClusterCriteria(NIDMObject): - - """ - Object representing a ClusterCriteria entity. - """ + """Object representing a ClusterCriteria entity.""" def __init__(self, contrast_num, connectivity, label=None, oid=None): - super(ClusterCriteria, self).__init__(oid=oid) + super().__init__(oid=oid) self.connectivity = connectivity self.type = NIDM_CLUSTER_DEFINITION_CRITERIA - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] if not label: - self.label = ("Cluster Connectivity Criterion: " + - str(self.connectivity)) + self.label = "Cluster Connectivity Criterion: " + str( + self.connectivity + ) else: self.label = label @@ -795,24 +906,26 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_ClusterDefinitionCriteria: prefix nidm_hasConnectivityCriterion: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_ClusterDefinitionCriteria: ; + """ + + oid_var + + """ a nidm_ClusterDefinitionCriteria: ; rdfs:label ?label ; nidm_hasConnectivityCriterion: ?connectivity . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ + """Create prov entities and activities.""" # Create "Cluster definition criteria" entity if isinstance(self.connectivity, int): if self.connectivity == 6: @@ -825,37 +938,56 @@ def export(self, nidm_version, export_dir): # FIXME if connectivity is missing if self.connectivity is not None: atts = ( - (PROV['type'], self.type), - (PROV['label'], self.label), - (NIDM_HAS_CONNECTIVITY_CRITERION, self.connectivity)) + (PROV["type"], self.type), + (PROV["label"], self.label), + (NIDM_HAS_CONNECTIVITY_CRITERION, self.connectivity), + ) else: atts = ( - (PROV['type'], NIDM_CLUSTER_DEFINITION_CRITERIA), - (PROV['label'], label)) + (PROV["type"], NIDM_CLUSTER_DEFINITION_CRITERIA), + (PROV["label"], label), + ) self.add_attributes(atts) class CenterOfGravity(NIDMObject): + """Object representing a CenterOfGravity entity.""" - """ - Object representing a CenterOfGravity entity. - """ - - def __init__(self, cluster_num, x=None, y=None, z=None, x_std=None, - y_std=None, z_std=None, oid=None, coord_vector=None, - coord_vector_std=None, label=None, coord_id=None): + def __init__( + self, + cluster_num, + x=None, + y=None, + z=None, + x_std=None, + y_std=None, + z_std=None, + oid=None, + coord_vector=None, + coord_vector_std=None, + label=None, + coord_id=None, + ): # Note: coord_id argument is only here for compatibility # with the query outputs - super(CenterOfGravity, self).__init__(oid=oid) + super().__init__(oid=oid) self.cluster_num = cluster_num - self.coordinate = Coordinate("%04d" % cluster_num, x=x, y=y, z=z, - x_std=x_std, y_std=y_std, z_std=z_std, - coord_vector_std=coord_vector_std, - coord_vector=coord_vector, oid=coord_id) + self.coordinate = Coordinate( + "%04d" % cluster_num, + x=x, + y=y, + z=z, + x_std=x_std, + y_std=y_std, + z_std=z_std, + coord_vector_std=coord_vector_std, + coord_vector=coord_vector, + oid=coord_id, + ) self.type = NIDM_CLUSTER_CENTER_OF_GRAVITY - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] if label is None: label = "Center of gravity " + str(self.cluster_num) self.label = label @@ -867,14 +999,17 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_ClusterCenterOfGravity: prefix nidm_coordinateVector: prefix nidm_coordinateVectorInVoxels: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_ClusterCenterOfGravity: ; + """ + + oid_var + + """ a nidm_ClusterCenterOfGravity: ; rdfs:label ?label ; prov:atLocation ?coord_id . @@ -884,39 +1019,55 @@ def get_query(klass, oid=None): OPTIONAL { ?coord_id nidm_coordinateVectorInVoxels: ?coord_vector .} . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ - self.add_attributes(( - (PROV['type'], self.type), - (PROV['label'], self.label), - (PROV['location'], self.coordinate.id))) + """Create prov entities and activities.""" + self.add_attributes( + ( + (PROV["type"], self.type), + (PROV["label"], self.label), + (PROV["location"], self.coordinate.id), + ) + ) class SearchSpace(NIDMObject): + """Object representing a SearchSpace entity.""" - """ - Object representing a SearchSpace entity. - """ - - def __init__(self, search_space_file, vol_in_voxels, vol_in_units, - vol_in_resels, resel_size_in_voxels, - random_field_stationarity, noise_fwhm_in_voxels, - noise_fwhm_in_units, coord_space, - expected_num_voxels=None, expected_num_clusters=None, - height_critical_fwe05=None, height_critical_fdr05=None, - extent_critical_fwe05=None, extent_critical_fdr05=None, - search_vol_geom=None, noise_roughness=None, - filename=None, sha=None, fmt=None, - label=None, oid=None, suffix=''): - super(SearchSpace, self).__init__(oid=oid) + def __init__( + self, + search_space_file, + vol_in_voxels, + vol_in_units, + vol_in_resels, + resel_size_in_voxels, + random_field_stationarity, + noise_fwhm_in_voxels, + noise_fwhm_in_units, + coord_space, + expected_num_voxels=None, + expected_num_clusters=None, + height_critical_fwe05=None, + height_critical_fdr05=None, + extent_critical_fwe05=None, + extent_critical_fdr05=None, + search_vol_geom=None, + noise_roughness=None, + filename=None, + sha=None, + fmt=None, + label=None, + oid=None, + suffix="", + ): + super().__init__(oid=oid) if not filename: - filename = 'SearchSpaceMask' + suffix + '.nii.gz' - self.file = NIDMFile(self.id, search_space_file, filename, - sha=sha, fmt=fmt) + filename = "SearchSpaceMask" + suffix + ".nii.gz" + self.file = NIDMFile( + self.id, search_space_file, filename, sha=sha, fmt=fmt + ) self.coord_space = coord_space self.resel_size_in_voxels = resel_size_in_voxels self.search_volume_in_voxels = vol_in_voxels @@ -926,7 +1077,7 @@ def __init__(self, search_space_file, vol_in_voxels, vol_in_units, self.noise_fwhm_in_voxels = noise_fwhm_in_voxels self.noise_fwhm_in_units = noise_fwhm_in_units self.type = NIDM_SEARCH_SPACE_MASK_MAP - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] self.label = "Search Space Mask Map" self.expected_num_voxels = expected_num_voxels self.expected_num_clusters = expected_num_clusters @@ -944,7 +1095,8 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_SearchSpaceMaskMap: prefix nidm_expectedNumberOfVoxelsPerCluster: @@ -970,7 +1122,9 @@ def get_query(klass, oid=None): SELECT DISTINCT * WHERE { -""" + oid_var + """ a nidm_SearchSpaceMaskMap: ; +""" + + oid_var + + """ a nidm_SearchSpaceMaskMap: ; rdfs:label ?label ; nidm_searchVolumeInVoxels: ?vol_in_voxels ; nidm_searchVolumeInUnits: ?vol_in_units ; @@ -985,153 +1139,212 @@ def get_query(klass, oid=None): nfo:fileName ?filename ; crypto:sha512 ?sha . - OPTIONAL {""" + oid_var + """ nidm_expectedNumberOfVoxelsPerCluster: ?expected_num_voxels } . - OPTIONAL {""" + oid_var + """ nidm_expectedNumberOfClusters: ?expected_num_clusters } . - OPTIONAL {""" + oid_var + """ nidm_heightCriticalThresholdFWE05: ?height_critical_fwe05 } . - OPTIONAL {""" + oid_var + """ nidm_heightCriticalThresholdFDR05: ?height_critical_fdr05 } . - OPTIONAL {""" + oid_var + """ spm_smallestSignificantClusterSizeInVoxelsFWE05: ?extent_critical_fwe05 } . - OPTIONAL {""" + oid_var + """ spm_smallestSignificantClusterSizeInVoxelsFDR05: ?extent_critical_fdr05 } . - OPTIONAL {""" + oid_var + """ spm_searchVolumeReselsGeometry: ?search_vol_geom } . - OPTIONAL {""" + oid_var + """ nidm_noiseRoughnessInVoxels: ?noise_roughness } . + OPTIONAL {""" + + oid_var + + """ nidm_expectedNumberOfVoxelsPerCluster: ?expected_num_voxels } . + OPTIONAL {""" + + oid_var + + """ nidm_expectedNumberOfClusters: ?expected_num_clusters } . + OPTIONAL {""" + + oid_var + + """ nidm_heightCriticalThresholdFWE05: ?height_critical_fwe05 } . + OPTIONAL {""" + + oid_var + + """ nidm_heightCriticalThresholdFDR05: ?height_critical_fdr05 } . + OPTIONAL {""" + + oid_var + + """ spm_smallestSignificantClusterSizeInVoxelsFWE05: ?extent_critical_fwe05 } . + OPTIONAL {""" + + oid_var + + """ spm_smallestSignificantClusterSizeInVoxelsFDR05: ?extent_critical_fdr05 } . + OPTIONAL {""" + + oid_var + + """ spm_searchVolumeReselsGeometry: ?search_vol_geom } . + OPTIONAL {""" + + oid_var + + """ nidm_noiseRoughnessInVoxels: ?noise_roughness } . } """ + ) return query # Generate prov for search space entity generated by the inference activity def export(self, version, export_dir): - """ - Create prov entities and activities. - """ + """Create prov entities and activities.""" atts = ( - (PROV['label'], self.label), - (PROV['type'], NIDM_SEARCH_SPACE_MASK_MAP), + (PROV["label"], self.label), + (PROV["type"], NIDM_SEARCH_SPACE_MASK_MAP), (NIDM_RANDOM_FIELD_STATIONARITY, self.rf_stationarity), (NIDM_IN_COORDINATE_SPACE, self.coord_space.id), (NIDM_SEARCH_VOLUME_IN_VOXELS, self.search_volume_in_voxels), (NIDM_SEARCH_VOLUME_IN_UNITS, self.search_volume_in_units), (NIDM_SEARCH_VOLUME_IN_RESELS, self.search_volume_in_resels), - (NIDM_RESEL_SIZE_IN_VOXELS, self.resel_size_in_voxels)) + (NIDM_RESEL_SIZE_IN_VOXELS, self.resel_size_in_voxels), + ) # Noise FWHM was introduced in NIDM-Results 1.1.0 if self.noise_fwhm_in_voxels is not None: - if (version['major'] > 1) or \ - (version['major'] >= 1 and - (version['minor'] > 0 or version['revision'] > 0)): + if (version["major"] > 1) or ( + version["major"] >= 1 + and (version["minor"] > 0 or version["revision"] > 0) + ): atts = atts + ( (NIDM_NOISE_FWHM_IN_VOXELS, self.noise_fwhm_in_voxels), - (NIDM_NOISE_FWHM_IN_UNITS, self.noise_fwhm_in_units)) + (NIDM_NOISE_FWHM_IN_UNITS, self.noise_fwhm_in_units), + ) if self.expected_num_voxels is not None: - atts = atts + ((NIDM_EXPECTED_NUMBER_OF_VOXELS_PER_CLUSTER, - self.expected_num_voxels),) + atts = atts + ( + ( + NIDM_EXPECTED_NUMBER_OF_VOXELS_PER_CLUSTER, + self.expected_num_voxels, + ), + ) if self.expected_num_clusters is not None: - atts = atts + ((NIDM_EXPECTED_NUMBER_OF_CLUSTERS, - self.expected_num_clusters),) + atts = atts + ( + (NIDM_EXPECTED_NUMBER_OF_CLUSTERS, self.expected_num_clusters), + ) if self.height_critical_fwe05 is not None: - atts = atts + ((NIDM_HEIGHT_CRITICAL_THRESHOLD_FWE_05, - self.height_critical_fwe05),) + atts = atts + ( + ( + NIDM_HEIGHT_CRITICAL_THRESHOLD_FWE_05, + self.height_critical_fwe05, + ), + ) if self.height_critical_fdr05 is not None: - atts = atts + ((NIDM_HEIGHT_CRITICAL_THRESHOLD_FDR_05, - self.height_critical_fdr05),) + atts = atts + ( + ( + NIDM_HEIGHT_CRITICAL_THRESHOLD_FDR_05, + self.height_critical_fdr05, + ), + ) if self.extent_critical_fwe05 is not None: - atts = atts + (( - SPM_SMALLEST_SIGNIFICANT_CLUSTER_SIZE_IN_VOXELS_FWE05, - self.extent_critical_fwe05),) + atts = atts + ( + ( + SPM_SMALLEST_SIGNIFICANT_CLUSTER_SIZE_IN_VOXELS_FWE05, + self.extent_critical_fwe05, + ), + ) if self.extent_critical_fdr05 is not None: - atts = atts + (( - SPM_SMALLEST_SIGNIFICANT_CLUSTER_SIZE_IN_VOXELS_FDR05, - self.extent_critical_fdr05),) + atts = atts + ( + ( + SPM_SMALLEST_SIGNIFICANT_CLUSTER_SIZE_IN_VOXELS_FDR05, + self.extent_critical_fdr05, + ), + ) if self.search_vol_geom is not None: - atts = atts + ((SPM_SEARCH_VOLUME_RESELS_GEOMETRY, - self.search_vol_geom),) + atts = atts + ( + (SPM_SEARCH_VOLUME_RESELS_GEOMETRY, self.search_vol_geom), + ) if self.noise_roughness: - atts = atts + ((NIDM_NOISE_ROUGHNESS_IN_VOXELS, - self.noise_roughness),) + atts = atts + ( + (NIDM_NOISE_ROUGHNESS_IN_VOXELS, self.noise_roughness), + ) # Create "Search Space Mask map" entity self.add_attributes(atts) class Coordinate(NIDMObject): + """Object representing a Coordinate entity.""" - """ - Object representing a Coordinate entity. - """ - - def __init__(self, label_id, coord_vector=None, coord_vector_std=None, - x=None, y=None, z=None, x_std=None, y_std=None, z_std=None, - label=None, oid=None): - - super(Coordinate, self).__init__(oid=oid) + def __init__( + self, + label_id, + coord_vector=None, + coord_vector_std=None, + x=None, + y=None, + z=None, + x_std=None, + y_std=None, + z_std=None, + label=None, + oid=None, + ): + + super().__init__(oid=oid) self.label_id = label_id if x is not None and y is not None and z is not None: self.coord_vector = [x, y, z] else: - if coord_vector and not type(coord_vector) is list: + if coord_vector and type(coord_vector) is not list: coord_vector = json.loads(coord_vector) self.coord_vector = coord_vector if x_std is not None and y_std is not None and z_std is not None: self.coord_vector_std = [x_std, y_std, z_std] else: - if coord_vector_std and not type(coord_vector_std) is list: + if coord_vector_std and type(coord_vector_std) is not list: coord_vector_std = json.loads(coord_vector_std) self.coord_vector_std = coord_vector_std self.type = NIDM_COORDINATE - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] if label is not None: self.label = label else: self.label = "Coordinate " + self.label_id def __str__(self): - return '%s\t%s' % (self.label, self.coord_vector) + return f"{self.label}\t{self.coord_vector}" def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ + """Create prov entities and activities.""" # We can not have this as a dictionary because we want to keep the # duplicate prov:type attribute atts = ( # (PROV['type'],PROV['Location']), - (PROV['type'], NIDM_COORDINATE), - (PROV['type'], PROV['Location']), - (PROV['label'], self.label) - ) + (PROV["type"], NIDM_COORDINATE), + (PROV["type"], PROV["Location"]), + (PROV["label"], self.label), + ) if self.coord_vector is not None: - atts = atts +\ - ((NIDM_COORDINATE_VECTOR_IN_VOXELS, - json.dumps(self.coord_vector)),) + atts = atts + ( + ( + NIDM_COORDINATE_VECTOR_IN_VOXELS, + json.dumps(self.coord_vector), + ), + ) # FSL unnormalised subject-level analyses do not provide coordinates in # voxels if self.coord_vector_std is not None: - atts = atts +\ - ((NIDM_COORDINATE_VECTOR, json.dumps(self.coord_vector_std)),) + atts = atts + ( + (NIDM_COORDINATE_VECTOR, json.dumps(self.coord_vector_std)), + ) self.add_attributes(atts) class Peak(NIDMObject): + """Object representing a Peak entity.""" - """ - Object representing a Peak entity. - """ - - def __init__(self, equiv_z, p_unc=None, p_fwer=None, label=None, - coord_label=None, exc_set_id=None, oid=None, suffix='', - p_fdr=None, value=None, coord_id=None, *args, **kwargs): - super(Peak, self).__init__(oid) + def __init__( + self, + equiv_z, + p_unc=None, + p_fwer=None, + label=None, + coord_label=None, + exc_set_id=None, + oid=None, + suffix="", + p_fdr=None, + value=None, + coord_id=None, + *args, + **kwargs, + ): + super().__init__(oid) # FIXME: Currently assumes less than 10 clusters per contrast # cluster_num = cluster_index # FIXME: Currently assumes less than 100 peaks @@ -1147,9 +1360,10 @@ def __init__(self, equiv_z, p_unc=None, p_fwer=None, label=None, self.p_unc = p_unc self.p_fwer = p_fwer self.coordinate = Coordinate( - str(peak_unique_id), label=coord_label, oid=coord_id, **kwargs) + str(peak_unique_id), label=coord_label, oid=coord_id, **kwargs + ) self.type = NIDM_PEAK - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] # self.cluster = cluster_id self.exc_set_id = exc_set_id self.value = value @@ -1162,7 +1376,8 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_Peak: prefix nidm_pValueUncorrected: prefix nidm_equivalentZStatistic: @@ -1173,7 +1388,9 @@ def get_query(klass, oid=None): prefix nidm_coordinateVector: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_Peak: ; + """ + + oid_var + + """ a nidm_Peak: ; rdfs:label ?label ; prov:atLocation ?coord_id . @@ -1183,59 +1400,70 @@ def get_query(klass, oid=None): OPTIONAL {?coord_id nidm_coordinateVectorInVoxels: ?coord_vector .} . - OPTIONAL {""" + oid_var + """ prov:value ?value .} . - OPTIONAL {""" + oid_var + """ nidm_pValueUncorrected: ?p_unc .} . - OPTIONAL {""" + oid_var + """ nidm_equivalentZStatistic: ?equiv_z .} . - OPTIONAL {""" + oid_var + """ nidm_pValueFWER: ?p_fwer .} . - OPTIONAL {""" + oid_var + """ nidm_qValueFDR: ?p_fdr .} . + OPTIONAL {""" + + oid_var + + """ prov:value ?value .} . + OPTIONAL {""" + + oid_var + + """ nidm_pValueUncorrected: ?p_unc .} . + OPTIONAL {""" + + oid_var + + """ nidm_equivalentZStatistic: ?equiv_z .} . + OPTIONAL {""" + + oid_var + + """ nidm_pValueFWER: ?p_fwer .} . + OPTIONAL {""" + + oid_var + + """ nidm_qValueFDR: ?p_fdr .} . } """ + ) return query def __str__(self): - return '%s \tz=%.2f \tp=%.2e (unc.) \t%s' % ( - self.label, self.equiv_z, self.p_unc, str(self.coordinate)) + return "{} \tz={:.2f} \tp={:.2e} (unc.) \t{}".format( + self.label, self.equiv_z, self.p_unc, str(self.coordinate) + ) def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ + """Create prov entities and activities.""" if self.p_unc is None: norm_cdf_z = (1.0 + erf(self.equiv_z / sqrt(2.0))) / 2.0 self.p_unc = 1 - norm_cdf_z atts = ( - (PROV['type'], self.type), - (PROV['label'], self.label), - (PROV['location'], self.coordinate.id)) + (PROV["type"], self.type), + (PROV["label"], self.label), + (PROV["location"], self.coordinate.id), + ) if self.value is not None: - atts = atts + ( - (PROV['value'], self.value), - ) + atts = atts + ((PROV["value"], self.value),) if self.p_unc is not None: atts = atts + ( - (NIDM_P_VALUE_UNCORRECTED, - Literal(self.p_unc, datatype=XSD_FLOAT)), - ) + ( + NIDM_P_VALUE_UNCORRECTED, + Literal(self.p_unc, datatype=XSD_FLOAT), + ), + ) if self.equiv_z is not None: atts = atts + ( - (NIDM_EQUIVALENT_ZSTATISTIC, - Literal(self.equiv_z, datatype=XSD_FLOAT)), - ) + ( + NIDM_EQUIVALENT_ZSTATISTIC, + Literal(self.equiv_z, datatype=XSD_FLOAT), + ), + ) if self.p_fdr is not None: atts = atts + ( - (NIDM_Q_VALUE_FDR, - Literal(self.p_fdr, datatype=XSD_FLOAT)), - ) + (NIDM_Q_VALUE_FDR, Literal(self.p_fdr, datatype=XSD_FLOAT)), + ) if self.p_fwer is not None: atts = atts + ( - (NIDM_P_VALUE_FWER, - Literal(self.p_fwer, datatype=XSD_FLOAT)), - ) + (NIDM_P_VALUE_FWER, Literal(self.p_fwer, datatype=XSD_FLOAT)), + ) self.add_attributes(atts) diff --git a/nidmresults/objects/modelfitting.py b/nidmresults/objects/modelfitting.py index 82b3fd3..1b7c39f 100644 --- a/nidmresults/objects/modelfitting.py +++ b/nidmresults/objects/modelfitting.py @@ -1,6 +1,5 @@ -""" -Objects describing the Model Parameters Estimation activity, its inputs and -outputs as specified in NIDM-Results. +"""Objects describing the Model Parameters Estimation activity, \ + its inputs and outputs as specified in NIDM-Results. Specification: http://nidm.nidash.org/specs/nidm-results.html @@ -8,29 +7,39 @@ @copyright: University of Warwick 2013-2014 """ -from prov.model import Identifier -import uuid -import numpy as np -import os -from nidmresults.objects.constants import * -import nibabel as nib -from nidmresults.objects.generic import * import json +import os import warnings -from numpy import genfromtxt + +import nibabel as nib +import numpy as np from prov.identifier import QualifiedName +from prov.model import Identifier +from nidmresults.objects.constants import * +from nidmresults.objects.generic import * -class ModelFitting(object): - """ - Object representing a Model fitting step: including a - ModelParametersEstimation activity, its inputs and outputs. +class ModelFitting: + """Object representing a Model fitting step. + + Include a ModelParametersEstimation activity, its inputs and outputs. """ - def __init__(self, activity, design_matrix, data, error_model, - param_estimates, rms_map, mask_map, grand_mean_map, - machine, subjects, rpv_map=None): + def __init__( + self, + activity, + design_matrix, + data, + error_model, + param_estimates, + rms_map, + mask_map, + grand_mean_map, + machine, + subjects, + rpv_map=None, + ): self.activity = activity self.design_matrix = design_matrix self.data = data @@ -45,28 +54,34 @@ def __init__(self, activity, design_matrix, data, error_model, class ImagingInstrument(NIDMObject): - """ - Object representing a ImagingInstrument entity. - """ + """Object representing a ImagingInstrument entity.""" def __init__(self, machine_type, label=None, oid=None): - super(ImagingInstrument, self).__init__(oid=oid) + super().__init__(oid=oid) if not isinstance(machine_type, QualifiedName): machine_type = machine_type.lower() machine_term = dict( - mri=NIF_MRI, eeg=NIF_EEG, meg=NIF_MEG, pet=NIF_PET, - spect=NIF_SPECT) + mri=NIF_MRI, + eeg=NIF_EEG, + meg=NIF_MEG, + pet=NIF_PET, + spect=NIF_SPECT, + ) machine_label = dict( - mri='MRI Scanner', eeg='EEG Machine', meg='MEG Machine', - pet='PET Scanner', spect='SPECT Machine') + mri="MRI Scanner", + eeg="EEG Machine", + meg="MEG Machine", + pet="PET Scanner", + spect="SPECT Machine", + ) - if not machine_type.startswith('http:'): + if not machine_type.startswith("http:"): self.type = machine_term[machine_type] else: self.type = machine_type - self.prov_type = PROV['Agent'] + self.prov_type = PROV["Agent"] if label is None: self.label = machine_label[machine_type] @@ -81,7 +96,8 @@ def get_query(klass, oid=None): oid_var = "<" + str(oid) + ">" # TODO: handle multiple basis - query = """ + query = ( + """ prefix nlx_Imaginginstrument: prefix nlx_MagneticResonanceImagingScanner: @@ -95,41 +111,55 @@ def get_query(klass, oid=None): xl_0050003> SELECT DISTINCT * WHERE { - {""" + oid_var + """ a nlx_Imaginginstrument: .} UNION - {""" + oid_var + """ a nlx_MagneticResonanceImagingScanner: .} UNION - {""" + oid_var + """ a nlx_PositronEmissionTomographyScanner: .} UNION - {""" + oid_var + """ a nlx_SinglePhotonEmissionComputedTomographyScanner: .} UNION - {""" + oid_var + """ a nlx_MagnetoencephalographyMachine: .} UNION - {""" + oid_var + """ a nlx_ElectroencephalographyMachine: .} - - """ + oid_var + """ rdfs:label ?label ; + {""" + + oid_var + + """ a nlx_Imaginginstrument: .} UNION + {""" + + oid_var + + """ a nlx_MagneticResonanceImagingScanner: .} UNION + {""" + + oid_var + + """ a nlx_PositronEmissionTomographyScanner: .} UNION + {""" + + oid_var + + """ a nlx_SinglePhotonEmissionComputedTomographyScanner: .} UNION + {""" + + oid_var + + """ a nlx_MagnetoencephalographyMachine: .} UNION + {""" + + oid_var + + """ a nlx_ElectroencephalographyMachine: .} + + """ + + oid_var + + """ rdfs:label ?label ; rdf:type ?machine_type . FILTER ( ?machine_type NOT IN (prov:Agent, prov:SoftwareAgent, nlx_Imaging\ instrument:) ) } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ - self.add_attributes(( - (PROV['type'], self.type), - (PROV['type'], NLX_IMAGING_INSTRUMENT), - (PROV['label'], self.label))) + """Create prov entities and activities.""" + self.add_attributes( + ( + (PROV["type"], self.type), + (PROV["type"], NLX_IMAGING_INSTRUMENT), + (PROV["label"], self.label), + ) + ) class Group(NIDMObject): - """ - Object representing a ImagingInstrument entity. - """ + """Object representing a ImagingInstrument entity.""" def __init__(self, num_subjects, group_name, label=None, oid=None): - super(Group, self).__init__(oid=oid) + super().__init__(oid=oid) self.type = STATO_GROUP - self.prov_type = PROV['Agent'] + self.prov_type = PROV["Agent"] self.group_name = group_name self.num_subjects = num_subjects if not label: @@ -143,40 +173,43 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix obo_studygrouppopulation: prefix nidm_groupName: prefix nidm_numberOfSubjects: SELECT DISTINCT * WHERE { - """ + oid_var + """ a obo_studygrouppopulation: ; + """ + + oid_var + + """ a obo_studygrouppopulation: ; rdfs:label ?label ; nidm_groupName: ?group_name ; nidm_numberOfSubjects: ?num_subjects . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ - self.add_attributes(( - (PROV['type'], self.type), - (NIDM_GROUP_NAME, self.group_name), - (NIDM_NUMBER_OF_SUBJECTS, self.num_subjects), - (PROV['label'], self.label))) + """Create prov entities and activities.""" + self.add_attributes( + ( + (PROV["type"], self.type), + (NIDM_GROUP_NAME, self.group_name), + (NIDM_NUMBER_OF_SUBJECTS, self.num_subjects), + (PROV["label"], self.label), + ) + ) class Person(NIDMObject): - """ - Object representing a ImagingInstrument entity. - """ + """Object representing a ImagingInstrument entity.""" - def __init__(self, label=None, oid=None): - super(Person, self).__init__(oid=oid) - self.prov_type = PROV['Agent'] - self.type = PROV['Person'] + def __init__(self, label=None, oid=None): + super().__init__(oid=oid) + self.prov_type = PROV["Agent"] + self.type = PROV["Person"] if not label: label = "Person" self.label = label @@ -188,43 +221,55 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ SELECT DISTINCT * WHERE { - """ + oid_var + """ a prov:Person ; + """ + + oid_var + + """ a prov:Person ; rdfs:label ?label . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ - self.add_attributes(( - (PROV['type'], self.prov_type), - (PROV['type'], self.type), - (PROV['label'], self.label))) + """Create prov entities and activities.""" + self.add_attributes( + ( + (PROV["type"], self.prov_type), + (PROV["type"], self.type), + (PROV["label"], self.label), + ) + ) class DesignMatrix(NIDMObject): - - """ - Object representing a DesignMatrix entity. - """ - - def __init__(self, matrix, image_file, regressors=None, - design_type=None, hrf_models=None, drift_model=None, - suffix='', csv_file=None, filename=None, label=None, - oid=None): - super(DesignMatrix, self).__init__(oid=oid) + """Object representing a DesignMatrix entity.""" + + def __init__( + self, + matrix, + image_file, + regressors=None, + design_type=None, + hrf_models=None, + drift_model=None, + suffix="", + csv_file=None, + filename=None, + label=None, + oid=None, + ): + super().__init__(oid=oid) self.type = NIDM_DESIGN_MATRIX - self.prov_type = PROV['Entity'] - img_filename = 'DesignMatrix' + suffix + '.png' + self.prov_type = PROV["Entity"] + img_filename = "DesignMatrix" + suffix + ".png" if isinstance(image_file, Image): self.image = image_file else: self.image = Image(image_file, img_filename) - if not type(regressors) is list: + if type(regressors) is not list: regressors = json.loads(regressors) self.regressors = regressors @@ -233,7 +278,7 @@ def __init__(self, matrix, image_file, regressors=None, self.drift_model = drift_model if csv_file is None: - self.csv_file = 'DesignMatrix' + suffix + '.csv' + self.csv_file = "DesignMatrix" + suffix + ".csv" self.matrix = matrix else: self.csv_file = csv_file @@ -242,7 +287,7 @@ def __init__(self, matrix, image_file, regressors=None, # self.matrix = genfromtxt(self.csv_file, delimiter=',') self.matrix = [] if filename is None: - self.filename = 'DesignMatrix' + suffix + '.csv' + self.filename = "DesignMatrix" + suffix + ".csv" else: self.filename = filename if label is not None: @@ -258,49 +303,57 @@ def get_query(klass, oid=None): oid_var = "<" + str(oid) + ">" # TODO: handle multiple basis - query = """ + query = ( + """ prefix nidm_ModelParameterEstimation: prefix nidm_withEstimationMethod: prefix nidm_hasHRFBasis: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_DesignMatrix: ; + """ + + oid_var + + """ a nidm_DesignMatrix: ; rdfs:label ?label ; prov:atLocation ?csv_file ; nfo:fileName ?filename . - OPTIONAL { """ + oid_var + """ nidm_regressorNames: ?regressors . } . + OPTIONAL { """ + + oid_var + + """ nidm_regressorNames: ?regressors . } . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ + """Create prov entities and activities.""" # Create cvs file containing design matrix - np.savetxt(os.path.join(export_dir, self.csv_file), - np.asarray(self.matrix), delimiter=",") + np.savetxt( + os.path.join(export_dir, self.csv_file), + np.asarray(self.matrix), + delimiter=",", + ) - if nidm_version['num'] in ["1.0.0", "1.1.0"]: + if nidm_version["num"] in ["1.0.0", "1.1.0"]: csv_location = Identifier("file://./" + self.csv_file) else: csv_location = Identifier(self.csv_file) - attributes = [(PROV['type'], self.type), - (PROV['label'], self.label), - (NIDM_REGRESSOR_NAMES, json.dumps(self.regressors)), - (DCT['format'], "text/csv"), - (NFO['fileName'], self.filename), - (DC['description'], self.image.id), - (PROV['location'], csv_location)] + attributes = [ + (PROV["type"], self.type), + (PROV["label"], self.label), + (NIDM_REGRESSOR_NAMES, json.dumps(self.regressors)), + (DCT["format"], "text/csv"), + (NFO["fileName"], self.filename), + (DC["description"], self.image.id), + (PROV["location"], csv_location), + ] if self.hrf_models is not None: - if nidm_version['num'] in ("1.0.0", "1.1.0"): + if nidm_version["num"] in ("1.0.0", "1.1.0"): if self.design_type is not None: - attributes.append( - (NIDM_HAS_FMRI_DESIGN, self.design_type)) + attributes.append((NIDM_HAS_FMRI_DESIGN, self.design_type)) else: warnings.warn("Design type is missing") @@ -316,13 +369,10 @@ def export(self, nidm_version, export_dir): class DriftModel(NIDMObject): - - """ - Object representing a DriftModel entity. - """ + """Object representing a DriftModel entity.""" def __init__(self, drift_type, parameter, label=None, oid=None): - super(DriftModel, self).__init__(oid=oid) + super().__init__(oid=oid) # if not isinstance(drift_type, QualifiedName): # drift_type = namespace_manager.valid_qualified_name(drift_type) @@ -330,7 +380,7 @@ def __init__(self, drift_type, parameter, label=None, oid=None): self.drift_type = drift_type self.parameter = parameter self.type = drift_type - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] if not label: if self.drift_type == FSL_GAUSSIAN_RUNNING_LINE_DRIFT_MODEL: self.label = "FSL's Gaussian Running Line Drift Model" @@ -344,32 +394,42 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_DesignMatrix: prefix spm_SPMsDriftCutoffPeriod: prefix fsl_driftCutoffPeriod: SELECT DISTINCT * WHERE { [] a nidm_DesignMatrix: ; - nidm_hasDriftModel: """ + oid_var + """ . + nidm_hasDriftModel: """ + + oid_var + + """ . - """ + oid_var + """ a ?drift_type ; + """ + + oid_var + + """ a ?drift_type ; rdfs:label ?label . - {""" + oid_var + """ spm_SPMsDriftCutoffPeriod: ?parameter .} UNION - {""" + oid_var + """ fsl_driftCutoffPeriod: ?parameter .} . + {""" + + oid_var + + """ spm_SPMsDriftCutoffPeriod: ?parameter .} UNION + {""" + + oid_var + + """ fsl_driftCutoffPeriod: ?parameter .} . FILTER ( ?drift_type NOT IN (prov:Entity) ) } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ - attributes = [(PROV['type'], self.drift_type), - (PROV['label'], self.label)] + """Create prov entities and activities.""" + attributes = [ + (PROV["type"], self.drift_type), + (PROV["label"], self.label), + ] if self.drift_type == FSL_GAUSSIAN_RUNNING_LINE_DRIFT_MODEL: attributes.append((FSL_DRIFT_CUTOFF_PERIOD, self.parameter)) @@ -382,18 +442,22 @@ def export(self, nidm_version, export_dir): class Data(NIDMObject): - - """ - Object representing a Data entity. - """ - - def __init__(self, grand_mean_scaling, target=None, mri_protocol=None, - label=None, group_or_sub=None, oid=None): - super(Data, self).__init__(oid=oid) + """Object representing a Data entity.""" + + def __init__( + self, + grand_mean_scaling, + target=None, + mri_protocol=None, + label=None, + group_or_sub=None, + oid=None, + ): + super().__init__(oid=oid) self.grand_mean_sc = grand_mean_scaling self.target_intensity = target self.type = NIDM_DATA - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] self.mri_protocol = mri_protocol if self.mri_protocol == "fmri": self.mri_protocol = NLX_FMRI_PROTOCOL @@ -409,7 +473,8 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_Data: prefix nidm_grandMeanScaling: prefix nidm_targetIntensity: @@ -419,55 +484,70 @@ def get_query(klass, oid=None): SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_Data: ; + """ + + oid_var + + """ a nidm_Data: ; rdfs:label ?label ; nidm_grandMeanScaling: $grand_mean_scaling . - OPTIONAL {""" + oid_var + """ nidm_targetIntensity: ?target . } . - OPTIONAL {""" + oid_var + """ nidm_hasMRIProtocol: ?mri_protocol . } . + OPTIONAL {""" + + oid_var + + """ nidm_targetIntensity: ?target . } . + OPTIONAL {""" + + oid_var + + """ nidm_hasMRIProtocol: ?mri_protocol . } . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ - if nidm_version['major'] < 1 or \ - (nidm_version['major'] == 1 and nidm_version['minor'] < 3): + """Create prov entities and activities.""" + if nidm_version["major"] < 1 or ( + nidm_version["major"] == 1 and nidm_version["minor"] < 3 + ): self.type = NIDM_DATA_SCALING - # Create "Data" entity + # Create "Data" entity # FIXME: grand mean scaling? # FIXME: medianIntensity - self.add_attributes(( - (PROV['type'], self.type), - (PROV['type'], PROV['Collection']), - (PROV['label'], self.label), - (NIDM_GRAND_MEAN_SCALING, self.grand_mean_sc), - (NIDM_TARGET_INTENSITY, self.target_intensity))) - - if nidm_version['major'] > 1 or \ - (nidm_version['major'] == 1 and nidm_version['minor'] > 2): + self.add_attributes( + ( + (PROV["type"], self.type), + (PROV["type"], PROV["Collection"]), + (PROV["label"], self.label), + (NIDM_GRAND_MEAN_SCALING, self.grand_mean_sc), + (NIDM_TARGET_INTENSITY, self.target_intensity), + ) + ) + + if nidm_version["major"] > 1 or ( + nidm_version["major"] == 1 and nidm_version["minor"] > 2 + ): if self.mri_protocol is not None: self.add_attributes( - [(NIDM_HAS_MRI_PROTOCOL, self.mri_protocol)]) + [(NIDM_HAS_MRI_PROTOCOL, self.mri_protocol)] + ) class ErrorModel(NIDMObject): - - """ - Object representing an ErrorModel entity. - """ - - def __init__(self, error_distribution, variance_homo, variance_spatial, - dependence, dependance_spatial=None, oid=None): - super(ErrorModel, self).__init__(oid=oid) + """Object representing an ErrorModel entity.""" + + def __init__( + self, + error_distribution, + variance_homo, + variance_spatial, + dependence, + dependance_spatial=None, + oid=None, + ): + super().__init__(oid=oid) self.error_distribution = error_distribution self.variance_homo = variance_homo self.variance_spatial = variance_spatial self.dependence = dependence self.dependance_spatial = dependance_spatial self.type = NIDM_ERROR_MODEL - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] @classmethod def get_query(klass, oid=None): @@ -476,7 +556,8 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_ErrorModel: prefix nidm_hasErrorDistribution: prefix nidm_errorVarianceHomogeneous: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_ErrorModel: ; + """ + + oid_var + + """ a nidm_ErrorModel: ; nidm_hasErrorDistribution: $error_distribution ; nidm_errorVarianceHomogeneous: $variance_homo ; nidm_varianceMapWiseDependence: $variance_spatial ; nidm_hasErrorDependence: $dependence . - OPTIONAL {""" + oid_var + """ rdfs:label ?label . } . - OPTIONAL {""" + oid_var + """ nidm_dependenceMapWiseDependence: ?dependance_spatial . } . + OPTIONAL {""" + + oid_var + + """ rdfs:label ?label . } . + OPTIONAL {""" + + oid_var + + """ nidm_dependenceMapWiseDependence: ?dependance_spatial . } . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ + """Create prov entities and activities.""" atts = ( - (PROV['type'], NIDM_ERROR_MODEL), + (PROV["type"], NIDM_ERROR_MODEL), (NIDM_HAS_ERROR_DISTRIBUTION, self.error_distribution), (NIDM_ERROR_VARIANCE_HOMOGENEOUS, self.variance_homo), (NIDM_VARIANCE_SPATIAL_MODEL, self.variance_spatial), - (NIDM_HAS_ERROR_DEPENDENCE, self.dependence)) + (NIDM_HAS_ERROR_DEPENDENCE, self.dependence), + ) # If the error covariance is independent then there is no associated # spatial model if self.dependance_spatial is not None: atts = atts + ( - ((NIDM_DEPENDENCE_SPATIAL_MODEL, self.dependance_spatial),)) + ((NIDM_DEPENDENCE_SPATIAL_MODEL, self.dependance_spatial),) + ) # Create "Error Model" entity self.add_attributes(atts) class ModelParametersEstimation(NIDMObject): + """Object representing an ModelParametersEstimation activity.""" - """ - Object representing an ModelParametersEstimation activity. - """ - - def __init__(self, estimation_method, software_id, data=None, label=None, - oid=None): - super(ModelParametersEstimation, self).__init__(oid=oid) + def __init__( + self, estimation_method, software_id, data=None, label=None, oid=None + ): + super().__init__(oid=oid) self.estimation_method = estimation_method self.software_id = software_id self.type = NIDM_MODEL_PARAMETERS_ESTIMATION - self.prov_type = PROV['Activity'] + self.prov_type = PROV["Activity"] # currently only used for reading self.data = data if label is None: @@ -547,54 +633,71 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_ModelParameterEstimation: prefix nidm_withEstimationMethod: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_ModelParameterEstimation: ; + """ + + oid_var + + """ a nidm_ModelParameterEstimation: ; rdfs:label ?label ; nidm_withEstimationMethod: ?estimation_method ; prov:wasAssociatedWith ?software_id . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ + """Create prov entities and activities.""" # Create "Model Parameter estimation" activity - self.add_attributes(( - (PROV['type'], self.type), - (NIDM_WITH_ESTIMATION_METHOD, self.estimation_method), - (PROV['label'], self.label))) + self.add_attributes( + ( + (PROV["type"], self.type), + (NIDM_WITH_ESTIMATION_METHOD, self.estimation_method), + (PROV["label"], self.label), + ) + ) class ParameterEstimateMap(NIDMObject): - - """ - Object representing an ParameterEstimateMap entity. - """ - - def __init__(self, coord_space, pe_file=None, pe_num=None, filename=None, - sha=None, label=None, suffix='', model_param_estimation=None, - oid=None, fmt=None, derfrom_id=None, derfrom_filename=None, - derfrom_fmt=None, derfrom_sha=None, isderfrommap=False): - super(ParameterEstimateMap, self).__init__(oid=oid) + """Object representing an ParameterEstimateMap entity.""" + + def __init__( + self, + coord_space, + pe_file=None, + pe_num=None, + filename=None, + sha=None, + label=None, + suffix="", + model_param_estimation=None, + oid=None, + fmt=None, + derfrom_id=None, + derfrom_filename=None, + derfrom_fmt=None, + derfrom_sha=None, + isderfrommap=False, + ): + super().__init__(oid=oid) # Column index in the corresponding design matrix self.num = pe_num self.coord_space = coord_space # Parameter Estimate Map is going to be copied over to export_dir if not filename: - filename = 'ParameterEstimate' + suffix + '.nii.gz' + filename = "ParameterEstimate" + suffix + ".nii.gz" - self.file = NIDMFile(self.id, pe_file, filename=filename, sha=sha, - fmt=fmt) + self.file = NIDMFile( + self.id, pe_file, filename=filename, sha=sha, fmt=fmt + ) self.type = NIDM_PARAMETER_ESTIMATE_MAP - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] if label is None: if self.num: label = "Parameter estimate " + str(self.num) @@ -607,9 +710,13 @@ def __init__(self, coord_space, pe_file=None, pe_num=None, filename=None, if derfrom_id is not None: self.derfrom = ParameterEstimateMap( - oid=derfrom_id, coord_space=coord_space, - filename=derfrom_filename, sha=derfrom_sha, - fmt=derfrom_fmt, isderfrommap=True) + oid=derfrom_id, + coord_space=coord_space, + filename=derfrom_filename, + sha=derfrom_sha, + fmt=derfrom_fmt, + isderfrommap=True, + ) else: self.derfrom = None self.isderfrommap = isderfrommap @@ -621,19 +728,26 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_ParameterEstimateMap: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_ParameterEstimateMap: ; + """ + + oid_var + + """ a nidm_ParameterEstimateMap: ; rdfs:label ?label ; nfo:fileName ?filename ; crypto:sha512 ?sha ; dct:format ?fmt . - OPTIONAL {""" + oid_var + """ prov:atLocation ?pe_file .} . + OPTIONAL {""" + + oid_var + + """ prov:atLocation ?pe_file .} . - OPTIONAL {""" + oid_var + """ prov:wasDerivedFrom ?derfrom_id . + OPTIONAL {""" + + oid_var + + """ prov:wasDerivedFrom ?derfrom_id . ?derfrom_id a nidm_ParameterEstimateMap: ; nfo:fileName ?derfrom_filename ; @@ -642,62 +756,77 @@ def get_query(klass, oid=None): } . } """ + ) -# ?derfrom_id a nidm_ParameterEstimateMap: ; -# nfo:fileName ?derfrom_filename ; -# dct:format ?derfrom_format ; -# crypto:sha512 ?derfrom_sha . } . + # ?derfrom_id a nidm_ParameterEstimateMap: ; + # nfo:fileName ?derfrom_filename ; + # dct:format ?derfrom_format ; + # crypto:sha512 ?derfrom_sha . } . return query # Generate prov for contrast map def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ - atts = ( - (PROV['type'], self.type),) + """Create prov entities and activities.""" + atts = ((PROV["type"], self.type),) if not self.isderfrommap: - atts = atts + ( - (NIDM_IN_COORDINATE_SPACE, self.coord_space.id),) + atts = atts + ((NIDM_IN_COORDINATE_SPACE, self.coord_space.id),) if self.label is not None: - atts = atts + ( - (PROV['label'], self.label),) + atts = atts + ((PROV["label"], self.label),) # Parameter estimate entity self.add_attributes(atts) class ResidualMeanSquares(NIDMObject): - - """ - Object representing an ResidualMeanSquares entity. - """ - - def __init__(self, residual_file, coord_space, - temporary=False, suffix='', fmt=None, filename=None, - sha=None, label=None, oid=None, - derfrom_id=None, derfrom_filename=None, derfrom_fmt=None, - derfrom_sha=None, isderfrommap=False): - super(ResidualMeanSquares, self).__init__(oid=oid) + """Object representing an ResidualMeanSquares entity.""" + + def __init__( + self, + residual_file, + coord_space, + temporary=False, + suffix="", + fmt=None, + filename=None, + sha=None, + label=None, + oid=None, + derfrom_id=None, + derfrom_filename=None, + derfrom_fmt=None, + derfrom_sha=None, + isderfrommap=False, + ): + super().__init__(oid=oid) self.coord_space = coord_space if filename is None: - filename = 'ResidualMeanSquares' + suffix + '.nii.gz' - self.file = NIDMFile(self.id, residual_file, filename, - temporary=temporary, fmt=fmt, sha=sha) + filename = "ResidualMeanSquares" + suffix + ".nii.gz" + self.file = NIDMFile( + self.id, + residual_file, + filename, + temporary=temporary, + fmt=fmt, + sha=sha, + ) if label is None: label = "Residual Mean Squares Map" self.label = label self.type = NIDM_RESIDUAL_MEAN_SQUARES_MAP - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] if derfrom_id is not None: self.derfrom = ResidualMeanSquares( - None, coord_space, - oid=derfrom_id, filename=derfrom_filename, - sha=derfrom_sha, fmt=derfrom_fmt, - isderfrommap=True) + None, + coord_space, + oid=derfrom_id, + filename=derfrom_filename, + sha=derfrom_sha, + fmt=derfrom_fmt, + isderfrommap=True, + ) else: self.derfrom = None self.isderfrommap = isderfrommap @@ -709,18 +838,23 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_ResidualMeanSquaresMap: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_ResidualMeanSquaresMap: ; + """ + + oid_var + + """ a nidm_ResidualMeanSquaresMap: ; rdfs:label ?label ; nfo:fileName ?filename ; crypto:sha512 ?sha ; prov:atLocation ?residual_file ; dct:format ?fmt . - OPTIONAL {""" + oid_var + """ prov:wasDerivedFrom ?derfrom_id . + OPTIONAL {""" + + oid_var + + """ prov:wasDerivedFrom ?derfrom_id . ?derfrom_id a nidm_ResidualMeanSquaresMap: ; nfo:fileName ?derfrom_filename ; @@ -730,52 +864,70 @@ def get_query(klass, oid=None): } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ + """Create prov entities and activities.""" atts = ( - (PROV['type'], self.type,), - ) + ( + PROV["type"], + self.type, + ), + ) if not self.isderfrommap: atts = atts + ( (NIDM_IN_COORDINATE_SPACE, self.coord_space.id), - (PROV['label'], self.label)) + (PROV["label"], self.label), + ) self.add_attributes(atts) class ReselsPerVoxelMap(NIDMObject): - - """ - Object representing an ResidualMeanSquares entity. - """ - - def __init__(self, rpv_file, coord_space, - temporary=False, suffix='', fmt=None, filename=None, - sha=None, label=None, oid=None, - derfrom_id=None, derfrom_filename=None, derfrom_fmt=None, - derfrom_sha=None, inf_id=None, isderfrommap=False): - super(ReselsPerVoxelMap, self).__init__(oid=oid) + """Object representing an ResidualMeanSquares entity.""" + + def __init__( + self, + rpv_file, + coord_space, + temporary=False, + suffix="", + fmt=None, + filename=None, + sha=None, + label=None, + oid=None, + derfrom_id=None, + derfrom_filename=None, + derfrom_fmt=None, + derfrom_sha=None, + inf_id=None, + isderfrommap=False, + ): + super().__init__(oid=oid) self.coord_space = coord_space if filename is None: - filename = 'ReselsPerVoxelMap' + suffix + '.nii.gz' - self.file = NIDMFile(self.id, rpv_file, filename, - temporary=temporary, fmt=fmt, sha=sha) + filename = "ReselsPerVoxelMap" + suffix + ".nii.gz" + self.file = NIDMFile( + self.id, rpv_file, filename, temporary=temporary, fmt=fmt, sha=sha + ) if label is None: label = "Resels Per Voxel File" self.label = label self.type = NIDM_RESELS_PER_VOXEL_MAP - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] if derfrom_id is not None: self.derfrom = ReselsPerVoxelMap( - None, coord_space, - oid=derfrom_id, filename=derfrom_filename, - sha=derfrom_sha, fmt=derfrom_fmt, - isderfrommap=True) + None, + coord_space, + oid=derfrom_id, + filename=derfrom_filename, + sha=derfrom_sha, + fmt=derfrom_fmt, + isderfrommap=True, + ) else: self.derfrom = None self.inf_id = inf_id @@ -788,20 +940,27 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_ReselsPerVoxelMap: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_ReselsPerVoxelMap: ; + """ + + oid_var + + """ a nidm_ReselsPerVoxelMap: ; rdfs:label ?label ; nfo:fileName ?filename ; crypto:sha512 ?sha ; prov:atLocation ?rpv_file ; dct:format ?fmt . - ?inf_id prov:used """ + oid_var + """ . + ?inf_id prov:used """ + + oid_var + + """ . - OPTIONAL {""" + oid_var + """ prov:wasDerivedFrom ?derfrom_id . + OPTIONAL {""" + + oid_var + + """ prov:wasDerivedFrom ?derfrom_id . ?derfrom_id a nidm_ReselsPerVoxelMap: ; nfo:fileName ?derfrom_filename ; @@ -810,53 +969,69 @@ def get_query(klass, oid=None): } . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ + """Create prov entities and activities.""" atts = ( - (PROV['type'], self.type,), - ) + ( + PROV["type"], + self.type, + ), + ) if not self.isderfrommap: atts = atts + ( (NIDM_IN_COORDINATE_SPACE, self.coord_space.id), - (PROV['label'], self.label)) + (PROV["label"], self.label), + ) self.add_attributes(atts) class MaskMap(NIDMObject): - - """ - Object representing an MaskMap entity. - """ - - def __init__(self, mask_file, coord_space, user_defined, - suffix='', filename=None, fmt=None, label=None, sha=None, - oid=None, - derfrom_id=None, derfrom_filename=None, derfrom_fmt=None, - derfrom_sha=None, isderfrommap=False): - super(MaskMap, self).__init__(oid=oid) + """Object representing an MaskMap entity.""" + + def __init__( + self, + mask_file, + coord_space, + user_defined, + suffix="", + filename=None, + fmt=None, + label=None, + sha=None, + oid=None, + derfrom_id=None, + derfrom_filename=None, + derfrom_fmt=None, + derfrom_sha=None, + isderfrommap=False, + ): + super().__init__(oid=oid) self.coord_space = coord_space if filename is None: - filename = 'Mask' + suffix + '.nii.gz' - self.file = NIDMFile(self.id, mask_file, filename, - sha=sha, fmt=fmt) + filename = "Mask" + suffix + ".nii.gz" + self.file = NIDMFile(self.id, mask_file, filename, sha=sha, fmt=fmt) self.user_defined = user_defined self.type = NIDM_MASK_MAP - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] if label is None: label = "Mask" self.label = label if derfrom_id is not None: self.derfrom = MaskMap( - None, coord_space, user_defined, - oid=derfrom_id, filename=derfrom_filename, - sha=derfrom_sha, fmt=derfrom_fmt, - isderfrommap=True) + None, + coord_space, + user_defined, + oid=derfrom_id, + filename=derfrom_filename, + sha=derfrom_sha, + fmt=derfrom_fmt, + isderfrommap=True, + ) else: self.derfrom = None self.isderfrommap = isderfrommap @@ -868,12 +1043,15 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_MaskMap: prefix nidm_isUserDefined: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_MaskMap: ; + """ + + oid_var + + """ a nidm_MaskMap: ; rdfs:label ?label ; nidm_isUserDefined: ?user_defined ; nfo:fileName ?filename ; @@ -881,7 +1059,9 @@ def get_query(klass, oid=None): prov:atLocation ?mask_file ; dct:format ?fmt . - OPTIONAL {""" + oid_var + """ prov:wasDerivedFrom ?derfrom_id . + OPTIONAL {""" + + oid_var + + """ prov:wasDerivedFrom ?derfrom_id . ?derfrom_id a nidm_MaskMap: ; nfo:fileName ?derfrom_filename ; @@ -890,44 +1070,53 @@ def get_query(klass, oid=None): } . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ + """Create prov entities and activities.""" atts = ( - (PROV['type'], self.type,), + ( + PROV["type"], + self.type, + ), ) if not self.isderfrommap: atts = atts + ( (NIDM_IN_COORDINATE_SPACE, self.coord_space.id), - (PROV['label'], self.label), - (NIDM_IS_USER_DEFINED, self.user_defined)) + (PROV["label"], self.label), + (NIDM_IS_USER_DEFINED, self.user_defined), + ) self.add_attributes(atts) class GrandMeanMap(NIDMObject): - - """ - Object representing an GrandMeanMap entity. - """ + """Object representing an GrandMeanMap entity.""" # TODO: we should remove mask_file here and ask for masked data instead? - def __init__(self, org_file, mask_file, coord_space, - suffix='', label=None, filename=None, sha=None, - fmt=None, masked_median=None, oid=None): - super(GrandMeanMap, self).__init__(oid=oid) + def __init__( + self, + org_file, + mask_file, + coord_space, + suffix="", + label=None, + filename=None, + sha=None, + fmt=None, + masked_median=None, + oid=None, + ): + super().__init__(oid=oid) if filename is None: - filename = 'GrandMean' + suffix + '.nii.gz' - self.file = NIDMFile(self.id, org_file, filename, - sha=sha, fmt=fmt) + filename = "GrandMean" + suffix + ".nii.gz" + self.file = NIDMFile(self.id, org_file, filename, sha=sha, fmt=fmt) self.mask_file = mask_file # needed to compute masked median self.coord_space = coord_space self.type = NIDM_GRAND_MEAN_MAP - self.prov_type = PROV['Entity'] + self.prov_type = PROV["Entity"] if label is None: label = "Grand Mean Map" self.label = label @@ -940,12 +1129,15 @@ def get_query(klass, oid=None): else: oid_var = "<" + str(oid) + ">" - query = """ + query = ( + """ prefix nidm_GrandMeanMap: prefix nidm_maskedMedian: SELECT DISTINCT * WHERE { - """ + oid_var + """ a nidm_GrandMeanMap: ; + """ + + oid_var + + """ a nidm_GrandMeanMap: ; rdfs:label ?label ; nidm_maskedMedian: ?masked_median; prov:atLocation ?org_file ; @@ -954,13 +1146,11 @@ def get_query(klass, oid=None): dct:format ?fmt . } """ + ) return query def export(self, nidm_version, export_dir): - """ - Create prov entities and activities. - """ - + """Create prov entities and activities.""" if self.masked_median is None: grand_mean_file = self.file.path grand_mean_img = nib.load(grand_mean_file) @@ -973,11 +1163,14 @@ def export(self, nidm_version, export_dir): grand_mean_data_in_mask = grand_mean_data[mask_data > 0] self.masked_median = np.median( - np.array(grand_mean_data_in_mask, dtype=float)) + np.array(grand_mean_data_in_mask, dtype=float) + ) - self.add_attributes(( - (PROV['type'], self.type), - (PROV['label'], self.label), - (NIDM_MASKED_MEDIAN, self.masked_median), - (NIDM_IN_COORDINATE_SPACE, self.coord_space.id)) + self.add_attributes( + ( + (PROV["type"], self.type), + (PROV["label"], self.label), + (NIDM_MASKED_MEDIAN, self.masked_median), + (NIDM_IN_COORDINATE_SPACE, self.coord_space.id), + ) ) diff --git a/nidmresults/owl/nidm-results_020.owl b/nidmresults/owl/nidm-results_020.owl index 25d07b7..9bef825 100644 --- a/nidmresults/owl/nidm-results_020.owl +++ b/nidmresults/owl/nidm-results_020.owl @@ -31,17 +31,17 @@ obo:IAO_0000111 rdf:type owl:AnnotationProperty . ### http://purl.obolibrary.org/obo/IAO_0000112 obo:IAO_0000112 rdf:type owl:AnnotationProperty ; - + rdfs:label "example of usage"@en ; - + obo:IAO_0000115 "A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not"@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "example"@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -49,15 +49,15 @@ obo:IAO_0000112 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000114 obo:IAO_0000114 rdf:type owl:AnnotationProperty ; - + rdfs:label "has curation status"@en ; - + obo:IAO_0000119 "OBI_0000281"@en ; - + obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en , "PERSON:Bill Bug"@en , "PERSON:Melanie Courtot"@en ; - + obo:IAO_0000111 "has curation status"@en . @@ -65,17 +65,17 @@ obo:IAO_0000114 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000115 obo:IAO_0000115 rdf:type owl:AnnotationProperty ; - + rdfs:label "definition"@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000115 "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en ; - + obo:IAO_0000111 "definition"@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -83,17 +83,17 @@ obo:IAO_0000115 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000116 obo:IAO_0000116 rdf:type owl:AnnotationProperty ; - + rdfs:label "editor note"@en ; - + obo:IAO_0000115 "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "editor note"@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -128,9 +128,9 @@ owl:sameAs rdf:type owl:AnnotationProperty . ### http://purl.org/dc/terms/format dct:format rdf:type owl:ObjectProperty ; - + rdfs:subPropertyOf owl:topObjectProperty ; - + rdfs:domain prov:Entity . @@ -138,9 +138,9 @@ dct:format rdf:type owl:ObjectProperty ; ### http://www.incf.org/ns/nidash/nidm#alternativeHypothesis nidm:alternativeHypothesis rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:domain nidm:Inference . @@ -148,11 +148,11 @@ nidm:alternativeHypothesis rdf:type owl:ObjectProperty ; ### http://www.incf.org/ns/nidash/nidm#atCoordinateSpace nidm:atCoordinateSpace rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "Property of a DataArray to associate a CoordinateSpace with a physical file." ; - + rdfs:range nidm:CoordinateSpace ; - + rdfs:domain nidm:Map . @@ -160,11 +160,11 @@ nidm:atCoordinateSpace rdf:type owl:ObjectProperty ; ### http://www.incf.org/ns/nidash/nidm#dependenceSpatialModel nidm:dependenceSpatialModel rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:domain nidm:NoiseModel ; - + rdfs:range nidm:SpatialModel . @@ -172,11 +172,11 @@ nidm:dependenceSpatialModel rdf:type owl:ObjectProperty ; ### http://www.incf.org/ns/nidash/nidm#hasAlternativeHypothesis nidm:hasAlternativeHypothesis rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:domain nidm:Inference ; - + rdfs:range nidm:OneTailedTest , nidm:TwoTailedTest . @@ -185,16 +185,16 @@ nidm:hasAlternativeHypothesis rdf:type owl:ObjectProperty ; ### http://www.incf.org/ns/nidash/nidm#hasClusterLabelsMap nidm:hasClusterLabelsMap rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "A map whose value at each location denotes cluster membership. Each cluster is denoted by a different integer." ; - - obo:IAO_0000116 """Range: Pathtoaniftiimage not found. BIRNLex or + + obo:IAO_0000116 """Range: Pathtoaniftiimage not found. BIRNLex or NIDM Concept ID: nidm_4. """ ; - + obo:IAO_0000112 "file:///path/to/cluster_labels.img" ; - + rdfs:range nidm:ClusterLabelsMap ; - + rdfs:domain nidm:ExcursionSet . @@ -202,11 +202,11 @@ NIDM Concept ID: nidm_4. """ ; ### http://www.incf.org/ns/nidash/nidm#hasMapHeader nidm:hasMapHeader rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:domain nidm:Map ; - + rdfs:range nidm:MapHeader . @@ -214,11 +214,11 @@ nidm:hasMapHeader rdf:type owl:ObjectProperty ; ### http://www.incf.org/ns/nidash/nidm#hasNoiseDependence nidm:hasNoiseDependence rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:range nidm:NoiseDependence ; - + rdfs:domain nidm:NoiseModel . @@ -226,11 +226,11 @@ nidm:hasNoiseDependence rdf:type owl:ObjectProperty ; ### http://www.incf.org/ns/nidash/nidm#hasNoiseDistribution nidm:hasNoiseDistribution rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:range nidm:NoiseDistribution ; - + rdfs:domain nidm:NoiseModel . @@ -238,16 +238,16 @@ nidm:hasNoiseDistribution rdf:type owl:ObjectProperty ; ### http://www.incf.org/ns/nidash/nidm#inWorldCoordinateSystem nidm:inWorldCoordinateSystem rdf:type owl:ObjectProperty ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_22. """ ; - + obo:IAO_0000115 "Type of coordinate system." ; - + obo:IAO_0000112 "nidm:MNICoordinateSystem" ; - + rdfs:domain nidm:CoordinateSpace ; - + rdfs:range nidm:WorldCoordinateSystem . @@ -255,11 +255,11 @@ NIDM Concept ID: nidm_22. """ ; ### http://www.incf.org/ns/nidash/nidm#objectModel nidm:objectModel rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:range nidm:NIDMObjectModel ; - + rdfs:domain prov:Bundle . @@ -267,13 +267,13 @@ nidm:objectModel rdf:type owl:ObjectProperty ; ### http://www.incf.org/ns/nidash/nidm#statisticType nidm:statisticType rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:domain nidm:ContrastWeights ; - + rdfs:range nidm:Statistic ; - + rdfs:domain nidm:StatisticMap . @@ -281,11 +281,11 @@ nidm:statisticType rdf:type owl:ObjectProperty ; ### http://www.incf.org/ns/nidash/nidm#varianceSpatialModel nidm:varianceSpatialModel rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:domain nidm:NoiseModel ; - + rdfs:range nidm:SpatialModel . @@ -293,17 +293,17 @@ nidm:varianceSpatialModel rdf:type owl:ObjectProperty ; ### http://www.incf.org/ns/nidash/nidm#visualisation nidm:visualisation rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "Graphical representation of an entity." ; - + obo:IAO_0000112 "file:///path/to/design_matrix.png" ; - - obo:IAO_0000116 """Range: Pathtoanimage(e.g.png) not found. BIRNLex or + + obo:IAO_0000116 """Range: Pathtoanimage(e.g.png) not found. BIRNLex or NIDM Concept ID: nidm_66. """ ; - + rdfs:domain nidm:DesignMatrix , nidm:ExcursionSet ; - + rdfs:range nidm:Image . @@ -311,11 +311,11 @@ NIDM Concept ID: nidm_66. """ ; ### http://www.incf.org/ns/nidash/nidm#withEstimationMethod nidm:withEstimationMethod rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:range nidm:EstimationMethod ; - + rdfs:domain nidm:ModelParametersEstimation . @@ -323,16 +323,16 @@ nidm:withEstimationMethod rdf:type owl:ObjectProperty ; ### http://www.incf.org/ns/nidash/spm#hasMaximumIntensityProjection spm:hasMaximumIntensityProjection rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "Maximum intensity projection of a map." ; - - obo:IAO_0000116 """Range: Pathtoanimage(e.g.png) not found. BIRNLex or + + obo:IAO_0000116 """Range: Pathtoanimage(e.g.png) not found. BIRNLex or NIDM Concept ID: spm_77. """ ; - + obo:IAO_0000112 "file:///path/to/MIP.png" ; - + rdfs:domain nidm:ExcursionSet ; - + rdfs:range nidm:Image . @@ -340,9 +340,9 @@ NIDM Concept ID: spm_77. """ ; ### http://www.w3.org/ns/prov#atLocation prov:atLocation rdf:type owl:ObjectProperty ; - + rdfs:domain prov:Entity ; - + rdfs:range prov:Location . @@ -350,9 +350,9 @@ prov:atLocation rdf:type owl:ObjectProperty ; ### http://www.w3.org/ns/prov#used prov:used rdf:type owl:ObjectProperty ; - + rdfs:domain prov:Activity ; - + rdfs:range prov:Entity . @@ -360,11 +360,11 @@ prov:used rdf:type owl:ObjectProperty ; ### http://www.w3.org/ns/prov#wasAssociatedWith prov:wasAssociatedWith rdf:type owl:ObjectProperty ; - + rdfs:subPropertyOf owl:topObjectProperty ; - + rdfs:domain prov:Activity ; - + rdfs:range prov:Agent . @@ -372,9 +372,9 @@ prov:wasAssociatedWith rdf:type owl:ObjectProperty ; ### http://www.w3.org/ns/prov#wasDerivedFrom prov:wasDerivedFrom rdf:type owl:ObjectProperty ; - + rdfs:range prov:Entity ; - + rdfs:domain prov:Entity . @@ -382,9 +382,9 @@ prov:wasDerivedFrom rdf:type owl:ObjectProperty ; ### http://www.w3.org/ns/prov#wasGeneratedBy prov:wasGeneratedBy rdf:type owl:ObjectProperty ; - + rdfs:range prov:Activity ; - + rdfs:domain prov:Entity . @@ -401,9 +401,9 @@ prov:wasGeneratedBy rdf:type owl:ObjectProperty ; ### http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512 crypto:sha512 rdf:type owl:DatatypeProperty ; - + rdfs:range xsd:string ; - + rdfs:domain prov:Entity . @@ -411,7 +411,7 @@ crypto:sha512 rdf:type owl:DatatypeProperty ; ### http://purl.org/dc/terms/format dct:format rdf:type owl:DatatypeProperty ; - + rdfs:range xsd:string . @@ -419,16 +419,16 @@ dct:format rdf:type owl:DatatypeProperty ; ### http://www.incf.org/ns/nidash/fsl#coordinate1InVoxels fsl:coordinate1InVoxels rdf:type owl:DatatypeProperty ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_16. """ ; - + obo:IAO_0000112 "-60" ; - + obo:IAO_0000115 "Coordinate along the first dimension in voxels." ; - + rdfs:domain nidm:Coordinate ; - + rdfs:range xsd:float . @@ -436,16 +436,16 @@ NIDM Concept ID: nidm_16. """ ; ### http://www.incf.org/ns/nidash/fsl#coordinate2InVoxels fsl:coordinate2InVoxels rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Coordinate along the second dimension in voxels." ; - + obo:IAO_0000112 "-28" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_18. """ ; - + rdfs:domain nidm:Coordinate ; - + rdfs:range xsd:float . @@ -453,16 +453,16 @@ NIDM Concept ID: nidm_18. """ ; ### http://www.incf.org/ns/nidash/fsl#coordinate3InVoxels fsl:coordinate3InVoxels rdf:type owl:DatatypeProperty ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_20. """ ; - + obo:IAO_0000112 "13" ; - + obo:IAO_0000115 "Coordinate along the third dimension in voxels" ; - + rdfs:domain nidm:Coordinate ; - + rdfs:range xsd:float . @@ -470,13 +470,13 @@ NIDM Concept ID: nidm_20. """ ; ### http://www.incf.org/ns/nidash/fsl#dlh fsl:dlh rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:comment "To be renamed" ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range xsd:float . @@ -484,9 +484,9 @@ fsl:dlh rdf:type owl:DatatypeProperty ; ### http://www.incf.org/ns/nidash/fsl#featVersion fsl:featVersion rdf:type owl:DatatypeProperty ; - + rdfs:domain nidm:FSL ; - + rdfs:range xsd:string . @@ -494,13 +494,13 @@ fsl:featVersion rdf:type owl:DatatypeProperty ; ### http://www.incf.org/ns/nidash/fsl#reselSizeInVoxels fsl:reselSizeInVoxels rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range xsd:float ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -508,15 +508,15 @@ fsl:reselSizeInVoxels rdf:type owl:DatatypeProperty ; ### http://www.incf.org/ns/nidash/fsl#searchVolumeInVoxels fsl:searchVolumeInVoxels rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:comment "Check if this can be merged with spm:searchVolumeInVoxels" ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range xsd:positiveInteger ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -524,16 +524,16 @@ fsl:searchVolumeInVoxels rdf:type owl:DatatypeProperty ; ### http://www.incf.org/ns/nidash/nidm#clusterLabelId nidm:clusterLabelId rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "5" ; - + obo:IAO_0000115 "Integer associated with a particular cluster as specified in the clusterLabelsMap." ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_3. """ ; - + rdfs:domain nidm:Cluster ; - + rdfs:range xsd:int . @@ -541,17 +541,17 @@ NIDM Concept ID: nidm_3. """ ; ### http://www.incf.org/ns/nidash/nidm#clusterSizeInVertices nidm:clusterSizeInVertices rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "10" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_5. """ ; - + obo:IAO_0000115 "Number of vertices that make up the cluster." ; - + rdfs:domain nidm:Cluster , nidm:ExtentThreshold ; - + rdfs:range xsd:positiveInteger . @@ -559,17 +559,17 @@ NIDM Concept ID: nidm_5. """ ; ### http://www.incf.org/ns/nidash/nidm#clusterSizeInVoxels nidm:clusterSizeInVoxels rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "18" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_6. """ ; - + obo:IAO_0000115 "Number of voxels that make up the cluster." ; - + rdfs:domain nidm:Cluster , nidm:ExtentThreshold ; - + rdfs:range xsd:positiveInteger . @@ -577,18 +577,18 @@ NIDM Concept ID: nidm_6. """ ; ### http://www.incf.org/ns/nidash/nidm#contrastName nidm:contrastName rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Name of the contrast." ; - + obo:IAO_0000112 "\"Listening > Rest\"" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_11. """ ; - + rdfs:domain nidm:ContrastMap , nidm:ContrastWeights , nidm:StatisticMap ; - + rdfs:range xsd:string . @@ -596,16 +596,16 @@ NIDM Concept ID: nidm_11. """ ; ### http://www.incf.org/ns/nidash/nidm#coordinate1 nidm:coordinate1 rdf:type owl:DatatypeProperty ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_15. """ ; - + obo:IAO_0000115 "Coordinate along the first dimension in voxel units." ; - + obo:IAO_0000112 "-60" ; - + rdfs:domain nidm:Coordinate ; - + rdfs:range xsd:float . @@ -613,16 +613,16 @@ NIDM Concept ID: nidm_15. """ ; ### http://www.incf.org/ns/nidash/nidm#coordinate2 nidm:coordinate2 rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "-28" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_17. """ ; - + obo:IAO_0000115 "Coordinate along the second dimension in voxel units." ; - + rdfs:domain nidm:Coordinate ; - + rdfs:range xsd:float . @@ -630,16 +630,16 @@ NIDM Concept ID: nidm_17. """ ; ### http://www.incf.org/ns/nidash/nidm#coordinate3 nidm:coordinate3 rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "13" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_19. """ ; - + obo:IAO_0000115 "Coordinate along the third dimension in voxel units." ; - + rdfs:domain nidm:Coordinate ; - + rdfs:range xsd:float . @@ -647,16 +647,16 @@ NIDM Concept ID: nidm_19. """ ; ### http://www.incf.org/ns/nidash/nidm#dimensionsInVoxels nidm:dimensionsInVoxels rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "[64 64 20]" ; - - obo:IAO_0000116 """Range: Vectorofintegers not found. BIRNLex or + + obo:IAO_0000116 """Range: Vectorofintegers not found. BIRNLex or NIDM Concept ID: nidm_25. """ ; - + obo:IAO_0000115 "Dimensions of some N-dimensional data." ; - + rdfs:domain nidm:CoordinateSpace ; - + rdfs:range xsd:string . @@ -664,16 +664,16 @@ NIDM Concept ID: nidm_25. """ ; ### http://www.incf.org/ns/nidash/nidm#effectDegreesOfFreedom nidm:effectDegreesOfFreedom rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "1" ; - - obo:IAO_0000116 """Range: Positivefloat not found. BIRNLex or + + obo:IAO_0000116 """Range: Positivefloat not found. BIRNLex or NIDM Concept ID: nidm_26. """ ; - + obo:IAO_0000115 "Degrees of freedom of the effect." ; - + rdfs:domain nidm:StatisticMap ; - + rdfs:range xsd:float . @@ -681,16 +681,16 @@ NIDM Concept ID: nidm_26. """ ; ### http://www.incf.org/ns/nidash/nidm#equivalentZStatistic nidm:equivalentZStatistic rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Statistic value transformed into Z units; the output of a process which takes a non-normal statistic and transforms it to an equivalent z score." ; - + obo:IAO_0000112 "3.5" ; - - obo:IAO_0000116 """Context: Functional. Parent: Data transformation; http://purl.obolibrary.org/obo/OBI_0200000 not found. BIRNLex or + + obo:IAO_0000116 """Context: Functional. Parent: Data transformation; http://purl.obolibrary.org/obo/OBI_0200000 not found. BIRNLex or NIDM Concept ID: nidm_27. new parent: Peak. """ ; - + rdfs:domain nidm:Peak ; - + rdfs:range xsd:float . @@ -698,13 +698,13 @@ NIDM Concept ID: nidm_27. new parent: Peak. """ ; ### http://www.incf.org/ns/nidash/nidm#errorDegreesOfFreedom nidm:errorDegreesOfFreedom rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Degrees of freedom of the error." ; - + obo:IAO_0000112 "72.999999" ; - + rdfs:domain nidm:StatisticMap ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -717,12 +717,12 @@ nidm:errorDegreesOfFreedom rdf:type owl:DatatypeProperty ; ### http://www.incf.org/ns/nidash/nidm#f-statistic nidm:f-statistic rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "The statistic from the F-test, a test of the hypothesis that the standard deviations of two normally distributed populations are equal, and thus that they are of comparable origin." ; - - obo:IAO_0000116 """Context: io terms. Domain or Attributes: not found. BIRNLex or + + obo:IAO_0000116 """Context: io terms. Domain or Attributes: not found. BIRNLex or NIDM Concept ID: nidm_31. """ ; - + rdfs:seeAlso "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#F-Test" . @@ -730,17 +730,17 @@ NIDM Concept ID: nidm_31. """ ; ### http://www.incf.org/ns/nidash/nidm#filename nidm:filename rdf:type owl:DatatypeProperty ; - + owl:sameAs "http://purl.obolibrary.org/obo/OBIws_0000001"^^xsd:anyURI ; - + obo:IAO_0000112 "con_0001.img" ; - + rdfs:domain nidm:DesignMatrix , nidm:ExcursionSet , nidm:Image , nidm:Map , nidm:MapHeader ; - + rdfs:range xsd:string . @@ -748,11 +748,11 @@ nidm:filename rdf:type owl:DatatypeProperty ; ### http://www.incf.org/ns/nidash/nidm#globalNullDegree nidm:globalNullDegree rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:domain spm:KConjunctionInference ; - + rdfs:range xsd:int . @@ -760,16 +760,16 @@ nidm:globalNullDegree rdf:type owl:DatatypeProperty ; ### http://www.incf.org/ns/nidash/nidm#grandMeanScaling nidm:grandMeanScaling rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "TRUE" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_96. """ ; - + obo:IAO_0000115 "Binary flag defining whether the data was scaled. Specifically, \"grand mean scaling\" refers to multipliciation of every voxel in every scan by a common value. Grand mean scaling is essential for first-level fMRI, to transform the arbitrary MRI units, but is generally not used with second level analyses." ; - + rdfs:domain nidm:Data ; - + rdfs:range xsd:boolean . @@ -777,12 +777,12 @@ NIDM Concept ID: nidm_96. """ ; ### http://www.incf.org/ns/nidash/nidm#inWorldCoordinateSystem nidm:inWorldCoordinateSystem rdf:type owl:DatatypeProperty ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_22. """ ; - + obo:IAO_0000115 "Type of coordinate system." ; - + obo:IAO_0000112 "nidm:MNICoordinateSystem" . @@ -790,18 +790,18 @@ NIDM Concept ID: nidm_22. """ ; ### http://www.incf.org/ns/nidash/nidm#maskedMedian nidm:maskedMedian rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "155.23" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_98. """ ; - + obo:IAO_0000115 "Median value considering only in-mask voxels. Useful diagnostic when computed on grand mean image when grandMeanScaling is TRUE, as the median should be close to targetIntensity." ; - + rdfs:seeAlso "http://purl.obolibrary.org/obo/OBI_0200119" ; - + rdfs:domain nidm:GrandMeanMap ; - + rdfs:range xsd:float . @@ -809,14 +809,14 @@ NIDM Concept ID: nidm_98. """ ; ### http://www.incf.org/ns/nidash/nidm#noiseFWHM nidm:noiseFWHM rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "2.35" ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the noise distribution." ; - + rdfs:seeAlso "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Full_Width_at_Half_Maximum" ; - - obo:IAO_0000116 """Context: Functional. Domain or Attributes: not found. BIRNLex or + + obo:IAO_0000116 """Context: Functional. Domain or Attributes: not found. BIRNLex or NIDM Concept ID: nidm_42. \"type\": SearchVol. """ . @@ -824,11 +824,11 @@ NIDM Concept ID: nidm_42. \"type\": SearchVol. """ . ### http://www.incf.org/ns/nidash/nidm#noiseVarianceHomogeneous nidm:noiseVarianceHomogeneous rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:domain nidm:NoiseModel ; - + rdfs:range xsd:boolean . @@ -836,13 +836,13 @@ nidm:noiseVarianceHomogeneous rdf:type owl:DatatypeProperty ; ### http://www.incf.org/ns/nidash/nidm#numberOfClusters nidm:numberOfClusters rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:domain nidm:ExcursionSet ; - + rdfs:range xsd:int ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -850,16 +850,16 @@ nidm:numberOfClusters rdf:type owl:DatatypeProperty ; ### http://www.incf.org/ns/nidash/nidm#numberOfDimensions nidm:numberOfDimensions rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Number of dimensions of a data matrix." ; - + obo:IAO_0000112 "3" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_43. """ ; - + rdfs:domain nidm:CoordinateSpace ; - + rdfs:range xsd:positiveInteger . @@ -867,22 +867,22 @@ NIDM Concept ID: nidm_43. """ ; ### http://www.incf.org/ns/nidash/nidm#pValue nidm:pValue rdf:type owl:DatatypeProperty ; - + owl:sameAs "http://purl.obolibrary.org/obo/OBI_0000175"^^xsd:anyURI ; - + rdfs:seeAlso """http://purl.obolibrary.org/obo/IAO_0000121 http://purl.obolibrary.org/obo/OBI_0000175 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P-Value""" ; - - obo:IAO_0000116 """Range: Floatbetween0and1 not found. BIRNLex or + + obo:IAO_0000116 """Range: Floatbetween0and1 not found. BIRNLex or NIDM Concept ID: nidm_47. """ ; - + obo:IAO_0000112 "8.95E-14" ; - + owl:sameAs "This definition is from OBI. Please update this note if the definition is modified." ; - + rdfs:domain nidm:ExcursionSet ; - + rdfs:range xsd:float . @@ -890,23 +890,23 @@ NIDM Concept ID: nidm_47. """ ; ### http://www.incf.org/ns/nidash/nidm#pValueFWER nidm:pValueFWER rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "0.05" ; - - obo:IAO_0000116 """Range: Floatbetween0and1 not found. BIRNLex or + + obo:IAO_0000116 """Range: Floatbetween0and1 not found. BIRNLex or NIDM Concept ID: nidm_48. """ ; - + owl:sameAs "This definition is from OBI. Please update this note if the definition is modified." ; - + obo:IAO_0000115 "\"A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests\"" ; - + rdfs:seeAlso "Synonym of \"nidm:pFWE\"" ; - + rdfs:domain nidm:Cluster , nidm:ExtentThreshold , nidm:HeightThreshold , nidm:Peak ; - + rdfs:range xsd:float . @@ -914,21 +914,21 @@ NIDM Concept ID: nidm_48. """ ; ### http://www.incf.org/ns/nidash/nidm#pValueUncorrected nidm:pValueUncorrected rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "0.0542" ; - + obo:IAO_0000115 "A p-value reported without correction for multiple testing. " ; - + rdfs:seeAlso "http://purl.obolibrary.org/obo/IAO_0000121" ; - - obo:IAO_0000116 """Parent: p-value i.e. nidm:nidm_0011 not found. Range: Floatbetween0and1 not found. BIRNLex or + + obo:IAO_0000116 """Parent: p-value i.e. nidm:nidm_0011 not found. Range: Floatbetween0and1 not found. BIRNLex or NIDM Concept ID: nidm_49. """ ; - + rdfs:domain nidm:Cluster , nidm:ExtentThreshold , nidm:HeightThreshold , nidm:Peak ; - + rdfs:range xsd:float . @@ -936,21 +936,21 @@ NIDM Concept ID: nidm_49. """ ; ### http://www.incf.org/ns/nidash/nidm#qValueFDR nidm:qValueFDR rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "P-value adjusted for the multiple testing, controlling for the False Discovery Rate" ; - + rdfs:seeAlso "http://purl.obolibrary.org/obo/OBI_0001442" ; - - obo:IAO_0000116 """Parent: p-value i.e. nidm:nidm_0011 not found. Range: Floatbetween0and1 not found. BIRNLex or + + obo:IAO_0000116 """Parent: p-value i.e. nidm:nidm_0011 not found. Range: Floatbetween0and1 not found. BIRNLex or NIDM Concept ID: nidm_50. """ ; - + obo:IAO_0000112 "0.000154" ; - + rdfs:domain nidm:Cluster , nidm:ExtentThreshold , nidm:HeightThreshold , nidm:Peak ; - + rdfs:range xsd:float . @@ -958,16 +958,16 @@ NIDM Concept ID: nidm_50. """ ; ### http://www.incf.org/ns/nidash/nidm#randomFieldStationarity nidm:randomFieldStationarity rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Is the random field assumed to be stationary across the entire search volume?" ; - + obo:IAO_0000112 "stationaryRandomField" ; - - obo:IAO_0000116 """Range: {nonStationaryRandomField not foundstationaryRandomField} not found. BIRNLex or + + obo:IAO_0000116 """Range: {nonStationaryRandomField not foundstationaryRandomField} not found. BIRNLex or NIDM Concept ID: nidm_51. """ ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range xsd:boolean . @@ -975,12 +975,12 @@ NIDM Concept ID: nidm_51. """ ; ### http://www.incf.org/ns/nidash/nidm#smoothingFWHM nidm:smoothingFWHM rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "[6 6 6]" ; - - obo:IAO_0000116 """Domain or Attributes: not found. BIRNLex or + + obo:IAO_0000116 """Domain or Attributes: not found. BIRNLex or NIDM Concept ID: nidm_54. """ ; - + obo:IAO_0000115 "Full width at half maximum of a Gaussian smoothing kernel in real world units (e.g. mm mm mm)." . @@ -988,16 +988,16 @@ NIDM Concept ID: nidm_54. """ ; ### http://www.incf.org/ns/nidash/nidm#softwareVersion nidm:softwareVersion rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "SPM99, SPM2, SPM5, SPM8, SPM12b, FSL5.0.0" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_55. """ ; - + obo:IAO_0000115 "Name and number that specifies the software version." ; - + rdfs:range xsd:string ; - + rdfs:domain prov:SoftwareAgent . @@ -1005,12 +1005,12 @@ NIDM Concept ID: nidm_55. """ ; ### http://www.incf.org/ns/nidash/nidm#standardError nidm:standardError rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "\"A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution.\"" ; - + owl:sameAs "This definition is from OBI. Please update this note if the definition is modified." ; - - obo:IAO_0000116 """Domain or Attributes: not found. BIRNLex or + + obo:IAO_0000116 """Domain or Attributes: not found. BIRNLex or NIDM Concept ID: nidm_58. """ . @@ -1018,16 +1018,16 @@ NIDM Concept ID: nidm_58. """ . ### http://www.incf.org/ns/nidash/nidm#targetIntensity nidm:targetIntensity rdf:type owl:DatatypeProperty ; - - obo:IAO_0000116 """Range: positivefloat not found. BIRNLex or + + obo:IAO_0000116 """Range: positivefloat not found. BIRNLex or NIDM Concept ID: nidm_97. """ ; - + obo:IAO_0000112 "100" ; - + obo:IAO_0000115 "Value to which the grand mean of the Data was scaled (applies only if grandMeanScaling is true)." ; - + rdfs:domain nidm:Data ; - + rdfs:range xsd:float . @@ -1035,17 +1035,17 @@ NIDM Concept ID: nidm_97. """ ; ### http://www.incf.org/ns/nidash/nidm#underlayFile nidm:underlayFile rdf:type owl:DatatypeProperty ; - - obo:IAO_0000116 """Parent: nidm:map not found. Range: PathtoaNIfTIimage not found. BIRNLex or + + obo:IAO_0000116 """Parent: nidm:map not found. Range: PathtoaNIfTIimage not found. BIRNLex or NIDM Concept ID: nidm_64. """ ; - + obo:IAO_0000112 "MNI152.nii.gz or cortex.surf.gii" ; - - obo:IAO_0000116 """Parent: nidm:map not found. Range: Pathtoaniftiimage not found. BIRNLex or + + obo:IAO_0000116 """Parent: nidm:map not found. Range: Pathtoaniftiimage not found. BIRNLex or NIDM Concept ID: nidm_64. """ ; - + obo:IAO_0000115 "Map or surface on which the associated results are displayed. " ; - + rdfs:domain nidm:ExcursionSet . @@ -1053,17 +1053,17 @@ NIDM Concept ID: nidm_64. """ ; ### http://www.incf.org/ns/nidash/nidm#userSpecifiedThresholdType nidm:userSpecifiedThresholdType rdf:type owl:DatatypeProperty ; - - obo:IAO_0000116 """Range: {'nidm:pValueFWER' not found'nidm:pValueFDR' not found'nidm:pValueUncorrected';'nidm:statistic'} not found. BIRNLex or + + obo:IAO_0000116 """Range: {'nidm:pValueFWER' not found'nidm:pValueFDR' not found'nidm:pValueUncorrected';'nidm:statistic'} not found. BIRNLex or NIDM Concept ID: nidm_65. """ ; - + obo:IAO_0000115 "Type of method used to define a threshold (e.g. statistic value, uncorrected P-value or corrected P-value)." ; - + obo:IAO_0000112 "nidm:pValueFWER" ; - + rdfs:domain nidm:ExtentThreshold , nidm:HeightThreshold ; - + rdfs:range xsd:string . @@ -1071,11 +1071,11 @@ NIDM Concept ID: nidm_65. """ ; ### http://www.incf.org/ns/nidash/nidm#version nidm:version rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:range xsd:string ; - + rdfs:domain prov:Bundle . @@ -1083,19 +1083,19 @@ nidm:version rdf:type owl:DatatypeProperty ; ### http://www.incf.org/ns/nidash/nidm#voxelSize nidm:voxelSize rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "[2 2 4]" ; - - rdfs:seeAlso """http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C95003 + + rdfs:seeAlso """http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C95003 """ ; - + obo:IAO_0000115 "3D size of a voxel measured in voxelUnits." ; - - obo:IAO_0000116 """Parent: size not found. Range: Vectoroffloats not found. BIRNLex or + + obo:IAO_0000116 """Parent: size not found. Range: Vectoroffloats not found. BIRNLex or NIDM Concept ID: nidm_67. """ ; - + rdfs:domain nidm:CoordinateSpace ; - + rdfs:range xsd:string . @@ -1103,16 +1103,16 @@ NIDM Concept ID: nidm_67. """ ; ### http://www.incf.org/ns/nidash/nidm#voxelToWorldMapping nidm:voxelToWorldMapping rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Homogeneous transformation matrix to map from voxel coordinate system to world coordinate system." ; - - obo:IAO_0000116 """Range: Matrixoffloat not found. BIRNLex or + + obo:IAO_0000116 """Range: Matrixoffloat not found. BIRNLex or NIDM Concept ID: nidm_68. """ ; - + obo:IAO_0000112 "[3 0 0 0;0 3 0 0;0 0 3 0; 0 0 0 1] " ; - + rdfs:domain nidm:CoordinateSpace ; - + rdfs:range xsd:string . @@ -1120,16 +1120,16 @@ NIDM Concept ID: nidm_68. """ ; ### http://www.incf.org/ns/nidash/nidm#voxelUnits nidm:voxelUnits rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Units associated with each dimensions of some N-dimensional data." ; - + obo:IAO_0000112 "{'mm' 'mm' 's'}" ; - - obo:IAO_0000116 """Range: Vectorofstrings not found. BIRNLex or + + obo:IAO_0000116 """Range: Vectorofstrings not found. BIRNLex or NIDM Concept ID: nidm_69. """ ; - + rdfs:domain nidm:CoordinateSpace ; - + rdfs:range xsd:string . @@ -1137,14 +1137,14 @@ NIDM Concept ID: nidm_69. """ ; ### http://www.incf.org/ns/nidash/spm#clusterSizeInResels spm:clusterSizeInResels rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Number of resels that make up a cluster." ; - + obo:IAO_0000112 "13" ; - + rdfs:domain nidm:Cluster , nidm:ExtentThreshold ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1157,13 +1157,13 @@ spm:clusterSizeInResels rdf:type owl:DatatypeProperty ; ### http://www.incf.org/ns/nidash/spm#expectedNumberOfClusters spm:expectedNumberOfClusters rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "9.51" ; - + obo:IAO_0000115 "Expected number of clusters in an excursion set." ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1176,16 +1176,16 @@ spm:expectedNumberOfClusters rdf:type owl:DatatypeProperty ; ### http://www.incf.org/ns/nidash/spm#expectedNumberOfVerticesPerCluster spm:expectedNumberOfVerticesPerCluster rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Expected number of vertices in a cluster." ; - - obo:IAO_0000116 """Range: Positivefloat not found. BIRNLex or + + obo:IAO_0000116 """Range: Positivefloat not found. BIRNLex or NIDM Concept ID: spm_72. """ ; - + obo:IAO_0000112 "60.632" ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1198,16 +1198,16 @@ NIDM Concept ID: spm_72. """ ; ### http://www.incf.org/ns/nidash/spm#expectedNumberOfVoxelsPerCluster spm:expectedNumberOfVoxelsPerCluster rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Expected number of voxels in a cluster." ; - - obo:IAO_0000116 """Range: Positivefloat not found. BIRNLex or + + obo:IAO_0000116 """Range: Positivefloat not found. BIRNLex or NIDM Concept ID: spm_73. """ ; - + obo:IAO_0000112 "60.632" ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1220,16 +1220,16 @@ NIDM Concept ID: spm_73. """ ; ### http://www.incf.org/ns/nidash/spm#heightCriticalThresholdFDR05 spm:heightCriticalThresholdFDR05 rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Peak statistic threshold corrected for false discovery rate at a level of alpha = 0.05. " ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: spm_74. """ ; - + obo:IAO_0000112 "5.896" ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range xsd:float . @@ -1237,16 +1237,16 @@ NIDM Concept ID: spm_74. """ ; ### http://www.incf.org/ns/nidash/spm#heightCriticalThresholdFWE05 spm:heightCriticalThresholdFWE05 rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Peak statistic threshold corrected for family-wise error at a level of alpha = 0.05. " ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: spm_75. """ ; - + obo:IAO_0000112 "4.913" ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range xsd:float . @@ -1254,18 +1254,18 @@ NIDM Concept ID: spm_75. """ ; ### http://www.incf.org/ns/nidash/spm#noiseFWHMInUnits spm:noiseFWHMInUnits rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the noise distribution in world units." ; - - obo:IAO_0000116 """Range: Vectorofpositivefloats not found. BIRNLex or + + obo:IAO_0000116 """Range: Vectorofpositivefloats not found. BIRNLex or NIDM Concept ID: spm_78. """ ; - + obo:IAO_0000112 "[8.87, 8.89, 7.83]" ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:subPropertyOf nidm:noiseFWHM ; - + rdfs:range xsd:string . @@ -1273,16 +1273,16 @@ NIDM Concept ID: spm_78. """ ; ### http://www.incf.org/ns/nidash/spm#noiseFWHMInVertices spm:noiseFWHMInVertices rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "[2.95, 2.96, 2.61]" ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the noise distribution in world vertices." ; - - obo:IAO_0000116 """Range: Vectorofpositivefloats not found. BIRNLex or + + obo:IAO_0000116 """Range: Vectorofpositivefloats not found. BIRNLex or NIDM Concept ID: spm_79. """ ; - + rdfs:domain nidm:MaskMap ; - + rdfs:subPropertyOf nidm:noiseFWHM . @@ -1290,20 +1290,20 @@ NIDM Concept ID: spm_79. """ ; ### http://www.incf.org/ns/nidash/spm#noiseFWHMInVoxels spm:noiseFWHMInVoxels rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "[3.7 3.7 3.1]" ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the noise distribution in voxels." ; - - obo:IAO_0000116 """Context: NoiseFWHM nidm_0009. Range: Vectorofpositivefloats not found. BIRNLex or + + obo:IAO_0000116 """Context: NoiseFWHM nidm_0009. Range: Vectorofpositivefloats not found. BIRNLex or NIDM Concept ID: spm_80. """ ; - + rdfs:seeAlso "Synonyms of or close match with nidm:NoiseFWHM" ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:subPropertyOf nidm:noiseFWHM ; - + rdfs:range xsd:string . @@ -1311,13 +1311,13 @@ NIDM Concept ID: spm_80. """ ; ### http://www.incf.org/ns/nidash/spm#reselSize spm:reselSize rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Size of one resel in voxels or vertices." ; - + obo:IAO_0000112 "22.325" ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1330,15 +1330,15 @@ spm:reselSize rdf:type owl:DatatypeProperty ; ### http://www.incf.org/ns/nidash/spm#searchVolumeInResels spm:searchVolumeInResels rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Total number of resels within the search volume." ; - + obo:IAO_0000112 "151.3" ; - + rdfs:seeAlso "Synonyms of nidm:volumeInResels" ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1351,16 +1351,16 @@ spm:searchVolumeInResels rdf:type owl:DatatypeProperty ; ### http://www.incf.org/ns/nidash/spm#searchVolumeInUnits spm:searchVolumeInUnits rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Total number of product of coordinate units within the search volume. The volume of the searched region in units determined by the current coordinate space units (e.g., mm^3 for axis units of mm in a three dimensional image, sec.Hz for a time by frequency two dimensional image)." ; - - obo:IAO_0000116 """Context: volumeInVoxels nidm_0025. Range: Positivefloat not found. BIRNLex or + + obo:IAO_0000116 """Context: volumeInVoxels nidm_0025. Range: Positivefloat not found. BIRNLex or NIDM Concept ID: spm_84. """ ; - + obo:IAO_0000112 "1771011" ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1373,13 +1373,13 @@ NIDM Concept ID: spm_84. """ ; ### http://www.incf.org/ns/nidash/spm#searchVolumeInVertices spm:searchVolumeInVertices rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "151.3" ; - + obo:IAO_0000115 "Total number of vertices within the search volume." ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1392,18 +1392,18 @@ spm:searchVolumeInVertices rdf:type owl:DatatypeProperty ; ### http://www.incf.org/ns/nidash/spm#searchVolumeInVoxels spm:searchVolumeInVoxels rdf:type owl:DatatypeProperty ; - + rdfs:seeAlso "Synonyms of nidm:volumeInVoxels" ; - + obo:IAO_0000115 "Total number of voxels within the search volume." ; - - obo:IAO_0000116 """Context: volumeInVoxels nidm_0025. BIRNLex or + + obo:IAO_0000116 """Context: volumeInVoxels nidm_0025. BIRNLex or NIDM Concept ID: spm_87. """ ; - + obo:IAO_0000112 "68656" ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range xsd:positiveInteger . @@ -1411,20 +1411,20 @@ NIDM Concept ID: spm_87. """ ; ### http://www.incf.org/ns/nidash/spm#searchVolumeReselsGeometry spm:searchVolumeReselsGeometry rdf:type owl:DatatypeProperty ; - - obo:IAO_0000116 """Context: volumeInResels nidm_0024. Range: Vectorof1positiveintegerand3positivefloats not found. BIRNLex or + + obo:IAO_0000116 """Context: volumeInResels nidm_0024. Range: Vectorof1positiveintegerand3positivefloats not found. BIRNLex or NIDM Concept ID: spm_88. """ ; - + obo:IAO_0000112 "[6 68.8 589.1 1475.5]" ; - + obo:IAO_0000115 "Description of geometry of search volume. As per Worsley et al. [ http://www.ncbi.nlm.nih.gov/pubmed/20408186 ], the first element is the Euler Characteristic of the search volume, the second element is twice the average caliper diameter, the third element is half the surface area, and the fourth element is the volume. With the exception of the first element (which is a unitless integer) all quantities are in units of Resels." ; - + rdfs:seeAlso "http://www.ncbi.nlm.nih.gov/pubmed/20408186" ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1432,16 +1432,16 @@ NIDM Concept ID: spm_88. """ ; ### http://www.incf.org/ns/nidash/spm#smallestSignifClusterSizeInVerticesFDR05 spm:smallestSignifClusterSizeInVerticesFDR05 rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "5" ; - + obo:IAO_0000115 "Smallest cluster size in vertices that are significant at a false discovery rate corrected alpha value of 0.05. " ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: spm_90. """ ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range xsd:positiveInteger . @@ -1449,17 +1449,17 @@ NIDM Concept ID: spm_90. """ ; ### http://www.incf.org/ns/nidash/spm#smallestSignifClusterSizeInVerticesFWE05 spm:smallestSignifClusterSizeInVerticesFWE05 rdf:type owl:DatatypeProperty ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: spm_91. """ ; - + obo:IAO_0000112 "2" ; - - obo:IAO_0000115 """Smallest cluster size in vertices significant at family-wise error rate corrected alpha value of 0.05. + + obo:IAO_0000115 """Smallest cluster size in vertices significant at family-wise error rate corrected alpha value of 0.05. """ ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range xsd:positiveInteger . @@ -1467,16 +1467,16 @@ NIDM Concept ID: spm_91. """ ; ### http://www.incf.org/ns/nidash/spm#smallestSignifClusterSizeInVoxelsFDR05 spm:smallestSignifClusterSizeInVoxelsFDR05 rdf:type owl:DatatypeProperty ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: spm_92. """ ; - + obo:IAO_0000115 "Smallest cluster size in voxels significant at false discovery rate corrected alpha value of 0.05. " ; - + obo:IAO_0000112 "3" ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range xsd:positiveInteger . @@ -1484,17 +1484,17 @@ NIDM Concept ID: spm_92. """ ; ### http://www.incf.org/ns/nidash/spm#smallestSignifClusterSizeInVoxelsFWE05 spm:smallestSignifClusterSizeInVoxelsFWE05 rdf:type owl:DatatypeProperty ; - - obo:IAO_0000115 """Smallest cluster size in voxels significant at family-wise error corrected alpha value of 0.05. + + obo:IAO_0000115 """Smallest cluster size in voxels significant at family-wise error corrected alpha value of 0.05. """ ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: spm_93. """ ; - + obo:IAO_0000112 "1" ; - + rdfs:domain nidm:SearchSpaceMap ; - + rdfs:range xsd:positiveInteger . @@ -1502,16 +1502,16 @@ NIDM Concept ID: spm_93. """ ; ### http://www.incf.org/ns/nidash/spm#softwareRevision spm:softwareRevision rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "5417" ; - + obo:IAO_0000115 "revision number of a piece of software." ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: spm_94. """ ; - + rdfs:range xsd:string ; - + rdfs:domain prov:SoftwareAgent . @@ -1528,19 +1528,19 @@ NIDM Concept ID: spm_94. """ ; ### http://www.incf.org/ns/nidash/fsl#CenterOfGravity fsl:CenterOfGravity rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Centre Of Gravity for the cluster, equivalent to the concept of Centre Of Gravity for a object with distributed mass, where intensity substitutes for mass in this case (definition from http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster)" ; - + obo:IAO_0000112 """entity(niiri:center_of_gravity_1, [prov:type = 'fsl:CenterOfGravity', prov:label = \"Center of gravity 1\", prov:location = 'niiri:COG_coordinate_0001'])""" ; - + rdfs:seeAlso "http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: fsl_102. """ . @@ -1548,16 +1548,16 @@ NIDM Concept ID: fsl_102. """ . ### http://www.incf.org/ns/nidash/fsl#ClusterMaximumStatistic fsl:ClusterMaximumStatistic rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 """entity(niiri:peak_0001, [prov:type = 'fsl:ClusterMaximumStatistic', prov:type = 'nidm:Peak', prov:label = \"Peak 1\" %% xsd:string, prov:location = 'niiri:coordinate_0001', nidm:equivalentZStatistic = \"6.14\" %% xsd:float])""" ; - + obo:IAO_0000115 "FIXME" . @@ -1565,9 +1565,9 @@ fsl:ClusterMaximumStatistic rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/fsl#VarCope fsl:VarCope rdf:type owl:Class ; - + rdfs:subClassOf nidm:Map ; - + obo:IAO_0000115 "FIXME" . @@ -1575,9 +1575,9 @@ fsl:VarCope rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/fsl#ZStatisticMap fsl:ZStatisticMap rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 """entity(niiri:z_statistical_map_id, [prov:type = 'nidm:StatisticMap', prov:type = 'fsl:ZStatisticalMap', @@ -1588,7 +1588,7 @@ fsl:ZStatisticMap rdf:type owl:Class ; nidm:atCoordinateSpace = 'niiri:coordinate_space_id_1', crypto:sha = \"400a2f07d99ed9be06577e6ecc89222cf4b688c654bc89067da558e88b73b97dd1b25e6c98f2a735fa0a1409598cff7e6025bda55abb6b9f5ef65d8d307eeba8\"]) """ ; - + obo:IAO_0000115 "A map whose value at each location is a Z-statistic value. " . @@ -1596,9 +1596,9 @@ fsl:ZStatisticMap rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#ArbitrarilyCorrelatedNoise nidm:ArbitrarilyCorrelatedNoise rdf:type owl:Class ; - + rdfs:subClassOf nidm:NoiseDependence ; - + obo:IAO_0000115 "FIXME" . @@ -1606,9 +1606,9 @@ nidm:ArbitrarilyCorrelatedNoise rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#BinomialDistribution nidm:BinomialDistribution rdf:type owl:Class ; - + rdfs:subClassOf nidm:NoiseDistribution ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000276"^^xsd:anyURI . @@ -1616,11 +1616,11 @@ nidm:BinomialDistribution rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#Cluster nidm:Cluster rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + rdfs:seeAlso "Child of \"nidm:Statistic\"" ; - + obo:IAO_0000112 """entity(niiri:cluster_0001, [prov:type = 'nidm:Cluster', prov:label = \"Cluster 0001\" %% xsd:string, @@ -1630,10 +1630,10 @@ nidm:Cluster rdf:type owl:Class ; nidm:pValueUncorrected = \"9.56276736481136e-52\" %% xsd:float, nidm:pValueFWER = \"0\" %% xsd:float, nidm:qValueFDR = \"7.65021389184909e-51\" %% xsd:float])""" ; - - obo:IAO_0000116 """Range: - not found. BIRNLex or + + obo:IAO_0000116 """Range: - not found. BIRNLex or NIDM Concept ID: nidm_7. """ ; - + obo:IAO_0000115 "Statistic defined at the cluster-level in an excusion set. In SPM it is defined as the cluster size. FIXME (now Cluster instead of ClusterStatistic)" . @@ -1641,11 +1641,11 @@ NIDM Concept ID: nidm_7. """ ; ### http://www.incf.org/ns/nidash/nidm#ClusterLabelsMap nidm:ClusterLabelsMap rdf:type owl:Class ; - + rdfs:subClassOf nidm:Map ; - + obo:IAO_0000115 "FIXME" ; - + obo:IAO_0000112 """entity(niiri:cluster_label_map_id, [prov:type = 'nidm:ClusterLabelsMap', prov:location = \"file:///path/to/ClusterLabels.nii.gz\" %% xsd:anyURI, @@ -1657,13 +1657,13 @@ nidm:ClusterLabelsMap rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#Colin27CoordinateSystem nidm:Colin27CoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:StandardizedCoordinateSystem ; - + obo:IAO_0000115 "Coordinate system defined by the \"stereotaxic average of 27 T1-weighted MRI scans of the same individual\"." ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres" ; - + rdfs:comment "used in SPM96 (cf. http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)" , "FIXME. This definition needs to be re-worked and reviewed." . @@ -1672,9 +1672,9 @@ nidm:Colin27CoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#CompoundSymmetricNoise nidm:CompoundSymmetricNoise rdf:type owl:Class ; - + rdfs:subClassOf nidm:NoiseDependence ; - + obo:IAO_0000115 "FIXME" . @@ -1682,13 +1682,13 @@ nidm:CompoundSymmetricNoise rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#ConjunctionInference nidm:ConjunctionInference rdf:type owl:Class ; - + rdfs:subClassOf nidm:Inference , prov:Activity ; - + obo:IAO_0000115 "Statistically testing for the joint significance of multiple effects, with emphasis on rejecting all (instead of one or more) of the respective null hypotheses." ; - - obo:IAO_0000116 """Range: - not found. BIRNLex or + + obo:IAO_0000116 """Range: - not found. BIRNLex or NIDM Concept ID: nidm_8. """ . @@ -1696,16 +1696,16 @@ NIDM Concept ID: nidm_8. """ . ### http://www.incf.org/ns/nidash/nidm#ContrastEstimation nidm:ContrastEstimation rdf:type owl:Class ; - + rdfs:subClassOf prov:Activity ; - + obo:IAO_0000112 """activity(niiri:contrast_estimation_id, [prov:type = 'nidm:ContrastEstimation', prov:label = \"Contrast estimation\"])""" ; - + obo:IAO_0000115 "The process of estimating a contrast from the estimated parameters of statistical model." ; - - obo:IAO_0000116 """Range: - not found. BIRNLex or + + obo:IAO_0000116 """Range: - not found. BIRNLex or NIDM Concept ID: nidm_9. """ . @@ -1713,15 +1713,15 @@ NIDM Concept ID: nidm_9. """ . ### http://www.incf.org/ns/nidash/nidm#ContrastMap nidm:ContrastMap rdf:type owl:Class ; - + rdfs:subClassOf nidm:Map , prov:Entity ; - + obo:IAO_0000115 "A map whose value at each location is statistical contrast estimate." ; - - obo:IAO_0000116 """Context: io terms. Parent: nidm:map, Scan Image not found. Range: - not found. BIRNLex or + + obo:IAO_0000116 """Context: io terms. Parent: nidm:map, Scan Image not found. Range: - not found. BIRNLex or NIDM Concept ID: nidm_10. """ ; - + obo:IAO_0000112 """entity(niiri:contrast_map_id, [prov:type = 'nidm:ContrastMap', prov:location = \"file:///path/to/Contrast.nii.gz\" %% xsd:anyURI, @@ -1737,11 +1737,11 @@ NIDM Concept ID: nidm_10. """ ; ### http://www.incf.org/ns/nidash/nidm#ContrastStandardErrorMap nidm:ContrastStandardErrorMap rdf:type owl:Class ; - + rdfs:subClassOf nidm:Map ; - + obo:IAO_0000115 "A map whose value at each location is the standard error of a given contrast." ; - + obo:IAO_0000112 """entity(niiri:contrast_standard_error_map_id, [prov:type = 'nidm:ContrastStandardErrorMap', prov:location = \"file:///path/to/ContrastStandardError.nii.gz\" %% xsd:anyURI, @@ -1750,8 +1750,8 @@ nidm:ContrastStandardErrorMap rdf:type owl:Class ; prov:label = \"Contrast Standard Error Map\" %% xsd:string, nidm:atCoordinateSpace = 'niiri:coordinate_space_id_1', crypto:sha512 = \"e43b6e01b0463fe7d40782137867a...\" %% xsd:string])""" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_12. """ . @@ -1759,19 +1759,19 @@ NIDM Concept ID: nidm_12. """ . ### http://www.incf.org/ns/nidash/nidm#ContrastWeights nidm:ContrastWeights rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Vector defining the linear combination associated with a particular contrast. " ; - + obo:IAO_0000112 """entity(niiri:contrast_weights_id, [prov:type = 'nidm:ContrastWeights', nidm:statisticType = 'nidm:TStatistic', nidm:contrastName = \"listening > rest\" %% xsd:string, prov:label = \"Contrast: Listening > Rest\" %% xsd:string, prov:value = \"[1, 0, 0]\" %% xsd:string])""" ; - - obo:IAO_0000116 """Range: Vectorofintegers not found. BIRNLex or + + obo:IAO_0000116 """Range: Vectorofintegers not found. BIRNLex or NIDM Concept ID: nidm_13. """ . @@ -1779,11 +1779,11 @@ NIDM Concept ID: nidm_13. """ . ### http://www.incf.org/ns/nidash/nidm#Coordinate nidm:Coordinate rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + owl:sameAs "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C44465"^^xsd:anyURI ; - + obo:IAO_0000112 """entity(niiri:coordinate_0001, [prov:type = 'prov:Location', prov:type = 'nidm:Coordinate', @@ -1791,13 +1791,13 @@ nidm:Coordinate rdf:type owl:Class ; nidm:coordinate1 = \"-60\" %% xsd:float, nidm:coordinate2 = \"-28\" %% xsd:float, nidm:coordinate3 = \"13\" %% xsd:float])""" ; - + obo:IAO_0000116 """Model: - search for coordinate uri - subclasses of coordinate -- additional properties (e.g. units) -. Context: Functional. BIRNLex or +- additional properties (e.g. units) +. Context: Functional. BIRNLex or NIDM Concept ID: nidm_14. """ ; - + obo:IAO_0000112 """entity(niiri:coordinate_0001, [prov:type = 'prov:Location', prov:type = 'nidm:Coordinate', @@ -1814,11 +1814,11 @@ NIDM Concept ID: nidm_14. """ ; ### http://www.incf.org/ns/nidash/nidm#CoordinateSpace nidm:CoordinateSpace rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "An entity with spatial attributes (e.g., dimensions, units, and voxel-to-world mapping) that provides context to a SpatialImage (e.g., a StatisticMap)." ; - + obo:IAO_0000112 """entity(niiri:coordinate_space_id_1, [prov:type = 'nidm:CoordinateSpace', prov:label = \"Coordinate space 1\" %% xsd:string, @@ -1828,8 +1828,8 @@ nidm:CoordinateSpace rdf:type owl:Class ; nidm:inWorldCoordinateSystem = 'nidm:MNICoordinateSystem', nidm:numberOfDimensions = \"3\" %% xsd:int, nidm:dimensionsInVoxels = \"[53,63,46]\" %% xsd:string])""" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_21. """ . @@ -1837,9 +1837,9 @@ NIDM Concept ID: nidm_21. """ . ### http://www.incf.org/ns/nidash/nidm#CustomCoordinateSystem nidm:CustomCoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:StandardizedCoordinateSystem ; - + rdfs:comment "FIXME. This definition needs to be re-worked and reviewed." . @@ -1847,12 +1847,12 @@ nidm:CustomCoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#CustomMaskMap nidm:CustomMaskMap rdf:type owl:Class ; - + rdfs:subClassOf nidm:Map ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_99. """ ; - + obo:IAO_0000112 """entity(niiri:custom_mask_id_1, [prov:type = 'nidm:CustomMaskMap', prov:location = \"file:///path/to/CustomMask.nii.gz\" %% xsd:anyURI, @@ -1861,7 +1861,7 @@ NIDM Concept ID: nidm_99. """ ; prov:label = \"Custom mask\" %% xsd:string, nidm:atCoordinateSpace = 'niiri:coordinate_space_id_1', crypto:sha512 = \"e43b6e01b0463fe7d40782137867a...\" %% xsd:string])""" ; - + obo:IAO_0000115 "mask defined by the user to restrain the space in which model fitting is performed." . @@ -1869,23 +1869,23 @@ NIDM Concept ID: nidm_99. """ ; ### http://www.incf.org/ns/nidash/nidm#Data nidm:Data rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "\"A collection or single item of factual information, derived from measurement or research, from which conclusions may be drawn.\"" ; - + obo:IAO_0000112 """entity(niiri:data_id, [prov:type = 'nidm:Data', prov:type = 'prov:Collection', prov:label = \"Data\" %% xsd:string, nidm:grandMeanScaling = \"true\" %%xsd:boolean, nidm:targetIntensity = \"100\" %% xsd:float])""" ; - + owl:sameAs "This definition is from NCIT. Please update this note if the definition is modified." ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_23. """ ; - + rdfs:seeAlso "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25474" . @@ -1893,12 +1893,12 @@ NIDM Concept ID: nidm_23. """ ; ### http://www.incf.org/ns/nidash/nidm#DesignMatrix nidm:DesignMatrix rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_24. """ ; - + obo:IAO_0000112 """entity(niiri:design_matrix_id, [prov:type = 'nidm:DesignMatrix', prov:location = \"file:///path/to/DesignMatrix.csv\" %% xsd:anyURI, @@ -1906,9 +1906,9 @@ NIDM Concept ID: nidm_24. """ ; nidm:filename = \"DesignMatrix.csv\", nidm:visualisation = 'niiri:design_matrix_png_id', prov:label = \"Design Matrix\" %% xsd:string])""" ; - + obo:IAO_0000115 "A matrix of values defining the explanatory variables used in a regression model. Each column corresponds to one explanatory variable, each row corresponds to one observation." ; - + rdfs:seeAlso "stato:design matrix" . @@ -1916,7 +1916,7 @@ NIDM Concept ID: nidm_24. """ ; ### http://www.incf.org/ns/nidash/nidm#EstimationMethod nidm:EstimationMethod rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity . @@ -1924,11 +1924,11 @@ nidm:EstimationMethod rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#ExchangeableNoise nidm:ExchangeableNoise rdf:type owl:Class ; - + rdfs:subClassOf nidm:NoiseDependence ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:comment "Under gaussianity assumption this is equivalent to compound symmetry but not in general." . @@ -1936,14 +1936,14 @@ nidm:ExchangeableNoise rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#ExcursionSet nidm:ExcursionSet rdf:type owl:Class ; - + rdfs:subClassOf nidm:Map ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_29. """ ; - + obo:IAO_0000115 "Set of map elements surviving a thresholding procedure." ; - + obo:IAO_0000112 """entity(niiri:excursion_set_id, [prov:type = 'nidm:ExcursionSet', prov:location = \"file:///path/to/ExcursionSet.nii.gz\" %% xsd:anyURI, @@ -1962,12 +1962,12 @@ NIDM Concept ID: nidm_29. """ ; ### http://www.incf.org/ns/nidash/nidm#ExtentThreshold nidm:ExtentThreshold rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 """A numerical value that establishes a bound on a range of cluster-sizes. / [from extentThresh:] Minimum cluster size used when thresholding a statistic image 5voxels """ ; - + obo:IAO_0000112 """entity(niiri:extent_threshold_id, [prov:type = 'nidm:ExtentThreshold', prov:label = \"Extent Threshold: k>=0\" %% xsd:string, @@ -1975,9 +1975,9 @@ nidm:ExtentThreshold rdf:type owl:Class ; spm:clusterSizeInResels = \"0\" %% xsd:float, nidm:pValueUncorrected = \"1\" %% xsd:float, nidm:pValueFWER = \"1\" %% xsd:float])""" ; - - obo:IAO_0000116 """Context: Attribute \"prov:value\" -of \"extentThresh\" nidm_0079. BIRNLex or + + obo:IAO_0000116 """Context: Attribute \"prov:value\" +of \"extentThresh\" nidm_0079. BIRNLex or NIDM Concept ID: nidm_30. new parent: Effect. """ . @@ -1985,14 +1985,14 @@ NIDM Concept ID: nidm_30. new parent: Effect. """ . ### http://www.incf.org/ns/nidash/nidm#FSL nidm:FSL rdf:type owl:Class ; - + rdfs:subClassOf prov:SoftwareAgent ; - + rdfs:seeAlso "http://fsl.fmrib.ox.ac.uk" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_57. """ ; - + obo:IAO_0000115 "FMRIB Software Library software package for the analysis of neuroimaging data from the FMRIB" . @@ -2000,15 +2000,15 @@ NIDM Concept ID: nidm_57. """ ; ### http://www.incf.org/ns/nidash/nidm#FSLResults nidm:FSLResults rdf:type owl:Class ; - + rdfs:subClassOf nidm:NIDMObjectModel ; - + obo:IAO_0000112 """entity(niiri:fsl_results_id, [prov:type = 'prov:Bundle', prov:label = \"FSL Results\", nidm:objectModel = 'nidm:FSLResults', nidm:version = \"0.2.0\"])""" ; - + obo:IAO_0000115 "FIXME" . @@ -2016,9 +2016,9 @@ nidm:FSLResults rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#FStatistic nidm:FStatistic rdf:type owl:Class ; - + rdfs:subClassOf nidm:Statistic ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000282"^^xsd:anyURI . @@ -2026,9 +2026,9 @@ nidm:FStatistic rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#GaussianDistribution nidm:GaussianDistribution rdf:type owl:Class ; - + rdfs:subClassOf nidm:NoiseDistribution ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000227"^^xsd:anyURI . @@ -2036,11 +2036,11 @@ nidm:GaussianDistribution rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#GeneralizedLeastSquares nidm:GeneralizedLeastSquares rdf:type owl:Class ; - + rdfs:subClassOf nidm:EstimationMethod ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:comment "GLS (both heteroscedasticity and dependence accounted for) OLS is a special case of WLS & GLS; WLS is a special case of GLS." . @@ -2048,9 +2048,9 @@ nidm:GeneralizedLeastSquares rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#GrandMeanMap nidm:GrandMeanMap rdf:type owl:Class ; - + rdfs:subClassOf nidm:Map ; - + obo:IAO_0000112 """entity(niiri:grand_mean_map_id, [prov:type = 'nidm:GrandMeanMap', prov:location = \"file:///path/to/GrandMean.nii.gz\" %% xsd:anyURI, @@ -2060,7 +2060,7 @@ nidm:GrandMeanMap rdf:type owl:Class ; nidm:maskedMedian = \"115\" %% xsd:float, nidm:atCoordinateSpace = 'niiri:coordinate_space_id_1', crypto:sha512 = \"e43b6e01b0463fe7d40782137867a...\" %% xsd:string])""" ; - + obo:IAO_0000115 "FIXME" . @@ -2068,16 +2068,16 @@ nidm:GrandMeanMap rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#HeightThreshold nidm:HeightThreshold rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000116 """Context: Attribute \"statistic\" nidm_0049 -of \"StatisticThresh\" nidm_0018. BIRNLex or +of \"StatisticThresh\" nidm_0018. BIRNLex or NIDM Concept ID: nidm_34. """ ; - + obo:IAO_0000115 """A numerical value that establishes a bound on a range of voxelwise or vertex-wise defined statistic. """ ; - + obo:IAO_0000112 """entity(niiri:height_threshold_id, [prov:type = 'nidm:HeightThreshold', prov:label = \"Height Threshold: p<0.05 (FWE)\" %% xsd:string, @@ -2091,13 +2091,13 @@ NIDM Concept ID: nidm_34. """ ; ### http://www.incf.org/ns/nidash/nidm#Icbm452AirCoordinateSystem nidm:Icbm452AirCoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:MNICoordinateSystem ; - + rdfs:seeAlso "http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml" ; - + obo:IAO_0000115 "Coordinate system defined by the \"average of 452 T1-weighted MRIs of normal young adult brains\" with \"linear transforms of the subjects into the atlas space using a 12-parameter affine transformation\"" ; - + rdfs:comment "FIXME. This definition needs to be re-worked and reviewed." . @@ -2105,13 +2105,13 @@ nidm:Icbm452AirCoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#Icbm452Warp5CoordinateSystem nidm:Icbm452Warp5CoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:MNICoordinateSystem ; - + rdfs:seeAlso "http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml" ; - + obo:IAO_0000115 "Coordinate system defined by the \"average of 452 T1-weighted MRIs of normal young adult brains\" \"based on a 5th order polynomial transformation into the atlas space\"" ; - + rdfs:comment "FIXME. This definition needs to be re-worked and reviewed." . @@ -2119,15 +2119,15 @@ nidm:Icbm452Warp5CoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#IcbmMni152LinearCoordinateSystem nidm:IcbmMni152LinearCoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:MNICoordinateSystem ; - + rdfs:comment "FIXME. This definition needs to be re-worked and reviewed." ; - + obo:IAO_0000115 "Coordinate system defined by the \"average of 152 T1-weighted MRI scans, linearly transformed to Talairach space\"." ; - + rdfs:comment "used in SPM99 to SPM8 (cf. http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach and spm8/spm_templates.man)" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin" . @@ -2135,13 +2135,13 @@ nidm:IcbmMni152LinearCoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#IcbmMni152NonLinear2009aAsymmetricCoordinateSystem nidm:IcbmMni152NonLinear2009aAsymmetricCoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:MNICoordinateSystem ; - + rdfs:comment "FIXME. This definition needs to be re-worked and reviewed." ; - + obo:IAO_0000115 "Coordinate system defined by the \"average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space\"." ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" . @@ -2149,13 +2149,13 @@ nidm:IcbmMni152NonLinear2009aAsymmetricCoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#IcbmMni152NonLinear2009aSymmetricCoordinateSystem nidm:IcbmMni152NonLinear2009aSymmetricCoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:MNICoordinateSystem ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000115 "Coordinate system defined by the \"average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space\"." ; - + rdfs:comment "FIXME. This definition needs to be re-worked and reviewed." . @@ -2163,13 +2163,13 @@ nidm:IcbmMni152NonLinear2009aSymmetricCoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#IcbmMni152NonLinear2009bAsymmetricCoordinateSystem nidm:IcbmMni152NonLinear2009bAsymmetricCoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:MNICoordinateSystem ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000115 "Coordinate system defined by the \"average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space\"." ; - + rdfs:comment "FIXME. This definition needs to be re-worked and reviewed." . @@ -2177,13 +2177,13 @@ nidm:IcbmMni152NonLinear2009bAsymmetricCoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#IcbmMni152NonLinear2009bSymmetricCoordinateSystem nidm:IcbmMni152NonLinear2009bSymmetricCoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:MNICoordinateSystem ; - + obo:IAO_0000115 "Coordinate system defined by the \"average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space\"." ; - + rdfs:comment "FIXME. This definition needs to be re-worked and reviewed." ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" . @@ -2191,15 +2191,15 @@ nidm:IcbmMni152NonLinear2009bSymmetricCoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#IcbmMni152NonLinear2009cAsymmetricCoordinateSystem nidm:IcbmMni152NonLinear2009cAsymmetricCoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:MNICoordinateSystem ; - + rdfs:comment "Used in DARTEL toolbox in SPM12b (cf. spm12b/spm_templates.man)" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000115 "Coordinate system defined by the \"average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space\"." ; - + rdfs:comment "FIXME. This definition needs to be re-worked and reviewed." . @@ -2207,13 +2207,13 @@ nidm:IcbmMni152NonLinear2009cAsymmetricCoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#IcbmMni152NonLinear2009cSymmetricCoordinateSystem nidm:IcbmMni152NonLinear2009cSymmetricCoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:MNICoordinateSystem ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000115 "Coordinate system defined by the \"average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space\"." ; - + rdfs:comment "FIXME. This definition needs to be re-worked and reviewed." . @@ -2221,13 +2221,13 @@ nidm:IcbmMni152NonLinear2009cSymmetricCoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#IcbmMni152NonLinear6thGenerationCoordinateSystem nidm:IcbmMni152NonLinear6thGenerationCoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:MNICoordinateSystem ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6"^^xsd:anyURI ; - + obo:IAO_0000115 "Coordinate system defined by the \"average of 152 T1-weighted MRI scans, linearly and non-linearly (6 iterations) transformed to form a symmetric model in Talairach space\"" ; - + rdfs:comment "Used in FSL (cf. http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases)" , "FIXME. This definition needs to be re-worked and reviewed." . @@ -2236,19 +2236,19 @@ nidm:IcbmMni152NonLinear6thGenerationCoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#Image nidm:Image rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 """entity(niiri:design_matrix_png_id, [prov:type = 'nidm:Image', prov:location = \"file:///path/to/DesignMatrix.png\" %% xsd:anyURI, nidm:filename = \"DesignMatrix.png\", dct:format = \"image/png\"])""" ; - + rdfs:comment "Class used to represent png, gif..." ; - + obo:IAO_0000115 "FIXME" ; - + obo:IAO_0000112 """entity(niiri:maximum_intensity_projection_id, [prov:type = 'nidm:Image', prov:location = \"file:///path/to/MaximumIntensityProjection.png\" %% xsd:anyURI, @@ -2260,9 +2260,9 @@ nidm:Image rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#IndependentNoise nidm:IndependentNoise rdf:type owl:Class ; - + rdfs:subClassOf nidm:NoiseDependence ; - + obo:IAO_0000115 "FIXME" . @@ -2270,17 +2270,17 @@ nidm:IndependentNoise rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#Inference nidm:Inference rdf:type owl:Class ; - + rdfs:subClassOf prov:Activity ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_35. """ ; - + obo:IAO_0000112 """activity(niiri:inference_id, [prov:type = 'nidm:Inference', nidm:hasAlternativeHypothesis = 'nidm:OneTailedTest', prov:label = \"Inference\"])""" ; - + obo:IAO_0000115 "The process of inferring the excursion set from a statistical map." . @@ -2288,15 +2288,15 @@ NIDM Concept ID: nidm_35. """ ; ### http://www.incf.org/ns/nidash/nidm#Ixi549Space nidm:Ixi549Space rdf:type owl:Class ; - + rdfs:subClassOf nidm:MNICoordinateSystem ; - + obo:IAO_0000115 "Coordinate system defined by the average of the \"549 [...] subjects from the IXI dataset\" linearly transformed to ICBM MNI 452." ; - + rdfs:comment "Used in SPM12b (cf. spm12b/spm_templates.man)" ; - + rdfs:seeAlso "http://biomedic.doc.ic.ac.uk/brain-development/index.php?n=Main.Datasets" ; - + rdfs:comment "FIXME. This definition needs to be re-worked and reviewed." . @@ -2304,16 +2304,16 @@ nidm:Ixi549Space rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#MNICoordinateSystem nidm:MNICoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:StandardizedCoordinateSystem ; - + rdfs:seeAlso "birnlex_2125" ; - + rdfs:comment "FIXME. This definition needs to be re-worked and reviewed." ; - - obo:IAO_0000116 """Context: io terms. Parent: reference atlas not found. BIRNLex or + + obo:IAO_0000116 """Context: io terms. Parent: reference atlas not found. BIRNLex or NIDM Concept ID: nidm:nidm_40. """ ; - + obo:IAO_0000115 "Coordinate system defined with reference to the MNI atlas." . @@ -2321,9 +2321,9 @@ NIDM Concept ID: nidm:nidm_40. """ ; ### http://www.incf.org/ns/nidash/nidm#Map nidm:Map rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Ordered set of values corresponding to the discrete sampling of some process (e.g. brain MRI data measured on a regular 3D lattice; or brain cortical surface data measured irregularly over the cortex)." . @@ -2331,9 +2331,9 @@ nidm:Map rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#MapHeader nidm:MapHeader rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "FIXME" . @@ -2341,15 +2341,15 @@ nidm:MapHeader rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#MaskMap nidm:MaskMap rdf:type owl:Class ; - + rdfs:subClassOf nidm:Map , prov:Entity ; - + obo:IAO_0000115 "map or surface on which the associated results are displayed. " ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_39. """ ; - + obo:IAO_0000112 """entity(niiri:mask_id_2, [prov:type = 'nidm:MaskMap', prov:location = \"file:///path/to/Mask.nii.gz\" %% xsd:anyURI, @@ -2364,13 +2364,13 @@ NIDM Concept ID: nidm_39. """ ; ### http://www.incf.org/ns/nidash/nidm#Mni305CoordinateSystem nidm:Mni305CoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:MNICoordinateSystem ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/MNI305" ; - + obo:IAO_0000115 "Coordinate system defined by the \"average of 305 T1-weighted MRI scans, linearly transformed to Talairach space\"." ; - + rdfs:comment "FIXME. This definition needs to be re-worked and reviewed." . @@ -2378,20 +2378,20 @@ nidm:Mni305CoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#ModelParametersEstimation nidm:ModelParametersEstimation rdf:type owl:Class ; - + rdfs:subClassOf prov:Activity ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_41. """ ; - + rdfs:seeAlso "stato:model parameter estimation" ; - + obo:IAO_0000112 """activity(niiri:model_pe_id, [prov:type = 'nidm:ModelParametersEstimation', prov:label = \"Model parameters estimation\", nidm:withEstimationMethod = 'nidm:OrdinaryLeastSquares' ])""" ; - + obo:IAO_0000115 "The process of estimating the parameters of a general linear model from the available data." . @@ -2399,9 +2399,9 @@ NIDM Concept ID: nidm_41. """ ; ### http://www.incf.org/ns/nidash/nidm#NIDMObjectModel nidm:NIDMObjectModel rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "FIXME" . @@ -2409,9 +2409,9 @@ nidm:NIDMObjectModel rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#NoiseDependence nidm:NoiseDependence rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "FIXME" . @@ -2419,7 +2419,7 @@ nidm:NoiseDependence rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#NoiseDistribution nidm:NoiseDistribution rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity . @@ -2427,9 +2427,9 @@ nidm:NoiseDistribution rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#NoiseModel nidm:NoiseModel rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 """entity(niiri:noise_model_id, [prov:type = 'nidm:NoiseModel', nidm:hasNoiseDistribution = 'nidm:GaussianDistribution', @@ -2437,7 +2437,7 @@ nidm:NoiseModel rdf:type owl:Class ; nidm:varianceSpatialModel = 'nidm:SpatiallyLocal', nidm:hasNoiseDependence = 'nidm:IndependentNoise', nidm:dependenceSpatialModel = 'nidm:SpatiallyLocal'])""" ; - + obo:IAO_0000115 "FIXME" . @@ -2445,9 +2445,9 @@ nidm:NoiseModel rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#NonParametricDistribution nidm:NonParametricDistribution rdf:type owl:Class ; - + rdfs:subClassOf nidm:NoiseDistribution ; - + obo:IAO_0000115 "FIXME" . @@ -2455,9 +2455,9 @@ nidm:NonParametricDistribution rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#NonParametricSymmetricDistribution nidm:NonParametricSymmetricDistribution rdf:type owl:Class ; - + rdfs:subClassOf nidm:NoiseDistribution ; - + obo:IAO_0000115 "FIXME" . @@ -2465,11 +2465,11 @@ nidm:NonParametricSymmetricDistribution rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#OneTailedTest nidm:OneTailedTest rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000286"^^xsd:anyURI ; - + obo:IAO_0000115 "Re-use \"one tailed test\" from STATO." . @@ -2477,11 +2477,11 @@ nidm:OneTailedTest rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#OrdinaryLeastSquares nidm:OrdinaryLeastSquares rdf:type owl:Class ; - + rdfs:subClassOf nidm:EstimationMethod ; - + rdfs:comment "OLS (no heteroscedasticity or dependence accounted for)" ; - + obo:IAO_0000115 "FIXME" . @@ -2489,9 +2489,9 @@ nidm:OrdinaryLeastSquares rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#ParameterEstimateMap nidm:ParameterEstimateMap rdf:type owl:Class ; - + rdfs:subClassOf nidm:Map ; - + obo:IAO_0000112 """entity(niiri:parameter_estimate_map_id_1, [prov:type = 'nidm:ParameterEstimateMap', prov:location = \"file:///path/to/ParameterEstimate_0001.nii.gz\" %% xsd:anyURI, @@ -2500,10 +2500,10 @@ nidm:ParameterEstimateMap rdf:type owl:Class ; dct:format = \"image/nifti\", nidm:atCoordinateSpace = 'niiri:coordinate_space_id_1', crypto:sha512 = \"e43b6e01b0463fe7d40782137867a...\" %% xsd:string])""" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_45. """ ; - + obo:IAO_0000115 "A map whose value at each location is the estimate of a model parameter." . @@ -2511,14 +2511,14 @@ NIDM Concept ID: nidm_45. """ ; ### http://www.incf.org/ns/nidash/nidm#Peak nidm:Peak rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Statistic defined at the peak-level in an excursion set. FIXME (now Peak instead of PeakStatistic)" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_46. """ ; - + obo:IAO_0000112 """entity(niiri:peak_0001, [prov:type = 'nidm:Peak', prov:label = \"Peak 0001\" %% xsd:string, @@ -2534,9 +2534,9 @@ NIDM Concept ID: nidm_46. """ ; ### http://www.incf.org/ns/nidash/nidm#PoissonDistribution nidm:PoissonDistribution rdf:type owl:Class ; - + rdfs:subClassOf nidm:NoiseDistribution ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000051"^^xsd:anyURI . @@ -2544,14 +2544,14 @@ nidm:PoissonDistribution rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#ResidualMeanSquaresMap nidm:ResidualMeanSquaresMap rdf:type owl:Class ; - + rdfs:subClassOf nidm:Map ; - + obo:IAO_0000115 """A map whose value at each location is the residual of the mean squares fit to the data. """ ; - + rdfs:seeAlso "This is a map of \"residuals\" as defined at http://bioportal.bioontology.org/ontologies/STATO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FSTATO_0000234 " ; - + obo:IAO_0000112 """entity(niiri:residual_mean_squares_map_id, [prov:type = 'nidm:ResidualMeanSquaresMap', prov:location = \"file:///path/to/ResidualMeanSquares.nii.gz\" %% xsd:anyURI, @@ -2560,8 +2560,8 @@ nidm:ResidualMeanSquaresMap rdf:type owl:Class ; prov:label = \"Residual Mean Squares Map\" %% xsd:string, nidm:atCoordinateSpace = 'niiri:coordinate_space_id_1', crypto:sha512 = \"e43b6e01b0463fe7d40782137867a...\" %% xsd:string])""" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_52. """ . @@ -2569,11 +2569,11 @@ NIDM Concept ID: nidm_52. """ . ### http://www.incf.org/ns/nidash/nidm#RobustIterativelyReweighedLeastSquares nidm:RobustIterativelyReweighedLeastSquares rdf:type owl:Class ; - + rdfs:subClassOf nidm:EstimationMethod ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:comment "used for automatically down-weighting outliers, using some given influence function (e.g. Huber; see [1] for a neuroimaging application)." . @@ -2581,21 +2581,21 @@ nidm:RobustIterativelyReweighedLeastSquares rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#SPM nidm:SPM rdf:type owl:Class ; - + rdfs:subClassOf prov:SoftwareAgent ; - + obo:IAO_0000112 """agent(niiri:software_id, [prov:type = 'nidm:SPM', prov:type = 'prov:SoftwareAgent', prov:label = \"SPM\" %% xsd:string, nidm:softwareVersion = \"SPM12b\" %% xsd:string, spm:softwareRevision = \"5853\" %% xsd:string])""" ; - + obo:IAO_0000115 "Statistical Parametric Mapping software package for the analysis of neuroimaging data from the FIL Methods Group." ; - + rdfs:seeAlso "http://www.fil.ion.ucl.ac.uk/spm/" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_56. """ . @@ -2603,11 +2603,11 @@ NIDM Concept ID: nidm_56. """ . ### http://www.incf.org/ns/nidash/nidm#SPMResults nidm:SPMResults rdf:type owl:Class ; - + rdfs:subClassOf nidm:NIDMObjectModel ; - + obo:IAO_0000115 "FIXME" ; - + obo:IAO_0000112 """entity(niiri:spm_results_id, [prov:type = 'prov:Bundle', prov:label = \"SPM Results\", @@ -2619,10 +2619,10 @@ nidm:SPMResults rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#SearchSpaceMap nidm:SearchSpaceMap rdf:type owl:Class ; - + rdfs:subClassOf nidm:Map , prov:Entity ; - + obo:IAO_0000112 """entity(niiri:stat_image_properties_id, [prov:type = 'nidm:SearchSpaceMap', prov:label = \"Statistical image properties\", @@ -2643,12 +2643,12 @@ nidm:SearchSpaceMap rdf:type owl:Class ; prov:label = \"Search Space Map\" %% xsd:string, fsl:searchVolumeInVoxels = \"45359\" %% xsd:int, fsl:reselSizeInVoxels = \"12.2251\" %%xsd:float])""" ; - + rdfs:seeAlso "http://purl.obolibrary.org/obo/OBI_0000235" ; - - obo:IAO_0000116 """Domain or Attributes: spm:searchVolumeInUnits not found. BIRNLex or + + obo:IAO_0000116 """Domain or Attributes: spm:searchVolumeInUnits not found. BIRNLex or NIDM Concept ID: nidm_100. """ ; - + obo:IAO_0000112 """entity(niiri:search_space_id, [prov:type = 'nidm:SearchSpaceMap', prov:location = \"file:///path/to/SearchSpace.nii.gz\" %% xsd:anyURI, @@ -2671,10 +2671,10 @@ NIDM Concept ID: nidm_100. """ ; spm:noiseFWHMInUnits = \"[8.87643567497404, 8.89885340008753, 7.83541276878791]\" %% xsd:string, nidm:randomFieldStationarity = \"false\" %%xsd:boolean, crypto:sha512 = \"e43b6e01b0463fe7d40782137867a...\" %% xsd:string])""" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: spm_95. """ ; - + obo:IAO_0000115 "mask in which the inference was performed / Properties of the underlying statistical process." . @@ -2682,9 +2682,9 @@ NIDM Concept ID: spm_95. """ ; ### http://www.incf.org/ns/nidash/nidm#SeriallyCorrelatedNoise nidm:SeriallyCorrelatedNoise rdf:type owl:Class ; - + rdfs:subClassOf nidm:NoiseDependence ; - + obo:IAO_0000115 "FIXME" . @@ -2692,9 +2692,9 @@ nidm:SeriallyCorrelatedNoise rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#SpatialModel nidm:SpatialModel rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "FIXME" . @@ -2702,9 +2702,9 @@ nidm:SpatialModel rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#SpatiallyGlobalModel nidm:SpatiallyGlobalModel rdf:type owl:Class ; - + rdfs:subClassOf nidm:SpatialModel ; - + obo:IAO_0000115 "FIXME" . @@ -2712,9 +2712,9 @@ nidm:SpatiallyGlobalModel rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#SpatiallyLocalModel nidm:SpatiallyLocalModel rdf:type owl:Class ; - + rdfs:subClassOf nidm:SpatialModel ; - + obo:IAO_0000115 "FIXME" . @@ -2722,9 +2722,9 @@ nidm:SpatiallyLocalModel rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#SpatiallyRegularizedModel nidm:SpatiallyRegularizedModel rdf:type owl:Class ; - + rdfs:subClassOf nidm:SpatialModel ; - + obo:IAO_0000115 "FIXME" . @@ -2732,11 +2732,11 @@ nidm:SpatiallyRegularizedModel rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#StandardizedCoordinateSystem nidm:StandardizedCoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:WorldCoordinateSystem ; - + obo:IAO_0000115 "Parent of all reference spaces except \"Subject\"." ; - + rdfs:comment "This is meant to be used for retrospective export when exact template is unknown." , "FIXME. This definition needs to be re-worked and reviewed." . @@ -2745,9 +2745,9 @@ nidm:StandardizedCoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#Statistic nidm:Statistic rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000039"^^xsd:anyURI . @@ -2755,10 +2755,10 @@ nidm:Statistic rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#StatisticMap nidm:StatisticMap rdf:type owl:Class ; - + rdfs:subClassOf nidm:Map , prov:Entity ; - + obo:IAO_0000112 """entity(niiri:statistic_map_id, [prov:type = 'nidm:StatisticMap', nidm:statisticType = 'nidm:TStatistic', @@ -2771,10 +2771,10 @@ nidm:StatisticMap rdf:type owl:Class ; nidm:effectDegreesOfFreedom = \"1\" %% xsd:float, nidm:atCoordinateSpace = 'niiri:coordinate_space_id_1', crypto:sha512 = \"e43b6e01b0463fe7d40782137867a...\" %% xsd:string])""" ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_60. """ ; - + obo:IAO_0000115 "A map whose value at each location is a statistic. " . @@ -2782,12 +2782,12 @@ NIDM Concept ID: nidm_60. """ ; ### http://www.incf.org/ns/nidash/nidm#SubVolumeMap nidm:SubVolumeMap rdf:type owl:Class ; - + rdfs:subClassOf nidm:Map ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_101. """ ; - + obo:IAO_0000112 """entity(niiri:sub_volume_id, [prov:type = 'nidm:SubVolumeMap', prov:location = \"file:///path/to/SubVolume.nii.gz\" %% xsd:anyURI, @@ -2796,7 +2796,7 @@ NIDM Concept ID: nidm_101. """ ; prov:label = \"Sub-volume Map\" %% xsd:string, nidm:atCoordinateSpace = 'niiri:coordinate_space_id_2', crypto:sha512 = \"e43b6e01b0463fe7d40782137867a...\" %% xsd:string])""" ; - + obo:IAO_0000115 "mask defined by the user to restrain the space in which inference is performed." . @@ -2804,11 +2804,11 @@ NIDM Concept ID: nidm_101. """ ; ### http://www.incf.org/ns/nidash/nidm#SubjectCoordinateSystem nidm:SubjectCoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:WorldCoordinateSystem ; - + obo:IAO_0000115 "Coordinate system defined by the subject brain (no spatial normalisation applied)." ; - + rdfs:comment "Used in FSL and SPM un-registered data." . @@ -2816,9 +2816,9 @@ nidm:SubjectCoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#TStatistic nidm:TStatistic rdf:type owl:Class ; - + rdfs:subClassOf nidm:Statistic ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000176"^^xsd:anyURI . @@ -2826,13 +2826,13 @@ nidm:TStatistic rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#TalairachCoordinateSystem nidm:TalairachCoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf nidm:StandardizedCoordinateSystem ; - + rdfs:comment "FIXME. This definition needs to be re-worked and reviewed." ; - + obo:IAO_0000115 "Reference space defined by the dissected brain used for the Talairach and Tournoux atlas." ; - + rdfs:seeAlso "http://www.talairach.org/" . @@ -2840,11 +2840,11 @@ nidm:TalairachCoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#TwoTailedTest nidm:TwoTailedTest rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Re-use \"two tailed test\" from STATO"^^xsd:anyURI ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000287"^^xsd:anyURI . @@ -2852,11 +2852,11 @@ nidm:TwoTailedTest rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#WeightedLeastSquares nidm:WeightedLeastSquares rdf:type owl:Class ; - + rdfs:subClassOf nidm:EstimationMethod ; - + obo:IAO_0000115 "FIXME" ; - + rdfs:comment "WLS (heteroscedasticity accounted for, but no dependence)" . @@ -2864,9 +2864,9 @@ nidm:WeightedLeastSquares rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#WorldCoordinateSystem nidm:WorldCoordinateSystem rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "FIXME" . @@ -2874,9 +2874,9 @@ nidm:WorldCoordinateSystem rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#ZStatistic nidm:ZStatistic rdf:type owl:Class ; - + rdfs:subClassOf nidm:Statistic ; - + obo:IAO_0000115 "FIXME" . @@ -2884,12 +2884,12 @@ nidm:ZStatistic rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/nidm#stationaryRandomField nidm:stationaryRandomField rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: nidm_59. """ ; - + obo:IAO_0000115 "Random-field that is constant across the search volume." . @@ -2897,9 +2897,9 @@ NIDM Concept ID: nidm_59. """ ; ### http://www.incf.org/ns/nidash/spm#KConjunctionInference spm:KConjunctionInference rdf:type owl:Class ; - + rdfs:subClassOf nidm:Inference ; - + obo:IAO_0000115 "FIXME" . @@ -2907,14 +2907,14 @@ spm:KConjunctionInference rdf:type owl:Class ; ### http://www.incf.org/ns/nidash/spm#ReselsPerVoxelMap spm:ReselsPerVoxelMap rdf:type owl:Class ; - + rdfs:subClassOf nidm:Map ; - + obo:IAO_0000115 "A map whose value at each location is the number of resels per voxel. " ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: spm_83. """ ; - + obo:IAO_0000112 """entity(niiri:resels_per_voxel_map_id, [prov:type = 'spm:ReselsPerVoxelMap', prov:location = \"file:///path/to/ReselsPerVoxel.nii.gz\" %% xsd:anyURI, @@ -2929,12 +2929,12 @@ NIDM Concept ID: spm_83. """ ; ### http://www.incf.org/ns/nidash/spm#kConjunctionInference spm:kConjunctionInference rdf:type owl:Class ; - + rdfs:subClassOf prov:Activity ; - + obo:IAO_0000115 "Inference testing for the joint significance of a subset of the effects." ; - - obo:IAO_0000116 """BIRNLex or + + obo:IAO_0000116 """BIRNLex or NIDM Concept ID: spm_76. """ . @@ -2942,14 +2942,14 @@ NIDM Concept ID: spm_76. """ . ### http://www.incf.org/ns/nidash/spm#nonStationaryRandomField spm:nonStationaryRandomField rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - - obo:IAO_0000116 """Range: not found. BIRNLex or + + obo:IAO_0000116 """Range: not found. BIRNLex or NIDM Concept ID: spm_81. """ ; - + obo:IAO_0000112 "" ; - + obo:IAO_0000115 "Random field that is variable across the search volume." . @@ -2969,7 +2969,7 @@ prov:Agent rdf:type owl:Class . ### http://www.w3.org/ns/prov#Bundle prov:Bundle rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity . @@ -2983,7 +2983,7 @@ prov:Entity rdf:type owl:Class . ### http://www.w3.org/ns/prov#Location prov:Location rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity . @@ -2991,11 +2991,10 @@ prov:Location rdf:type owl:Class ; ### http://www.w3.org/ns/prov#SoftwareAgent prov:SoftwareAgent rdf:type owl:Class ; - + rdfs:subClassOf prov:Agent . ### Generated by the OWL API (version 3.5.0) http://owlapi.sourceforge.net - diff --git a/nidmresults/owl/nidm-results_100.owl b/nidmresults/owl/nidm-results_100.owl index 543dbe3..ad1ea3d 100644 --- a/nidmresults/owl/nidm-results_100.owl +++ b/nidmresults/owl/nidm-results_100.owl @@ -63,17 +63,17 @@ dc:description rdfs:range dctype:Image . ### http://purl.org/nidash/nidm#NIDM_0000010 nidm:NIDM_0000010 rdf:type owl:ObjectProperty ; - + rdfs:label "has fMRI Design" ; - + obo:IAO_0000115 "A property that associates an fMRI design to a design matrix in first-level fMRI analyses." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/299" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000019 ; - + rdfs:range nidm:NIDM_0000155 . @@ -81,17 +81,17 @@ nidm:NIDM_0000010 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000088 nidm:NIDM_0000088 rdf:type owl:ObjectProperty ; - + rdfs:label "has Drift Model" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000115 "A property that associates a drift model to a design matrix (only used for first-level fMRI experiments)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000019 ; - + rdfs:range nidm:NIDM_0000087 . @@ -99,17 +99,17 @@ nidm:NIDM_0000088 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000089 nidm:NIDM_0000089 rdf:type owl:ObjectProperty ; - + rdfs:label "dependence Map-Wise Dependence" ; - + obo:IAO_0000115 "Property that associates an Error Parameter Map-Wise Dependence to the dependence of an error model." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000023 ; - + rdfs:range nidm:NIDM_0000071 . @@ -117,20 +117,20 @@ nidm:NIDM_0000089 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000097 nidm:NIDM_0000097 rdf:type owl:ObjectProperty ; - + rdfs:label "has Alternative Hypothesis" ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/pull/81" ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000208" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000049 ; - + rdfs:range nidm:NIDM_0000060 , nidm:NIDM_0000079 ; - + rdfs:subPropertyOf owl:topObjectProperty . @@ -138,17 +138,17 @@ nidm:NIDM_0000097 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000098 nidm:NIDM_0000098 rdf:type owl:ObjectProperty ; - + rdfs:label "has Cluster Labels Map" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/282" ; - + obo:IAO_0000115 "A property that associates a clusters label map to the excursion set." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range nidm:NIDM_0000008 ; - + rdfs:domain nidm:NIDM_0000025 . @@ -156,17 +156,17 @@ nidm:NIDM_0000098 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000099 nidm:NIDM_0000099 rdf:type owl:ObjectProperty ; - + rdfs:label "has Connectivity Criterion" ; - + obo:IAO_0000115 "Property that associates a ConnectivityCriterion with a ClusterDefinitionCriteria." ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000007 ; - + rdfs:range nidm:NIDM_0000012 . @@ -174,15 +174,15 @@ nidm:NIDM_0000099 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000100 nidm:NIDM_0000100 rdf:type owl:ObjectProperty ; - + rdfs:label "has Error Dependence" ; - + obo:IAO_0000115 "Property that associates a covariance structure representing the dependence structure of the error, used as part of model estimation with an Error Model." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range obo:STATO_0000346 ; - + rdfs:domain nidm:NIDM_0000023 . @@ -190,15 +190,15 @@ nidm:NIDM_0000100 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000101 nidm:NIDM_0000101 rdf:type owl:ObjectProperty ; - + rdfs:label "has Error Distribution" ; - + obo:IAO_0000115 "Property that associates an ErrorDistribution with an ErrorModel." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range nidm:NIDM_0000022 ; - + rdfs:domain nidm:NIDM_0000023 . @@ -206,17 +206,17 @@ nidm:NIDM_0000101 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000102 nidm:NIDM_0000102 rdf:type owl:ObjectProperty ; - + rdfs:label "has HRF Basis" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "A property that associates a set of functions that, when convolved with the anticipated neural responses, yield a set of regressors to model the anticipated hemodynamic responses in a design matrix." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000019 ; - + rdfs:range nidm:NIDM_0000036 . @@ -224,17 +224,17 @@ nidm:NIDM_0000102 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000103 nidm:NIDM_0000103 rdf:type owl:ObjectProperty ; - + rdfs:label "has Map Header" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/289" ; - + obo:IAO_0000115 "A Property that associates an additional file containing the map header with a map" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000052 ; - + rdfs:range nidm:NIDM_0000053 . @@ -242,17 +242,17 @@ nidm:NIDM_0000103 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000104 nidm:NIDM_0000104 rdf:type owl:ObjectProperty ; - + rdfs:label "in Coordinate Space" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/171 by NN JT CM SG KH TN." ; - + obo:IAO_0000115 "Property of a DataArray to associate a CoordinateSpace with a physical file." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range nidm:NIDM_0000016 ; - + rdfs:domain nidm:NIDM_0000052 . @@ -260,17 +260,17 @@ nidm:NIDM_0000104 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000105 nidm:NIDM_0000105 rdf:type owl:ObjectProperty ; - + rdfs:label "in World Coordinate System" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Property that associates a world coordinate system to the coordinate space." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range nidm:NIDM_0000081 . @@ -278,15 +278,15 @@ nidm:NIDM_0000105 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000113 nidm:NIDM_0000113 rdf:type owl:ObjectProperty ; - + rdfs:label "object Model" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/pull/137" ; - + obo:IAO_0000114 obo:IAO_0000124 ; - + rdfs:range nidm:NIDM_0000057 ; - + rdfs:domain prov:Bundle . @@ -294,17 +294,17 @@ nidm:NIDM_0000113 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000123 nidm:NIDM_0000123 rdf:type owl:ObjectProperty ; - + rdfs:label "statistic Type" ; - + obo:IAO_0000115 "Property that associates a [stato:\"statistic\"](http://purl.obolibrary.org/obo/STATO_0000039) with a StatisticMap or a ContrastWeights entity." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/293" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range obo:STATO_0000039 ; - + rdfs:domain obo:STATO_0000323 , nidm:NIDM_0000076 . @@ -313,17 +313,17 @@ nidm:NIDM_0000123 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000126 nidm:NIDM_0000126 rdf:type owl:ObjectProperty ; - + rdfs:label "variance Map-Wise Dependence" ; - + obo:IAO_0000115 "Property that associates an Error Parameter Map-Wise Dependence to the variance of an error model" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000023 ; - + rdfs:range nidm:NIDM_0000071 . @@ -331,17 +331,17 @@ nidm:NIDM_0000126 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000134 nidm:NIDM_0000134 rdf:type owl:ObjectProperty ; - + rdfs:label "with Estimation Method" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/293" ; - + obo:IAO_0000115 "Property that associates a [stato:\"model parameter estimation\"](http://purl.obolibrary.org/obo/STATO_0000119) method with a model parameter estimation" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range obo:STATO_0000119 ; - + rdfs:domain nidm:NIDM_0000056 . @@ -349,17 +349,17 @@ nidm:NIDM_0000134 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000138 nidm:NIDM_0000138 rdf:type owl:ObjectProperty ; - + rdfs:label "has Maximum Intensity Projection" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/293" ; - + obo:IAO_0000115 "Property that associates an image of the maximum intensity projection with an excursion set map." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range dctype:Image ; - + rdfs:domain nidm:NIDM_0000025 . @@ -382,7 +382,7 @@ dc:description rdf:type owl:DatatypeProperty . ### http://purl.org/dc/terms/format dct:format rdf:type owl:DatatypeProperty ; - + rdfs:range xsd:string . @@ -390,17 +390,17 @@ dct:format rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/fsl#FSL_0000004 fsl:FSL_0000004 rdf:type owl:DatatypeProperty ; - + rdfs:label "drift Cutoff Period" ; - + obo:IAO_0000115 "Full Width at Half Maximum in seconds of the Gaussian weight function used in the running line smoother." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain fsl:FSL_0000002 ; - + rdfs:range xsd:float . @@ -408,17 +408,17 @@ fsl:FSL_0000004 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/fsl#FSL_0000005 fsl:FSL_0000005 rdf:type owl:DatatypeProperty ; - + rdfs:label "feat Version" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/291" ; - + obo:IAO_0000115 "Version of the FEAT software." ; - + rdfs:domain nlx:birnlex_2067 ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range xsd:string . @@ -430,17 +430,17 @@ fsl:FSL_0000005 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000021 nidm:NIDM_0000021 rdf:type owl:DatatypeProperty ; - + rdfs:label "regressor Names" ; - + obo:IAO_0000115 "A list of abstract names associated with each column of the design matrix (e.g. [\"motor_left\", \"motor_right\"])." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/299" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000019 ; - + rdfs:range xsd:string . @@ -448,19 +448,19 @@ nidm:NIDM_0000021 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000082 nidm:NIDM_0000082 rdf:type owl:DatatypeProperty ; - + rdfs:label "cluster Label Id" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/271" ; - + obo:IAO_0000115 "Integer value used in the cluster label map to identify the location of the cluster within the excursion set." ; - + obo:IAO_0000112 "5" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000070 ; - + rdfs:range xsd:int . @@ -468,18 +468,18 @@ nidm:NIDM_0000082 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000083 nidm:NIDM_0000083 rdf:type owl:DatatypeProperty ; - + rdfs:label "cluster Size In Vertices" ; - + obo:IAO_0000115 "Number of vertices that make up the cluster." ; - + obo:IAO_0000112 "10" ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000070 ; - + rdfs:range xsd:positiveInteger . @@ -487,18 +487,18 @@ nidm:NIDM_0000083 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000084 nidm:NIDM_0000084 rdf:type owl:DatatypeProperty ; - + rdfs:label "cluster Size In Voxels" ; - + obo:IAO_0000112 "18" ; - + obo:IAO_0000115 "Number of voxels that make up the cluster." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000070 ; - + rdfs:range xsd:positiveInteger . @@ -506,19 +506,19 @@ nidm:NIDM_0000084 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000085 nidm:NIDM_0000085 rdf:type owl:DatatypeProperty ; - + rdfs:label "contrast Name" ; - + obo:IAO_0000115 "Name of the contrast." ; - + obo:IAO_0000112 "\"Listening > Rest\"" ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain obo:STATO_0000323 , nidm:NIDM_0000002 , nidm:NIDM_0000076 ; - + rdfs:range xsd:string . @@ -526,19 +526,19 @@ nidm:NIDM_0000085 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000086 nidm:NIDM_0000086 rdf:type owl:DatatypeProperty ; - + rdfs:label "coordinate Vector" ; - + obo:IAO_0000112 "[-60, 32, 54]"^^xsd:string ; - + obo:IAO_0000115 "A vector with one number per dimension. The first element corresponds to the coordinate along the first dimension measured in map elements (e.g., pixels, voxels, vertices, or faces), the second element to the coordinate along the second dimension etc." ; - + obo:IAO_0000116 "Under discussion at: https://github.com/incf-nidash/nidm/pull/270 and https://github.com/incf-nidash/nidm/issues/145" ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000015 ; - + rdfs:range xsd:string . @@ -546,19 +546,19 @@ nidm:NIDM_0000086 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000090 nidm:NIDM_0000090 rdf:type owl:DatatypeProperty ; - + rdfs:label "dimensions In Voxels" ; - + obo:IAO_0000115 "Number of voxels in each of the dimensions of the data array. For example, \"91 109 91\" indicates there are 91 voxels in the first dimension, 109 in the second dimension, and 91 in the third dimension." ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/issues/146" ; - + obo:IAO_0000112 "[64 64 20]" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:string . @@ -566,19 +566,19 @@ nidm:NIDM_0000090 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000091 nidm:NIDM_0000091 rdf:type owl:DatatypeProperty ; - + rdfs:label "effect Degrees Of Freedom" ; - + obo:IAO_0000115 "In the context of a general linear model, the effect degrees of freedom is the rank of the contrast. For example, a contrast comprising of a vector has effect degrees of freedom of 1 and can be tested with a F-test with numerator degrees of freedom of 1." ; - + obo:IAO_0000112 "1" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/issues/277" ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000076 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -591,17 +591,17 @@ nidm:NIDM_0000091 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000092 nidm:NIDM_0000092 rdf:type owl:DatatypeProperty ; - + rdfs:label "equivalent ZStatistic" ; - + obo:IAO_0000115 "Statistic value transformed into Z units; the output of a process which takes a non-normal statistic and transforms it to an equivalent z score." ; - + obo:IAO_0000112 "3.5" ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain nidm:NIDM_0000062 ; - + rdfs:range xsd:float . @@ -609,19 +609,19 @@ nidm:NIDM_0000092 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000093 nidm:NIDM_0000093 rdf:type owl:DatatypeProperty ; - + rdfs:label "error Degrees Of Freedom" ; - + obo:IAO_0000112 "72.999999" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/issues/277" ; - + obo:IAO_0000115 "In the context of a general linear model, the error degrees of freedom are the number of observations less the rank of the design matrix." ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000076 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -634,15 +634,15 @@ nidm:NIDM_0000093 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000094 nidm:NIDM_0000094 rdf:type owl:DatatypeProperty ; - + rdfs:label "error Variance Homogeneous" ; - + obo:IAO_0000115 "A boolean value reflecting how the variance of the error is modeled during parameter estimation; TRUE for constant variance over all observations in the model, FALSE for heterogeneous variance." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000023 ; - + rdfs:range xsd:boolean . @@ -650,17 +650,17 @@ nidm:NIDM_0000094 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000095 nidm:NIDM_0000095 rdf:type owl:DatatypeProperty ; - + rdfs:label "partial Conjunction Degree" ; - + obo:IAO_0000115 "The number of non-null effects permitted in a partial conjunction null, as part of a partial conjunction inference" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/294" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain spm:SPM_0000005 ; - + rdfs:range xsd:int . @@ -668,19 +668,19 @@ nidm:NIDM_0000095 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000096 nidm:NIDM_0000096 rdf:type owl:DatatypeProperty ; - + rdfs:label "grand Mean Scaling" ; - + obo:IAO_0000115 "Binary flag defining whether the data was scaled (true for scaled). Specifically, \"grand mean scaling\" refers to multiplication of every voxel in every scan by a common (or session-specific) value." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/285" ; - + obo:IAO_0000112 "TRUE" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000018 ; - + rdfs:range xsd:boolean . @@ -688,13 +688,13 @@ nidm:NIDM_0000096 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000105 nidm:NIDM_0000105 rdf:type owl:DatatypeProperty ; - + rdfs:label "in World Coordinate System" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Property that associates a world coordinate system to the coordinate space." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -702,17 +702,17 @@ nidm:NIDM_0000105 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000106 nidm:NIDM_0000106 rdf:type owl:DatatypeProperty ; - + rdfs:label "is User Defined" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/pull/258" ; - + obo:IAO_0000115 "A binary flag defining whether the mask was specified by the user (true) or automatically generated during the analysis (false)" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000004 ; - + rdfs:range xsd:boolean . @@ -720,21 +720,21 @@ nidm:NIDM_0000106 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000107 nidm:NIDM_0000107 rdf:type owl:DatatypeProperty ; - + rdfs:label "masked Median" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/288, naming previously discussed at: https://github.com/incf-nidash/nidm/issues/70" ; - + obo:IAO_0000115 "Median value considering only in-mask voxels. Useful diagnostic when computed on grand mean image when grandMeanScaling is TRUE, as the median should be close to targetIntensity." ; - + rdfs:seeAlso "http://purl.obolibrary.org/obo/OBI_0200119" ; - + obo:IAO_0000112 "155.23" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000033 ; - + rdfs:range xsd:float . @@ -742,17 +742,17 @@ nidm:NIDM_0000107 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000108 nidm:NIDM_0000108 rdf:type owl:DatatypeProperty ; - + rdfs:label "max Number Of Peaks Per Cluster" ; - + obo:IAO_0000115 "Maximum number of peaks to be reported after inference within a cluster." ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/200" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000063 ; - + rdfs:range xsd:int . @@ -760,17 +760,17 @@ nidm:NIDM_0000108 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000109 nidm:NIDM_0000109 rdf:type owl:DatatypeProperty ; - + rdfs:label "min Distance Between Peaks" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/200" ; - + obo:IAO_0000115 "Minimum distance between two peaks to be reported after inference." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000063 ; - + rdfs:range xsd:float . @@ -778,19 +778,19 @@ nidm:NIDM_0000109 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000111 nidm:NIDM_0000111 rdf:type owl:DatatypeProperty ; - + rdfs:label "number Of Significant Clusters" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/292" ; - + obo:IAO_0000115 "Number of significant clusters found by the inference activity. This is SPM's set level statistic." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000025 ; - + rdfs:range xsd:int ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -798,19 +798,19 @@ nidm:NIDM_0000111 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000112 nidm:NIDM_0000112 rdf:type owl:DatatypeProperty ; - + rdfs:label "number Of Dimensions" ; - + obo:IAO_0000115 "Number of dimensions of the data matrix (e.g. 3 for volumetric data)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/295" ; - + obo:IAO_0000112 "3" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:positiveInteger . @@ -818,23 +818,23 @@ nidm:NIDM_0000112 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000114 nidm:NIDM_0000114 rdf:type owl:DatatypeProperty ; - + rdfs:label "p Value" ; - + owl:sameAs "http://purl.obolibrary.org/obo/OBI_0000175"^^xsd:anyURI ; - + obo:IAO_0000112 "8.95E-14" ; - + rdfs:seeAlso """http://purl.obolibrary.org/obo/IAO_0000121 http://purl.obolibrary.org/obo/OBI_0000175 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P-Value""" ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/38" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000025 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -849,26 +849,26 @@ http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P-Value""" ; ### http://purl.org/nidash/nidm#NIDM_0000115 nidm:NIDM_0000115 rdf:type owl:DatatypeProperty ; - + rdfs:label "p Value FWER" ; - + obo:IAO_0000112 "0.05" ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/38" ; - + obo:IAO_0000115 "\"A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests\"" ; - + owl:sameAs "This definition is from OBI. Please update this note if the definition is modified." ; - + rdfs:seeAlso "Synonym of \"nidm:pFWE\"" ; - + obo:IAO_0000114 obo:IAO_0000423 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000034 , nidm:NIDM_0000062 , nidm:NIDM_0000070 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -883,24 +883,24 @@ nidm:NIDM_0000115 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000116 nidm:NIDM_0000116 rdf:type owl:DatatypeProperty ; - + rdfs:label "p Value Uncorrected" ; - + obo:IAO_0000115 "A p-value reported without correction for multiple testing. " ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/38" ; - + obo:IAO_0000112 "0.0542" ; - + rdfs:seeAlso "http://purl.obolibrary.org/obo/IAO_0000121" ; - + obo:IAO_0000114 obo:IAO_0000423 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000034 , nidm:NIDM_0000062 , nidm:NIDM_0000070 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -915,24 +915,24 @@ nidm:NIDM_0000116 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000119 nidm:NIDM_0000119 rdf:type owl:DatatypeProperty ; - + rdfs:label "q Value FDR" ; - + obo:IAO_0000112 "0.000154" ; - + obo:IAO_0000115 "A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level (same as OBI_0001442)." ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/38" ; - + owl:sameAs "http://purl.obolibrary.org/obo/OBI_0001442" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000034 , nidm:NIDM_0000062 , nidm:NIDM_0000070 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -947,17 +947,17 @@ nidm:NIDM_0000119 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000120 nidm:NIDM_0000120 rdf:type owl:DatatypeProperty ; - + rdfs:label "random Field Stationarity" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/130" ; - + obo:IAO_0000115 "A binary flag that indicates whether Random Field Theory methods assumed smoothness that was homogeneous over the map (true), or allowed for smoothness that varies over the map (false)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:boolean . @@ -965,21 +965,21 @@ nidm:NIDM_0000120 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000121 nidm:NIDM_0000121 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume In Voxels" ; - + obo:IAO_0000112 "68656" ; - + rdfs:seeAlso "Synonyms of nidm:volumeInVoxels" ; - + obo:IAO_0000115 "Total number of voxels within the search volume." ; - + obo:IAO_0000114 obo:IAO_0000124 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -987,19 +987,19 @@ nidm:NIDM_0000121 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000122 nidm:NIDM_0000122 rdf:type owl:DatatypeProperty ; - + rdfs:label "software Version" ; - + obo:IAO_0000112 8.6225 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/291" ; - + obo:IAO_0000115 "Name and number that specifies the software version. For SPM, this includes the main software version followed by the revision number (e.g. 8.6225 for SPM8 revision 6225)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range xsd:string ; - + rdfs:domain prov:SoftwareAgent . @@ -1007,19 +1007,19 @@ nidm:NIDM_0000122 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000124 nidm:NIDM_0000124 rdf:type owl:DatatypeProperty ; - + rdfs:label "target Intensity" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/285" ; - + obo:IAO_0000115 "Value to which the grand mean of the Data was scaled (applies only if grand mean scaling is true)." ; - + obo:IAO_0000112 "100" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000018 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1032,22 +1032,22 @@ nidm:NIDM_0000124 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000125 nidm:NIDM_0000125 rdf:type owl:DatatypeProperty ; - + rdfs:label "user Specified Threshold Type" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/150" ; - + obo:IAO_0000112 "nidm:pValueFWER" ; - + obo:IAO_0000115 "Type of method used to define a threshold (e.g. statistic value, uncorrected P-value or corrected P-value)." ; - + rdfs:comment "Range is currently string but should be limited to {'nidm:pValueFWER' not found'nidm:pValueFDR' not found'nidm:pValueUncorrected';'nidm:statistic'}?" ; - + obo:IAO_0000114 obo:IAO_0000428 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000034 ; - + rdfs:range xsd:string . @@ -1055,15 +1055,15 @@ nidm:NIDM_0000125 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000127 nidm:NIDM_0000127 rdf:type owl:DatatypeProperty ; - + rdfs:label "version" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/pull/137" ; - + obo:IAO_0000114 obo:IAO_0000124 ; - + rdfs:range xsd:string ; - + rdfs:domain prov:Bundle . @@ -1071,19 +1071,19 @@ nidm:NIDM_0000127 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000131 nidm:NIDM_0000131 rdf:type owl:DatatypeProperty ; - + rdfs:label "voxel Size" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/295" ; - + obo:IAO_0000115 "3D size of a voxel measured in voxel units (e.g. [2, 2, 4])" ; - + obo:IAO_0000112 "[2, 2, 4]" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:string . @@ -1091,21 +1091,21 @@ nidm:NIDM_0000131 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000132 nidm:NIDM_0000132 rdf:type owl:DatatypeProperty ; - + rdfs:label "voxel To World Mapping" ; - + obo:IAO_0000116 "Range: Matrix of float." ; - + obo:IAO_0000112 "[3 0 0 0;0 3 0 0;0 0 3 0; 0 0 0 1] " ; - + obo:IAO_0000115 "Homogeneous transformation matrix to map from voxel coordinate system to world coordinate system." ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/148" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:string . @@ -1113,21 +1113,21 @@ nidm:NIDM_0000132 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000133 nidm:NIDM_0000133 rdf:type owl:DatatypeProperty ; - + rdfs:label "voxel Units" ; - + rdfs:comment "Range: Vector of strings." ; - + obo:IAO_0000112 "['mm', 'mm', 's']" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/295 and https://github.com/incf-nidash/nidm/issues/147" ; - + obo:IAO_0000115 "Set of units associated with the dimensions of some N-dimensional data (e.g. [mm, mm, mm])" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:string . @@ -1135,21 +1135,21 @@ nidm:NIDM_0000133 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000136 nidm:NIDM_0000136 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume In Units" ; - + obo:IAO_0000117 "Discussed at https://github.com/incf-nidash/nidm/pull/131" ; - + obo:IAO_0000115 "The volume of the searched region in units determined by the current coordinate space units (e.g., mm^3 for axis units of mm in a three dimensional image, sec.Hz for a time by frequency two dimensional image)." ; - + obo:IAO_0000116 "Context: volumeInVoxels nidm_0025. Range: Positivefloat not found." ; - + obo:IAO_0000112 "1771011" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1162,17 +1162,17 @@ nidm:NIDM_0000136 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000137 nidm:NIDM_0000137 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume In Vertices" ; - + obo:IAO_0000112 "151.3" ; - + obo:IAO_0000115 "Total number of vertices within the search volume." ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1185,19 +1185,19 @@ nidm:NIDM_0000137 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000139 nidm:NIDM_0000139 rdf:type owl:DatatypeProperty ; - + rdfs:label "coordinate Vector In Voxels" ; - + obo:IAO_0000115 "Coordinate along the first dimension in voxels. (This definition needs to be re-worked as this term was renamed from coordinate1 to coordinate in https://github.com/incf-nidash/nidm/issues/270)" ; - + obo:IAO_0000112 "[12 51 48]" ; - + obo:IAO_0000116 "Under discussion at: https://github.com/incf-nidash/nidm/pull/270" ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain nidm:NIDM_0000015 ; - + rdfs:range xsd:string . @@ -1205,17 +1205,17 @@ nidm:NIDM_0000139 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000141 nidm:NIDM_0000141 rdf:type owl:DatatypeProperty ; - + rdfs:label "expected Number Of Clusters" ; - + obo:IAO_0000112 "9.51" ; - + obo:IAO_0000115 "Expected number of clusters in an excursion set under the null hypothesis." ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1228,17 +1228,17 @@ nidm:NIDM_0000141 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000142 nidm:NIDM_0000142 rdf:type owl:DatatypeProperty ; - + rdfs:label "expected Number Of Vertices Per Cluster" ; - + obo:IAO_0000115 "Expected number of vertices in a cluster under the null hypothesis." ; - + obo:IAO_0000112 "60.632" ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1251,17 +1251,17 @@ nidm:NIDM_0000142 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000143 nidm:NIDM_0000143 rdf:type owl:DatatypeProperty ; - + rdfs:label "expected Number Of Voxels Per Cluster" ; - + obo:IAO_0000115 "Expected number of voxels in a cluster under the null hypothesis." ; - + obo:IAO_0000112 "60.632" ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1274,17 +1274,17 @@ nidm:NIDM_0000143 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000145 nidm:NIDM_0000145 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise Roughness In Voxels" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/214 and https://github.com/incf-nidash/nidm/issues/275" ; - + obo:IAO_0000115 "Estimated spatial roughness of the noise process in voxel units, as measured by the square-root determinant of the variance-covariance matrix of spatial derivatives of the noise process (Lambda matrix)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:float . @@ -1292,17 +1292,17 @@ nidm:NIDM_0000145 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000146 nidm:NIDM_0000146 rdf:type owl:DatatypeProperty ; - + rdfs:label "height Critical Threshold FDR 05" ; - + obo:IAO_0000112 "5.896" ; - + obo:IAO_0000115 "Peak statistic threshold corrected for false discovery rate at a level of alpha = 0.05. " ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:float . @@ -1310,17 +1310,17 @@ nidm:NIDM_0000146 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000147 nidm:NIDM_0000147 rdf:type owl:DatatypeProperty ; - + rdfs:label "height Critical Threshold FWE 05" ; - + obo:IAO_0000112 "4.913" ; - + obo:IAO_0000115 "Peak statistic threshold corrected for family-wise error at a level of alpha = 0.05. " ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:float . @@ -1328,23 +1328,23 @@ nidm:NIDM_0000147 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000148 nidm:NIDM_0000148 rdf:type owl:DatatypeProperty ; - + rdfs:label "resel Size In Voxels" ; - + obo:IAO_0000112 "22.325" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/275" ; - + obo:IAO_0000115 "Size of one resel in elements (e.g., pixels, voxels or vertices)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:float ; - + rdfs:subPropertyOf owl:topDataProperty ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1357,19 +1357,19 @@ nidm:NIDM_0000148 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000149 nidm:NIDM_0000149 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume In Resels" ; - + obo:IAO_0000112 "151.3" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/275" ; - + obo:IAO_0000115 "Size of search volume measured in resels." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1382,20 +1382,20 @@ nidm:NIDM_0000149 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000156 nidm:NIDM_0000156 rdf:type owl:DatatypeProperty ; - + rdfs:label "cluster Size In Resels" ; - + obo:IAO_0000117 "Under discussion at: https://github.com/incf-nidash/nidm/issues/127" ; - + obo:IAO_0000112 "13" ; - + obo:IAO_0000115 "Size of cluster measured in resels." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000070 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1408,17 +1408,17 @@ nidm:NIDM_0000156 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000001 spm:SPM_0000001 rdf:type owl:DatatypeProperty ; - + rdfs:label "SPM's Drift Cut-off Period" ; - + obo:IAO_0000115 "Discrete Cosine Transform basis cut-off, specified as period length in seconds and ensures that all basis elements will have period of this duration or longer." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain spm:SPM_0000002 ; - + rdfs:range xsd:float . @@ -1426,23 +1426,23 @@ spm:SPM_0000001 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000007 spm:SPM_0000007 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Units" ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + obo:IAO_0000112 "[8.87, 8.89, 7.83]" ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in world units (e.g. mm^2 or mm^3, in subject or atlas space)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1450,21 +1450,21 @@ spm:SPM_0000007 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000008 spm:SPM_0000008 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Vertices" ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in vertices." ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + obo:IAO_0000112 "[2.95, 2.96, 2.61]" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000054 ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1472,25 +1472,25 @@ spm:SPM_0000008 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000009 spm:SPM_0000009 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Voxels" ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in voxels." ; - + obo:IAO_0000112 "[3.7 3.7 3.1]" ; - + rdfs:seeAlso "Synonyms of or close match with nidm:NoiseFWHM" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1498,25 +1498,25 @@ spm:SPM_0000009 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000010 spm:SPM_0000010 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume Resels Geometry" ; - + obo:IAO_0000112 "[6 68.8 589.1 1475.5]" ; - + rdfs:comment "Range: Vector of 1 positive integer and 3 positive floats." ; - + rdfs:seeAlso "http://www.ncbi.nlm.nih.gov/pubmed/20408186" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000115 "Description of geometry of search volume. As per Worsley et al. [ http://www.ncbi.nlm.nih.gov/pubmed/20408186 ], for space dimension 3 the first element is the Euler Characteristic of the search volume, the second element is twice the average caliper diameter, the third element is half the surface area, and the fourth element is the volume. With the exception of the first element (which is a unitless integer) all quantities are in units of Resels." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1524,19 +1524,19 @@ spm:SPM_0000010 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000011 spm:SPM_0000011 rdf:type owl:DatatypeProperty ; - + rdfs:label "smallest Significant Cluster Size In Vertices FDR 05" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000112 "5" ; - + obo:IAO_0000115 "Smallest cluster size in vertices that is significant at the false discovery rate of 0.05. " ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger . @@ -1544,19 +1544,19 @@ spm:SPM_0000011 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000012 spm:SPM_0000012 rdf:type owl:DatatypeProperty ; - + rdfs:label "smallest Significant Cluster Size In Vertices FWE 05" ; - + obo:IAO_0000115 "Smallest cluster size in vertices that is significant at the family-wise corrected type I error rate (alpha value) value of 0.05." ; - + obo:IAO_0000112 "2" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger . @@ -1564,19 +1564,19 @@ spm:SPM_0000012 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000013 spm:SPM_0000013 rdf:type owl:DatatypeProperty ; - + rdfs:label "smallest Significant Cluster Size In Voxels FDR 05" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000112 "3" ; - + obo:IAO_0000115 "Smallest cluster size in voxels that is significant at the false discovery rate of 0.05. " ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger . @@ -1584,20 +1584,20 @@ spm:SPM_0000013 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000014 spm:SPM_0000014 rdf:type owl:DatatypeProperty ; - + rdfs:label "smallest Significant Cluster Size In Voxels FWE 05" ; - - obo:IAO_0000115 """Smallest cluster size in voxels that is significant at the family-wise error corrected type I error rate (alpha value) of 0.05. + + obo:IAO_0000115 """Smallest cluster size in voxels that is significant at the family-wise error corrected type I error rate (alpha value) of 0.05. """ ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000112 "1" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger . @@ -1605,9 +1605,9 @@ spm:SPM_0000014 rdf:type owl:DatatypeProperty ; ### http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#fileName nfo:fileName rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "con_0001.img" ; - + rdfs:range xsd:string . @@ -1648,9 +1648,9 @@ obo:STATO_0000119 rdfs:subClassOf prov:Activity . ### http://purl.obolibrary.org/obo/STATO_0000323 obo:STATO_0000323 rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/ContrastWeights.txt" . @@ -1664,7 +1664,7 @@ obo:STATO_0000346 rdfs:subClassOf prov:Entity . ### http://purl.org/dc/dcmitype/Image dctype:Image rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity , [ rdf:type owl:Restriction ; owl:onProperty dct:format ; @@ -1690,15 +1690,15 @@ dctype:Image rdf:type owl:Class ; ### http://purl.org/nidash/fsl#FSL_0000002 fsl:FSL_0000002 rdf:type owl:Class ; - + rdfs:label "Gaussian Running Line Drift Model" ; - + rdfs:subClassOf nidm:NIDM_0000087 ; - + obo:IAO_0000115 "A drift model in which the drifts are modeled with a Gaussian-weighted running line smoother, fit to and subtracted from the data and each column of the design matrix." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1706,17 +1706,17 @@ fsl:FSL_0000002 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000001 nidm:NIDM_0000001 rdf:type owl:Class ; - + rdfs:label "Contrast Estimation" ; - + rdfs:subClassOf prov:Activity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/ContrastEstimation.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "The process of performing a [obo:contrast estimation](http://purl.obolibrary.org/obo/STATO_0000383) at each element (e.g., pixel, voxel, vertex, or face) of a map" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/276 and https://github.com/ISA-tools/stato/issues/23" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1724,17 +1724,17 @@ nidm:NIDM_0000001 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000002 nidm:NIDM_0000002 rdf:type owl:Class ; - + rdfs:label "Contrast Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [contrast estimate](http://purl.obolibrary.org/obo/STATO_0000384)."^^xsd:string ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/ContrastMap.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/255" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1742,15 +1742,15 @@ nidm:NIDM_0000002 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000003 nidm:NIDM_0000003 rdf:type owl:Class ; - + rdfs:label "Arbitrarily Correlated Error" ; - + rdfs:subClassOf obo:STATO_0000346 ; - + obo:IAO_0000117 "TN" ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/28" ; - + obo:IAO_0000114 obo:IAO_0000423 . @@ -1758,15 +1758,15 @@ nidm:NIDM_0000003 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000004 nidm:NIDM_0000004 rdf:type owl:Class ; - + rdfs:label "Binary Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000115 "A map in which all values are 0, 1 or NaN. Usually, selected elements (e.g., pixels, voxels, vertices, or faces) have a value of 1 and excluded elements (i.e. the background) have a value of 0 or NaN" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/258" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1774,15 +1774,15 @@ nidm:NIDM_0000004 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000005 nidm:NIDM_0000005 rdf:type owl:Class ; - + rdfs:label "Binomial Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000276"^^xsd:anyURI ; - + obo:IAO_0000115 "The binomial distribution is a discrete probability distribution which describes the probability of k successes in n draws with replacement from a finite population of size N. The binomial distribution is frequently used to model the number of successes in a sample of size n drawn with replacement from a population of size N. The binomial distribution gives the discrete probability distribution of obtaining exactly n successes out of N Bernoulli trials (where the result of each Bernoulli trial is true with probability p and false with probability q=1-p ) notation: B(n,p) The mean is N*p The variance is N*p*q. (Definition from STATO)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1790,15 +1790,15 @@ nidm:NIDM_0000005 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000006 nidm:NIDM_0000006 rdf:type owl:Class ; - + rdfs:label "Cluster" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "A collection of elements related by one or more criteria."^^xsd:string ; - + prov:editorialNote "Discussed in https://github.com/incf-nidash/nidm/issues/71."^^xsd:string ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1806,15 +1806,15 @@ nidm:NIDM_0000006 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000007 nidm:NIDM_0000007 rdf:type owl:Class ; - + rdfs:label "Cluster Definition Criteria" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Set of criterion specified a priori to define the clusters reported after inference (e.g. pixel or voxel connectivity criterion)." ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/ClusterDefinitionCriteria.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1822,17 +1822,17 @@ nidm:NIDM_0000007 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000008 nidm:NIDM_0000008 rdf:type owl:Class ; - + rdfs:label "Cluster Labels Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/ClusterLabelsMap.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) denotes cluster membership within the excursion set. Each cluster is denoted by a different integer and all members of the same cluster have the same value." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/282" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1840,15 +1840,15 @@ nidm:NIDM_0000008 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000011 nidm:NIDM_0000011 rdf:type owl:Class ; - + rdfs:label "Conjunction Inference" ; - + rdfs:subClassOf nidm:NIDM_0000049 ; - + obo:IAO_0000115 "Statistically testing for the joint significance of multiple effects, with emphasis on rejecting all (instead of one or more) of the respective null hypotheses." ; - + obo:IAO_0000116 "Term discussed in https://github.com/incf-nidash/nidm/pull/134" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1856,17 +1856,17 @@ nidm:NIDM_0000011 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000012 nidm:NIDM_0000012 rdf:type owl:Class ; - + rdfs:label "Connectivity Criterion" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000117 "TN, KH, CM" ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "The criterion used to characterize two voxels, pixels or vertices as 'connected'." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1874,17 +1874,17 @@ nidm:NIDM_0000012 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000013 nidm:NIDM_0000013 rdf:type owl:Class ; - + rdfs:label "Contrast Standard Error Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/255."^^xsd:anyURI ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/ContrastStandardErrorMap.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [standard error of a contrast estimate](http://purl.obolibrary.org/obo/STATO_0000385)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1892,17 +1892,17 @@ nidm:NIDM_0000013 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000015 nidm:NIDM_0000015 rdf:type owl:Class ; - + rdfs:label "Coordinate" ; - + rdfs:subClassOf prov:Entity ; - + owl:sameAs "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C44465"^^xsd:anyURI ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/Coordinate.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/pull/144 and https://github.com/incf-nidash/nidm/pull/172" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1910,17 +1910,17 @@ nidm:NIDM_0000015 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000016 nidm:NIDM_0000016 rdf:type owl:Class ; - + rdfs:label "Coordinate Space" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/CoordinateSpace.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "An entity with spatial attributes (e.g., dimensions, units, and voxel-to-world mapping) that provides context to a Map (e.g., a Statistic Map, a Contrast Map...)." ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/issues/290" ; - + obo:IAO_0000114 obo:IAO_0000125 . @@ -1928,15 +1928,15 @@ nidm:NIDM_0000016 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000017 nidm:NIDM_0000017 rdf:type owl:Class ; - + rdfs:label "Custom Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000075 ; - + obo:IAO_0000115 "Custom (unknown) reference space selected by the user" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1944,17 +1944,17 @@ nidm:NIDM_0000017 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000018 nidm:NIDM_0000018 rdf:type owl:Class ; - + rdfs:label "Data Scaling" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/Data.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Scaling applied to the data before parameter estimation, including specification of the target intensity." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/285" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1962,9 +1962,9 @@ nidm:NIDM_0000018 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000019 nidm:NIDM_0000019 rdf:type owl:Class ; - + rdfs:label "Design Matrix" ; - + rdfs:subClassOf prov:Entity , [ rdf:type owl:Restriction ; owl:onProperty dc:description ; @@ -1981,15 +1981,15 @@ nidm:NIDM_0000019 rdf:type owl:Class ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ; owl:onDataRange xsd:string ] ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/DesignMatrix.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/274" ; - + rdfs:seeAlso "stato:design matrix" ; - + obo:IAO_0000115 "A [stato:design matrix](http://purl.obolibrary.org/obo/STATO_0000289), with additional neuroimaging attributes, including HRF and drift for first level fMRI models" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1997,17 +1997,17 @@ nidm:NIDM_0000019 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000020 nidm:NIDM_0000020 rdf:type owl:Class ; - + rdfs:label "Display Mask Map" ; - + rdfs:subClassOf nidm:NIDM_0000004 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/DisplayMaskMap.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/258 and https://github.com/incf-nidash/nidm/pull/157" ; - + obo:IAO_0000115 "A binary map used by an activity that changed the voxels displayed, but did not alter the space in which the activity was performed (e.g. at the level of inference, this mask is called \"contrast masking\" in both FSL & SPM and does not alter voxel-wise corrected p-values)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2015,13 +2015,13 @@ nidm:NIDM_0000020 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000022 nidm:NIDM_0000022 rdf:type owl:Class ; - + rdfs:label "Error Distribution" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Probability distribution used to model the error." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2029,15 +2029,15 @@ nidm:NIDM_0000022 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000023 nidm:NIDM_0000023 rdf:type owl:Class ; - + rdfs:label "Error Model" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/ErrorModel.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Model used to describe the random variation of the error term as part of parameter estimation, including specification of the error probability distribution, its variance and dependence both spatially and across observations." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2045,17 +2045,17 @@ nidm:NIDM_0000023 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000024 nidm:NIDM_0000024 rdf:type owl:Class ; - + rdfs:label "Exchangeable Error" ; - + rdfs:subClassOf obo:STATO_0000346 ; - + rdfs:comment "Under gaussianity assumption this is equivalent to compound symmetry but not in general." ; - + obo:IAO_0000117 "TN" ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/28" ; - + obo:IAO_0000114 obo:IAO_0000423 . @@ -2063,22 +2063,22 @@ nidm:NIDM_0000024 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000025 nidm:NIDM_0000025 rdf:type owl:Class ; - + rdfs:label "Excursion Set Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 , [ rdf:type owl:Restriction ; owl:onProperty dc:description ; owl:onClass dctype:Image ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ] ; - + obo:IAO_0000116 "Discussed in the Neuroimaging terms spreadsheet and in https://github.com/incf-nidash/nidm/issues/256." ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/ExcursionSetMap.txt" ; - + obo:IAO_0000115 "A map in which the set of elements (e.g., pixels, voxels, vertices, or faces) not selected by the inference activity is set to zero or NaN" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2086,17 +2086,17 @@ nidm:NIDM_0000025 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000026 nidm:NIDM_0000026 rdf:type owl:Class ; - + rdfs:label "Extent Threshold" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/ExtentThreshold.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A numerical value that establishes a lower bound on cluster-sizes and can be specified by the user in terms of FWER-corrected p-value, uncorrected p-value or minimum cluster size in voxels" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/273" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2104,15 +2104,15 @@ nidm:NIDM_0000026 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000027 nidm:NIDM_0000027 rdf:type owl:Class ; - + rdfs:label "NIDM-Results" ; - + rdfs:subClassOf nidm:NIDM_0000057 ; - + obo:IAO_0000115 "NIDM Object model representing the results of a mass univariate neuroimaging study and targeting the application of meta-analysis. The specification is available at: http://nidm.nidash.org/specs/nidm-results.html" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/137" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2120,15 +2120,15 @@ nidm:NIDM_0000027 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000028 nidm:NIDM_0000028 rdf:type owl:Class ; - + rdfs:label "Finite Impulse Response Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000115 "Set of Finite impulse response (FIR) filters, with FIR the convolution kernel is represented as a set of discrete fixed-width \"impulses\" (definition adapted from [FSL wiki](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html))" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2136,15 +2136,15 @@ nidm:NIDM_0000028 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000029 nidm:NIDM_0000029 rdf:type owl:Class ; - + rdfs:label "Gamma Difference HRF" ; - + rdfs:subClassOf nidm:NIDM_0000035 ; - + obo:IAO_0000115 "Hemodynamic response function which is a difference of two gamma probability density functions." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2152,15 +2152,15 @@ nidm:NIDM_0000029 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000030 nidm:NIDM_0000030 rdf:type owl:Class ; - + rdfs:label "Gamma Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000115 "Set of gamma probability density functions." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2168,15 +2168,15 @@ nidm:NIDM_0000030 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000031 nidm:NIDM_0000031 rdf:type owl:Class ; - + rdfs:label "Gamma HRF" ; - + rdfs:subClassOf nidm:NIDM_0000035 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "Hemodynamic response function which is a gamma probability density function." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2184,15 +2184,15 @@ nidm:NIDM_0000031 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000032 nidm:NIDM_0000032 rdf:type owl:Class ; - + rdfs:label "Gaussian Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000227"^^xsd:anyURI ; - + obo:IAO_0000115 "A normal distribution is a continuous probability distribution described by a probability distribution function described here: http://mathworld.wolfram.com/NormalDistribution.html (Definition from STATO)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2200,17 +2200,17 @@ nidm:NIDM_0000032 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000033 nidm:NIDM_0000033 rdf:type owl:Class ; - + rdfs:label "Grand Mean Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/GrandMeanMap.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/288" ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is the mean over all observations of that element in the input maps (after any scaling of those input maps)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2218,17 +2218,17 @@ nidm:NIDM_0000033 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000034 nidm:NIDM_0000034 rdf:type owl:Class ; - + rdfs:label "Height Threshold" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/HeightThreshold_P.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A numerical value that establishes a lower bound on statistic values and can be specified by the user in terms of FWER-corrected p-value, uncorrected p-value or minimum statistic value." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/280" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2236,15 +2236,15 @@ nidm:NIDM_0000034 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000035 nidm:NIDM_0000035 rdf:type owl:Class ; - + rdfs:label "Hemodynamic Response Function" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "Hemodynamic response function basis that can on its own be used to represent the idealised hemodynamic response function." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2252,15 +2252,15 @@ nidm:NIDM_0000035 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000036 nidm:NIDM_0000036 rdf:type owl:Class ; - + rdfs:label "Convolution Basis Set" ; - + rdfs:subClassOf prov:Entity ; - + rdfs:isDefinedBy "A set of functions that, when convolved with the anticipated neural responses, yield a set of regressors to model the anticipated hemodynamic responses."^^xsd:string ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000124 . @@ -2268,15 +2268,15 @@ nidm:NIDM_0000036 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000037 nidm:NIDM_0000037 rdf:type owl:Class ; - + rdfs:label "Hemodynamic Response Function Derivative" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000115 "Hemodynamic response function basis which is the derivative of an hemodynamic response function." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2284,15 +2284,15 @@ nidm:NIDM_0000037 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000048 nidm:NIDM_0000048 rdf:type owl:Class ; - + rdfs:label "Independent Error" ; - + rdfs:subClassOf obo:STATO_0000346 ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/28" ; - + obo:IAO_0000117 "TN" ; - + obo:IAO_0000114 obo:IAO_0000423 . @@ -2300,17 +2300,17 @@ nidm:NIDM_0000048 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000049 nidm:NIDM_0000049 rdf:type owl:Class ; - + rdfs:label "Inference" ; - + rdfs:subClassOf prov:Activity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/Inference.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Statistical inference is a process of drawing conclusions following data analysis using statistical methods (statistical tests) and evaluating whether to reject or accept null hypothesis. (definition from STATO)." ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000299" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2318,17 +2318,17 @@ nidm:NIDM_0000049 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000051 nidm:NIDM_0000051 rdf:type owl:Class ; - + rdfs:label "MNI Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000075 ; - + rdfs:seeAlso "birnlex_2125" ; - + obo:IAO_0000115 "MNI 305 coordinate system or any coordinate system derived from MNI 305." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2336,9 +2336,9 @@ nidm:NIDM_0000051 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000052 nidm:NIDM_0000052 rdf:type owl:Class ; - + rdfs:label "Map" ; - + rdfs:subClassOf prov:Entity , [ rdf:type owl:Restriction ; owl:onProperty nfo:fileName ; @@ -2355,11 +2355,11 @@ nidm:NIDM_0000052 rdf:type owl:Class ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ; owl:onDataRange xsd:string ] ; - + obo:IAO_0000115 "Ordered set of values corresponding to the discrete sampling of some process (e.g. brain MRI data measured on a regular 3D lattice; or brain cortical surface data measured irregularly over the cortex)." ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/pull/149" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2367,9 +2367,9 @@ nidm:NIDM_0000052 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000053 nidm:NIDM_0000053 rdf:type owl:Class ; - + rdfs:label "Map Header" ; - + rdfs:subClassOf prov:Entity , [ rdf:type owl:Restriction ; owl:onProperty nfo:fileName ; @@ -2386,11 +2386,11 @@ nidm:NIDM_0000053 rdf:type owl:Class ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ; owl:onDataRange xsd:string ] ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/289" ; - + obo:IAO_0000115 "A file associated with a Map to provide header information (e.g. NIfTI header file)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2398,17 +2398,17 @@ nidm:NIDM_0000053 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000054 nidm:NIDM_0000054 rdf:type owl:Class ; - + rdfs:label "Mask Map" ; - + rdfs:subClassOf nidm:NIDM_0000004 ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/258 and https://github.com/incf-nidash/nidm/issues/155" ; - + obo:IAO_0000115 "A binary map representing the exact set of elements (e.g., pixels, voxels, vertices, and faces) in which an activity was performed (e.g. the mask map generated by the model parameter estimation activity represents the exact set of voxels in which the mass univariate model was estimated) and/or restraining the space in which an activity was performed (e.g. the mask map used by inference)" ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/MaskMap.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2416,17 +2416,17 @@ nidm:NIDM_0000054 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000056 nidm:NIDM_0000056 rdf:type owl:Class ; - + rdfs:label "Model Parameters Estimation" ; - + rdfs:subClassOf prov:Activity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/ModelParametersEstimation.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "the process of performing a [obo:model parameter estimation](http://purl.obolibrary.org/obo/STATO_0000119) at each element (e.g., pixel, voxel, vertex, or face) of a map" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/issues/141" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2434,15 +2434,15 @@ nidm:NIDM_0000056 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000057 nidm:NIDM_0000057 rdf:type owl:Class ; - + rdfs:label "NIDM Object Model" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Abstraction on the data model, developed for a specific application/use-case/task at hand, that specifies the components and relations necessary for use by these applications. The same object model can be reused by multiple applications (e.g., meta-analysis, Neurovault)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/137" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2450,13 +2450,13 @@ nidm:NIDM_0000057 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000058 nidm:NIDM_0000058 rdf:type owl:Class ; - + rdfs:label "Non Parametric Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + obo:IAO_0000115 "Probability distribution estimated empirically on the data without assumptions on the shape of the probability distribution." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2464,13 +2464,13 @@ nidm:NIDM_0000058 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000059 nidm:NIDM_0000059 rdf:type owl:Class ; - + rdfs:label "Non Parametric Symmetric Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + obo:IAO_0000115 "Probability distribution estimated empirically on the data assuming only symmetry of the probability distribution." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2478,15 +2478,15 @@ nidm:NIDM_0000059 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000060 nidm:NIDM_0000060 rdf:type owl:Class ; - + rdfs:label "One Tailed Test" ; - + rdfs:subClassOf prov:Entity ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000286"^^xsd:anyURI ; - + obo:IAO_0000116 "Re-use \"one tailed test\" from STATO." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2494,17 +2494,17 @@ nidm:NIDM_0000060 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000061 nidm:NIDM_0000061 rdf:type owl:Class ; - + rdfs:label "Parameter Estimate Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/ParameterEstimateMap.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/255 and https://github.com/incf-nidash/nidm/issues/141 (see also https://github.com/ISA-tools/stato/issues/18)" ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [model parameter estimate](http://purl.obolibrary.org/obo/STATO_0000144)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2512,17 +2512,17 @@ nidm:NIDM_0000061 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000062 nidm:NIDM_0000062 rdf:type owl:Class ; - + rdfs:label "Peak" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "A map element (e.g., pixel, voxel, vertex, or face) which is a local maximum in the significant cluster and complies with the peak definition criteria." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/283" ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/Peak_ValueP.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2530,17 +2530,17 @@ nidm:NIDM_0000062 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000063 nidm:NIDM_0000063 rdf:type owl:Class ; - + rdfs:label "Peak Definition Criteria" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/PeakDefinitionCriteria_MaxPeaks.txt"^^xsd:anyURI ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/200" ; - + obo:IAO_0000115 "Set of criterion specified a priori to define the peaks reported after inference (e.g. maximum number of peaks within a cluster, minimum distance between peaks)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2548,15 +2548,15 @@ nidm:NIDM_0000063 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000064 nidm:NIDM_0000064 rdf:type owl:Class ; - + rdfs:label "Pixel Connectivity Criterion" ; - + rdfs:subClassOf nidm:NIDM_0000012 ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "The criterion used to characterize two pixels as 'connected'. In two dimensions voxels that are connected can share an edge (4-connected) or, edge or corner (8-connected)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2564,15 +2564,15 @@ nidm:NIDM_0000064 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000065 nidm:NIDM_0000065 rdf:type owl:Class ; - + rdfs:label "Poisson Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000051"^^xsd:anyURI ; - + obo:IAO_0000115 "Poisson distribution is a probability distribution used to model the number of events occurring within a given time interval. It is defined by a real number (λ) and an integer k representing the number of events and a function. The expected value of a Poisson-distributed random variable is equal to λ and so is its variance. (Definition from STATO)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2580,17 +2580,17 @@ nidm:NIDM_0000065 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000066 nidm:NIDM_0000066 rdf:type owl:Class ; - + rdfs:label "Residual Mean Squares Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/255." ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [residual mean square](http://purl.obolibrary.org/obo/STATO_0000375)." ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/ResidualMeanSquaresMap.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2598,15 +2598,15 @@ nidm:NIDM_0000066 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000067 nidm:NIDM_0000067 rdf:type owl:Class ; - + rdfs:label "Custom Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "Customised set of basis functions." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2614,17 +2614,17 @@ nidm:NIDM_0000067 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000068 nidm:NIDM_0000068 rdf:type owl:Class ; - + rdfs:label "Search Space Mask Map" ; - + rdfs:subClassOf nidm:NIDM_0000054 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/SearchSpaceMaskMap.txt" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/258" ; - + obo:IAO_0000115 "A mask map representing the set of elements (e.g., pixels, voxels, vertices, or faces) in which the inference was performed" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2632,15 +2632,15 @@ nidm:NIDM_0000068 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000069 nidm:NIDM_0000069 rdf:type owl:Class ; - + rdfs:label "Fourier Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000115 "Set of Fourier basis." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2648,17 +2648,17 @@ nidm:NIDM_0000069 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000070 nidm:NIDM_0000070 rdf:type owl:Class ; - + rdfs:label "Significant Cluster" ; - + rdfs:subClassOf nidm:NIDM_0000006 ; - + obo:IAO_0000115 "A cluster of map elements (e.g., pixels, voxels, vertices, and faces) that were selected by the inference activity and are contiguous according to the cluster connectivity criteria."^^xsd:string ; - + prov:editorialNote "Discussed in https://github.com/incf-nidash/nidm/issues/71."^^xsd:string ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/SignificantCluster.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2666,15 +2666,15 @@ nidm:NIDM_0000070 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000071 nidm:NIDM_0000071 rdf:type owl:Class ; - + rdfs:label "Error Parameter Map-Wise Dependence" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Map-wise dependence structure of a parameter in the error model (i.e. variance or dependence parameter). For example, whether a temporal autocorrelation parameter is estimated at each element separately, estimated using data in a local neighbourhood, or estimated using all elements in the map." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2682,15 +2682,15 @@ nidm:NIDM_0000071 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000072 nidm:NIDM_0000072 rdf:type owl:Class ; - + rdfs:label "Constant Parameter" ; - + rdfs:subClassOf nidm:NIDM_0000071 ; - + obo:IAO_0000115 "Parameter estimated as constant over a entire set of elements considered (e.g. those in the analysis mask)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2698,15 +2698,15 @@ nidm:NIDM_0000072 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000073 nidm:NIDM_0000073 rdf:type owl:Class ; - + rdfs:label "Independent Parameter" ; - + rdfs:subClassOf nidm:NIDM_0000071 ; - + obo:IAO_0000115 "Parameter whose estimation at a given element does not depend on any other element." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2714,15 +2714,15 @@ nidm:NIDM_0000073 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000074 nidm:NIDM_0000074 rdf:type owl:Class ; - + rdfs:label "Regularized Parameter" ; - + rdfs:subClassOf nidm:NIDM_0000071 ; - + obo:IAO_0000115 "Parameter whose estimation at a given element depends on a local neighborhood of elements" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2730,17 +2730,17 @@ nidm:NIDM_0000074 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000075 nidm:NIDM_0000075 rdf:type owl:Class ; - + rdfs:label "Standardized Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000081 ; - + rdfs:comment "This is meant to be used for retrospective export when exact template is unknown." ; - + obo:IAO_0000115 "Parent of all reference spaces except \"Subject\"." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -2748,17 +2748,17 @@ nidm:NIDM_0000075 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000076 nidm:NIDM_0000076 rdf:type owl:Class ; - + rdfs:label "Statistic Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/StatisticMap_T.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/255" ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [statistic](http://purl.obolibrary.org/obo/STATO_0000039)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2766,17 +2766,17 @@ nidm:NIDM_0000076 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000077 nidm:NIDM_0000077 rdf:type owl:Class ; - + rdfs:label "Subject Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000081 ; - + obo:IAO_0000115 "Reference space corresponding to the subject brain (no spatial normalization applied)." ; - + rdfs:comment "Used in FSL and SPM un-registered data." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -2784,17 +2784,17 @@ nidm:NIDM_0000077 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000078 nidm:NIDM_0000078 rdf:type owl:Class ; - + rdfs:label "Talairach Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000075 ; - + obo:IAO_0000115 "Reference space defined by the dissected brain used for the Talairach and Tournoux atlas (cf. http://www.talairach.org/about.html)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + rdfs:seeAlso "http://www.talairach.org/" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2802,15 +2802,15 @@ nidm:NIDM_0000078 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000079 nidm:NIDM_0000079 rdf:type owl:Class ; - + rdfs:label "Two Tailed Test" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Re-use \"two tailed test\" from STATO"^^xsd:anyURI ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000287"^^xsd:anyURI ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2818,15 +2818,15 @@ nidm:NIDM_0000079 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000080 nidm:NIDM_0000080 rdf:type owl:Class ; - + rdfs:label "Voxel Connectivity Criterion" ; - + rdfs:subClassOf nidm:NIDM_0000012 ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "The criterion used to characterize two voxels as 'connected'. In three dimensions voxels that are connected can share a voxel face (6-connected), face or edge (18-connectec), or face, edge, or corner (26-connected)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2834,16 +2834,16 @@ nidm:NIDM_0000080 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000081 nidm:NIDM_0000081 rdf:type owl:Class ; - + rdfs:label "World Coordinate System" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 """Reference space on which real-world positions are expressed (cf. [Nifti-1 FAQ question 14](http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q14) and [Understanding affines on nipy](http://nipy.org/nipy/stable/devel/code_discussions/understanding_affines.html) ). A world coordinate system can be represented by an image obtained by registering an initial set of images, using a given normalization algorithm to match a target template.""" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2851,18 +2851,18 @@ nidm:NIDM_0000081 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000087 nidm:NIDM_0000087 rdf:type owl:Class ; - + rdfs:label "Drift Model" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/FSL_DriftModel.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/SPM_DriftModel.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000115 "A model used to compensate for low frequency baseline drifts when analyzing functional MRI data at the subject level." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2870,15 +2870,15 @@ nidm:NIDM_0000087 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000110 nidm:NIDM_0000110 rdf:type owl:Class ; - + rdfs:label "Gaussian HRF" ; - + rdfs:subClassOf nidm:NIDM_0000035 ; - + obo:IAO_0000115 "Hemodynamic response function which is a gaussian kernel." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2886,15 +2886,15 @@ nidm:NIDM_0000110 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000135 nidm:NIDM_0000135 rdf:type owl:Class ; - + rdfs:label "Contrast Variance Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a contrast variance (i.e. the square of a [standard error of a contrast estimate](http://purl.obolibrary.org/obo/STATO_0000385))" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/287" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2902,19 +2902,19 @@ nidm:NIDM_0000135 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000140 nidm:NIDM_0000140 rdf:type owl:Class ; - + rdfs:label "Cluster Center Of Gravity" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/257" ; - + obo:IAO_0000115 "A centre of gravity of the cluster, equivalent to the concept of Centre Of Gravity for a object with distributed mass, where intensity substitutes for mass in this case. The coordinate of the centre of gravity is the weighted average of the cluster element (e.g., pixels, voxels, vertices, or faces) coordinates, where the weighting factors are the cluster element intensities. (definition adapted from http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster)" ; - + rdfs:seeAlso "http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster" ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/FSL_ClusterCenterOfGravity.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2922,15 +2922,15 @@ nidm:NIDM_0000140 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000144 nidm:NIDM_0000144 rdf:type owl:Class ; - + rdfs:label "Resels Per Voxel Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.0.0/nidm/nidm-results/terms/examples/SPM_ReselsPerVoxelMap.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) location is the number of resels per voxel." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2938,15 +2938,15 @@ nidm:NIDM_0000144 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000150 nidm:NIDM_0000150 rdf:type owl:Class ; - + rdfs:label "Linear Spline Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "A Linear (order 1) spline, providing an estimate that is continuous over time (in contrast to a FIR basis, which is discontinuous between each time bin). This is called TENT in AFNI's 3dDeconvolve program." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2954,15 +2954,15 @@ nidm:NIDM_0000150 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000151 nidm:NIDM_0000151 rdf:type owl:Class ; - + rdfs:label "Sine Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "A set of Sine waves of differing frequencies (definition adapted from [FSL wiki](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html))." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2970,15 +2970,15 @@ nidm:NIDM_0000151 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000155 nidm:NIDM_0000155 rdf:type owl:Class ; - + rdfs:label "fMRI Design Type" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/299" ; - + obo:IAO_0000115 "The type of stimulus presentation used in the data acquisition, one of block-based design event-related design or mixed design." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2986,15 +2986,15 @@ nidm:NIDM_0000155 rdf:type owl:Class ; ### http://purl.org/nidash/spm#SPM_0000002 spm:SPM_0000002 rdf:type owl:Class ; - + rdfs:label "DCT Drift Model" ; - + rdfs:subClassOf nidm:NIDM_0000087 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000115 "A drift model in which the drifts are modeled by a Discrete Cosine Transform basis added to regression model" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3002,15 +3002,15 @@ spm:SPM_0000002 rdf:type owl:Class ; ### http://purl.org/nidash/spm#SPM_0000005 spm:SPM_0000005 rdf:type owl:Class ; - + rdfs:label "Partial Conjunction Inference" ; - + rdfs:subClassOf nidm:NIDM_0000049 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/294" ; - + obo:IAO_0000115 "The process of testing the joint significance of multiple effects to infer that some (not necessarily all) of the respective effects are real (i.e. their null hypotheses are false). If there are K effects considered, the partial conjunction degree u is the number non-null effects allowed as part of partial conjunction null hypothesis; if the partial conjunction null is rejected, it may be inferred that u+1 or more effects are real. The case of u=K-1 corresponds to proper \"conjunction inference\", while the case of u=0 corresponds to \"global null\" conjunction test. See [Friston et al. (2005). Conjunction revisited. NeuroImage, 25(3), 661-7.](http://dx.doi.org/10.1016/j.neuroimage.2005.01.013)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3032,13 +3032,13 @@ spm:SPM_0000005 rdf:type owl:Class ; fsl:FSL_0000001 rdf:type nidm:NIDM_0000029 , owl:NamedIndividual ; - + rdfs:label "FSL's Gamma Difference HRF" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "Hemodynamic response function which is a fixed difference of two gamma probability density functions - a standard positive function at normal lag, and a small, delayed, negated gamma probability density function, which attempts to model the late undershoot (definition adapted [FSL wiki](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html)). This is the default in FSL." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3047,13 +3047,13 @@ fsl:FSL_0000001 rdf:type nidm:NIDM_0000029 , fsl:FSL_0000003 rdf:type nidm:NIDM_0000037 , owl:NamedIndividual ; - + rdfs:label "FSL's Temporal Derivative" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "Hemodynamic response function basis that is the derivative with respect to time of the FSL's Gamma Difference heamodynamic response function." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3062,17 +3062,17 @@ fsl:FSL_0000003 rdf:type nidm:NIDM_0000037 , nidm:NIDM_0000009 rdf:type nidm:NIDM_0000075 , owl:NamedIndividual ; - + rdfs:label "Colin27 Coordinate System" ; - + obo:IAO_0000115 "Reference space defined as the stereotaxic average of 27 T1-weighted MRI scans of the same individual transformed into the Talairach stereotaxic space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres and http://neuro.debian.net/pkgs/mni-colin27-nifti.html). This is the default in SPM96 (cf. [MRC CBSU Wiki](http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach))." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + rdfs:comment "used in SPM96 (cf. http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3081,15 +3081,15 @@ nidm:NIDM_0000009 rdf:type nidm:NIDM_0000075 , nidm:NIDM_0000038 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm452 Air Coordinate System" ; - + obo:IAO_0000115 "Reference space defined as the average of 452 T1-weighted MRIs of normal young adult brains after 12 parameter AIR linear transform to the MNI 305 space (cf. http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml and http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)" ; - + rdfs:seeAlso "http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3098,15 +3098,15 @@ nidm:NIDM_0000038 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000039 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm452 Warp5 Coordinate System" ; - + rdfs:seeAlso "http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml" ; - + obo:IAO_0000115 "Reference space defined as the average of 452 T1-weighted MRIs of normal young adult brains after affine and 5 order polynomial non-linear warping to the MNI 305 space (cf. http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml and http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3115,17 +3115,17 @@ nidm:NIDM_0000039 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000040 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Linear Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin" ; - + rdfs:comment "used in SPM99 to SPM8 (cf. http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach and spm8/spm_templates.man)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Reference space which is the average of 152 T1-weighted MRI scans, linearly transformed onto the MNI 305 reference space (definition adapted from: http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin). This is the default in SPM99 to SPM8 (cf. [MRC CBSU Wiki](http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach) and spm8/spm_templates.man." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3134,15 +3134,15 @@ nidm:NIDM_0000040 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000041 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009a Asymmetric Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3151,15 +3151,15 @@ nidm:NIDM_0000041 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000042 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009a Symmetric Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to to form a symmetric model in MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3168,15 +3168,15 @@ nidm:NIDM_0000042 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000043 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009b Asymmetric Coordinate System" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans in high-resolution, non-linearly transformed to MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3185,15 +3185,15 @@ nidm:NIDM_0000043 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000044 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009b Symmetric Coordinate System" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans in high-resolution, non-linearly transformed to form a symmetric model in MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3202,17 +3202,17 @@ nidm:NIDM_0000044 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000045 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009c Asymmetric Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space using the N3 algorithm (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + rdfs:comment "Used in DARTEL toolbox in SPM12b (cf. spm12b/spm_templates.man)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3221,15 +3221,15 @@ nidm:NIDM_0000045 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000046 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009c Symmetric Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to form a symmetric model in MNI152 linear space using the N3 algorithm (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details). This is the default for DARTEL toolbox in SPM12b (cf. spm12/spm_templates.man)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3238,17 +3238,17 @@ nidm:NIDM_0000046 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000047 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear6th Generation Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6"^^xsd:anyURI ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, linearly and non-linearly (6 iterations) transformed to form a symmetric model in Talairach space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6)" ; - + rdfs:comment "Used in FSL (cf. http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3257,17 +3257,17 @@ nidm:NIDM_0000047 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000050 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Ixi549 Coordinate System" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Reference space defined by the average of the 549 subjects from the IXI dataset linearly transformed to the ICBM MNI 452 (cf. spm12/spm\\_templates.man and http://biomedic.doc.ic.ac.uk/brain-development/index.php?n=Main.Datasets). This is the default in SPM12 (cf. spm12/spm_templates.man)." ; - + rdfs:seeAlso "http://biomedic.doc.ic.ac.uk/brain-development/index.php?n=Main.Datasets" ; - + rdfs:comment "Used in SPM12b (cf. spm12b/spm_templates.man)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3276,15 +3276,15 @@ nidm:NIDM_0000050 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000055 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Mni305 Coordinate System" ; - + obo:IAO_0000115 "Reference space defined as the average of 305 T1-weighted MRI scans, linearly transformed to Talairach space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/MNI305 for more details)" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/MNI305" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3293,13 +3293,13 @@ nidm:NIDM_0000055 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000117 rdf:type nidm:NIDM_0000064 , owl:NamedIndividual ; - + rdfs:label "pixel4connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of pixels are 4-Connected if they share an edge." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3308,13 +3308,13 @@ nidm:NIDM_0000117 rdf:type nidm:NIDM_0000064 , nidm:NIDM_0000118 rdf:type nidm:NIDM_0000064 , owl:NamedIndividual ; - + rdfs:label "pixel8connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of pixels are 8-Connected if they share an edge or corner." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3323,13 +3323,13 @@ nidm:NIDM_0000118 rdf:type nidm:NIDM_0000064 , nidm:NIDM_0000128 rdf:type nidm:NIDM_0000080 , owl:NamedIndividual ; - + rdfs:label "voxel18connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of voxels are 18-Connected if they share a face or edge." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3338,13 +3338,13 @@ nidm:NIDM_0000128 rdf:type nidm:NIDM_0000080 , nidm:NIDM_0000129 rdf:type nidm:NIDM_0000080 , owl:NamedIndividual ; - + rdfs:label "voxel26connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of voxels are 26-Connected if they share a face, edge or corner." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3353,13 +3353,13 @@ nidm:NIDM_0000129 rdf:type nidm:NIDM_0000080 , nidm:NIDM_0000130 rdf:type nidm:NIDM_0000080 , owl:NamedIndividual ; - + rdfs:label "voxel6connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of voxels are 6-Connected if they share a face." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3368,13 +3368,13 @@ nidm:NIDM_0000130 rdf:type nidm:NIDM_0000080 , nidm:NIDM_0000152 rdf:type nidm:NIDM_0000155 , owl:NamedIndividual ; - + rdfs:label "Block-Based Design" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/299" ; - + obo:IAO_0000115 "An fMRI design comprised of epochs of stimulus and/or behavior." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3383,13 +3383,13 @@ nidm:NIDM_0000152 rdf:type nidm:NIDM_0000155 , nidm:NIDM_0000153 rdf:type nidm:NIDM_0000155 , owl:NamedIndividual ; - + rdfs:label "Event-Related Design" ; - + obo:IAO_0000115 "An fMRI design comprised of discrete events of stimulus and/or behavior." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/299" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3398,13 +3398,13 @@ nidm:NIDM_0000153 rdf:type nidm:NIDM_0000155 , nidm:NIDM_0000154 rdf:type nidm:NIDM_0000155 , owl:NamedIndividual ; - + rdfs:label "Mixed Design" ; - + obo:IAO_0000115 "An fMRI design comprised of both epochs & discrete events of stimulus and/or behavior." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/299" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3413,13 +3413,13 @@ nidm:NIDM_0000154 rdf:type nidm:NIDM_0000155 , spm:SPM_0000003 rdf:type nidm:NIDM_0000037 , owl:NamedIndividual ; - + rdfs:label "SPM's Dispersion Derivative" ; - + obo:IAO_0000115 "Hemodynamic response function basis that is the derivative with respect to spatial dispersion of the SPM's Canonical heamodynamic response function." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3428,13 +3428,13 @@ spm:SPM_0000003 rdf:type nidm:NIDM_0000037 , spm:SPM_0000004 rdf:type nidm:NIDM_0000029 , owl:NamedIndividual ; - + rdfs:label "SPM's Canonical HRF" ; - + obo:IAO_0000115 "Hemodynamic response function which is a fixed difference of two gamma probability density functions and is denoted by \"canonical HRF\" in SPM. This is the default in SPM" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3443,13 +3443,13 @@ spm:SPM_0000004 rdf:type nidm:NIDM_0000029 , spm:SPM_0000006 rdf:type nidm:NIDM_0000037 , owl:NamedIndividual ; - + rdfs:label "SPM's Temporal Derivative" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "Hemodynamic response function basis that is the derivative with respect to time of the SPM's Canonical heamodynamic response function." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3473,9 +3473,9 @@ spm:SPM_0000006 rdf:type nidm:NIDM_0000037 , ### http://purl.org/dc/terms/format crypto:sha512 rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Secure Hash Algorithm 512." ; - + rdfs:comment "SHA stands for Secure Hash Algorithm. Hash algorithms compute a fixed-length digital representation (known as a message digest) of an input data sequence (the message) of any length." . ##### Imports from dc ##### . @@ -3493,9 +3493,9 @@ crypto:sha512 rdf:type owl:DatatypeProperty ; ### http://purl.org/dc/elements/1.1/description dc:description rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "An account of the resource." ; - + rdfs:comment "Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource." . @@ -3512,9 +3512,9 @@ dc:description rdf:type owl:ObjectProperty ; ### http://purl.org/dc/terms/format dct:format rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "The file format, physical medium, or dimensions of the resource." ; - + rdfs:comment "Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME]." . @@ -3531,9 +3531,9 @@ dct:format rdf:type owl:DatatypeProperty ; ### http://purl.org/dc/dcmitype/Image dctype:Image rdf:type owl:Class ; - + obo:IAO_0000115 "A visual representation other than text." ; - + rdfs:comment "Examples include images and photographs of physical objects, paintings, prints, drawings, other images and graphics, animations and moving pictures, film, diagrams, maps, musical notation. Note that Image may include both electronic and physical representations." . @@ -3546,18 +3546,18 @@ dctype:Image rdf:type owl:Class ; ##### Imports from iao ##### . rdf:type owl:Ontology ; - + dc:date "2009-07-31"^^xsd:date ; - + owl:versionInfo "2015-02-23"^^xsd:string ; - + rdfs:comment "An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/"^^xsd:string , "IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999"^^xsd:string , "IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999"^^xsd:string , "This file is based on checkout of our SVN repository revision $Revision: 717 $ "^^xsd:string ; - + protege:defaultLanguage "en"^^xsd:string ; - + dc:contributor "Adam Goldstein"@en , "Alan Ruttenberg"@en , "Albert Goldfain"@en , @@ -3593,11 +3593,11 @@ dctype:Image rdf:type owl:Class ; "William Duncan"@en , "William Hogan"@en , "Yongqun (Oliver) He"@en ; - + foaf:homepage ; - + dc:license ; - + owl:versionIRI iao:iao.owl . @@ -3617,13 +3617,13 @@ protege:defaultLanguage rdf:type owl:AnnotationProperty . ### http://purl.obolibrary.org/obo/BFO_0000179 obo:BFO_0000179 rdf:type owl:AnnotationProperty ; - + rdfs:label "BFO OWL specification label"@en ; - + obo:IAO_0000232 "Really of interest to developers only"@en ; - + obo:IAO_0000115 "Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification."@en ; - + rdfs:subPropertyOf rdfs:label . @@ -3631,15 +3631,15 @@ obo:BFO_0000179 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/BFO_0000180 obo:BFO_0000180 rdf:type owl:AnnotationProperty ; - + rdfs:label "BFO CLIF specification label"@en ; - + obo:IAO_0000119 "Person:Alan Ruttenberg" ; - + obo:IAO_0000232 "Really of interest to developers only"@en ; - + obo:IAO_0000115 "Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2"@en ; - + rdfs:subPropertyOf rdfs:label . @@ -3647,24 +3647,24 @@ obo:BFO_0000180 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000111 obo:IAO_0000111 rdf:type owl:AnnotationProperty ; - + rdfs:label "editor preferred term" , "editor preferred label"@en , "editor preferred term"@en ; - + obo:IAO_0000111 "editor preferred term" ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000115 "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)"@en ; - + obo:IAO_0000111 "editor preferred label"@en , "editor preferred term"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3672,20 +3672,20 @@ obo:IAO_0000111 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000112 obo:IAO_0000112 rdf:type owl:AnnotationProperty ; - + rdfs:label "example of usage"@en ; - + obo:IAO_0000115 "A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not"@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "example"@en , "example of usage"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3693,15 +3693,15 @@ obo:IAO_0000112 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000114 obo:IAO_0000114 rdf:type owl:AnnotationProperty ; - + rdfs:label "has curation status"@en ; - + obo:IAO_0000119 "OBI_0000281"@en ; - + obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en , "PERSON:Bill Bug"@en , "PERSON:Melanie Courtot"@en ; - + obo:IAO_0000111 "has curation status"@en . @@ -3709,27 +3709,27 @@ obo:IAO_0000114 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000115 obo:IAO_0000115 rdf:type owl:AnnotationProperty ; - + rdfs:label "definition"^^xsd:string , "textual definition"^^xsd:string , "definition" , "definition"@en ; - + obo:IAO_0000111 "definition"^^xsd:string , "textual definition"^^xsd:string , "definition" ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000115 "The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en , "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en ; - + obo:IAO_0000111 "definition"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3737,19 +3737,19 @@ obo:IAO_0000115 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000116 obo:IAO_0000116 rdf:type owl:AnnotationProperty ; - + rdfs:label "editor note"@en ; - + obo:IAO_0000115 "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "editor note"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3757,21 +3757,21 @@ obo:IAO_0000116 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000117 obo:IAO_0000117 rdf:type owl:AnnotationProperty ; - + rdfs:label "term editor"@en ; - + obo:IAO_0000116 "20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115."@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000115 "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "term editor"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3779,19 +3779,19 @@ obo:IAO_0000117 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000118 obo:IAO_0000118 rdf:type owl:AnnotationProperty ; - + rdfs:label "alternative term"@en ; - + obo:IAO_0000115 "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)"@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "alternative term"@en ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:isDefinedBy . @@ -3799,20 +3799,20 @@ obo:IAO_0000118 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000119 obo:IAO_0000119 rdf:type owl:AnnotationProperty ; - + rdfs:label "definition source"@en ; - + obo:IAO_0000119 "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"^^xsd:string , "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "definition source"@en ; - + obo:IAO_0000115 "formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3820,17 +3820,17 @@ obo:IAO_0000119 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000232 obo:IAO_0000232 rdf:type owl:AnnotationProperty ; - + rdfs:label "curator note"@en ; - + obo:IAO_0000115 "An administrative note of use for a curator but of no use for a user"@en ; - + obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en ; - + obo:IAO_0000111 "curator note"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3838,20 +3838,20 @@ obo:IAO_0000232 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000412 obo:IAO_0000412 rdf:type owl:AnnotationProperty ; - + rdfs:label "imported from"@en ; - + obo:IAO_0000115 "For external terms/classes, the ontology from which the term was imported"@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en , "PERSON:Melanie Courtot"@en ; - + obo:IAO_0000111 "imported from"@en ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:isDefinedBy . @@ -3859,17 +3859,17 @@ obo:IAO_0000412 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000600 obo:IAO_0000600 rdf:type owl:AnnotationProperty ; - + rdfs:label "elucidation"@en ; - + obo:IAO_0000119 "Person:Barry Smith"@en ; - + obo:IAO_0000600 "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms"@en ; - + obo:IAO_0000111 "elucidation"@en ; - + obo:IAO_0000117 "person:Alan Ruttenberg"@en ; - + rdfs:isDefinedBy . @@ -3877,9 +3877,9 @@ obo:IAO_0000600 rdf:type owl:AnnotationProperty ; ### http://purl.org/dc/elements/1.1/contributor dc:contributor rdf:type owl:AnnotationProperty ; - + rdfs:label "Contributor"@en-us ; - + rdfs:isDefinedBy dc: . @@ -3887,9 +3887,9 @@ dc:contributor rdf:type owl:AnnotationProperty ; ### http://purl.org/dc/elements/1.1/date dc:date rdf:type owl:AnnotationProperty ; - + rdfs:label "Date"@en-us ; - + rdfs:isDefinedBy dc: . @@ -3930,19 +3930,19 @@ foaf:homepage rdf:type owl:AnnotationProperty . ### http://purl.obolibrary.org/obo/IAO_0000136 obo:IAO_0000136 rdf:type owl:ObjectProperty ; - + rdfs:label "is about"@en ; - + obo:IAO_0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en ; - + obo:IAO_0000112 "This document is about information artifacts and their representations"@en ; - + obo:IAO_0000115 "is_about is a (currently) primitive relation that relates an information artifact to an entity."@en ; - + obo:IAO_0000117 "person:Alan Ruttenberg"@en ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + obo:IAO_0000412 . @@ -3959,9 +3959,9 @@ obo:IAO_0000136 rdf:type owl:ObjectProperty ; ### http://usefulinc.com/ns/doap#revision doap:revision rdf:type owl:DatatypeProperty ; - + obo:IAO_0000412 ; - + rdfs:isDefinedBy ns:doap . @@ -3984,7 +3984,7 @@ doap:revision rdf:type owl:DatatypeProperty ; ### http://purl.obolibrary.org/obo/IAO_0000002 obo:IAO_0000002 rdf:type owl:NamedIndividual ; - + rdfs:label "example to be eventually removed"@en . @@ -3992,9 +3992,9 @@ obo:IAO_0000002 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000120 obo:IAO_0000120 rdf:type owl:NamedIndividual ; - + rdfs:label "metadata complete"@en ; - + obo:IAO_0000115 "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en . @@ -4002,9 +4002,9 @@ obo:IAO_0000120 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000121 obo:IAO_0000121 rdf:type owl:NamedIndividual ; - + rdfs:label "organizational term"@en ; - + obo:IAO_0000115 "term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en . @@ -4012,9 +4012,9 @@ obo:IAO_0000121 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000122 obo:IAO_0000122 rdf:type owl:NamedIndividual ; - + rdfs:label "ready for release"@en ; - + obo:IAO_0000115 "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en . @@ -4022,9 +4022,9 @@ obo:IAO_0000122 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000123 obo:IAO_0000123 rdf:type owl:NamedIndividual ; - + rdfs:label "metadata incomplete"@en ; - + obo:IAO_0000115 "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en . @@ -4032,9 +4032,9 @@ obo:IAO_0000123 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000124 obo:IAO_0000124 rdf:type owl:NamedIndividual ; - + rdfs:label "uncurated"@en ; - + obo:IAO_0000115 "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en . @@ -4042,9 +4042,9 @@ obo:IAO_0000124 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000125 obo:IAO_0000125 rdf:type owl:NamedIndividual ; - + rdfs:label "pending final vetting"@en ; - + obo:IAO_0000115 "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en . @@ -4052,13 +4052,13 @@ obo:IAO_0000125 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000423 obo:IAO_0000423 rdf:type owl:NamedIndividual ; - + rdfs:label "to be replaced with external ontology term"@en ; - + obo:IAO_0000117 "Alan Ruttenberg"@en ; - + obo:IAO_0000115 "Terms with this status should eventually replaced with a term from another ontology."@en ; - + obo:IAO_0000119 "group:OBI"@en . @@ -4066,13 +4066,13 @@ obo:IAO_0000423 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000428 obo:IAO_0000428 rdf:type owl:NamedIndividual ; - + rdfs:label "requires discussion"@en ; - + obo:IAO_0000115 "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en ; - + obo:IAO_0000117 "Alan Ruttenberg"@en ; - + obo:IAO_0000119 "group:OBI"@en . @@ -4086,14 +4086,14 @@ obo:IAO_0000428 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/iao/2015-02-23/iao.owl iao:iao.owl rdf:type owl:NamedIndividual ; - + rdfs:label "IAO Release 2015-02-23" ; - + doap:revision "SVN $Revision: 717 $" ; - + doap:file-release , iao:iao.owl ; - + rdfs:seeAlso . @@ -4149,13 +4149,13 @@ obo:IAO_0000115 rdf:type owl:AnnotationProperty . ### http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#fileName nfo:fileName rdf:type owl:DatatypeProperty ; - + rdfs:label "fileName" ; - + nrl:maxCardinality "1" ; - + obo:IAO_0000115 "Name of the file, together with the extension" ; - + rdfs:range xsd:string . @@ -4195,9 +4195,9 @@ obo:IAO_0000115 rdf:type owl:AnnotationProperty . ### http://neurolex.org/wiki/birnlex_2067 nlx:birnlex_2067 rdf:type owl:Class ; - + rdfs:label "FSL" ; - + obo:IAO_0000115 "A comprehensive library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. The tools include registration, atlases, Diffusion MRI tools for parameter reconstruction and probabilistic taractography, and a viewer. FSL runs on Apple and PCs (Linux and Windows), and is very easy to install. Most of the tools can be run both from the command line and as GUIs ('point-and-click' graphical user interfaces). Several complementary brain atlases, integrated into FSLView and Featquery, allowing viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Atlases included with FSL: * Harvard-Oxford cortical and subcortical structural atlases * Julich histological atlas * JHU DTI-based white-matter atlases * Oxford thalamic connectivity atlas * Talairach atlas * MNI structural atlas * Cerebellum atlas FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK." . @@ -4205,9 +4205,9 @@ nlx:birnlex_2067 rdf:type owl:Class ; ### http://neurolex.org/wiki/nif-0000-00343 nlx:nif-0000-00343 rdf:type owl:Class ; - + rdfs:label "SPM" ; - + obo:IAO_0000115 "Software package for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG." . @@ -4334,20 +4334,20 @@ obo:OBI_0000299 rdf:type owl:ObjectProperty . ### http://purl.obolibrary.org/obo/STATO_0000030 obo:STATO_0000030 rdf:type owl:Class ; - + rdfs:label "Chi-Squared statistic"@en ; - + rdfs:subClassOf obo:STATO_0000039 ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string , "Alejandra Gonzalez-Beltran"@en ; - + obo:IAO_0000115 "Chi-squared statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Chi-Squared distribution."@en ; - + obo:IAO_0000117 "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO"@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -4355,22 +4355,22 @@ obo:STATO_0000030 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000039 obo:STATO_0000039 rdf:type owl:Class ; - + rdfs:label "statistic"@en ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string ; - + obo:IAO_0000112 ""@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic)."@en ; - + obo:IAO_0000115 "a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data."@en ; - + obo:STATO_0000032 "statistic"@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -4378,21 +4378,21 @@ obo:STATO_0000039 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000119 obo:STATO_0000119 rdf:type owl:Class ; - + rdfs:label "model parameter estimation"@en ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string ; - + obo:IAO_0000119 ""@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000115 "model parameter estimation is a data transformation that finds parameter values (the model parameter estimates) most compatible with the data as judged by the model."@en ; - + obo:IAO_0000116 """textual definition modified following contributiong by Thomas Nichols: https://github.com/ISA-tools/stato/issues/18"""@en ; - + obo:IAO_0000114 obo:IAO_0000125 . @@ -4400,22 +4400,22 @@ https://github.com/ISA-tools/stato/issues/18"""@en ; ### http://purl.obolibrary.org/obo/STATO_0000176 obo:STATO_0000176 rdf:type owl:Class ; - + rdfs:label "t-statistic"@en ; - + rdfs:subClassOf obo:STATO_0000039 ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string ; - + obo:STATO_0000032 ""@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO"@en ; - + obo:IAO_0000115 "t-statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Student's t distribution."@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -4423,20 +4423,20 @@ obo:STATO_0000176 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000282 obo:STATO_0000282 rdf:type owl:Class ; - + rdfs:label "F-statistic"@en ; - + rdfs:subClassOf obo:STATO_0000039 ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string , "Alejandra Gonzalez-Beltran"@en ; - + obo:IAO_0000115 "F statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a F distribution. the F statistic is the ratio of two scaled sums of squares reflecting different sources of variability"@en ; - + obo:IAO_0000117 "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO"@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -4444,22 +4444,22 @@ obo:STATO_0000282 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000323 obo:STATO_0000323 rdf:type owl:Class ; - + rdfs:label "contrast weight matrix"@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Camille Maumet"@en , "Orlaith Burke"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO"@en ; - + obo:IAO_0000117 "Tom Nichols"@en ; - + obo:IAO_0000112 "[1,0,0]"@en ; - + obo:IAO_0000115 "a contrast weight matrix is a information content entity which holds a set of contrast weight, coefficient used in a weighting sum of means defining a contrast"@en ; - + obo:STATO_0000032 "contrast weights"@en . @@ -4467,19 +4467,19 @@ obo:STATO_0000323 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000346 obo:STATO_0000346 rdf:type owl:Class ; - + rdfs:label "covariance structure"@en ; - + obo:IAO_0000117 "Camille Maumet" , "Orlaith Burke" , "Tom Nichols" , "Alejandra Gonzalez-Beltran" , "Philippe Rocca-Serra" ; - + obo:IAO_0000115 "a covariance structure is a data item which is part of a regression model and which indicates a pattern in the covariance matrix. The nature of covariance structure is specified before the regression analysis and various covariance structure may be tested and evaluated using information criteria to help choose the most suitable model"@en ; - + obo:IAO_0000119 "http://www3.nd.edu/~kyuan/courses/sem/readpapers/benter.pdf" ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4487,27 +4487,27 @@ obo:STATO_0000346 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000357 obo:STATO_0000357 rdf:type owl:Class ; - + rdfs:label "Toeplitz covariance structure"@en ; - + rdfs:subClassOf obo:STATO_0000346 ; - + obo:IAO_0000117 "Orlaith Burke" ; - + obo:IAO_0000115 ""@en ; - + obo:STATO_0000041 ""@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Camille Maumet"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000118 "TOEP"@en ; - + obo:IAO_0000117 "Tom Nichols"@en ; - + obo:IAO_0000119 "http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm"@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4515,26 +4515,26 @@ obo:STATO_0000357 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000362 obo:STATO_0000362 rdf:type owl:Class ; - + rdfs:label "compound symmetry covariance structure"@en ; - + rdfs:subClassOf obo:STATO_0000346 ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en ; - + obo:IAO_0000118 "CS"@en ; - + obo:IAO_0000117 "Camille Maumet"@en , "Orlaith Burke" , "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000115 "compound symmetry covariance structure is a covariance structure which means that all the variances are equal and all the covariances are equal."@en ; - + obo:STATO_0000041 "http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corCompSymm.html"@en ; - + obo:IAO_0000119 "http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm"@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4542,25 +4542,25 @@ obo:STATO_0000362 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000370 obo:STATO_0000370 rdf:type owl:Class ; - + rdfs:label "ordinary least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000119 ; - + obo:STATO_0000032 "OLS estimation" ; - + obo:STATO_0000041 ""@en , "https://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html" ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Camille Maumet"@en , "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000119 "http://en.wikipedia.org/wiki/Ordinary_least_squares and Tom Nichols"@en ; - + obo:IAO_0000115 "the ordinary least squares estimation is a model parameter estimation for a linear regression model when the errors are uncorrelated and equal in variance. Is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption."@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4568,25 +4568,25 @@ obo:STATO_0000370 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000371 obo:STATO_0000371 rdf:type owl:Class ; - + rdfs:label "weighted least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000119 ; - + obo:STATO_0000032 "WLS estimation" ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Camille Maumet"@en , "Orlaith Burke"@en , "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000119 "http://en.wikipedia.org/wiki/Least_squares#Weighted_least_squares and Tom Nichols"@en ; - + obo:STATO_0000041 "https://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html"@en ; - + obo:IAO_0000115 "the weighted least squares estimation is a model parameter estimation for a linear regression model with errors that independent but have heterogeneous variance. Difficult to use use in practice, as weights must be set based on the variance which is usually unknown. If true variance is known, it is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption."@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4594,22 +4594,22 @@ obo:STATO_0000371 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000372 obo:STATO_0000372 rdf:type owl:Class ; - + rdfs:label "generalized least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000119 ; - + obo:STATO_0000032 "GLS estimation" ; - + obo:IAO_0000117 "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000119 "http://en.wikipedia.org/wiki/Generalized_least_squares and Tom Nichols"@en ; - + obo:STATO_0000041 "http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/gls.html"@en ; - + obo:IAO_0000115 "the generalized least squares estimation is a model parameter estimation for a linear regression model with errors that are dependent and (possibly) have heterogeneous variance. Difficult to use use in practice, as covariance matrix of the errors must known to \"whiten\" data and model. If true covariance is known, it is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption."@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4617,25 +4617,25 @@ obo:STATO_0000372 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000373 obo:STATO_0000373 rdf:type owl:Class ; - + rdfs:label "iteratively reweighted least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000119 ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran" , "Camille Maumet" , "Orlaith Burke" ; - + obo:STATO_0000041 ""@en ; - + obo:IAO_0000117 "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "Tom Nichols"@en ; - + obo:IAO_0000117 "Tom Nichols"@en ; - + obo:IAO_0000115 "the iteratively reweighted least squares estimation is a model parameter estimation which is a practical implementation of Weighted Least Squares, where the heterogeneous variances of the errors are estimated from the residuals of the regression model, providing an estimate for the weights. Each successive estimate of the weights improves the estimation of the regression parameters, which in turn are used to compute residuals and update the weights"@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4643,22 +4643,22 @@ obo:STATO_0000373 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000374 obo:STATO_0000374 rdf:type owl:Class ; - + rdfs:label "feasible generalized least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000372 ; - + obo:IAO_0000115 "the feasible generalized least squares estimation is a model parameter estimation which is a practical implementation of Generalised Least Squares, where the covariance of the errors is estimated from the residuals of the regression model, providing the information needed to whiten the data and model. Each successive estimate of the whitening matrix improves the estimation of the regression parameters, which in turn are used to compute residuals and update the whitening matrix." ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Orlaith Burke"@en ; - + obo:IAO_0000119 "Tom Nichols" ; - + obo:IAO_0000117 "Camille Maumet" , "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4666,20 +4666,20 @@ obo:STATO_0000374 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000376 obo:STATO_0000376 rdf:type owl:Class ; - + rdfs:label "Z-statistic" ; - + rdfs:subClassOf obo:STATO_0000039 ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran" , "Camille Maument" , "Philippe Rocca-Serra" , "Thomas Nichols" ; - + obo:IAO_0000119 "http://en.wikipedia.org/wiki/Z-test" ; - + obo:IAO_0000115 "Z-statistic is a statistic computed from observations and used to produce a p-value when compared to a Standard Normal Distribution in a statistical test called the Z-test." ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -5521,7 +5521,7 @@ prov:qualifiedEnd prov:qualifiedForm a owl:AnnotationProperty ; - rdfs:comment """This annotation property links a subproperty of prov:wasInfluencedBy with the subclass of prov:Influence and the qualifying property that are used to qualify it. + rdfs:comment """This annotation property links a subproperty of prov:wasInfluencedBy with the subclass of prov:Influence and the qualifying property that are used to qualify it. Example annotation: @@ -5534,7 +5534,7 @@ Then this unqualified assertion: can be qualified by adding: prov:entity1 prov:qualifiedGeneration prov:entity1Gen . - prov:entity1Gen + prov:entity1Gen a prov:Generation, prov:Influence; prov:activity prov:activity1; prov:customValue 1337 . @@ -5835,7 +5835,7 @@ prov:wasInfluencedBy Subproperties of prov:wasInfluencedBy may also be asserted directly without being qualified. -prov:wasInfluencedBy should not be used without also using one of its subproperties. +prov:wasInfluencedBy should not be used without also using one of its subproperties. """@en ; prov:inverse "influenced" ; prov:qualifiedForm prov:Influence, prov:qualifiedInfluence ; @@ -5922,7 +5922,7 @@ prov:wasStartedBy a owl:Ontology ; - rdfs:comment """This document is published by the Provenance Working Group (http://www.w3.org/2011/prov/wiki/Main_Page). + rdfs:comment """This document is published by the Provenance Working Group (http://www.w3.org/2011/prov/wiki/Main_Page). If you wish to make comments regarding this document, please send them to public-prov-comments@w3.org (subscribe public-prov-comments-request@w3.org, archives http://lists.w3.org/Archives/Public/public-prov-comments/). All feedback is welcome."""@en ; rdfs:label "W3C PROVenance Interchange Ontology (PROV-O)"@en ; @@ -5999,9 +5999,8 @@ If you wish to make comments regarding this document, please send them to public [] a owl:Axiom ; - rdfs:comment """Revision is a derivation (see http://www.w3.org/TR/prov-dm/#term-Revision). Moreover, according to + rdfs:comment """Revision is a derivation (see http://www.w3.org/TR/prov-dm/#term-Revision). Moreover, according to http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#term-Revision 23 April 2012 'wasRevisionOf is a strict sub-relation of wasDerivedFrom since two entities e2 and e1 may satisfy wasDerivedFrom(e2,e1) without being a variant of each other.'""" ; owl:annotatedProperty rdfs:subPropertyOf ; owl:annotatedSource prov:wasRevisionOf ; owl:annotatedTarget prov:wasDerivedFrom . - diff --git a/nidmresults/owl/nidm-results_110.owl b/nidmresults/owl/nidm-results_110.owl index 860ef36..291b28b 100644 --- a/nidmresults/owl/nidm-results_110.owl +++ b/nidmresults/owl/nidm-results_110.owl @@ -63,17 +63,17 @@ dc:description rdfs:range dctype:Image . ### http://purl.org/nidash/nidm#NIDM_0000010 nidm:NIDM_0000010 rdf:type owl:ObjectProperty ; - + rdfs:label "has fMRI Design" ; - + obo:IAO_0000115 "A property that associates an fMRI design to a design matrix in first-level fMRI analyses." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/299" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000019 ; - + rdfs:range nidm:NIDM_0000155 . @@ -81,17 +81,17 @@ nidm:NIDM_0000010 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000088 nidm:NIDM_0000088 rdf:type owl:ObjectProperty ; - + rdfs:label "has Drift Model" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000115 "A property that associates a drift model to a design matrix (only used for first-level fMRI experiments)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000019 ; - + rdfs:range nidm:NIDM_0000087 . @@ -99,17 +99,17 @@ nidm:NIDM_0000088 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000089 nidm:NIDM_0000089 rdf:type owl:ObjectProperty ; - + rdfs:label "dependence Map-Wise Dependence" ; - + obo:IAO_0000115 "Property that associates an Error Parameter Map-Wise Dependence to the dependence of an error model." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000023 ; - + rdfs:range nidm:NIDM_0000071 . @@ -117,20 +117,20 @@ nidm:NIDM_0000089 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000097 nidm:NIDM_0000097 rdf:type owl:ObjectProperty ; - + rdfs:label "has Alternative Hypothesis" ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/pull/81" ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000208" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000049 ; - + rdfs:range nidm:NIDM_0000060 , nidm:NIDM_0000079 ; - + rdfs:subPropertyOf owl:topObjectProperty . @@ -138,17 +138,17 @@ nidm:NIDM_0000097 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000098 nidm:NIDM_0000098 rdf:type owl:ObjectProperty ; - + rdfs:label "has Cluster Labels Map" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/282" ; - + obo:IAO_0000115 "A property that associates a clusters label map to the excursion set." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range nidm:NIDM_0000008 ; - + rdfs:domain nidm:NIDM_0000025 . @@ -156,17 +156,17 @@ nidm:NIDM_0000098 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000099 nidm:NIDM_0000099 rdf:type owl:ObjectProperty ; - + rdfs:label "has Connectivity Criterion" ; - + obo:IAO_0000115 "Property that associates a ConnectivityCriterion with a ClusterDefinitionCriteria." ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000007 ; - + rdfs:range nidm:NIDM_0000012 . @@ -174,15 +174,15 @@ nidm:NIDM_0000099 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000100 nidm:NIDM_0000100 rdf:type owl:ObjectProperty ; - + rdfs:label "has Error Dependence" ; - + obo:IAO_0000115 "Property that associates a covariance structure representing the dependence structure of the error, used as part of model estimation with an Error Model." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range obo:STATO_0000346 ; - + rdfs:domain nidm:NIDM_0000023 . @@ -190,15 +190,15 @@ nidm:NIDM_0000100 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000101 nidm:NIDM_0000101 rdf:type owl:ObjectProperty ; - + rdfs:label "has Error Distribution" ; - + obo:IAO_0000115 "Property that associates an ErrorDistribution with an ErrorModel." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range nidm:NIDM_0000022 ; - + rdfs:domain nidm:NIDM_0000023 . @@ -206,17 +206,17 @@ nidm:NIDM_0000101 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000102 nidm:NIDM_0000102 rdf:type owl:ObjectProperty ; - + rdfs:label "has HRF Basis" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "A property that associates a set of functions that, when convolved with the anticipated neural responses, yield a set of regressors to model the anticipated hemodynamic responses in a design matrix." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000019 ; - + rdfs:range nidm:NIDM_0000036 . @@ -224,17 +224,17 @@ nidm:NIDM_0000102 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000103 nidm:NIDM_0000103 rdf:type owl:ObjectProperty ; - + rdfs:label "has Map Header" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/289" ; - + obo:IAO_0000115 "A Property that associates an additional file containing the map header with a map" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000052 ; - + rdfs:range nidm:NIDM_0000053 . @@ -242,17 +242,17 @@ nidm:NIDM_0000103 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000104 nidm:NIDM_0000104 rdf:type owl:ObjectProperty ; - + rdfs:label "in Coordinate Space" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/171 by NN JT CM SG KH TN." ; - + obo:IAO_0000115 "Property of a DataArray to associate a CoordinateSpace with a physical file." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range nidm:NIDM_0000016 ; - + rdfs:domain nidm:NIDM_0000052 . @@ -260,17 +260,17 @@ nidm:NIDM_0000104 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000105 nidm:NIDM_0000105 rdf:type owl:ObjectProperty ; - + rdfs:label "in World Coordinate System" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Property that associates a world coordinate system to the coordinate space." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range nidm:NIDM_0000081 . @@ -278,15 +278,15 @@ nidm:NIDM_0000105 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000113 nidm:NIDM_0000113 rdf:type owl:ObjectProperty ; - + rdfs:label "object Model" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/pull/137" ; - + obo:IAO_0000114 obo:IAO_0000124 ; - + rdfs:range nidm:NIDM_0000057 ; - + rdfs:domain prov:Bundle . @@ -294,17 +294,17 @@ nidm:NIDM_0000113 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000123 nidm:NIDM_0000123 rdf:type owl:ObjectProperty ; - + rdfs:label "statistic Type" ; - + obo:IAO_0000115 "Property that associates a [stato:\"statistic\"](http://purl.obolibrary.org/obo/STATO_0000039) with a StatisticMap or a ContrastWeights entity." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/293" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range obo:STATO_0000039 ; - + rdfs:domain obo:STATO_0000323 , nidm:NIDM_0000076 . @@ -313,17 +313,17 @@ nidm:NIDM_0000123 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000126 nidm:NIDM_0000126 rdf:type owl:ObjectProperty ; - + rdfs:label "variance Map-Wise Dependence" ; - + obo:IAO_0000115 "Property that associates an Error Parameter Map-Wise Dependence to the variance of an error model" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000023 ; - + rdfs:range nidm:NIDM_0000071 . @@ -331,17 +331,17 @@ nidm:NIDM_0000126 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000134 nidm:NIDM_0000134 rdf:type owl:ObjectProperty ; - + rdfs:label "with Estimation Method" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/293" ; - + obo:IAO_0000115 "Property that associates a [stato:\"model parameter estimation\"](http://purl.obolibrary.org/obo/STATO_0000119) method with a model parameter estimation" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range obo:STATO_0000119 ; - + rdfs:domain nidm:NIDM_0000056 . @@ -349,17 +349,17 @@ nidm:NIDM_0000134 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000138 nidm:NIDM_0000138 rdf:type owl:ObjectProperty ; - + rdfs:label "has Maximum Intensity Projection" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/293" ; - + obo:IAO_0000115 "Property that associates an image of the maximum intensity projection with an excursion set map." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range dctype:Image ; - + rdfs:domain nidm:NIDM_0000025 . @@ -367,17 +367,17 @@ nidm:NIDM_0000138 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000161 nidm:NIDM_0000161 rdf:type owl:ObjectProperty ; - + rdfs:label "equivalent Threshold" ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/329" ; - + obo:IAO_0000115 "Property that associates another Threshold that is equivalent (e.g. if the user specified a threshold in terms of FWE-corrected p-value, this property can be used to associate the corresponding uncorrected p-value)." ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:range nidm:NIDM_0000162 ; - + rdfs:domain nidm:NIDM_0000162 . @@ -400,7 +400,7 @@ dc:description rdf:type owl:DatatypeProperty . ### http://purl.org/dc/terms/format dct:format rdf:type owl:DatatypeProperty ; - + rdfs:range xsd:string . @@ -408,17 +408,17 @@ dct:format rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/fsl#FSL_0000004 fsl:FSL_0000004 rdf:type owl:DatatypeProperty ; - + rdfs:label "drift Cutoff Period" ; - + obo:IAO_0000115 "Full Width at Half Maximum in seconds of the Gaussian weight function used in the running line smoother." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain fsl:FSL_0000002 ; - + rdfs:range xsd:float . @@ -426,17 +426,17 @@ fsl:FSL_0000004 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/fsl#FSL_0000005 fsl:FSL_0000005 rdf:type owl:DatatypeProperty ; - + rdfs:label "feat Version" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/291" ; - + obo:IAO_0000115 "Version of the FEAT software." ; - + rdfs:domain nlx:birnlex_2067 ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range xsd:string . @@ -448,17 +448,17 @@ fsl:FSL_0000005 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000021 nidm:NIDM_0000021 rdf:type owl:DatatypeProperty ; - + rdfs:label "regressor Names" ; - + obo:IAO_0000115 "A list of abstract names associated with each column of the design matrix (e.g. [\"motor_left\", \"motor_right\"])." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/299" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000019 ; - + rdfs:range xsd:string . @@ -466,19 +466,19 @@ nidm:NIDM_0000021 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000082 nidm:NIDM_0000082 rdf:type owl:DatatypeProperty ; - + rdfs:label "cluster Label Id" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/271" ; - + obo:IAO_0000115 "Integer value used in the cluster label map to identify the location of the cluster within the excursion set." ; - + obo:IAO_0000112 "5" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000070 ; - + rdfs:range xsd:int . @@ -486,18 +486,18 @@ nidm:NIDM_0000082 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000083 nidm:NIDM_0000083 rdf:type owl:DatatypeProperty ; - + rdfs:label "cluster Size In Vertices" ; - + obo:IAO_0000115 "Number of vertices that make up the cluster." ; - + obo:IAO_0000112 "10" ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000070 ; - + rdfs:range xsd:positiveInteger . @@ -505,18 +505,18 @@ nidm:NIDM_0000083 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000084 nidm:NIDM_0000084 rdf:type owl:DatatypeProperty ; - + rdfs:label "cluster Size In Voxels" ; - + obo:IAO_0000112 "18" ; - + obo:IAO_0000115 "Number of voxels that make up the cluster." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000070 ; - + rdfs:range xsd:positiveInteger . @@ -524,19 +524,19 @@ nidm:NIDM_0000084 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000085 nidm:NIDM_0000085 rdf:type owl:DatatypeProperty ; - + rdfs:label "contrast Name" ; - + obo:IAO_0000115 "Name of the contrast." ; - + obo:IAO_0000112 "\"Listening > Rest\"" ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain obo:STATO_0000323 , nidm:NIDM_0000002 , nidm:NIDM_0000076 ; - + rdfs:range xsd:string . @@ -544,19 +544,19 @@ nidm:NIDM_0000085 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000086 nidm:NIDM_0000086 rdf:type owl:DatatypeProperty ; - + rdfs:label "coordinate Vector" ; - + obo:IAO_0000112 "[-60, 32, 54]"^^xsd:string ; - + obo:IAO_0000115 "A vector with one number per dimension. The first element corresponds to the coordinate along the first dimension measured in map elements (e.g., pixels, voxels, vertices, or faces), the second element to the coordinate along the second dimension etc." ; - + obo:IAO_0000116 "Under discussion at: https://github.com/incf-nidash/nidm/pull/270 and https://github.com/incf-nidash/nidm/issues/145" ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000015 ; - + rdfs:range xsd:string . @@ -564,19 +564,19 @@ nidm:NIDM_0000086 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000090 nidm:NIDM_0000090 rdf:type owl:DatatypeProperty ; - + rdfs:label "dimensions In Voxels" ; - + obo:IAO_0000115 "Number of voxels in each of the dimensions of the data array. For example, \"91 109 91\" indicates there are 91 voxels in the first dimension, 109 in the second dimension, and 91 in the third dimension." ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/issues/146" ; - + obo:IAO_0000112 "[64 64 20]" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:string . @@ -584,19 +584,19 @@ nidm:NIDM_0000090 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000091 nidm:NIDM_0000091 rdf:type owl:DatatypeProperty ; - + rdfs:label "effect Degrees Of Freedom" ; - + obo:IAO_0000115 "In the context of a general linear model, the effect degrees of freedom is the rank of the contrast. For example, a contrast comprising of a vector has effect degrees of freedom of 1 and can be tested with a F-test with numerator degrees of freedom of 1." ; - + obo:IAO_0000112 "1" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/issues/277" ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000076 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -609,17 +609,17 @@ nidm:NIDM_0000091 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000092 nidm:NIDM_0000092 rdf:type owl:DatatypeProperty ; - + rdfs:label "equivalent ZStatistic" ; - + obo:IAO_0000115 "Statistic value transformed into Z units; the output of a process which takes a non-normal statistic and transforms it to an equivalent z score." ; - + obo:IAO_0000112 "3.5" ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain nidm:NIDM_0000062 ; - + rdfs:range xsd:float . @@ -627,19 +627,19 @@ nidm:NIDM_0000092 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000093 nidm:NIDM_0000093 rdf:type owl:DatatypeProperty ; - + rdfs:label "error Degrees Of Freedom" ; - + obo:IAO_0000112 "72.999999" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/issues/277" ; - + obo:IAO_0000115 "In the context of a general linear model, the error degrees of freedom are the number of observations less the rank of the design matrix." ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000076 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -652,15 +652,15 @@ nidm:NIDM_0000093 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000094 nidm:NIDM_0000094 rdf:type owl:DatatypeProperty ; - + rdfs:label "error Variance Homogeneous" ; - + obo:IAO_0000115 "A boolean value reflecting how the variance of the error is modeled during parameter estimation; TRUE for constant variance over all observations in the model, FALSE for heterogeneous variance." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000023 ; - + rdfs:range xsd:boolean . @@ -668,19 +668,19 @@ nidm:NIDM_0000094 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000095 nidm:NIDM_0000095 rdf:type owl:DatatypeProperty ; - + rdfs:label "partial Conjunction Degree" ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000115 "The number of non-null effects permitted in a partial conjunction null, as part of a partial conjunction inference" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/294" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain spm:SPM_0000005 ; - + rdfs:range xsd:int . @@ -688,19 +688,19 @@ nidm:NIDM_0000095 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000096 nidm:NIDM_0000096 rdf:type owl:DatatypeProperty ; - + rdfs:label "grand Mean Scaling" ; - + obo:IAO_0000115 "Binary flag defining whether the data was scaled (true for scaled). Specifically, \"grand mean scaling\" refers to multiplication of every voxel in every scan by a common (or session-specific) value." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/285" ; - + obo:IAO_0000112 "TRUE" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000018 ; - + rdfs:range xsd:boolean . @@ -708,13 +708,13 @@ nidm:NIDM_0000096 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000105 nidm:NIDM_0000105 rdf:type owl:DatatypeProperty ; - + rdfs:label "in World Coordinate System" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Property that associates a world coordinate system to the coordinate space." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -722,17 +722,17 @@ nidm:NIDM_0000105 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000106 nidm:NIDM_0000106 rdf:type owl:DatatypeProperty ; - + rdfs:label "is User Defined" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/pull/258" ; - + obo:IAO_0000115 "A binary flag defining whether the mask was specified by the user (true) or automatically generated during the analysis (false)" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000004 ; - + rdfs:range xsd:boolean . @@ -740,21 +740,21 @@ nidm:NIDM_0000106 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000107 nidm:NIDM_0000107 rdf:type owl:DatatypeProperty ; - + rdfs:label "masked Median" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/288, naming previously discussed at: https://github.com/incf-nidash/nidm/issues/70" ; - + obo:IAO_0000115 "Median value considering only in-mask voxels. Useful diagnostic when computed on grand mean image when grandMeanScaling is TRUE, as the median should be close to targetIntensity." ; - + rdfs:seeAlso "http://purl.obolibrary.org/obo/OBI_0200119" ; - + obo:IAO_0000112 "155.23" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000033 ; - + rdfs:range xsd:float . @@ -762,17 +762,17 @@ nidm:NIDM_0000107 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000108 nidm:NIDM_0000108 rdf:type owl:DatatypeProperty ; - + rdfs:label "max Number Of Peaks Per Cluster" ; - + obo:IAO_0000115 "Maximum number of peaks to be reported after inference within a cluster." ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/200" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000063 ; - + rdfs:range xsd:int . @@ -780,17 +780,17 @@ nidm:NIDM_0000108 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000109 nidm:NIDM_0000109 rdf:type owl:DatatypeProperty ; - + rdfs:label "min Distance Between Peaks" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/200" ; - + obo:IAO_0000115 "Minimum distance between two peaks to be reported after inference." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000063 ; - + rdfs:range xsd:float . @@ -798,19 +798,19 @@ nidm:NIDM_0000109 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000111 nidm:NIDM_0000111 rdf:type owl:DatatypeProperty ; - + rdfs:label "number Of Significant Clusters" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/292" ; - + obo:IAO_0000115 "Number of significant clusters found by the inference activity. This is SPM's set level statistic." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000025 ; - + rdfs:range xsd:int ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -818,19 +818,19 @@ nidm:NIDM_0000111 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000112 nidm:NIDM_0000112 rdf:type owl:DatatypeProperty ; - + rdfs:label "number Of Dimensions" ; - + obo:IAO_0000115 "Number of dimensions of the data matrix (e.g. 3 for volumetric data)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/295" ; - + obo:IAO_0000112 "3" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:positiveInteger . @@ -838,23 +838,23 @@ nidm:NIDM_0000112 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000114 nidm:NIDM_0000114 rdf:type owl:DatatypeProperty ; - + rdfs:label "p Value" ; - + owl:sameAs "http://purl.obolibrary.org/obo/OBI_0000175"^^xsd:anyURI ; - + obo:IAO_0000112 "8.95E-14" ; - + rdfs:seeAlso """http://purl.obolibrary.org/obo/IAO_0000121 http://purl.obolibrary.org/obo/OBI_0000175 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P-Value""" ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/38" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000025 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -869,24 +869,24 @@ http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P-Value""" ; ### http://purl.org/nidash/nidm#NIDM_0000115 nidm:NIDM_0000115 rdf:type owl:DatatypeProperty ; - + rdfs:label "p Value FWER" ; - + obo:IAO_0000112 "0.05" ; - + obo:IAO_0000115 "\"A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests\"" ; - + owl:sameAs "This definition is from OBI. Please update this note if the definition is modified." ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/38" ; - + rdfs:seeAlso "Synonym of \"nidm:pFWE\"" ; - + obo:IAO_0000114 obo:IAO_0000423 ; - + rdfs:domain nidm:NIDM_0000062 , nidm:NIDM_0000070 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -901,22 +901,22 @@ nidm:NIDM_0000115 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000116 nidm:NIDM_0000116 rdf:type owl:DatatypeProperty ; - + rdfs:label "p Value Uncorrected" ; - + obo:IAO_0000115 "A p-value reported without correction for multiple testing. " ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/38" ; - + obo:IAO_0000112 "0.0542" ; - + rdfs:seeAlso "http://purl.obolibrary.org/obo/IAO_0000121" ; - + obo:IAO_0000114 obo:IAO_0000423 ; - + rdfs:domain nidm:NIDM_0000062 , nidm:NIDM_0000070 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -931,22 +931,22 @@ nidm:NIDM_0000116 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000119 nidm:NIDM_0000119 rdf:type owl:DatatypeProperty ; - + rdfs:label "q Value FDR" ; - + obo:IAO_0000112 "0.000154" ; - + obo:IAO_0000115 "A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level (same as OBI_0001442)." ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/38" ; - + owl:sameAs "http://purl.obolibrary.org/obo/OBI_0001442" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000062 , nidm:NIDM_0000070 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -961,17 +961,17 @@ nidm:NIDM_0000119 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000120 nidm:NIDM_0000120 rdf:type owl:DatatypeProperty ; - + rdfs:label "random Field Stationarity" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/130" ; - + obo:IAO_0000115 "A binary flag that indicates whether Random Field Theory methods assumed smoothness that was homogeneous over the map (true), or allowed for smoothness that varies over the map (false)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:boolean . @@ -979,21 +979,21 @@ nidm:NIDM_0000120 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000121 nidm:NIDM_0000121 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume In Voxels" ; - + obo:IAO_0000112 "68656" ; - + rdfs:seeAlso "Synonyms of nidm:volumeInVoxels" ; - + obo:IAO_0000115 "Total number of voxels within the search volume." ; - + obo:IAO_0000114 obo:IAO_0000124 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1001,19 +1001,19 @@ nidm:NIDM_0000121 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000122 nidm:NIDM_0000122 rdf:type owl:DatatypeProperty ; - + rdfs:label "software Version" ; - + obo:IAO_0000112 8.6225 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/291" ; - + obo:IAO_0000115 "Name and number that specifies the software version. For SPM, this includes the main software version followed by the revision number (e.g. 8.6225 for SPM8 revision 6225)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range xsd:string ; - + rdfs:domain prov:SoftwareAgent . @@ -1021,19 +1021,19 @@ nidm:NIDM_0000122 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000124 nidm:NIDM_0000124 rdf:type owl:DatatypeProperty ; - + rdfs:label "target Intensity" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/285" ; - + obo:IAO_0000115 "Value to which the grand mean of the Data was scaled (applies only if grand mean scaling is true)." ; - + obo:IAO_0000112 "100" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000018 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1046,24 +1046,24 @@ nidm:NIDM_0000124 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000125 nidm:NIDM_0000125 rdf:type owl:DatatypeProperty ; - + rdfs:label "user Specified Threshold Type" ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/150" ; - + obo:IAO_0000112 "nidm:pValueFWER" ; - + obo:IAO_0000115 "Type of method used to define a threshold (e.g. statistic value, uncorrected P-value or corrected P-value)." ; - + rdfs:comment "Range is currently string but should be limited to {'nidm:pValueFWER' not found'nidm:pValueFDR' not found'nidm:pValueUncorrected';'nidm:statistic'}?" ; - + obo:IAO_0000114 obo:IAO_0000428 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000034 ; - + rdfs:range xsd:string . @@ -1071,15 +1071,15 @@ nidm:NIDM_0000125 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000127 nidm:NIDM_0000127 rdf:type owl:DatatypeProperty ; - + rdfs:label "version" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/pull/137" ; - + obo:IAO_0000114 obo:IAO_0000124 ; - + rdfs:range xsd:string ; - + rdfs:domain prov:Bundle . @@ -1087,19 +1087,19 @@ nidm:NIDM_0000127 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000131 nidm:NIDM_0000131 rdf:type owl:DatatypeProperty ; - + rdfs:label "voxel Size" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/295" ; - + obo:IAO_0000115 "3D size of a voxel measured in voxel units (e.g. [2, 2, 4])" ; - + obo:IAO_0000112 "[2, 2, 4]" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:string . @@ -1107,21 +1107,21 @@ nidm:NIDM_0000131 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000132 nidm:NIDM_0000132 rdf:type owl:DatatypeProperty ; - + rdfs:label "voxel To World Mapping" ; - + obo:IAO_0000116 "Range: Matrix of float." ; - + obo:IAO_0000112 "[3 0 0 0;0 3 0 0;0 0 3 0; 0 0 0 1] " ; - + obo:IAO_0000115 "Homogeneous transformation matrix to map from voxel coordinate system to world coordinate system." ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/148" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:string . @@ -1129,21 +1129,21 @@ nidm:NIDM_0000132 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000133 nidm:NIDM_0000133 rdf:type owl:DatatypeProperty ; - + rdfs:label "voxel Units" ; - + rdfs:comment "Range: Vector of strings." ; - + obo:IAO_0000112 "['mm', 'mm', 's']" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/295 and https://github.com/incf-nidash/nidm/issues/147" ; - + obo:IAO_0000115 "Set of units associated with the dimensions of some N-dimensional data (e.g. [mm, mm, mm])" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:string . @@ -1151,21 +1151,21 @@ nidm:NIDM_0000133 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000136 nidm:NIDM_0000136 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume In Units" ; - + obo:IAO_0000117 "Discussed at https://github.com/incf-nidash/nidm/pull/131" ; - + obo:IAO_0000115 "The volume of the searched region in units determined by the current coordinate space units (e.g., mm^3 for axis units of mm in a three dimensional image, sec.Hz for a time by frequency two dimensional image)." ; - + obo:IAO_0000116 "Context: volumeInVoxels nidm_0025. Range: Positivefloat not found." ; - + obo:IAO_0000112 "1771011" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1178,17 +1178,17 @@ nidm:NIDM_0000136 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000137 nidm:NIDM_0000137 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume In Vertices" ; - + obo:IAO_0000112 "151.3" ; - + obo:IAO_0000115 "Total number of vertices within the search volume." ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1201,19 +1201,19 @@ nidm:NIDM_0000137 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000139 nidm:NIDM_0000139 rdf:type owl:DatatypeProperty ; - + rdfs:label "coordinate Vector In Voxels" ; - + obo:IAO_0000115 "Coordinate along the first dimension in voxels. (This definition needs to be re-worked as this term was renamed from coordinate1 to coordinate in https://github.com/incf-nidash/nidm/issues/270)" ; - + obo:IAO_0000112 "[12 51 48]" ; - + obo:IAO_0000116 "Under discussion at: https://github.com/incf-nidash/nidm/pull/270" ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain nidm:NIDM_0000015 ; - + rdfs:range xsd:string . @@ -1221,17 +1221,17 @@ nidm:NIDM_0000139 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000141 nidm:NIDM_0000141 rdf:type owl:DatatypeProperty ; - + rdfs:label "expected Number Of Clusters" ; - + obo:IAO_0000112 "9.51" ; - + obo:IAO_0000115 "Expected number of clusters in an excursion set under the null hypothesis." ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1244,17 +1244,17 @@ nidm:NIDM_0000141 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000142 nidm:NIDM_0000142 rdf:type owl:DatatypeProperty ; - + rdfs:label "expected Number Of Vertices Per Cluster" ; - + obo:IAO_0000115 "Expected number of vertices in a cluster under the null hypothesis." ; - + obo:IAO_0000112 "60.632" ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1267,17 +1267,17 @@ nidm:NIDM_0000142 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000143 nidm:NIDM_0000143 rdf:type owl:DatatypeProperty ; - + rdfs:label "expected Number Of Voxels Per Cluster" ; - + obo:IAO_0000115 "Expected number of voxels in a cluster under the null hypothesis." ; - + obo:IAO_0000112 "60.632" ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1290,17 +1290,17 @@ nidm:NIDM_0000143 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000145 nidm:NIDM_0000145 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise Roughness In Voxels" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/214 and https://github.com/incf-nidash/nidm/issues/275" ; - + obo:IAO_0000115 "Estimated spatial roughness of the noise process in voxel units, as measured by the square-root determinant of the variance-covariance matrix of spatial derivatives of the noise process (Lambda matrix)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:float . @@ -1308,17 +1308,17 @@ nidm:NIDM_0000145 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000146 nidm:NIDM_0000146 rdf:type owl:DatatypeProperty ; - + rdfs:label "height Critical Threshold FDR 05" ; - + obo:IAO_0000112 "5.896" ; - + obo:IAO_0000115 "Peak statistic threshold corrected for false discovery rate at a level of alpha = 0.05. " ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:float . @@ -1326,17 +1326,17 @@ nidm:NIDM_0000146 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000147 nidm:NIDM_0000147 rdf:type owl:DatatypeProperty ; - + rdfs:label "height Critical Threshold FWE 05" ; - + obo:IAO_0000112 "4.913" ; - + obo:IAO_0000115 "Peak statistic threshold corrected for family-wise error at a level of alpha = 0.05. " ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:float . @@ -1344,23 +1344,23 @@ nidm:NIDM_0000147 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000148 nidm:NIDM_0000148 rdf:type owl:DatatypeProperty ; - + rdfs:label "resel Size In Voxels" ; - + obo:IAO_0000112 "22.325" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/275" ; - + obo:IAO_0000115 "Size of one resel in elements (e.g., pixels, voxels or vertices)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:float ; - + rdfs:subPropertyOf owl:topDataProperty ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1373,19 +1373,19 @@ nidm:NIDM_0000148 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000149 nidm:NIDM_0000149 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume In Resels" ; - + obo:IAO_0000112 "151.3" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/275" ; - + obo:IAO_0000115 "Size of search volume measured in resels." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1398,20 +1398,20 @@ nidm:NIDM_0000149 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000156 nidm:NIDM_0000156 rdf:type owl:DatatypeProperty ; - + rdfs:label "cluster Size In Resels" ; - + obo:IAO_0000117 "Under discussion at: https://github.com/incf-nidash/nidm/issues/127" ; - + obo:IAO_0000112 "13" ; - + obo:IAO_0000115 "Size of cluster measured in resels." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000070 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1424,23 +1424,23 @@ nidm:NIDM_0000156 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000157 nidm:NIDM_0000157 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Units" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + obo:IAO_0000112 "[8.87, 8.89, 7.83]" ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in world units (e.g. mm^2 or mm^3, in subject or atlas space)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1448,21 +1448,21 @@ nidm:NIDM_0000157 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000158 nidm:NIDM_0000158 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Vertices" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in vertices." ; - + obo:IAO_0000112 "[2.95, 2.96, 2.61]" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000054 ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1470,25 +1470,25 @@ nidm:NIDM_0000158 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000159 nidm:NIDM_0000159 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Voxels" ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in voxels." ; - + obo:IAO_0000112 "[3.7 3.7 3.1]" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + rdfs:seeAlso "Synonyms of or close match with nidm:NoiseFWHM" ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1496,17 +1496,17 @@ nidm:NIDM_0000159 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000001 spm:SPM_0000001 rdf:type owl:DatatypeProperty ; - + rdfs:label "SPM's Drift Cut-off Period" ; - + obo:IAO_0000115 "Discrete Cosine Transform basis cut-off, specified as period length in seconds and ensures that all basis elements will have period of this duration or longer." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain spm:SPM_0000002 ; - + rdfs:range xsd:float . @@ -1514,25 +1514,25 @@ spm:SPM_0000001 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000007 spm:SPM_0000007 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Units" ; - + owl:deprecated "true"^^xsd:boolean ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + obo:IAO_0000112 "[8.87, 8.89, 7.83]" ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in world units (e.g. mm^2 or mm^3, in subject or atlas space)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1540,23 +1540,23 @@ spm:SPM_0000007 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000008 spm:SPM_0000008 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Vertices" ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in vertices." ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + obo:IAO_0000112 "[2.95, 2.96, 2.61]" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000054 ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1564,27 +1564,27 @@ spm:SPM_0000008 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000009 spm:SPM_0000009 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Voxels" ; - + owl:deprecated "true"^^xsd:boolean ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in voxels." ; - + obo:IAO_0000112 "[3.7 3.7 3.1]" ; - + rdfs:seeAlso "Synonyms of or close match with nidm:NoiseFWHM" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1592,25 +1592,25 @@ spm:SPM_0000009 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000010 spm:SPM_0000010 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume Resels Geometry" ; - + obo:IAO_0000112 "[6 68.8 589.1 1475.5]" ; - + rdfs:comment "Range: Vector of 1 positive integer and 3 positive floats." ; - + rdfs:seeAlso "http://www.ncbi.nlm.nih.gov/pubmed/20408186" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000115 "Description of geometry of search volume. As per Worsley et al. [ http://www.ncbi.nlm.nih.gov/pubmed/20408186 ], for space dimension 3 the first element is the Euler Characteristic of the search volume, the second element is twice the average caliper diameter, the third element is half the surface area, and the fourth element is the volume. With the exception of the first element (which is a unitless integer) all quantities are in units of Resels." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1618,19 +1618,19 @@ spm:SPM_0000010 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000011 spm:SPM_0000011 rdf:type owl:DatatypeProperty ; - + rdfs:label "smallest Significant Cluster Size In Vertices FDR 05" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000112 "5" ; - + obo:IAO_0000115 "Smallest cluster size in vertices that is significant at the false discovery rate of 0.05. " ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger . @@ -1638,19 +1638,19 @@ spm:SPM_0000011 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000012 spm:SPM_0000012 rdf:type owl:DatatypeProperty ; - + rdfs:label "smallest Significant Cluster Size In Vertices FWE 05" ; - + obo:IAO_0000115 "Smallest cluster size in vertices that is significant at the family-wise corrected type I error rate (alpha value) value of 0.05." ; - + obo:IAO_0000112 "2" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger . @@ -1658,19 +1658,19 @@ spm:SPM_0000012 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000013 spm:SPM_0000013 rdf:type owl:DatatypeProperty ; - + rdfs:label "smallest Significant Cluster Size In Voxels FDR 05" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000112 "3" ; - + obo:IAO_0000115 "Smallest cluster size in voxels that is significant at the false discovery rate of 0.05. " ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger . @@ -1678,20 +1678,20 @@ spm:SPM_0000013 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000014 spm:SPM_0000014 rdf:type owl:DatatypeProperty ; - + rdfs:label "smallest Significant Cluster Size In Voxels FWE 05" ; - - obo:IAO_0000115 """Smallest cluster size in voxels that is significant at the family-wise error corrected type I error rate (alpha value) of 0.05. + + obo:IAO_0000115 """Smallest cluster size in voxels that is significant at the family-wise error corrected type I error rate (alpha value) of 0.05. """ ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000112 "1" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger . @@ -1699,17 +1699,17 @@ spm:SPM_0000014 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000015 spm:SPM_0000015 rdf:type owl:DatatypeProperty ; - + rdfs:label "partial Conjunction Degree" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/294" ; - + obo:IAO_0000115 "The number of non-null effects permitted in a partial conjunction null, as part of a partial conjunction inference" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain spm:SPM_0000005 ; - + rdfs:range xsd:int . @@ -1717,9 +1717,9 @@ spm:SPM_0000015 rdf:type owl:DatatypeProperty ; ### http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#fileName nfo:fileName rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "con_0001.img" ; - + rdfs:range xsd:string . @@ -1772,9 +1772,9 @@ obo:STATO_0000119 rdfs:subClassOf prov:Activity . ### http://purl.obolibrary.org/obo/STATO_0000323 obo:STATO_0000323 rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/ContrastWeights.txt" . @@ -1788,7 +1788,7 @@ obo:STATO_0000346 rdfs:subClassOf prov:Entity . ### http://purl.org/dc/dcmitype/Image dctype:Image rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity , [ rdf:type owl:Restriction ; owl:onProperty nfo:fileName ; @@ -1814,15 +1814,15 @@ dctype:Image rdf:type owl:Class ; ### http://purl.org/nidash/fsl#FSL_0000002 fsl:FSL_0000002 rdf:type owl:Class ; - + rdfs:label "Gaussian Running Line Drift Model" ; - + rdfs:subClassOf nidm:NIDM_0000087 ; - + obo:IAO_0000115 "A drift model in which the drifts are modeled with a Gaussian-weighted running line smoother, fit to and subtracted from the data and each column of the design matrix." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1830,17 +1830,17 @@ fsl:FSL_0000002 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000001 nidm:NIDM_0000001 rdf:type owl:Class ; - + rdfs:label "Contrast Estimation" ; - + rdfs:subClassOf prov:Activity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/ContrastEstimation.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "The process of performing a [obo:contrast estimation](http://purl.obolibrary.org/obo/STATO_0000383) at each element (e.g., pixel, voxel, vertex, or face) of a map" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/276 and https://github.com/ISA-tools/stato/issues/23" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1848,17 +1848,17 @@ nidm:NIDM_0000001 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000002 nidm:NIDM_0000002 rdf:type owl:Class ; - + rdfs:label "Contrast Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [contrast estimate](http://purl.obolibrary.org/obo/STATO_0000384)."^^xsd:string ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/ContrastMap.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/255" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1866,15 +1866,15 @@ nidm:NIDM_0000002 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000003 nidm:NIDM_0000003 rdf:type owl:Class ; - + rdfs:label "Arbitrarily Correlated Error" ; - + rdfs:subClassOf obo:STATO_0000346 ; - + obo:IAO_0000117 "TN" ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/28" ; - + obo:IAO_0000114 obo:IAO_0000423 . @@ -1882,15 +1882,15 @@ nidm:NIDM_0000003 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000004 nidm:NIDM_0000004 rdf:type owl:Class ; - + rdfs:label "Binary Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000115 "A map in which all values are 0, 1 or NaN. Usually, selected elements (e.g., pixels, voxels, vertices, or faces) have a value of 1 and excluded elements (i.e. the background) have a value of 0 or NaN" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/258" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1898,15 +1898,15 @@ nidm:NIDM_0000004 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000005 nidm:NIDM_0000005 rdf:type owl:Class ; - + rdfs:label "Binomial Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000276"^^xsd:anyURI ; - + obo:IAO_0000115 "The binomial distribution is a discrete probability distribution which describes the probability of k successes in n draws with replacement from a finite population of size N. The binomial distribution is frequently used to model the number of successes in a sample of size n drawn with replacement from a population of size N. The binomial distribution gives the discrete probability distribution of obtaining exactly n successes out of N Bernoulli trials (where the result of each Bernoulli trial is true with probability p and false with probability q=1-p ) notation: B(n,p) The mean is N*p The variance is N*p*q. (Definition from STATO)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1914,15 +1914,15 @@ nidm:NIDM_0000005 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000006 nidm:NIDM_0000006 rdf:type owl:Class ; - + rdfs:label "Cluster" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "A collection of elements related by one or more criteria."^^xsd:string ; - + prov:editorialNote "Discussed in https://github.com/incf-nidash/nidm/issues/71."^^xsd:string ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1930,15 +1930,15 @@ nidm:NIDM_0000006 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000007 nidm:NIDM_0000007 rdf:type owl:Class ; - + rdfs:label "Cluster Definition Criteria" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Set of criterion specified a priori to define the clusters reported after inference (e.g. pixel or voxel connectivity criterion)." ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/ClusterDefinitionCriteria.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1946,17 +1946,17 @@ nidm:NIDM_0000007 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000008 nidm:NIDM_0000008 rdf:type owl:Class ; - + rdfs:label "Cluster Labels Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/ClusterLabelsMap.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) denotes cluster membership within the excursion set. Each cluster is denoted by a different integer and all members of the same cluster have the same value." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/282" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1964,15 +1964,15 @@ nidm:NIDM_0000008 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000011 nidm:NIDM_0000011 rdf:type owl:Class ; - + rdfs:label "Conjunction Inference" ; - + rdfs:subClassOf nidm:NIDM_0000049 ; - + obo:IAO_0000115 "Statistically testing for the joint significance of multiple effects, with emphasis on rejecting all (instead of one or more) of the respective null hypotheses." ; - + obo:IAO_0000116 "Term discussed in https://github.com/incf-nidash/nidm/pull/134" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1980,17 +1980,17 @@ nidm:NIDM_0000011 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000012 nidm:NIDM_0000012 rdf:type owl:Class ; - + rdfs:label "Connectivity Criterion" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000117 "TN, KH, CM" ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "The criterion used to characterize two voxels, pixels or vertices as 'connected'." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1998,17 +1998,17 @@ nidm:NIDM_0000012 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000013 nidm:NIDM_0000013 rdf:type owl:Class ; - + rdfs:label "Contrast Standard Error Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/255."^^xsd:anyURI ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/ContrastStandardErrorMap.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [standard error of a contrast estimate](http://purl.obolibrary.org/obo/STATO_0000385)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2016,17 +2016,17 @@ nidm:NIDM_0000013 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000015 nidm:NIDM_0000015 rdf:type owl:Class ; - + rdfs:label "Coordinate" ; - + rdfs:subClassOf prov:Entity ; - + owl:sameAs "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C44465"^^xsd:anyURI ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/Coordinate.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/pull/144 and https://github.com/incf-nidash/nidm/pull/172" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2034,17 +2034,17 @@ nidm:NIDM_0000015 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000016 nidm:NIDM_0000016 rdf:type owl:Class ; - + rdfs:label "Coordinate Space" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/CoordinateSpace.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "An entity with spatial attributes (e.g., dimensions, units, and voxel-to-world mapping) that provides context to a Map (e.g., a Statistic Map, a Contrast Map...)." ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/issues/290" ; - + obo:IAO_0000114 obo:IAO_0000125 . @@ -2052,15 +2052,15 @@ nidm:NIDM_0000016 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000017 nidm:NIDM_0000017 rdf:type owl:Class ; - + rdfs:label "Custom Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000075 ; - + obo:IAO_0000115 "Custom (unknown) reference space selected by the user" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2068,17 +2068,17 @@ nidm:NIDM_0000017 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000018 nidm:NIDM_0000018 rdf:type owl:Class ; - + rdfs:label "Data Scaling" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/Data.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Scaling applied to the data before parameter estimation, including specification of the target intensity." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/285" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2086,9 +2086,9 @@ nidm:NIDM_0000018 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000019 nidm:NIDM_0000019 rdf:type owl:Class ; - + rdfs:label "Design Matrix" ; - + rdfs:subClassOf prov:Entity , [ rdf:type owl:Restriction ; owl:onProperty dc:description ; @@ -2105,15 +2105,15 @@ nidm:NIDM_0000019 rdf:type owl:Class ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ; owl:onDataRange xsd:string ] ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/DesignMatrix.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/274" ; - + rdfs:seeAlso "stato:design matrix" ; - + obo:IAO_0000115 "A [stato:design matrix](http://purl.obolibrary.org/obo/STATO_0000289), with additional neuroimaging attributes, including HRF and drift for first level fMRI models" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2121,17 +2121,17 @@ nidm:NIDM_0000019 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000020 nidm:NIDM_0000020 rdf:type owl:Class ; - + rdfs:label "Display Mask Map" ; - + rdfs:subClassOf nidm:NIDM_0000004 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/DisplayMaskMap.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/258 and https://github.com/incf-nidash/nidm/pull/157" ; - + obo:IAO_0000115 "A binary map used by an activity that changed the voxels displayed, but did not alter the space in which the activity was performed (e.g. at the level of inference, this mask is called \"contrast masking\" in both FSL & SPM and does not alter voxel-wise corrected p-values)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2139,13 +2139,13 @@ nidm:NIDM_0000020 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000022 nidm:NIDM_0000022 rdf:type owl:Class ; - + rdfs:label "Error Distribution" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Probability distribution used to model the error." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2153,15 +2153,15 @@ nidm:NIDM_0000022 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000023 nidm:NIDM_0000023 rdf:type owl:Class ; - + rdfs:label "Error Model" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/ErrorModel.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Model used to describe the random variation of the error term as part of parameter estimation, including specification of the error probability distribution, its variance and dependence both spatially and across observations." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2169,17 +2169,17 @@ nidm:NIDM_0000023 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000024 nidm:NIDM_0000024 rdf:type owl:Class ; - + rdfs:label "Exchangeable Error" ; - + rdfs:subClassOf obo:STATO_0000346 ; - + rdfs:comment "Under gaussianity assumption this is equivalent to compound symmetry but not in general." ; - + obo:IAO_0000117 "TN" ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/28" ; - + obo:IAO_0000114 obo:IAO_0000423 . @@ -2187,22 +2187,22 @@ nidm:NIDM_0000024 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000025 nidm:NIDM_0000025 rdf:type owl:Class ; - + rdfs:label "Excursion Set Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 , [ rdf:type owl:Restriction ; owl:onProperty dc:description ; owl:onClass dctype:Image ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ] ; - + obo:IAO_0000116 "Discussed in the Neuroimaging terms spreadsheet and in https://github.com/incf-nidash/nidm/issues/256." ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/ExcursionSetMap.txt" ; - + obo:IAO_0000115 "A map in which the set of elements (e.g., pixels, voxels, vertices, or faces) not selected by the inference activity is set to zero or NaN" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2210,20 +2210,20 @@ nidm:NIDM_0000025 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000026 nidm:NIDM_0000026 rdf:type owl:Class ; - + rdfs:label "Extent Threshold" ; - + rdfs:subClassOf nidm:NIDM_0000162 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/ExtentThreshold-FDR.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/ExtentThreshold-Unc.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/ExtentThresholdStat.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/ExtentThreshold_equivThresh-FWER.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A numerical value that establishes a lower bound on cluster-sizes and can be specified by the user in terms of FWER-corrected p-value, uncorrected p-value or minimum cluster size in voxels" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/273" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2231,15 +2231,15 @@ nidm:NIDM_0000026 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000027 nidm:NIDM_0000027 rdf:type owl:Class ; - + rdfs:label "NIDM-Results" ; - + rdfs:subClassOf nidm:NIDM_0000057 ; - + obo:IAO_0000115 "NIDM Object model representing the results of a mass univariate neuroimaging study and targeting the application of meta-analysis. The specification is available at: http://nidm.nidash.org/specs/nidm-results.html" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/137" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2247,15 +2247,15 @@ nidm:NIDM_0000027 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000028 nidm:NIDM_0000028 rdf:type owl:Class ; - + rdfs:label "Finite Impulse Response Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000115 "Set of Finite impulse response (FIR) filters, with FIR the convolution kernel is represented as a set of discrete fixed-width \"impulses\" (definition adapted from [FSL wiki](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html))" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2263,15 +2263,15 @@ nidm:NIDM_0000028 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000029 nidm:NIDM_0000029 rdf:type owl:Class ; - + rdfs:label "Gamma Difference HRF" ; - + rdfs:subClassOf nidm:NIDM_0000035 ; - + obo:IAO_0000115 "Hemodynamic response function which is a difference of two gamma probability density functions." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2279,15 +2279,15 @@ nidm:NIDM_0000029 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000030 nidm:NIDM_0000030 rdf:type owl:Class ; - + rdfs:label "Gamma Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000115 "Set of gamma probability density functions." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2295,15 +2295,15 @@ nidm:NIDM_0000030 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000031 nidm:NIDM_0000031 rdf:type owl:Class ; - + rdfs:label "Gamma HRF" ; - + rdfs:subClassOf nidm:NIDM_0000035 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "Hemodynamic response function which is a gamma probability density function." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2311,15 +2311,15 @@ nidm:NIDM_0000031 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000032 nidm:NIDM_0000032 rdf:type owl:Class ; - + rdfs:label "Gaussian Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000227"^^xsd:anyURI ; - + obo:IAO_0000115 "A normal distribution is a continuous probability distribution described by a probability distribution function described here: http://mathworld.wolfram.com/NormalDistribution.html (Definition from STATO)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2327,17 +2327,17 @@ nidm:NIDM_0000032 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000033 nidm:NIDM_0000033 rdf:type owl:Class ; - + rdfs:label "Grand Mean Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/GrandMeanMap.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/288" ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is the mean over all observations of that element in the input maps (after any scaling of those input maps)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2345,20 +2345,20 @@ nidm:NIDM_0000033 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000034 nidm:NIDM_0000034 rdf:type owl:Class ; - + rdfs:label "Height Threshold" ; - + rdfs:subClassOf nidm:NIDM_0000162 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/HeightThreshold-FDR.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/HeightThreshold-Stat.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/HeightThreshold-Unc.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/HeightThreshold_equivThresh-FWER.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A numerical value that establishes a lower bound on statistic values and can be specified by the user in terms of FWER-corrected p-value, uncorrected p-value or minimum statistic value." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/280" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2366,15 +2366,15 @@ nidm:NIDM_0000034 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000035 nidm:NIDM_0000035 rdf:type owl:Class ; - + rdfs:label "Hemodynamic Response Function" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "Hemodynamic response function basis that can on its own be used to represent the idealised hemodynamic response function." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2382,15 +2382,15 @@ nidm:NIDM_0000035 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000036 nidm:NIDM_0000036 rdf:type owl:Class ; - + rdfs:label "Convolution Basis Set" ; - + rdfs:subClassOf prov:Entity ; - + rdfs:isDefinedBy "A set of functions that, when convolved with the anticipated neural responses, yield a set of regressors to model the anticipated hemodynamic responses."^^xsd:string ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000124 . @@ -2398,15 +2398,15 @@ nidm:NIDM_0000036 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000037 nidm:NIDM_0000037 rdf:type owl:Class ; - + rdfs:label "Hemodynamic Response Function Derivative" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000115 "Hemodynamic response function basis which is the derivative of an hemodynamic response function." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2414,15 +2414,15 @@ nidm:NIDM_0000037 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000048 nidm:NIDM_0000048 rdf:type owl:Class ; - + rdfs:label "Independent Error" ; - + rdfs:subClassOf obo:STATO_0000346 ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/28" ; - + obo:IAO_0000117 "TN" ; - + obo:IAO_0000114 obo:IAO_0000423 . @@ -2430,17 +2430,17 @@ nidm:NIDM_0000048 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000049 nidm:NIDM_0000049 rdf:type owl:Class ; - + rdfs:label "Inference" ; - + rdfs:subClassOf prov:Activity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/Inference.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Statistical inference is a process of drawing conclusions following data analysis using statistical methods (statistical tests) and evaluating whether to reject or accept null hypothesis. (definition from STATO)." ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000299" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2448,17 +2448,17 @@ nidm:NIDM_0000049 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000051 nidm:NIDM_0000051 rdf:type owl:Class ; - + rdfs:label "MNI Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000075 ; - + rdfs:seeAlso "birnlex_2125" ; - + obo:IAO_0000115 "MNI 305 coordinate system or any coordinate system derived from MNI 305." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2466,9 +2466,9 @@ nidm:NIDM_0000051 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000052 nidm:NIDM_0000052 rdf:type owl:Class ; - + rdfs:label "Map" ; - + rdfs:subClassOf prov:Entity , [ rdf:type owl:Restriction ; owl:onProperty crypto:sha512 ; @@ -2485,11 +2485,11 @@ nidm:NIDM_0000052 rdf:type owl:Class ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ; owl:onDataRange xsd:string ] ; - + obo:IAO_0000115 "Ordered set of values corresponding to the discrete sampling of some process (e.g. brain MRI data measured on a regular 3D lattice; or brain cortical surface data measured irregularly over the cortex)." ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/pull/149" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2497,9 +2497,9 @@ nidm:NIDM_0000052 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000053 nidm:NIDM_0000053 rdf:type owl:Class ; - + rdfs:label "Map Header" ; - + rdfs:subClassOf prov:Entity , [ rdf:type owl:Restriction ; owl:onProperty nfo:fileName ; @@ -2516,11 +2516,11 @@ nidm:NIDM_0000053 rdf:type owl:Class ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ; owl:onDataRange xsd:string ] ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/289" ; - + obo:IAO_0000115 "A file associated with a Map to provide header information (e.g. NIfTI header file)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2528,17 +2528,17 @@ nidm:NIDM_0000053 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000054 nidm:NIDM_0000054 rdf:type owl:Class ; - + rdfs:label "Mask Map" ; - + rdfs:subClassOf nidm:NIDM_0000004 ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/258 and https://github.com/incf-nidash/nidm/issues/155" ; - + obo:IAO_0000115 "A binary map representing the exact set of elements (e.g., pixels, voxels, vertices, and faces) in which an activity was performed (e.g. the mask map generated by the model parameter estimation activity represents the exact set of voxels in which the mass univariate model was estimated) and/or restraining the space in which an activity was performed (e.g. the mask map used by inference)" ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/MaskMap.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2546,17 +2546,17 @@ nidm:NIDM_0000054 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000056 nidm:NIDM_0000056 rdf:type owl:Class ; - + rdfs:label "Model Parameters Estimation" ; - + rdfs:subClassOf prov:Activity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/ModelParametersEstimation.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "the process of performing a [obo:model parameter estimation](http://purl.obolibrary.org/obo/STATO_0000119) at each element (e.g., pixel, voxel, vertex, or face) of a map" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/issues/141" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2564,15 +2564,15 @@ nidm:NIDM_0000056 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000057 nidm:NIDM_0000057 rdf:type owl:Class ; - + rdfs:label "NIDM Object Model" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Abstraction on the data model, developed for a specific application/use-case/task at hand, that specifies the components and relations necessary for use by these applications. The same object model can be reused by multiple applications (e.g., meta-analysis, Neurovault)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/137" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2580,13 +2580,13 @@ nidm:NIDM_0000057 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000058 nidm:NIDM_0000058 rdf:type owl:Class ; - + rdfs:label "Non Parametric Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + obo:IAO_0000115 "Probability distribution estimated empirically on the data without assumptions on the shape of the probability distribution." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2594,13 +2594,13 @@ nidm:NIDM_0000058 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000059 nidm:NIDM_0000059 rdf:type owl:Class ; - + rdfs:label "Non Parametric Symmetric Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + obo:IAO_0000115 "Probability distribution estimated empirically on the data assuming only symmetry of the probability distribution." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2608,15 +2608,15 @@ nidm:NIDM_0000059 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000060 nidm:NIDM_0000060 rdf:type owl:Class ; - + rdfs:label "One Tailed Test" ; - + rdfs:subClassOf prov:Entity ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000286"^^xsd:anyURI ; - + obo:IAO_0000116 "Re-use \"one tailed test\" from STATO." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2624,17 +2624,17 @@ nidm:NIDM_0000060 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000061 nidm:NIDM_0000061 rdf:type owl:Class ; - + rdfs:label "Parameter Estimate Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/ParameterEstimateMap.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/255 and https://github.com/incf-nidash/nidm/issues/141 (see also https://github.com/ISA-tools/stato/issues/18)" ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [model parameter estimate](http://purl.obolibrary.org/obo/STATO_0000144)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2642,17 +2642,17 @@ nidm:NIDM_0000061 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000062 nidm:NIDM_0000062 rdf:type owl:Class ; - + rdfs:label "Peak" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "A map element (e.g., pixel, voxel, vertex, or face) which is a local maximum in the significant cluster and complies with the peak definition criteria." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/283" ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/Peak_ValueP.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2660,17 +2660,17 @@ nidm:NIDM_0000062 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000063 nidm:NIDM_0000063 rdf:type owl:Class ; - + rdfs:label "Peak Definition Criteria" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/PeakDefinitionCriteria_MaxPeaks.txt"^^xsd:anyURI ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/200" ; - + obo:IAO_0000115 "Set of criterion specified a priori to define the peaks reported after inference (e.g. maximum number of peaks within a cluster, minimum distance between peaks)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2678,15 +2678,15 @@ nidm:NIDM_0000063 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000064 nidm:NIDM_0000064 rdf:type owl:Class ; - + rdfs:label "Pixel Connectivity Criterion" ; - + rdfs:subClassOf nidm:NIDM_0000012 ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "The criterion used to characterize two pixels as 'connected'. In two dimensions voxels that are connected can share an edge (4-connected) or, edge or corner (8-connected)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2694,15 +2694,15 @@ nidm:NIDM_0000064 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000065 nidm:NIDM_0000065 rdf:type owl:Class ; - + rdfs:label "Poisson Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000051"^^xsd:anyURI ; - + obo:IAO_0000115 "Poisson distribution is a probability distribution used to model the number of events occurring within a given time interval. It is defined by a real number (λ) and an integer k representing the number of events and a function. The expected value of a Poisson-distributed random variable is equal to λ and so is its variance. (Definition from STATO)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2710,17 +2710,17 @@ nidm:NIDM_0000065 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000066 nidm:NIDM_0000066 rdf:type owl:Class ; - + rdfs:label "Residual Mean Squares Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/255." ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [residual mean square](http://purl.obolibrary.org/obo/STATO_0000375)." ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/ResidualMeanSquaresMap.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2728,15 +2728,15 @@ nidm:NIDM_0000066 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000067 nidm:NIDM_0000067 rdf:type owl:Class ; - + rdfs:label "Custom Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "Customised set of basis functions." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2744,17 +2744,17 @@ nidm:NIDM_0000067 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000068 nidm:NIDM_0000068 rdf:type owl:Class ; - + rdfs:label "Search Space Mask Map" ; - + rdfs:subClassOf nidm:NIDM_0000054 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/SearchSpaceMaskMap.txt" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/258" ; - + obo:IAO_0000115 "A mask map representing the set of elements (e.g., pixels, voxels, vertices, or faces) in which the inference was performed" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2762,15 +2762,15 @@ nidm:NIDM_0000068 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000069 nidm:NIDM_0000069 rdf:type owl:Class ; - + rdfs:label "Fourier Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000115 "Set of Fourier basis." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2778,17 +2778,17 @@ nidm:NIDM_0000069 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000070 nidm:NIDM_0000070 rdf:type owl:Class ; - + rdfs:label "Significant Cluster" ; - + rdfs:subClassOf nidm:NIDM_0000006 ; - + obo:IAO_0000115 "A cluster of map elements (e.g., pixels, voxels, vertices, and faces) that were selected by the inference activity and are contiguous according to the cluster connectivity criteria."^^xsd:string ; - + prov:editorialNote "Discussed in https://github.com/incf-nidash/nidm/issues/71."^^xsd:string ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/SignificantCluster.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2796,15 +2796,15 @@ nidm:NIDM_0000070 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000071 nidm:NIDM_0000071 rdf:type owl:Class ; - + rdfs:label "Error Parameter Map-Wise Dependence" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Map-wise dependence structure of a parameter in the error model (i.e. variance or dependence parameter). For example, whether a temporal autocorrelation parameter is estimated at each element separately, estimated using data in a local neighbourhood, or estimated using all elements in the map." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2812,15 +2812,15 @@ nidm:NIDM_0000071 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000072 nidm:NIDM_0000072 rdf:type owl:Class ; - + rdfs:label "Constant Parameter" ; - + rdfs:subClassOf nidm:NIDM_0000071 ; - + obo:IAO_0000115 "Parameter estimated as constant over a entire set of elements considered (e.g. those in the analysis mask)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2828,15 +2828,15 @@ nidm:NIDM_0000072 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000073 nidm:NIDM_0000073 rdf:type owl:Class ; - + rdfs:label "Independent Parameter" ; - + rdfs:subClassOf nidm:NIDM_0000071 ; - + obo:IAO_0000115 "Parameter whose estimation at a given element does not depend on any other element." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2844,15 +2844,15 @@ nidm:NIDM_0000073 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000074 nidm:NIDM_0000074 rdf:type owl:Class ; - + rdfs:label "Regularized Parameter" ; - + rdfs:subClassOf nidm:NIDM_0000071 ; - + obo:IAO_0000115 "Parameter whose estimation at a given element depends on a local neighborhood of elements" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2860,17 +2860,17 @@ nidm:NIDM_0000074 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000075 nidm:NIDM_0000075 rdf:type owl:Class ; - + rdfs:label "Standardized Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000081 ; - + rdfs:comment "This is meant to be used for retrospective export when exact template is unknown." ; - + obo:IAO_0000115 "Parent of all reference spaces except \"Subject\"." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -2878,17 +2878,17 @@ nidm:NIDM_0000075 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000076 nidm:NIDM_0000076 rdf:type owl:Class ; - + rdfs:label "Statistic Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/StatisticMap_T.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/255" ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [statistic](http://purl.obolibrary.org/obo/STATO_0000039)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2896,17 +2896,17 @@ nidm:NIDM_0000076 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000077 nidm:NIDM_0000077 rdf:type owl:Class ; - + rdfs:label "Subject Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000081 ; - + obo:IAO_0000115 "Reference space corresponding to the subject brain (no spatial normalization applied)." ; - + rdfs:comment "Used in FSL and SPM un-registered data." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -2914,17 +2914,17 @@ nidm:NIDM_0000077 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000078 nidm:NIDM_0000078 rdf:type owl:Class ; - + rdfs:label "Talairach Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000075 ; - + obo:IAO_0000115 "Reference space defined by the dissected brain used for the Talairach and Tournoux atlas (cf. http://www.talairach.org/about.html)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + rdfs:seeAlso "http://www.talairach.org/" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2932,15 +2932,15 @@ nidm:NIDM_0000078 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000079 nidm:NIDM_0000079 rdf:type owl:Class ; - + rdfs:label "Two Tailed Test" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Re-use \"two tailed test\" from STATO"^^xsd:anyURI ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000287"^^xsd:anyURI ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2948,15 +2948,15 @@ nidm:NIDM_0000079 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000080 nidm:NIDM_0000080 rdf:type owl:Class ; - + rdfs:label "Voxel Connectivity Criterion" ; - + rdfs:subClassOf nidm:NIDM_0000012 ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "The criterion used to characterize two voxels as 'connected'. In three dimensions voxels that are connected can share a voxel face (6-connected), face or edge (18-connectec), or face, edge, or corner (26-connected)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2964,16 +2964,16 @@ nidm:NIDM_0000080 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000081 nidm:NIDM_0000081 rdf:type owl:Class ; - + rdfs:label "World Coordinate System" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 """Reference space on which real-world positions are expressed (cf. [Nifti-1 FAQ question 14](http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q14) and [Understanding affines on nipy](http://nipy.org/nipy/stable/devel/code_discussions/understanding_affines.html) ). A world coordinate system can be represented by an image obtained by registering an initial set of images, using a given normalization algorithm to match a target template.""" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2981,18 +2981,18 @@ nidm:NIDM_0000081 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000087 nidm:NIDM_0000087 rdf:type owl:Class ; - + rdfs:label "Drift Model" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/FSL_DriftModel.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/SPM_DriftModel.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000115 "A model used to compensate for low frequency baseline drifts when analyzing functional MRI data at the subject level." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3000,15 +3000,15 @@ nidm:NIDM_0000087 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000110 nidm:NIDM_0000110 rdf:type owl:Class ; - + rdfs:label "Gaussian HRF" ; - + rdfs:subClassOf nidm:NIDM_0000035 ; - + obo:IAO_0000115 "Hemodynamic response function which is a gaussian kernel." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3016,15 +3016,15 @@ nidm:NIDM_0000110 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000135 nidm:NIDM_0000135 rdf:type owl:Class ; - + rdfs:label "Contrast Variance Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a contrast variance (i.e. the square of a [standard error of a contrast estimate](http://purl.obolibrary.org/obo/STATO_0000385))" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/287" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3032,19 +3032,19 @@ nidm:NIDM_0000135 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000140 nidm:NIDM_0000140 rdf:type owl:Class ; - + rdfs:label "Cluster Center Of Gravity" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/257" ; - + obo:IAO_0000115 "A centre of gravity of the cluster, equivalent to the concept of Centre Of Gravity for a object with distributed mass, where intensity substitutes for mass in this case. The coordinate of the centre of gravity is the weighted average of the cluster element (e.g., pixels, voxels, vertices, or faces) coordinates, where the weighting factors are the cluster element intensities. (definition adapted from http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster)" ; - + rdfs:seeAlso "http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster" ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/FSL_ClusterCenterOfGravity.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3052,15 +3052,15 @@ nidm:NIDM_0000140 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000144 nidm:NIDM_0000144 rdf:type owl:Class ; - + rdfs:label "Resels Per Voxel Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.1.0/nidm/nidm-results/terms/examples/SPM_ReselsPerVoxelMap.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) location is the number of resels per voxel." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3068,15 +3068,15 @@ nidm:NIDM_0000144 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000150 nidm:NIDM_0000150 rdf:type owl:Class ; - + rdfs:label "Linear Spline Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "A Linear (order 1) spline, providing an estimate that is continuous over time (in contrast to a FIR basis, which is discontinuous between each time bin). This is called TENT in AFNI's 3dDeconvolve program." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3084,15 +3084,15 @@ nidm:NIDM_0000150 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000151 nidm:NIDM_0000151 rdf:type owl:Class ; - + rdfs:label "Sine Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "A set of Sine waves of differing frequencies (definition adapted from [FSL wiki](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html))." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3100,15 +3100,15 @@ nidm:NIDM_0000151 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000155 nidm:NIDM_0000155 rdf:type owl:Class ; - + rdfs:label "fMRI Design Type" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/299" ; - + obo:IAO_0000115 "The type of stimulus presentation used in the data acquisition, one of block-based design event-related design or mixed design." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3116,15 +3116,15 @@ nidm:NIDM_0000155 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000160 nidm:NIDM_0000160 rdf:type owl:Class ; - + rdfs:label "P-Value Uncorrected" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "A p-value reported without correction for multiple testing."^^xsd:string ; - + obo:IAO_0000116 "Discussed in [Neuroimaging terms spreadsheet](https://docs.google.com/spreadsheets/d/16pC2cDsdxlzv2CzlNMtStqt5-xHwDEsU6MjZVxWhrE4/edit?usp=sharing)"^^xsd:string ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3132,13 +3132,13 @@ nidm:NIDM_0000160 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000162 nidm:NIDM_0000162 rdf:type owl:Class ; - + rdfs:label "Threshold"^^xsd:string ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "A numerical value that establishes a bound on a set of statistic values and can be specified by the user in terms of FWER-corrected p-value, uncorrected p-value, FDR-corrected q-value or statistic value"^^xsd:string ; - + obo:IAO_0000114 obo:IAO_0000125 . @@ -3146,15 +3146,15 @@ nidm:NIDM_0000162 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000163 nidm:NIDM_0000163 rdf:type owl:Class ; - + rdfs:label "Contrast Explained Mean Square Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is the extra sum of squares divided by the effect degrees of freedom (i.e. the denumerator of an F-statistic)." ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/235" ; - + obo:IAO_0000114 obo:IAO_0000125 . @@ -3162,15 +3162,15 @@ nidm:NIDM_0000163 rdf:type owl:Class ; ### http://purl.org/nidash/spm#SPM_0000002 spm:SPM_0000002 rdf:type owl:Class ; - + rdfs:label "DCT Drift Model" ; - + rdfs:subClassOf nidm:NIDM_0000087 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000115 "A drift model in which the drifts are modeled by a Discrete Cosine Transform basis added to regression model" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3178,15 +3178,15 @@ spm:SPM_0000002 rdf:type owl:Class ; ### http://purl.org/nidash/spm#SPM_0000005 spm:SPM_0000005 rdf:type owl:Class ; - + rdfs:label "Partial Conjunction Inference" ; - + rdfs:subClassOf nidm:NIDM_0000049 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/294" ; - + obo:IAO_0000115 "The process of testing the joint significance of multiple effects to infer that some (not necessarily all) of the respective effects are real (i.e. their null hypotheses are false). If there are K effects considered, the partial conjunction degree u is the number non-null effects allowed as part of partial conjunction null hypothesis; if the partial conjunction null is rejected, it may be inferred that u+1 or more effects are real. The case of u=K-1 corresponds to proper \"conjunction inference\", while the case of u=0 corresponds to \"global null\" conjunction test. See [Friston et al. (2005). Conjunction revisited. NeuroImage, 25(3), 661-7.](http://dx.doi.org/10.1016/j.neuroimage.2005.01.013)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3208,13 +3208,13 @@ spm:SPM_0000005 rdf:type owl:Class ; fsl:FSL_0000001 rdf:type nidm:NIDM_0000029 , owl:NamedIndividual ; - + rdfs:label "FSL's Gamma Difference HRF" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "Hemodynamic response function which is a fixed difference of two gamma probability density functions - a standard positive function at normal lag, and a small, delayed, negated gamma probability density function, which attempts to model the late undershoot (definition adapted [FSL wiki](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html)). This is the default in FSL." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3223,13 +3223,13 @@ fsl:FSL_0000001 rdf:type nidm:NIDM_0000029 , fsl:FSL_0000003 rdf:type nidm:NIDM_0000037 , owl:NamedIndividual ; - + rdfs:label "FSL's Temporal Derivative" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "Hemodynamic response function basis that is the derivative with respect to time of the FSL's Gamma Difference heamodynamic response function." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3238,17 +3238,17 @@ fsl:FSL_0000003 rdf:type nidm:NIDM_0000037 , nidm:NIDM_0000009 rdf:type nidm:NIDM_0000075 , owl:NamedIndividual ; - + rdfs:label "Colin27 Coordinate System" ; - + obo:IAO_0000115 "Reference space defined as the stereotaxic average of 27 T1-weighted MRI scans of the same individual transformed into the Talairach stereotaxic space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres and http://neuro.debian.net/pkgs/mni-colin27-nifti.html). This is the default in SPM96 (cf. [MRC CBSU Wiki](http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach))." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + rdfs:comment "used in SPM96 (cf. http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3257,15 +3257,15 @@ nidm:NIDM_0000009 rdf:type nidm:NIDM_0000075 , nidm:NIDM_0000038 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm452 Air Coordinate System" ; - + obo:IAO_0000115 "Reference space defined as the average of 452 T1-weighted MRIs of normal young adult brains after 12 parameter AIR linear transform to the MNI 305 space (cf. http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml and http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)" ; - + rdfs:seeAlso "http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3274,15 +3274,15 @@ nidm:NIDM_0000038 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000039 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm452 Warp5 Coordinate System" ; - + rdfs:seeAlso "http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml" ; - + obo:IAO_0000115 "Reference space defined as the average of 452 T1-weighted MRIs of normal young adult brains after affine and 5 order polynomial non-linear warping to the MNI 305 space (cf. http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml and http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3291,17 +3291,17 @@ nidm:NIDM_0000039 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000040 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Linear Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin" ; - + rdfs:comment "used in SPM99 to SPM8 (cf. http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach and spm8/spm_templates.man)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Reference space which is the average of 152 T1-weighted MRI scans, linearly transformed onto the MNI 305 reference space (definition adapted from: http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin). This is the default in SPM99 to SPM8 (cf. [MRC CBSU Wiki](http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach) and spm8/spm_templates.man." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3310,15 +3310,15 @@ nidm:NIDM_0000040 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000041 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009a Asymmetric Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3327,15 +3327,15 @@ nidm:NIDM_0000041 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000042 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009a Symmetric Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to to form a symmetric model in MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3344,15 +3344,15 @@ nidm:NIDM_0000042 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000043 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009b Asymmetric Coordinate System" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans in high-resolution, non-linearly transformed to MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3361,15 +3361,15 @@ nidm:NIDM_0000043 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000044 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009b Symmetric Coordinate System" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans in high-resolution, non-linearly transformed to form a symmetric model in MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3378,17 +3378,17 @@ nidm:NIDM_0000044 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000045 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009c Asymmetric Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space using the N3 algorithm (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + rdfs:comment "Used in DARTEL toolbox in SPM12b (cf. spm12b/spm_templates.man)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3397,15 +3397,15 @@ nidm:NIDM_0000045 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000046 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009c Symmetric Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to form a symmetric model in MNI152 linear space using the N3 algorithm (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details). This is the default for DARTEL toolbox in SPM12b (cf. spm12/spm_templates.man)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3414,17 +3414,17 @@ nidm:NIDM_0000046 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000047 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear6th Generation Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6"^^xsd:anyURI ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, linearly and non-linearly (6 iterations) transformed to form a symmetric model in Talairach space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6)" ; - + rdfs:comment "Used in FSL (cf. http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3433,17 +3433,17 @@ nidm:NIDM_0000047 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000050 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Ixi549 Coordinate System" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Reference space defined by the average of the 549 subjects from the IXI dataset linearly transformed to the ICBM MNI 452 (cf. spm12/spm\\_templates.man and http://biomedic.doc.ic.ac.uk/brain-development/index.php?n=Main.Datasets). This is the default in SPM12 (cf. spm12/spm_templates.man)." ; - + rdfs:seeAlso "http://biomedic.doc.ic.ac.uk/brain-development/index.php?n=Main.Datasets" ; - + rdfs:comment "Used in SPM12b (cf. spm12b/spm_templates.man)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3452,15 +3452,15 @@ nidm:NIDM_0000050 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000055 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Mni305 Coordinate System" ; - + obo:IAO_0000115 "Reference space defined as the average of 305 T1-weighted MRI scans, linearly transformed to Talairach space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/MNI305 for more details)" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/MNI305" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3469,13 +3469,13 @@ nidm:NIDM_0000055 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000117 rdf:type nidm:NIDM_0000064 , owl:NamedIndividual ; - + rdfs:label "pixel4connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of pixels are 4-Connected if they share an edge." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3484,13 +3484,13 @@ nidm:NIDM_0000117 rdf:type nidm:NIDM_0000064 , nidm:NIDM_0000118 rdf:type nidm:NIDM_0000064 , owl:NamedIndividual ; - + rdfs:label "pixel8connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of pixels are 8-Connected if they share an edge or corner." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3499,13 +3499,13 @@ nidm:NIDM_0000118 rdf:type nidm:NIDM_0000064 , nidm:NIDM_0000128 rdf:type nidm:NIDM_0000080 , owl:NamedIndividual ; - + rdfs:label "voxel18connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of voxels are 18-Connected if they share a face or edge." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3514,13 +3514,13 @@ nidm:NIDM_0000128 rdf:type nidm:NIDM_0000080 , nidm:NIDM_0000129 rdf:type nidm:NIDM_0000080 , owl:NamedIndividual ; - + rdfs:label "voxel26connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of voxels are 26-Connected if they share a face, edge or corner." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3529,13 +3529,13 @@ nidm:NIDM_0000129 rdf:type nidm:NIDM_0000080 , nidm:NIDM_0000130 rdf:type nidm:NIDM_0000080 , owl:NamedIndividual ; - + rdfs:label "voxel6connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of voxels are 6-Connected if they share a face." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3544,13 +3544,13 @@ nidm:NIDM_0000130 rdf:type nidm:NIDM_0000080 , nidm:NIDM_0000152 rdf:type nidm:NIDM_0000155 , owl:NamedIndividual ; - + rdfs:label "Block-Based Design" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/299" ; - + obo:IAO_0000115 "An fMRI design comprised of epochs of stimulus and/or behavior." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3559,13 +3559,13 @@ nidm:NIDM_0000152 rdf:type nidm:NIDM_0000155 , nidm:NIDM_0000153 rdf:type nidm:NIDM_0000155 , owl:NamedIndividual ; - + rdfs:label "Event-Related Design" ; - + obo:IAO_0000115 "An fMRI design comprised of discrete events of stimulus and/or behavior." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/299" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3574,13 +3574,13 @@ nidm:NIDM_0000153 rdf:type nidm:NIDM_0000155 , nidm:NIDM_0000154 rdf:type nidm:NIDM_0000155 , owl:NamedIndividual ; - + rdfs:label "Mixed Design" ; - + obo:IAO_0000115 "An fMRI design comprised of both epochs & discrete events of stimulus and/or behavior." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/299" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3589,13 +3589,13 @@ nidm:NIDM_0000154 rdf:type nidm:NIDM_0000155 , spm:SPM_0000003 rdf:type nidm:NIDM_0000037 , owl:NamedIndividual ; - + rdfs:label "SPM's Dispersion Derivative" ; - + obo:IAO_0000115 "Hemodynamic response function basis that is the derivative with respect to spatial dispersion of the SPM's Canonical heamodynamic response function." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3604,13 +3604,13 @@ spm:SPM_0000003 rdf:type nidm:NIDM_0000037 , spm:SPM_0000004 rdf:type nidm:NIDM_0000029 , owl:NamedIndividual ; - + rdfs:label "SPM's Canonical HRF" ; - + obo:IAO_0000115 "Hemodynamic response function which is a fixed difference of two gamma probability density functions and is denoted by \"canonical HRF\" in SPM. This is the default in SPM" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3619,13 +3619,13 @@ spm:SPM_0000004 rdf:type nidm:NIDM_0000029 , spm:SPM_0000006 rdf:type nidm:NIDM_0000037 , owl:NamedIndividual ; - + rdfs:label "SPM's Temporal Derivative" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "Hemodynamic response function basis that is the derivative with respect to time of the SPM's Canonical heamodynamic response function." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3638,18 +3638,18 @@ spm:SPM_0000006 rdf:type nidm:NIDM_0000037 , ##### Imports from iao ##### . rdf:type owl:Ontology ; - + dc:date "2009-07-31"^^xsd:date ; - + owl:versionInfo "2015-02-23"^^xsd:string ; - + rdfs:comment "An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/"^^xsd:string , "IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999"^^xsd:string , "IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999"^^xsd:string , "This file is based on checkout of our SVN repository revision $Revision: 717 $ "^^xsd:string ; - + protege:defaultLanguage "en"^^xsd:string ; - + dc:contributor "Adam Goldstein"@en , "Alan Ruttenberg"@en , "Albert Goldfain"@en , @@ -3685,11 +3685,11 @@ spm:SPM_0000006 rdf:type nidm:NIDM_0000037 , "William Duncan"@en , "William Hogan"@en , "Yongqun (Oliver) He"@en ; - + foaf:homepage ; - + dc:license ; - + owl:versionIRI iao:iao.owl . @@ -3709,13 +3709,13 @@ protege:defaultLanguage rdf:type owl:AnnotationProperty . ### http://purl.obolibrary.org/obo/BFO_0000179 obo:BFO_0000179 rdf:type owl:AnnotationProperty ; - + rdfs:label "BFO OWL specification label"@en ; - + obo:IAO_0000232 "Really of interest to developers only"@en ; - + obo:IAO_0000115 "Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification."@en ; - + rdfs:subPropertyOf rdfs:label . @@ -3723,15 +3723,15 @@ obo:BFO_0000179 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/BFO_0000180 obo:BFO_0000180 rdf:type owl:AnnotationProperty ; - + rdfs:label "BFO CLIF specification label"@en ; - + obo:IAO_0000119 "Person:Alan Ruttenberg" ; - + obo:IAO_0000232 "Really of interest to developers only"@en ; - + obo:IAO_0000115 "Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2"@en ; - + rdfs:subPropertyOf rdfs:label . @@ -3739,24 +3739,24 @@ obo:BFO_0000180 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000111 obo:IAO_0000111 rdf:type owl:AnnotationProperty ; - + rdfs:label "editor preferred term" , "editor preferred label"@en , "editor preferred term"@en ; - + obo:IAO_0000111 "editor preferred term" ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000115 "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)"@en ; - + obo:IAO_0000111 "editor preferred label"@en , "editor preferred term"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3764,20 +3764,20 @@ obo:IAO_0000111 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000112 obo:IAO_0000112 rdf:type owl:AnnotationProperty ; - + rdfs:label "example of usage"@en ; - + obo:IAO_0000115 "A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not"@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "example"@en , "example of usage"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3785,15 +3785,15 @@ obo:IAO_0000112 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000114 obo:IAO_0000114 rdf:type owl:AnnotationProperty ; - + rdfs:label "has curation status"@en ; - + obo:IAO_0000119 "OBI_0000281"@en ; - + obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en , "PERSON:Bill Bug"@en , "PERSON:Melanie Courtot"@en ; - + obo:IAO_0000111 "has curation status"@en . @@ -3801,27 +3801,27 @@ obo:IAO_0000114 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000115 obo:IAO_0000115 rdf:type owl:AnnotationProperty ; - + rdfs:label "definition"^^xsd:string , "textual definition"^^xsd:string , "definition" , "definition"@en ; - + obo:IAO_0000111 "definition"^^xsd:string , "textual definition"^^xsd:string , "definition" ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000115 "The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en , "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en ; - + obo:IAO_0000111 "definition"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3829,19 +3829,19 @@ obo:IAO_0000115 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000116 obo:IAO_0000116 rdf:type owl:AnnotationProperty ; - + rdfs:label "editor note"@en ; - + obo:IAO_0000115 "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "editor note"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3849,21 +3849,21 @@ obo:IAO_0000116 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000117 obo:IAO_0000117 rdf:type owl:AnnotationProperty ; - + rdfs:label "term editor"@en ; - + obo:IAO_0000116 "20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115."@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000115 "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "term editor"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3871,19 +3871,19 @@ obo:IAO_0000117 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000118 obo:IAO_0000118 rdf:type owl:AnnotationProperty ; - + rdfs:label "alternative term"@en ; - + obo:IAO_0000115 "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)"@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "alternative term"@en ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:isDefinedBy . @@ -3891,20 +3891,20 @@ obo:IAO_0000118 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000119 obo:IAO_0000119 rdf:type owl:AnnotationProperty ; - + rdfs:label "definition source"@en ; - + obo:IAO_0000119 "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"^^xsd:string , "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "definition source"@en ; - + obo:IAO_0000115 "formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3912,17 +3912,17 @@ obo:IAO_0000119 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000232 obo:IAO_0000232 rdf:type owl:AnnotationProperty ; - + rdfs:label "curator note"@en ; - + obo:IAO_0000115 "An administrative note of use for a curator but of no use for a user"@en ; - + obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en ; - + obo:IAO_0000111 "curator note"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3930,20 +3930,20 @@ obo:IAO_0000232 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000412 obo:IAO_0000412 rdf:type owl:AnnotationProperty ; - + rdfs:label "imported from"@en ; - + obo:IAO_0000115 "For external terms/classes, the ontology from which the term was imported"@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en , "PERSON:Melanie Courtot"@en ; - + obo:IAO_0000111 "imported from"@en ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:isDefinedBy . @@ -3951,17 +3951,17 @@ obo:IAO_0000412 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000600 obo:IAO_0000600 rdf:type owl:AnnotationProperty ; - + rdfs:label "elucidation"@en ; - + obo:IAO_0000119 "Person:Barry Smith"@en ; - + obo:IAO_0000600 "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms"@en ; - + obo:IAO_0000111 "elucidation"@en ; - + obo:IAO_0000117 "person:Alan Ruttenberg"@en ; - + rdfs:isDefinedBy . @@ -3969,9 +3969,9 @@ obo:IAO_0000600 rdf:type owl:AnnotationProperty ; ### http://purl.org/dc/elements/1.1/contributor dc:contributor rdf:type owl:AnnotationProperty ; - + rdfs:label "Contributor"@en-us ; - + rdfs:isDefinedBy dc: . @@ -3979,9 +3979,9 @@ dc:contributor rdf:type owl:AnnotationProperty ; ### http://purl.org/dc/elements/1.1/date dc:date rdf:type owl:AnnotationProperty ; - + rdfs:label "Date"@en-us ; - + rdfs:isDefinedBy dc: . @@ -4022,19 +4022,19 @@ foaf:homepage rdf:type owl:AnnotationProperty . ### http://purl.obolibrary.org/obo/IAO_0000136 obo:IAO_0000136 rdf:type owl:ObjectProperty ; - + rdfs:label "is about"@en ; - + obo:IAO_0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en ; - + obo:IAO_0000112 "This document is about information artifacts and their representations"@en ; - + obo:IAO_0000115 "is_about is a (currently) primitive relation that relates an information artifact to an entity."@en ; - + obo:IAO_0000117 "person:Alan Ruttenberg"@en ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + obo:IAO_0000412 . @@ -4051,9 +4051,9 @@ obo:IAO_0000136 rdf:type owl:ObjectProperty ; ### http://usefulinc.com/ns/doap#revision doap:revision rdf:type owl:DatatypeProperty ; - + obo:IAO_0000412 ; - + rdfs:isDefinedBy ns:doap . @@ -4076,7 +4076,7 @@ doap:revision rdf:type owl:DatatypeProperty ; ### http://purl.obolibrary.org/obo/IAO_0000002 obo:IAO_0000002 rdf:type owl:NamedIndividual ; - + rdfs:label "example to be eventually removed"@en . @@ -4084,9 +4084,9 @@ obo:IAO_0000002 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000120 obo:IAO_0000120 rdf:type owl:NamedIndividual ; - + rdfs:label "metadata complete"@en ; - + obo:IAO_0000115 "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en . @@ -4094,9 +4094,9 @@ obo:IAO_0000120 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000121 obo:IAO_0000121 rdf:type owl:NamedIndividual ; - + rdfs:label "organizational term"@en ; - + obo:IAO_0000115 "term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en . @@ -4104,9 +4104,9 @@ obo:IAO_0000121 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000122 obo:IAO_0000122 rdf:type owl:NamedIndividual ; - + rdfs:label "ready for release"@en ; - + obo:IAO_0000115 "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en . @@ -4114,9 +4114,9 @@ obo:IAO_0000122 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000123 obo:IAO_0000123 rdf:type owl:NamedIndividual ; - + rdfs:label "metadata incomplete"@en ; - + obo:IAO_0000115 "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en . @@ -4124,9 +4124,9 @@ obo:IAO_0000123 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000124 obo:IAO_0000124 rdf:type owl:NamedIndividual ; - + rdfs:label "uncurated"@en ; - + obo:IAO_0000115 "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en . @@ -4134,9 +4134,9 @@ obo:IAO_0000124 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000125 obo:IAO_0000125 rdf:type owl:NamedIndividual ; - + rdfs:label "pending final vetting"@en ; - + obo:IAO_0000115 "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en . @@ -4144,13 +4144,13 @@ obo:IAO_0000125 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000423 obo:IAO_0000423 rdf:type owl:NamedIndividual ; - + rdfs:label "to be replaced with external ontology term"@en ; - + obo:IAO_0000117 "Alan Ruttenberg"@en ; - + obo:IAO_0000115 "Terms with this status should eventually replaced with a term from another ontology."@en ; - + obo:IAO_0000119 "group:OBI"@en . @@ -4158,57 +4158,57 @@ obo:IAO_0000423 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000428 obo:IAO_0000428 rdf:type owl:NamedIndividual ; - + rdfs:label "requires discussion"@en ; - + obo:IAO_0000115 "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en ; - + obo:IAO_0000117 "Alan Ruttenberg"@en ; - + obo:IAO_0000119 "group:OBI"@en . ### http://purl.obolibrary.org/obo/OBI_0001442 obo:OBI_0001442 rdf:type owl:Class ; - + rdfs:label "q-value"^^xsd:string ; - + obo:IAO_0000112 """PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines. \"After controlling the false discovery rate (FDR , iao:iao.owl ; - + rdfs:seeAlso . @@ -4263,9 +4263,9 @@ ns:doap rdf:type owl:NamedIndividual . ### http://purl.org/dc/terms/format crypto:sha512 rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Secure Hash Algorithm 512." ; - + rdfs:comment "SHA stands for Secure Hash Algorithm. Hash algorithms compute a fixed-length digital representation (known as a message digest) of an input data sequence (the message) of any length." . ##### Imports from dc ##### . @@ -4283,9 +4283,9 @@ crypto:sha512 rdf:type owl:DatatypeProperty ; ### http://purl.org/dc/elements/1.1/description dc:description rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "An account of the resource." ; - + rdfs:comment "Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource." . @@ -4302,9 +4302,9 @@ dc:description rdf:type owl:ObjectProperty ; ### http://purl.org/dc/terms/format dct:format rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "The file format, physical medium, or dimensions of the resource." ; - + rdfs:comment "Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME]." . @@ -4321,9 +4321,9 @@ dct:format rdf:type owl:DatatypeProperty ; ### http://purl.org/dc/dcmitype/Image dctype:Image rdf:type owl:Class ; - + obo:IAO_0000115 "A visual representation other than text." ; - + rdfs:comment "Examples include images and photographs of physical objects, paintings, prints, drawings, other images and graphics, animations and moving pictures, film, diagrams, maps, musical notation. Note that Image may include both electronic and physical representations." . @@ -4367,13 +4367,13 @@ obo:IAO_0000115 rdf:type owl:AnnotationProperty . ### http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#fileName nfo:fileName rdf:type owl:DatatypeProperty ; - + rdfs:label "fileName" ; - + nrl:maxCardinality "1" ; - + obo:IAO_0000115 "Name of the file, together with the extension" ; - + rdfs:range xsd:string . @@ -4413,9 +4413,9 @@ obo:IAO_0000115 rdf:type owl:AnnotationProperty . ### http://neurolex.org/wiki/birnlex_2067 nlx:birnlex_2067 rdf:type owl:Class ; - + rdfs:label "FSL" ; - + obo:IAO_0000115 "A comprehensive library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. The tools include registration, atlases, Diffusion MRI tools for parameter reconstruction and probabilistic taractography, and a viewer. FSL runs on Apple and PCs (Linux and Windows), and is very easy to install. Most of the tools can be run both from the command line and as GUIs ('point-and-click' graphical user interfaces). Several complementary brain atlases, integrated into FSLView and Featquery, allowing viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Atlases included with FSL: * Harvard-Oxford cortical and subcortical structural atlases * Julich histological atlas * JHU DTI-based white-matter atlases * Oxford thalamic connectivity atlas * Talairach atlas * MNI structural atlas * Cerebellum atlas FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK." . @@ -4423,9 +4423,9 @@ nlx:birnlex_2067 rdf:type owl:Class ; ### http://neurolex.org/wiki/nif-0000-00343 nlx:nif-0000-00343 rdf:type owl:Class ; - + rdfs:label "SPM" ; - + obo:IAO_0000115 "Software package for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG." . @@ -4552,20 +4552,20 @@ obo:OBI_0000299 rdf:type owl:ObjectProperty . ### http://purl.obolibrary.org/obo/STATO_0000030 obo:STATO_0000030 rdf:type owl:Class ; - + rdfs:label "Chi-Squared statistic"@en ; - + rdfs:subClassOf obo:STATO_0000039 ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string , "Alejandra Gonzalez-Beltran"@en ; - + obo:IAO_0000115 "Chi-squared statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Chi-Squared distribution."@en ; - + obo:IAO_0000117 "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO"@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -4573,22 +4573,22 @@ obo:STATO_0000030 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000039 obo:STATO_0000039 rdf:type owl:Class ; - + rdfs:label "statistic"@en ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string ; - + obo:IAO_0000112 ""@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic)."@en ; - + obo:IAO_0000115 "a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data."@en ; - + obo:STATO_0000032 "statistic"@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -4596,21 +4596,21 @@ obo:STATO_0000039 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000119 obo:STATO_0000119 rdf:type owl:Class ; - + rdfs:label "model parameter estimation"@en ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string ; - + obo:IAO_0000119 ""@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000115 "model parameter estimation is a data transformation that finds parameter values (the model parameter estimates) most compatible with the data as judged by the model."@en ; - + obo:IAO_0000116 """textual definition modified following contributiong by Thomas Nichols: https://github.com/ISA-tools/stato/issues/18"""@en ; - + obo:IAO_0000114 obo:IAO_0000125 . @@ -4618,22 +4618,22 @@ https://github.com/ISA-tools/stato/issues/18"""@en ; ### http://purl.obolibrary.org/obo/STATO_0000176 obo:STATO_0000176 rdf:type owl:Class ; - + rdfs:label "t-statistic"@en ; - + rdfs:subClassOf obo:STATO_0000039 ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string ; - + obo:STATO_0000032 ""@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO"@en ; - + obo:IAO_0000115 "t-statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Student's t distribution."@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -4641,20 +4641,20 @@ obo:STATO_0000176 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000282 obo:STATO_0000282 rdf:type owl:Class ; - + rdfs:label "F-statistic"@en ; - + rdfs:subClassOf obo:STATO_0000039 ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string , "Alejandra Gonzalez-Beltran"@en ; - + obo:IAO_0000115 "F statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a F distribution. the F statistic is the ratio of two scaled sums of squares reflecting different sources of variability"@en ; - + obo:IAO_0000117 "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO"@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -4662,22 +4662,22 @@ obo:STATO_0000282 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000323 obo:STATO_0000323 rdf:type owl:Class ; - + rdfs:label "contrast weight matrix"@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Camille Maumet"@en , "Orlaith Burke"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO"@en ; - + obo:IAO_0000117 "Tom Nichols"@en ; - + obo:IAO_0000112 "[1,0,0]"@en ; - + obo:IAO_0000115 "a contrast weight matrix is a information content entity which holds a set of contrast weight, coefficient used in a weighting sum of means defining a contrast"@en ; - + obo:STATO_0000032 "contrast weights"@en . @@ -4685,19 +4685,19 @@ obo:STATO_0000323 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000346 obo:STATO_0000346 rdf:type owl:Class ; - + rdfs:label "covariance structure"@en ; - + obo:IAO_0000117 "Camille Maumet" , "Orlaith Burke" , "Tom Nichols" , "Alejandra Gonzalez-Beltran" , "Philippe Rocca-Serra" ; - + obo:IAO_0000115 "a covariance structure is a data item which is part of a regression model and which indicates a pattern in the covariance matrix. The nature of covariance structure is specified before the regression analysis and various covariance structure may be tested and evaluated using information criteria to help choose the most suitable model"@en ; - + obo:IAO_0000119 "http://www3.nd.edu/~kyuan/courses/sem/readpapers/benter.pdf" ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4705,27 +4705,27 @@ obo:STATO_0000346 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000357 obo:STATO_0000357 rdf:type owl:Class ; - + rdfs:label "Toeplitz covariance structure"@en ; - + rdfs:subClassOf obo:STATO_0000346 ; - + obo:IAO_0000117 "Orlaith Burke" ; - + obo:IAO_0000115 ""@en ; - + obo:STATO_0000041 ""@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Camille Maumet"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000118 "TOEP"@en ; - + obo:IAO_0000117 "Tom Nichols"@en ; - + obo:IAO_0000119 "http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm"@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4733,26 +4733,26 @@ obo:STATO_0000357 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000362 obo:STATO_0000362 rdf:type owl:Class ; - + rdfs:label "compound symmetry covariance structure"@en ; - + rdfs:subClassOf obo:STATO_0000346 ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en ; - + obo:IAO_0000118 "CS"@en ; - + obo:IAO_0000117 "Camille Maumet"@en , "Orlaith Burke" , "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000115 "compound symmetry covariance structure is a covariance structure which means that all the variances are equal and all the covariances are equal."@en ; - + obo:STATO_0000041 "http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corCompSymm.html"@en ; - + obo:IAO_0000119 "http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm"@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4760,25 +4760,25 @@ obo:STATO_0000362 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000370 obo:STATO_0000370 rdf:type owl:Class ; - + rdfs:label "ordinary least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000119 ; - + obo:STATO_0000032 "OLS estimation" ; - + obo:STATO_0000041 ""@en , "https://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html" ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Camille Maumet"@en , "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000119 "http://en.wikipedia.org/wiki/Ordinary_least_squares and Tom Nichols"@en ; - + obo:IAO_0000115 "the ordinary least squares estimation is a model parameter estimation for a linear regression model when the errors are uncorrelated and equal in variance. Is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption."@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4786,25 +4786,25 @@ obo:STATO_0000370 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000371 obo:STATO_0000371 rdf:type owl:Class ; - + rdfs:label "weighted least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000119 ; - + obo:STATO_0000032 "WLS estimation" ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Camille Maumet"@en , "Orlaith Burke"@en , "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000119 "http://en.wikipedia.org/wiki/Least_squares#Weighted_least_squares and Tom Nichols"@en ; - + obo:STATO_0000041 "https://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html"@en ; - + obo:IAO_0000115 "the weighted least squares estimation is a model parameter estimation for a linear regression model with errors that independent but have heterogeneous variance. Difficult to use use in practice, as weights must be set based on the variance which is usually unknown. If true variance is known, it is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption."@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4812,22 +4812,22 @@ obo:STATO_0000371 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000372 obo:STATO_0000372 rdf:type owl:Class ; - + rdfs:label "generalized least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000119 ; - + obo:STATO_0000032 "GLS estimation" ; - + obo:IAO_0000117 "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000119 "http://en.wikipedia.org/wiki/Generalized_least_squares and Tom Nichols"@en ; - + obo:STATO_0000041 "http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/gls.html"@en ; - + obo:IAO_0000115 "the generalized least squares estimation is a model parameter estimation for a linear regression model with errors that are dependent and (possibly) have heterogeneous variance. Difficult to use use in practice, as covariance matrix of the errors must known to \"whiten\" data and model. If true covariance is known, it is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption."@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4835,25 +4835,25 @@ obo:STATO_0000372 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000373 obo:STATO_0000373 rdf:type owl:Class ; - + rdfs:label "iteratively reweighted least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000119 ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran" , "Camille Maumet" , "Orlaith Burke" ; - + obo:STATO_0000041 ""@en ; - + obo:IAO_0000117 "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "Tom Nichols"@en ; - + obo:IAO_0000117 "Tom Nichols"@en ; - + obo:IAO_0000115 "the iteratively reweighted least squares estimation is a model parameter estimation which is a practical implementation of Weighted Least Squares, where the heterogeneous variances of the errors are estimated from the residuals of the regression model, providing an estimate for the weights. Each successive estimate of the weights improves the estimation of the regression parameters, which in turn are used to compute residuals and update the weights"@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4861,22 +4861,22 @@ obo:STATO_0000373 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000374 obo:STATO_0000374 rdf:type owl:Class ; - + rdfs:label "feasible generalized least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000372 ; - + obo:IAO_0000115 "the feasible generalized least squares estimation is a model parameter estimation which is a practical implementation of Generalised Least Squares, where the covariance of the errors is estimated from the residuals of the regression model, providing the information needed to whiten the data and model. Each successive estimate of the whitening matrix improves the estimation of the regression parameters, which in turn are used to compute residuals and update the whitening matrix." ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Orlaith Burke"@en ; - + obo:IAO_0000119 "Tom Nichols" ; - + obo:IAO_0000117 "Camille Maumet" , "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4884,20 +4884,20 @@ obo:STATO_0000374 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000376 obo:STATO_0000376 rdf:type owl:Class ; - + rdfs:label "Z-statistic" ; - + rdfs:subClassOf obo:STATO_0000039 ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran" , "Camille Maument" , "Philippe Rocca-Serra" , "Thomas Nichols" ; - + obo:IAO_0000119 "http://en.wikipedia.org/wiki/Z-test" ; - + obo:IAO_0000115 "Z-statistic is a statistic computed from observations and used to produce a p-value when compared to a Standard Normal Distribution in a statistical test called the Z-test." ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -5739,7 +5739,7 @@ prov:qualifiedEnd prov:qualifiedForm a owl:AnnotationProperty ; - rdfs:comment """This annotation property links a subproperty of prov:wasInfluencedBy with the subclass of prov:Influence and the qualifying property that are used to qualify it. + rdfs:comment """This annotation property links a subproperty of prov:wasInfluencedBy with the subclass of prov:Influence and the qualifying property that are used to qualify it. Example annotation: @@ -5752,7 +5752,7 @@ Then this unqualified assertion: can be qualified by adding: prov:entity1 prov:qualifiedGeneration prov:entity1Gen . - prov:entity1Gen + prov:entity1Gen a prov:Generation, prov:Influence; prov:activity prov:activity1; prov:customValue 1337 . @@ -6053,7 +6053,7 @@ prov:wasInfluencedBy Subproperties of prov:wasInfluencedBy may also be asserted directly without being qualified. -prov:wasInfluencedBy should not be used without also using one of its subproperties. +prov:wasInfluencedBy should not be used without also using one of its subproperties. """@en ; prov:inverse "influenced" ; prov:qualifiedForm prov:Influence, prov:qualifiedInfluence ; @@ -6140,7 +6140,7 @@ prov:wasStartedBy a owl:Ontology ; - rdfs:comment """This document is published by the Provenance Working Group (http://www.w3.org/2011/prov/wiki/Main_Page). + rdfs:comment """This document is published by the Provenance Working Group (http://www.w3.org/2011/prov/wiki/Main_Page). If you wish to make comments regarding this document, please send them to public-prov-comments@w3.org (subscribe public-prov-comments-request@w3.org, archives http://lists.w3.org/Archives/Public/public-prov-comments/). All feedback is welcome."""@en ; rdfs:label "W3C PROVenance Interchange Ontology (PROV-O)"@en ; @@ -6217,9 +6217,8 @@ If you wish to make comments regarding this document, please send them to public [] a owl:Axiom ; - rdfs:comment """Revision is a derivation (see http://www.w3.org/TR/prov-dm/#term-Revision). Moreover, according to + rdfs:comment """Revision is a derivation (see http://www.w3.org/TR/prov-dm/#term-Revision). Moreover, according to http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#term-Revision 23 April 2012 'wasRevisionOf is a strict sub-relation of wasDerivedFrom since two entities e2 and e1 may satisfy wasDerivedFrom(e2,e1) without being a variant of each other.'""" ; owl:annotatedProperty rdfs:subPropertyOf ; owl:annotatedSource prov:wasRevisionOf ; owl:annotatedTarget prov:wasDerivedFrom . - diff --git a/nidmresults/owl/nidm-results_120.owl b/nidmresults/owl/nidm-results_120.owl index d6f46ea..db1cb39 100644 --- a/nidmresults/owl/nidm-results_120.owl +++ b/nidmresults/owl/nidm-results_120.owl @@ -59,17 +59,17 @@ dc:description rdfs:range dctype:Image . ### http://purl.org/nidash/nidm#NIDM_0000088 nidm:NIDM_0000088 rdf:type owl:ObjectProperty ; - + rdfs:label "has Drift Model" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000115 "A property that associates a 'Drift Model' to a 'Design Matrix' (only used for first-level fMRI experiments)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000019 ; - + rdfs:range nidm:NIDM_0000087 . @@ -77,17 +77,17 @@ nidm:NIDM_0000088 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000089 nidm:NIDM_0000089 rdf:type owl:ObjectProperty ; - + rdfs:label "dependence Map-Wise Dependence" ; - + obo:IAO_0000115 "Property that associates an 'Error Parameter Map-Wise Dependence' to the dependence of an 'Error Model'." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000023 ; - + rdfs:range nidm:NIDM_0000071 . @@ -95,20 +95,20 @@ nidm:NIDM_0000089 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000097 nidm:NIDM_0000097 rdf:type owl:ObjectProperty ; - + rdfs:label "has Alternative Hypothesis" ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/pull/81" ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000208" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000049 ; - + rdfs:range nidm:NIDM_0000060 , nidm:NIDM_0000079 ; - + rdfs:subPropertyOf owl:topObjectProperty . @@ -116,17 +116,17 @@ nidm:NIDM_0000097 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000098 nidm:NIDM_0000098 rdf:type owl:ObjectProperty ; - + rdfs:label "has Cluster Labels Map" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/282" ; - + obo:IAO_0000115 "A property that associates a clusters label map to the excursion set." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range nidm:NIDM_0000008 ; - + rdfs:domain nidm:NIDM_0000025 . @@ -134,17 +134,17 @@ nidm:NIDM_0000098 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000099 nidm:NIDM_0000099 rdf:type owl:ObjectProperty ; - + rdfs:label "has Connectivity Criterion" ; - + obo:IAO_0000115 "Property that associates a 'Connectivity Criterion' with a 'Cluster Definition Criteria'." ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000007 ; - + rdfs:range nidm:NIDM_0000012 . @@ -152,15 +152,15 @@ nidm:NIDM_0000099 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000100 nidm:NIDM_0000100 rdf:type owl:ObjectProperty ; - + rdfs:label "has Error Dependence" ; - + obo:IAO_0000115 "Property that associates a covariance structure representing the dependence structure of the error, used as part of model estimation with an 'Error Model'." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range obo:STATO_0000346 ; - + rdfs:domain nidm:NIDM_0000023 . @@ -168,15 +168,15 @@ nidm:NIDM_0000100 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000101 nidm:NIDM_0000101 rdf:type owl:ObjectProperty ; - + rdfs:label "has Error Distribution" ; - + obo:IAO_0000115 "Property that associates a Probability distribution used to model the error with an ErrorModel." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range obo:STATO_0000225 ; - + rdfs:domain nidm:NIDM_0000023 . @@ -184,17 +184,17 @@ nidm:NIDM_0000101 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000102 nidm:NIDM_0000102 rdf:type owl:ObjectProperty ; - + rdfs:label "has HRF Basis" ; - + obo:IAO_0000115 "A property that associates a set of functions that, when convolved with the anticipated neural responses, yields a set of regressors to model the anticipated hemodynamic responses in a 'Design Matrix'." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000019 ; - + rdfs:range nidm:NIDM_0000036 . @@ -202,17 +202,17 @@ nidm:NIDM_0000102 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000103 nidm:NIDM_0000103 rdf:type owl:ObjectProperty ; - + rdfs:label "has Map Header" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/289" ; - + obo:IAO_0000115 "A Property that associates an additional file containing the 'Map Header' with a map" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000052 ; - + rdfs:range nidm:NIDM_0000053 . @@ -220,17 +220,17 @@ nidm:NIDM_0000103 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000104 nidm:NIDM_0000104 rdf:type owl:ObjectProperty ; - + rdfs:label "in Coordinate Space" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/171 by NN JT CM SG KH TN." ; - + obo:IAO_0000115 "Property of a DataArray to associate a 'Coordinate Space' with a physical file." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range nidm:NIDM_0000016 ; - + rdfs:domain nidm:NIDM_0000052 . @@ -238,17 +238,17 @@ nidm:NIDM_0000104 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000105 nidm:NIDM_0000105 rdf:type owl:ObjectProperty ; - + rdfs:label "in World Coordinate System" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Property that associates a 'World Coordinate System' to the 'Coordinate Space'." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range nidm:NIDM_0000081 . @@ -256,15 +256,15 @@ nidm:NIDM_0000105 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000113 nidm:NIDM_0000113 rdf:type owl:ObjectProperty ; - + rdfs:label "object Model" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/pull/137" ; - + obo:IAO_0000114 obo:IAO_0000124 ; - + rdfs:range nidm:NIDM_0000057 ; - + rdfs:domain prov:Bundle . @@ -272,17 +272,17 @@ nidm:NIDM_0000113 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000123 nidm:NIDM_0000123 rdf:type owl:ObjectProperty ; - + rdfs:label "statistic Type" ; - + obo:IAO_0000115 "Property that associates a [stato:\"statistic\"](http://purl.obolibrary.org/obo/STATO_0000039) with a StatisticMap or a ContrastWeights entity." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/293" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range obo:STATO_0000039 ; - + rdfs:domain obo:STATO_0000323 , nidm:NIDM_0000076 . @@ -291,17 +291,17 @@ nidm:NIDM_0000123 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000126 nidm:NIDM_0000126 rdf:type owl:ObjectProperty ; - + rdfs:label "variance Map-Wise Dependence" ; - + obo:IAO_0000115 "Property that associates an 'Error Parameter Map-Wise Dependence' to the variance of an 'Error Model'" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000023 ; - + rdfs:range nidm:NIDM_0000071 . @@ -309,17 +309,17 @@ nidm:NIDM_0000126 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000134 nidm:NIDM_0000134 rdf:type owl:ObjectProperty ; - + rdfs:label "with Estimation Method" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/293" ; - + obo:IAO_0000115 "Property that associates a [stato:\"model parameter estimation\"](http://purl.obolibrary.org/obo/STATO_0000119) method with a model parameter estimation" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range obo:STATO_0000119 ; - + rdfs:domain nidm:NIDM_0000056 . @@ -327,17 +327,17 @@ nidm:NIDM_0000134 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000138 nidm:NIDM_0000138 rdf:type owl:ObjectProperty ; - + rdfs:label "has Maximum Intensity Projection" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/293" ; - + obo:IAO_0000115 "Property that associates an image of the maximum intensity projection with an 'Excursion Set Map'." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range dctype:Image ; - + rdfs:domain nidm:NIDM_0000025 . @@ -345,17 +345,17 @@ nidm:NIDM_0000138 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000161 nidm:NIDM_0000161 rdf:type owl:ObjectProperty ; - + rdfs:label "equivalent Threshold" ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/329" ; - + obo:IAO_0000115 "Property that associates another 'Threshold' that is equivalent (e.g. if the user specified a 'Threshold' in terms of FWE-corrected p-value, this property can be used to associate the corresponding uncorrected p-value)." ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:range nidm:NIDM_0000162 ; - + rdfs:domain nidm:NIDM_0000162 . @@ -363,7 +363,7 @@ nidm:NIDM_0000161 rdf:type owl:ObjectProperty ; ### http://www.w3.org/ns/prov#atLocation prov:atLocation prov:definition "The Location of any resource" ; - + obo:IAO_0000115 "The Location of any resource." . @@ -386,7 +386,7 @@ dc:description rdf:type owl:DatatypeProperty . ### http://purl.org/dc/terms/format dct:format rdf:type owl:DatatypeProperty ; - + rdfs:range xsd:string . @@ -394,17 +394,17 @@ dct:format rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/fsl#FSL_0000004 fsl:FSL_0000004 rdf:type owl:DatatypeProperty ; - + rdfs:label "drift Cutoff Period" ; - + obo:IAO_0000115 "Full Width at Half Maximum in seconds of the Gaussian weight function used in the running line smoother." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain fsl:FSL_0000002 ; - + rdfs:range xsd:float . @@ -412,17 +412,17 @@ fsl:FSL_0000004 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/fsl#FSL_0000005 fsl:FSL_0000005 rdf:type owl:DatatypeProperty ; - + rdfs:label "feat Version" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/291" ; - + obo:IAO_0000115 "Version of the FEAT software." ; - + rdfs:domain nlx:birnlex_2067 ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range xsd:string . @@ -430,17 +430,17 @@ fsl:FSL_0000005 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000014 nidm:NIDM_0000014 rdf:type owl:DatatypeProperty ; - + rdfs:label "Legendre Polynomial Order" ; - + obo:IAO_0000115 "The number of basis in the 'Drift Model' (1 = linear, 2 = quadratic, etc.)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain afni:LegendrePolynomialDriftModel ; - + rdfs:range xsd:int . @@ -448,17 +448,17 @@ nidm:NIDM_0000014 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000021 nidm:NIDM_0000021 rdf:type owl:DatatypeProperty ; - + rdfs:label "regressor Names" ; - + obo:IAO_0000115 "A list of abstract names associated with each column of the 'Design Matrix' (e.g. [\"motor_left\", \"motor_right\"])." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/299" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000019 ; - + rdfs:range xsd:string . @@ -466,19 +466,19 @@ nidm:NIDM_0000021 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000082 nidm:NIDM_0000082 rdf:type owl:DatatypeProperty ; - + rdfs:label "cluster Label Id" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/271" ; - + obo:IAO_0000115 "Integer value used in the cluster label map to identify the location of the cluster within the excursion set." ; - + obo:IAO_0000112 "5" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000070 ; - + rdfs:range xsd:int . @@ -486,18 +486,18 @@ nidm:NIDM_0000082 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000083 nidm:NIDM_0000083 rdf:type owl:DatatypeProperty ; - + rdfs:label "cluster Size In Vertices" ; - + obo:IAO_0000115 "Number of vertices that make up the cluster." ; - + obo:IAO_0000112 "10" ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000070 ; - + rdfs:range xsd:positiveInteger . @@ -505,18 +505,18 @@ nidm:NIDM_0000083 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000084 nidm:NIDM_0000084 rdf:type owl:DatatypeProperty ; - + rdfs:label "cluster Size In Voxels" ; - + obo:IAO_0000112 "18" ; - + obo:IAO_0000115 "Number of voxels that make up the cluster." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000070 ; - + rdfs:range xsd:positiveInteger . @@ -524,19 +524,19 @@ nidm:NIDM_0000084 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000085 nidm:NIDM_0000085 rdf:type owl:DatatypeProperty ; - + rdfs:label "contrast Name" ; - + obo:IAO_0000115 "Name of the contrast." ; - + obo:IAO_0000112 "\"Listening > Rest\"" ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain obo:STATO_0000323 , nidm:NIDM_0000002 , nidm:NIDM_0000076 ; - + rdfs:range xsd:string . @@ -544,19 +544,19 @@ nidm:NIDM_0000085 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000086 nidm:NIDM_0000086 rdf:type owl:DatatypeProperty ; - + rdfs:label "coordinate Vector" ; - + obo:IAO_0000112 "[-60, 32, 54]"^^xsd:string ; - + obo:IAO_0000115 "A vector with one number per dimension. The first element corresponds to the 'Coordinate' along the first dimension measured in map elements (e.g., pixels, voxels, vertices, or faces), the second element to the 'Coordinate' along the second dimension etc." ; - + obo:IAO_0000116 "Under discussion at: https://github.com/incf-nidash/nidm/pull/270 and https://github.com/incf-nidash/nidm/issues/145" ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000015 ; - + rdfs:range xsd:string . @@ -564,19 +564,19 @@ nidm:NIDM_0000086 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000090 nidm:NIDM_0000090 rdf:type owl:DatatypeProperty ; - + rdfs:label "dimensions In Voxels" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/issues/146" ; - + obo:IAO_0000115 "Number of voxels in each of the dimensions of the data array. For example, \"[91, 109, 91]\" indicates there are 91 voxels in the first dimension, 109 in the second dimension, and 91 in the third dimension." ; - + obo:IAO_0000112 "[64, 64, 20]" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:string . @@ -584,19 +584,19 @@ nidm:NIDM_0000090 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000091 nidm:NIDM_0000091 rdf:type owl:DatatypeProperty ; - + rdfs:label "effect Degrees Of Freedom" ; - + obo:IAO_0000115 "In the context of a general linear model, the effect degrees of freedom is the rank of the contrast. For example, a contrast comprising of a vector has effect degrees of freedom of 1 and can be tested with a F-test with numerator degrees of freedom of 1." ; - + obo:IAO_0000112 "1" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/issues/277" ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000076 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -609,17 +609,17 @@ nidm:NIDM_0000091 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000092 nidm:NIDM_0000092 rdf:type owl:DatatypeProperty ; - + rdfs:label "equivalent ZStatistic" ; - + obo:IAO_0000115 "Statistic value transformed into Z units; the output of a process which takes a non-normal statistic and transforms it to an equivalent z score." ; - + obo:IAO_0000112 "3.5" ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain nidm:NIDM_0000062 ; - + rdfs:range xsd:float . @@ -627,19 +627,19 @@ nidm:NIDM_0000092 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000093 nidm:NIDM_0000093 rdf:type owl:DatatypeProperty ; - + rdfs:label "error Degrees Of Freedom" ; - + obo:IAO_0000112 "72.999999" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/issues/277" ; - + obo:IAO_0000115 "In the context of a general linear model, the error degrees of freedom are the number of observations less the rank of the 'Design Matrix'." ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000076 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -652,15 +652,15 @@ nidm:NIDM_0000093 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000094 nidm:NIDM_0000094 rdf:type owl:DatatypeProperty ; - + rdfs:label "error Variance Homogeneous" ; - + obo:IAO_0000115 "A boolean value reflecting how the variance of the error is modeled during parameter estimation; TRUE for constant variance over all observations in the model, FALSE for heterogeneous variance." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000023 ; - + rdfs:range xsd:boolean . @@ -668,19 +668,19 @@ nidm:NIDM_0000094 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000095 nidm:NIDM_0000095 rdf:type owl:DatatypeProperty ; - + rdfs:label "partial Conjunction Degree" ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000115 "The number of non-null effects permitted in a partial conjunction null, as part of a 'Partial Conjunction Inference'" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/294" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain spm:SPM_0000005 ; - + rdfs:range xsd:int . @@ -688,19 +688,19 @@ nidm:NIDM_0000095 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000096 nidm:NIDM_0000096 rdf:type owl:DatatypeProperty ; - + rdfs:label "grand Mean Scaling" ; - + obo:IAO_0000115 "Binary flag defining whether the data was scaled (true for scaled). Specifically, \"grand mean scaling\" refers to multiplication of every voxel in every scan by a common (or session-specific) value." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/285" ; - + obo:IAO_0000112 "TRUE" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000018 ; - + rdfs:range xsd:boolean . @@ -708,13 +708,13 @@ nidm:NIDM_0000096 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000105 nidm:NIDM_0000105 rdf:type owl:DatatypeProperty ; - + rdfs:label "in World Coordinate System" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Property that associates a 'World Coordinate System' to the 'Coordinate Space'." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -722,17 +722,17 @@ nidm:NIDM_0000105 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000106 nidm:NIDM_0000106 rdf:type owl:DatatypeProperty ; - + rdfs:label "is User Defined" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/pull/258" ; - + obo:IAO_0000115 "A binary flag defining whether the mask was specified by the user (true) or automatically generated during the analysis (false)" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000004 ; - + rdfs:range xsd:boolean . @@ -740,21 +740,21 @@ nidm:NIDM_0000106 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000107 nidm:NIDM_0000107 rdf:type owl:DatatypeProperty ; - + rdfs:label "masked Median" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/288, naming previously discussed at: https://github.com/incf-nidash/nidm/issues/70" ; - + obo:IAO_0000115 "Median value considering only in-mask voxels. Useful diagnostic when computed on grand mean image when grandMeanScaling is TRUE, as the median should be close to targetIntensity." ; - + rdfs:seeAlso "http://purl.obolibrary.org/obo/OBI_0200119" ; - + obo:IAO_0000112 "155.23" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000033 ; - + rdfs:range xsd:float . @@ -762,17 +762,17 @@ nidm:NIDM_0000107 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000108 nidm:NIDM_0000108 rdf:type owl:DatatypeProperty ; - + rdfs:label "max Number Of Peaks Per Cluster" ; - + obo:IAO_0000115 "Maximum number of 'Peak's to be reported after 'Inference' within a cluster." ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/200" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000063 ; - + rdfs:range xsd:int . @@ -780,17 +780,17 @@ nidm:NIDM_0000108 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000109 nidm:NIDM_0000109 rdf:type owl:DatatypeProperty ; - + rdfs:label "min Distance Between Peaks" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/200" ; - + obo:IAO_0000115 "Minimum distance between two 'Peak's to be reported after 'Inference'." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000063 ; - + rdfs:range xsd:float . @@ -798,19 +798,19 @@ nidm:NIDM_0000109 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000111 nidm:NIDM_0000111 rdf:type owl:DatatypeProperty ; - + rdfs:label "number Of Significant Clusters" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/292" ; - + obo:IAO_0000115 "Number of significant clusters found by the 'Inference' activity. This is SPM's set level statistic." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000025 ; - + rdfs:range xsd:int ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -818,19 +818,19 @@ nidm:NIDM_0000111 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000112 nidm:NIDM_0000112 rdf:type owl:DatatypeProperty ; - + rdfs:label "number Of Dimensions" ; - + obo:IAO_0000115 "Number of dimensions of the data matrix (e.g. 3 for volumetric data)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/295" ; - + obo:IAO_0000112 "3" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:positiveInteger . @@ -838,23 +838,23 @@ nidm:NIDM_0000112 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000114 nidm:NIDM_0000114 rdf:type owl:DatatypeProperty ; - + rdfs:label "p Value" ; - + owl:sameAs "http://purl.obolibrary.org/obo/OBI_0000175"^^xsd:anyURI ; - + obo:IAO_0000112 "8.95E-14" ; - + rdfs:seeAlso """http://purl.obolibrary.org/obo/IAO_0000121 http://purl.obolibrary.org/obo/OBI_0000175 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P-Value""" ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/38" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000025 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:maxInclusive "1.0"^^xsd:float @@ -869,24 +869,24 @@ http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P-Value""" ; ### http://purl.org/nidash/nidm#NIDM_0000115 nidm:NIDM_0000115 rdf:type owl:DatatypeProperty ; - + rdfs:label "p Value FWER" ; - + obo:IAO_0000112 "0.05" ; - + obo:IAO_0000115 "\"A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests\"" ; - + owl:sameAs "This definition is from OBI. Please update this note if the definition is modified." ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/38" ; - + rdfs:seeAlso "Synonym of \"nidm:pFWE\"" ; - + obo:IAO_0000114 obo:IAO_0000423 ; - + rdfs:domain nidm:NIDM_0000062 , nidm:NIDM_0000070 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:maxInclusive "1.0"^^xsd:float @@ -901,22 +901,22 @@ nidm:NIDM_0000115 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000116 nidm:NIDM_0000116 rdf:type owl:DatatypeProperty ; - + rdfs:label "p Value Uncorrected" ; - + obo:IAO_0000115 "A p-value reported without correction for multiple testing. " ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/38" ; - + obo:IAO_0000112 "0.0542" ; - + rdfs:seeAlso "http://purl.obolibrary.org/obo/IAO_0000121" ; - + obo:IAO_0000114 obo:IAO_0000423 ; - + rdfs:domain nidm:NIDM_0000062 , nidm:NIDM_0000070 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:maxInclusive "1.0"^^xsd:float @@ -931,22 +931,22 @@ nidm:NIDM_0000116 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000119 nidm:NIDM_0000119 rdf:type owl:DatatypeProperty ; - + rdfs:label "q Value FDR" ; - + obo:IAO_0000112 "0.000154" ; - + obo:IAO_0000115 "A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level (same as OBI_0001442)." ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/38" ; - + owl:sameAs "http://purl.obolibrary.org/obo/OBI_0001442" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000062 , nidm:NIDM_0000070 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:maxInclusive "1.0"^^xsd:float @@ -961,17 +961,17 @@ nidm:NIDM_0000119 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000120 nidm:NIDM_0000120 rdf:type owl:DatatypeProperty ; - + rdfs:label "random Field Stationarity" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/130" ; - + obo:IAO_0000115 "A binary flag that indicates whether Random Field Theory methods assumed smoothness that was homogeneous over the map (true), or allowed for smoothness that varies over the map (false)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:boolean . @@ -979,21 +979,21 @@ nidm:NIDM_0000120 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000121 nidm:NIDM_0000121 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume In Voxels" ; - + obo:IAO_0000112 "68656" ; - + rdfs:seeAlso "Synonyms of nidm:volumeInVoxels" ; - + obo:IAO_0000115 "Total number of voxels within the search volume." ; - + obo:IAO_0000114 obo:IAO_0000124 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1001,19 +1001,19 @@ nidm:NIDM_0000121 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000122 nidm:NIDM_0000122 rdf:type owl:DatatypeProperty ; - + rdfs:label "software Version" ; - + obo:IAO_0000112 8.6225 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/291" ; - + obo:IAO_0000115 "Name and number that specifies the software version. For SPM, this includes the main software version followed by the revision number (e.g. 8.6225 for SPM8 revision 6225)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range xsd:string ; - + rdfs:domain prov:SoftwareAgent . @@ -1021,19 +1021,19 @@ nidm:NIDM_0000122 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000124 nidm:NIDM_0000124 rdf:type owl:DatatypeProperty ; - + rdfs:label "target Intensity" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/285" ; - + obo:IAO_0000115 "Value to which the grand mean of the Data was scaled (applies only if 'grand Mean Scaling' is true)." ; - + obo:IAO_0000112 "100" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000018 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1046,24 +1046,24 @@ nidm:NIDM_0000124 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000125 nidm:NIDM_0000125 rdf:type owl:DatatypeProperty ; - + rdfs:label "user Specified Threshold Type" ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/150" ; - + obo:IAO_0000112 "nidm:pValueFWER" ; - + obo:IAO_0000115 "Type of method used to define a 'Threshold' (e.g. statistic value, uncorrected P-value or corrected P-value)." ; - + rdfs:comment "Range is currently string but should be limited to {'nidm:pValueFWER' not found'nidm:pValueFDR' not found'nidm:pValueUncorrected';'nidm:statistic'}?" ; - + obo:IAO_0000114 obo:IAO_0000428 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000034 ; - + rdfs:range xsd:string . @@ -1071,17 +1071,17 @@ nidm:NIDM_0000125 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000127 nidm:NIDM_0000127 rdf:type owl:DatatypeProperty ; - + rdfs:label "version" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/137" ; - + obo:IAO_0000115 "Version of NIDM in use in the document." ; - + obo:IAO_0000114 obo:IAO_0000124 ; - + rdfs:domain nidm:NIDM_0000057 ; - + rdfs:range xsd:string . @@ -1089,19 +1089,19 @@ nidm:NIDM_0000127 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000131 nidm:NIDM_0000131 rdf:type owl:DatatypeProperty ; - + rdfs:label "voxel Size" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/295" ; - + obo:IAO_0000115 "3D size of a voxel measured in 'voxel Units' (e.g. [2, 2, 4])" ; - + obo:IAO_0000112 "[2, 2, 4]" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:string . @@ -1109,21 +1109,21 @@ nidm:NIDM_0000131 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000132 nidm:NIDM_0000132 rdf:type owl:DatatypeProperty ; - + rdfs:label "voxel To World Mapping" ; - + obo:IAO_0000116 "Range: Matrix of float." ; - + obo:IAO_0000112 "[3 0 0 0;0 3 0 0;0 0 3 0; 0 0 0 1] " ; - + obo:IAO_0000115 "Homogeneous transformation matrix to map from voxel coordinate system to 'World Coordinate System'." ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/148" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:string . @@ -1131,21 +1131,21 @@ nidm:NIDM_0000132 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000133 nidm:NIDM_0000133 rdf:type owl:DatatypeProperty ; - + rdfs:label "voxel Units" ; - + rdfs:comment "Range: Vector of strings." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/295 and https://github.com/incf-nidash/nidm/issues/147" ; - + obo:IAO_0000112 "'[\"mm\", \"mm\", \"s\"]'" ; - + obo:IAO_0000115 "Set of units associated with the dimensions of some N-dimensional data (e.g. '[\"mm\", \"mm\", \"mm\"]')" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:string . @@ -1153,21 +1153,21 @@ nidm:NIDM_0000133 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000136 nidm:NIDM_0000136 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume In Units" ; - + obo:IAO_0000117 "Discussed at https://github.com/incf-nidash/nidm/pull/131" ; - + obo:IAO_0000115 "The volume of the searched region in units determined by the current 'Coordinate Space' units (e.g., mm^3 for axis units of mm in a three dimensional image, sec.Hz for a time by frequency two dimensional image)." ; - + obo:IAO_0000116 "Context: volumeInVoxels nidm_0025. Range: Positivefloat not found." ; - + obo:IAO_0000112 "1771011" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1180,17 +1180,17 @@ nidm:NIDM_0000136 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000137 nidm:NIDM_0000137 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume In Vertices" ; - + obo:IAO_0000112 "151.3" ; - + obo:IAO_0000115 "Total number of vertices within the search volume." ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1203,19 +1203,19 @@ nidm:NIDM_0000137 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000139 nidm:NIDM_0000139 rdf:type owl:DatatypeProperty ; - + rdfs:label "coordinate Vector In Voxels" ; - + obo:IAO_0000115 "Coordinate along the first dimension in voxels. (This definition needs to be re-worked as this term was renamed from coordinate1 to coordinate in https://github.com/incf-nidash/nidm/issues/270)" ; - + obo:IAO_0000112 "[12 51 48]" ; - + obo:IAO_0000116 "Under discussion at: https://github.com/incf-nidash/nidm/pull/270" ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain nidm:NIDM_0000015 ; - + rdfs:range xsd:string . @@ -1223,17 +1223,17 @@ nidm:NIDM_0000139 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000141 nidm:NIDM_0000141 rdf:type owl:DatatypeProperty ; - + rdfs:label "expected Number Of Clusters" ; - + obo:IAO_0000112 "9.51" ; - + obo:IAO_0000115 "Expected number of clusters in an excursion set under the null hypothesis." ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1246,17 +1246,17 @@ nidm:NIDM_0000141 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000142 nidm:NIDM_0000142 rdf:type owl:DatatypeProperty ; - + rdfs:label "expected Number Of Vertices Per Cluster" ; - + obo:IAO_0000115 "Expected number of vertices in a cluster under the null hypothesis." ; - + obo:IAO_0000112 "60.632" ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1269,17 +1269,17 @@ nidm:NIDM_0000142 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000143 nidm:NIDM_0000143 rdf:type owl:DatatypeProperty ; - + rdfs:label "expected Number Of Voxels Per Cluster" ; - + obo:IAO_0000115 "Expected number of voxels in a cluster under the null hypothesis." ; - + obo:IAO_0000112 "60.632" ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1292,17 +1292,17 @@ nidm:NIDM_0000143 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000145 nidm:NIDM_0000145 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise Roughness In Voxels" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/214 and https://github.com/incf-nidash/nidm/issues/275" ; - + obo:IAO_0000115 "Estimated spatial roughness of the noise process in 'voxel Units', as measured by the square-root determinant of the variance-covariance matrix of spatial derivatives of the noise process (Lambda matrix)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:float . @@ -1310,17 +1310,17 @@ nidm:NIDM_0000145 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000146 nidm:NIDM_0000146 rdf:type owl:DatatypeProperty ; - + rdfs:label "height Critical Threshold FDR 05" ; - + obo:IAO_0000112 "5.896" ; - + obo:IAO_0000115 "'Peak' statistic 'Threshold' corrected for false discovery rate at a level of alpha = 0.05. " ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:float . @@ -1328,17 +1328,17 @@ nidm:NIDM_0000146 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000147 nidm:NIDM_0000147 rdf:type owl:DatatypeProperty ; - + rdfs:label "height Critical Threshold FWE 05" ; - + obo:IAO_0000112 "4.913" ; - + obo:IAO_0000115 "'Peak' statistic 'Threshold' corrected for family-wise error at a level of alpha = 0.05. " ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:float . @@ -1346,23 +1346,23 @@ nidm:NIDM_0000147 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000148 nidm:NIDM_0000148 rdf:type owl:DatatypeProperty ; - + rdfs:label "resel Size In Voxels" ; - + obo:IAO_0000112 "22.325" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/275" ; - + obo:IAO_0000115 "Size of one resel in elements (e.g., pixels, voxels or vertices)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:float ; - + rdfs:subPropertyOf owl:topDataProperty ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1375,19 +1375,19 @@ nidm:NIDM_0000148 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000149 nidm:NIDM_0000149 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume In Resels" ; - + obo:IAO_0000112 "151.3" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/275" ; - + obo:IAO_0000115 "Size of search volume measured in resels." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1400,20 +1400,20 @@ nidm:NIDM_0000149 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000156 nidm:NIDM_0000156 rdf:type owl:DatatypeProperty ; - + rdfs:label "cluster Size In Resels" ; - + obo:IAO_0000117 "Under discussion at: https://github.com/incf-nidash/nidm/issues/127" ; - + obo:IAO_0000112 "13" ; - + obo:IAO_0000115 "Size of cluster measured in resels." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000070 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1426,23 +1426,23 @@ nidm:NIDM_0000156 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000157 nidm:NIDM_0000157 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Units" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + obo:IAO_0000112 "[8.87, 8.89, 7.83]" ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in world units (e.g. mm^2 or mm^3, in subject or atlas space)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1450,21 +1450,21 @@ nidm:NIDM_0000157 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000158 nidm:NIDM_0000158 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Vertices" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in vertices." ; - + obo:IAO_0000112 "[2.95, 2.96, 2.61]" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000054 ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1472,25 +1472,25 @@ nidm:NIDM_0000158 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000159 nidm:NIDM_0000159 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Voxels" ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in voxels." ; - + obo:IAO_0000112 "[3.7 3.7 3.1]" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + rdfs:seeAlso "Synonyms of or close match with nidm:NoiseFWHM" ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1498,17 +1498,17 @@ nidm:NIDM_0000159 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000001 spm:SPM_0000001 rdf:type owl:DatatypeProperty ; - + rdfs:label "SPM's Drift Cut-off Period" ; - + obo:IAO_0000115 "Discrete Cosine Transform basis cut-off, specified as period length in seconds and ensures that all basis elements will have period of this duration or longer." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain spm:SPM_0000002 ; - + rdfs:range xsd:float . @@ -1516,25 +1516,25 @@ spm:SPM_0000001 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000007 spm:SPM_0000007 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Units" ; - + owl:deprecated "true"^^xsd:boolean ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + obo:IAO_0000112 "[8.87, 8.89, 7.83]" ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in world units (e.g. mm^2 or mm^3, in subject or atlas space)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1542,23 +1542,23 @@ spm:SPM_0000007 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000008 spm:SPM_0000008 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Vertices" ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in vertices." ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + obo:IAO_0000112 "[2.95, 2.96, 2.61]" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000054 ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1566,27 +1566,27 @@ spm:SPM_0000008 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000009 spm:SPM_0000009 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Voxels" ; - + owl:deprecated "true"^^xsd:boolean ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in voxels." ; - + obo:IAO_0000112 "[3.7 3.7 3.1]" ; - + rdfs:seeAlso "Synonyms of or close match with nidm:NoiseFWHM" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1594,25 +1594,25 @@ spm:SPM_0000009 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000010 spm:SPM_0000010 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume Resels Geometry" ; - + obo:IAO_0000112 "[6 68.8 589.1 1475.5]" ; - + rdfs:comment "Range: Vector of 1 positive integer and 3 positive floats." ; - + rdfs:seeAlso "http://www.ncbi.nlm.nih.gov/pubmed/20408186" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000115 "Description of geometry of search volume. As per Worsley et al. [ http://www.ncbi.nlm.nih.gov/pubmed/20408186 ], for space dimension 3 the first element is the Euler Characteristic of the search volume, the second element is twice the average caliper diameter, the third element is half the surface area, and the fourth element is the volume. With the exception of the first element (which is a unitless integer) all quantities are in units of Resels." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1620,19 +1620,19 @@ spm:SPM_0000010 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000011 spm:SPM_0000011 rdf:type owl:DatatypeProperty ; - + rdfs:label "smallest Significant Cluster Size In Vertices FDR 05" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000112 "5" ; - + obo:IAO_0000115 "Smallest cluster size in vertices that is significant at the false discovery rate of 0.05. " ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger . @@ -1640,19 +1640,19 @@ spm:SPM_0000011 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000012 spm:SPM_0000012 rdf:type owl:DatatypeProperty ; - + rdfs:label "smallest Significant Cluster Size In Vertices FWE 05" ; - + obo:IAO_0000115 "Smallest cluster size in vertices that is significant at the family-wise corrected type I error rate (alpha value) value of 0.05." ; - + obo:IAO_0000112 "2" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger . @@ -1660,19 +1660,19 @@ spm:SPM_0000012 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000013 spm:SPM_0000013 rdf:type owl:DatatypeProperty ; - + rdfs:label "smallest Significant Cluster Size In Voxels FDR 05" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000112 "3" ; - + obo:IAO_0000115 "Smallest cluster size in voxels that is significant at the false discovery rate of 0.05. " ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger . @@ -1680,20 +1680,20 @@ spm:SPM_0000013 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000014 spm:SPM_0000014 rdf:type owl:DatatypeProperty ; - + rdfs:label "smallest Significant Cluster Size In Voxels FWE 05" ; - - obo:IAO_0000115 """Smallest cluster size in voxels that is significant at the family-wise error corrected type I error rate (alpha value) of 0.05. + + obo:IAO_0000115 """Smallest cluster size in voxels that is significant at the family-wise error corrected type I error rate (alpha value) of 0.05. """ ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000112 "1" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger . @@ -1701,17 +1701,17 @@ spm:SPM_0000014 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000015 spm:SPM_0000015 rdf:type owl:DatatypeProperty ; - + rdfs:label "partial Conjunction Degree" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/294" ; - + obo:IAO_0000115 "The number of non-null effects permitted in a partial conjunction null, as part of a 'Partial Conjunction Inference'" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain spm:SPM_0000005 ; - + rdfs:range xsd:int . @@ -1719,9 +1719,9 @@ spm:SPM_0000015 rdf:type owl:DatatypeProperty ; ### http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#fileName nfo:fileName rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "con_0001.img" ; - + rdfs:range xsd:string . @@ -1738,7 +1738,7 @@ nfo:fileName rdf:type owl:DatatypeProperty ; ### http://neurolex.org/wiki/birnlex_2067 nlx:birnlex_2067 rdfs:subClassOf nidm:NIDM_0000164 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/FSL_Software.txt"^^xsd:anyURI . @@ -1746,7 +1746,7 @@ nlx:birnlex_2067 rdfs:subClassOf nidm:NIDM_0000164 ; ### http://neurolex.org/wiki/nif-0000-00343 nlx:nif-0000-00343 rdfs:subClassOf nidm:NIDM_0000164 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/SPM_Software.txt"^^xsd:anyURI . @@ -1754,7 +1754,7 @@ nlx:nif-0000-00343 rdfs:subClassOf nidm:NIDM_0000164 ; ### http://purl.obolibrary.org/obo/OBI_0000251 obo:OBI_0000251 rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity . @@ -1762,7 +1762,7 @@ obo:OBI_0000251 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/OBI_0001265 obo:OBI_0001265 rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity . @@ -1770,7 +1770,7 @@ obo:OBI_0001265 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/OBI_0001442 obo:OBI_0001442 rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity . @@ -1796,9 +1796,9 @@ obo:STATO_0000225 rdfs:subClassOf prov:Entity . ### http://purl.obolibrary.org/obo/STATO_0000323 obo:STATO_0000323 rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ContrastWeights.txt" . @@ -1812,7 +1812,7 @@ obo:STATO_0000346 rdfs:subClassOf prov:Entity . ### http://purl.org/dc/dcmitype/Image dctype:Image rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity , [ rdf:type owl:Restriction ; owl:onProperty nfo:fileName ; @@ -1830,13 +1830,13 @@ dctype:Image rdf:type owl:Class ; ### http://purl.org/nidash/afni#BLOCK afni:BLOCK rdf:type owl:Class ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + prov:editorialNote "We will have to determine if afni:BLOCK is child of a more specific nidm HRFBasis sub-class."^^xsd:string ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000124 . @@ -1844,15 +1844,15 @@ afni:BLOCK rdf:type owl:Class ; ### http://purl.org/nidash/afni#LegendrePolynomialDriftModel afni:LegendrePolynomialDriftModel rdf:type owl:Class ; - + rdfs:label "AFNI's Legendre Polynomial Drift Model" ; - + rdfs:subClassOf nidm:NIDM_0000087 ; - + obo:IAO_0000115 "A 'Drift Model' in which the drifts are modeled by a Legendre orthogonal polynomial basis added to the regression model" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1860,17 +1860,17 @@ afni:LegendrePolynomialDriftModel rdf:type owl:Class ; ### http://purl.org/nidash/fsl#FSL_0000002 fsl:FSL_0000002 rdf:type owl:Class ; - + rdfs:label "Gaussian Running Line Drift Model" ; - + rdfs:subClassOf nidm:NIDM_0000087 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/FSL_DriftModel.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A 'Drift Model' in which the drifts are modeled with a Gaussian-weighted running line smoother, fit to and subtracted from the data and each column of the 'Design Matrix'." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1878,17 +1878,17 @@ fsl:FSL_0000002 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000001 nidm:NIDM_0000001 rdf:type owl:Class ; - + rdfs:label "Contrast Estimation" ; - + rdfs:subClassOf prov:Activity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ContrastEstimation.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "The process of performing a [obo:contrast estimation](http://purl.obolibrary.org/obo/STATO_0000383) at each element (e.g., pixel, voxel, vertex, or face) of a map" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/276 and https://github.com/ISA-tools/stato/issues/23" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1896,17 +1896,17 @@ nidm:NIDM_0000001 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000002 nidm:NIDM_0000002 rdf:type owl:Class ; - + rdfs:label "Contrast Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [contrast estimate](http://purl.obolibrary.org/obo/STATO_0000384)."^^xsd:string ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ContrastMap.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/255" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1914,17 +1914,17 @@ nidm:NIDM_0000002 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000003 nidm:NIDM_0000003 rdf:type owl:Class ; - + rdfs:label "Arbitrarily Correlated Error" ; - owl:deprecated "true"^^xsd:boolean ; - + owl:deprecated "true"^^xsd:boolean ; + rdfs:subClassOf obo:STATO_0000346 ; - + obo:IAO_0000117 "TN" ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/28" ; - + obo:IAO_0000114 obo:IAO_0000423 . @@ -1932,15 +1932,15 @@ nidm:NIDM_0000003 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000004 nidm:NIDM_0000004 rdf:type owl:Class ; - + rdfs:label "Binary Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000115 "A map in which all values are 0, 1 or NaN. Usually, selected elements (e.g., pixels, voxels, vertices, or faces) have a value of 1 and excluded elements (i.e. the background) have a value of 0 or NaN" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/258" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1948,17 +1948,17 @@ nidm:NIDM_0000004 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000005 nidm:NIDM_0000005 rdf:type owl:Class ; - + rdfs:label "Binomial Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000276"^^xsd:anyURI ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000115 "The 'Binomial Distribution' is a discrete probability distribution which describes the probability of k successes in n draws with replacement from a finite population of size N. The 'Binomial Distribution' is frequently used to model the number of successes in a sample of size n drawn with replacement from a population of size N. The 'Binomial Distribution' gives the discrete probability distribution of obtaining exactly n successes out of N Bernoulli trials (where the result of each Bernoulli trial is true with probability p and false with probability q=1-p ) notation: B(n,p) The mean is N*p The variance is N*p*q. (Definition from STATO)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1966,17 +1966,17 @@ nidm:NIDM_0000005 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000006 nidm:NIDM_0000006 rdf:type owl:Class ; - + rdfs:label "Cluster" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "A collection of elements related by one or more criteria."^^xsd:string ; - + prov:editorialNote "Discussed in https://github.com/incf-nidash/nidm/issues/71."^^xsd:string ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1984,16 +1984,16 @@ nidm:NIDM_0000006 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000007 nidm:NIDM_0000007 rdf:type owl:Class ; - + rdfs:label "Cluster Definition Criteria" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Set of criterion specified a priori to define the clusters reported after 'Inference' (e.g. pixel or voxel 'Connectivity Criterion')." ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ClusterDefinitionCriteria.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2001,17 +2001,17 @@ nidm:NIDM_0000007 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000008 nidm:NIDM_0000008 rdf:type owl:Class ; - + rdfs:label "Cluster Labels Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ClusterLabelsMap.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) denotes cluster membership within the excursion set. Each cluster is denoted by a different integer and all members of the same cluster have the same value." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/282" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2019,17 +2019,17 @@ nidm:NIDM_0000008 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000011 nidm:NIDM_0000011 rdf:type owl:Class ; - + rdfs:label "Conjunction Inference" ; - + rdfs:subClassOf nidm:NIDM_0000049 ; - obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ConjunctionInference.txt"^^xsd:anyURI ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ConjunctionInference.txt"^^xsd:anyURI ; + obo:IAO_0000115 "Statistically testing for the joint significance of multiple effects, with emphasis on rejecting all (instead of one or more) of the respective null hypotheses." ; - + obo:IAO_0000116 "Term discussed in https://github.com/incf-nidash/nidm/pull/134" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2037,17 +2037,17 @@ nidm:NIDM_0000011 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000012 nidm:NIDM_0000012 rdf:type owl:Class ; - + rdfs:label "Connectivity Criterion" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000117 "TN, KH, CM" ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "The criterion used to characterize two voxels, pixels or vertices as 'connected'." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2055,17 +2055,17 @@ nidm:NIDM_0000012 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000013 nidm:NIDM_0000013 rdf:type owl:Class ; - + rdfs:label "Contrast Standard Error Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/255."^^xsd:anyURI ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ContrastStandardErrorMap.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [standard error of a contrast estimate](http://purl.obolibrary.org/obo/STATO_0000385)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2073,17 +2073,17 @@ nidm:NIDM_0000013 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000015 nidm:NIDM_0000015 rdf:type owl:Class ; - + rdfs:label "Coordinate" ; - + rdfs:subClassOf prov:Entity ; - + owl:sameAs "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C44465"^^xsd:anyURI ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/Coordinate.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/pull/144 and https://github.com/incf-nidash/nidm/pull/172" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2091,17 +2091,17 @@ nidm:NIDM_0000015 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000016 nidm:NIDM_0000016 rdf:type owl:Class ; - + rdfs:label "Coordinate Space" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/CoordinateSpace.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "An entity with spatial attributes (e.g., dimensions, units, and voxel-to-world mapping) that provides context to a 'Map' (e.g., a 'Statistic Map', a 'Contrast Map'...)." ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/issues/290" ; - + obo:IAO_0000114 obo:IAO_0000125 . @@ -2109,15 +2109,15 @@ nidm:NIDM_0000016 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000017 nidm:NIDM_0000017 rdf:type owl:Class ; - + rdfs:label "Custom Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000075 ; - + obo:IAO_0000115 "Custom (unknown) reference space selected by the user" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2125,17 +2125,17 @@ nidm:NIDM_0000017 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000018 nidm:NIDM_0000018 rdf:type owl:Class ; - + rdfs:label "Data Scaling" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/Data.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Scaling applied to the data before parameter estimation, including specification of the 'target Intensity'." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/285" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2143,9 +2143,9 @@ nidm:NIDM_0000018 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000019 nidm:NIDM_0000019 rdf:type owl:Class ; - + rdfs:label "Design Matrix" ; - + rdfs:subClassOf prov:Entity , [ rdf:type owl:Restriction ; owl:onProperty dc:description ; @@ -2162,16 +2162,16 @@ nidm:NIDM_0000019 rdf:type owl:Class ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ; owl:onDataRange xsd:string ] ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/DesignMatrix.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/DesignMatrix_1stLevel.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/274" ; - + obo:IAO_0000115 "A [stato:design matrix](http://purl.obolibrary.org/obo/STATO_0000289), with additional neuroimaging attributes, including HRF and drift for first-level fMRI models" ; - + rdfs:seeAlso "stato:design matrix" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2179,17 +2179,17 @@ nidm:NIDM_0000019 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000020 nidm:NIDM_0000020 rdf:type owl:Class ; - + rdfs:label "Display Mask Map" ; - + rdfs:subClassOf nidm:NIDM_0000004 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/DisplayMaskMap.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/258 and https://github.com/incf-nidash/nidm/pull/157" ; - + obo:IAO_0000115 "A 'Binary Map' used by an activity that changed the voxels displayed, but did not alter the space in which the activity was performed (e.g. at the level of 'Inference', this mask is called \"contrast masking\" in both FSL & SPM and does not alter voxel-wise corrected p-values)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2197,15 +2197,15 @@ nidm:NIDM_0000020 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000022 nidm:NIDM_0000022 rdf:type owl:Class ; - + rdfs:label "Error Distribution" ; - + rdfs:subClassOf prov:Entity ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000115 "Probability distribution used to model the error." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2213,15 +2213,15 @@ nidm:NIDM_0000022 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000023 nidm:NIDM_0000023 rdf:type owl:Class ; - + rdfs:label "Error Model" ; - + rdfs:subClassOf prov:Entity ; - - obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ErrorModel.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ErrorModel-SPMnonSphericity.txt" ; - + + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ErrorModel.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ErrorModel-SPMnonSphericity.txt" ; + obo:IAO_0000115 "Model used to describe the random variation of the error term as part of parameter estimation, including specification of the error probability distribution, its variance and dependence both spatially and across observations." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2229,17 +2229,17 @@ nidm:NIDM_0000023 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000024 nidm:NIDM_0000024 rdf:type owl:Class ; - + rdfs:label "Exchangeable Error" ; - + rdfs:subClassOf obo:STATO_0000346 ; - + rdfs:comment "Under gaussianity assumption this is equivalent to compound symmetry but not in general." ; - + obo:IAO_0000117 "TN" ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/28" ; - + obo:IAO_0000114 obo:IAO_0000423 . @@ -2247,22 +2247,22 @@ nidm:NIDM_0000024 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000025 nidm:NIDM_0000025 rdf:type owl:Class ; - + rdfs:label "Excursion Set Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 , [ rdf:type owl:Restriction ; owl:onProperty dc:description ; owl:onClass dctype:Image ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ] ; - + obo:IAO_0000116 "Discussed in the Neuroimaging terms spreadsheet and in https://github.com/incf-nidash/nidm/issues/256." ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ExcursionSetMap.txt" ; - + obo:IAO_0000115 "A map in which the set of elements (e.g., pixels, voxels, vertices, or faces) not selected by the 'Inference' activity is set to zero or NaN" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2270,20 +2270,20 @@ nidm:NIDM_0000025 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000026 nidm:NIDM_0000026 rdf:type owl:Class ; - + rdfs:label "Extent Threshold" ; - + rdfs:subClassOf nidm:NIDM_0000162 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ExtentThreshold-FDR.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ExtentThreshold-Unc.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ExtentThresholdStat.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ExtentThreshold_equivThresh-FWER.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A numerical value that establishes a lower bound on cluster-sizes and can be specified by the user in terms of FWER-corrected p-value, uncorrected p-value or minimum cluster size in voxels" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/273" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2291,17 +2291,17 @@ nidm:NIDM_0000026 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000027 nidm:NIDM_0000027 rdf:type owl:Class ; - + rdfs:label "NIDM-Results" ; - + rdfs:subClassOf nidm:NIDM_0000057 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/NIDMBundle.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "'NIDM Object Model' representing the results of a mass univariate neuroimaging study and targeting the application of meta-analysis. The specification is available at: http://nidm.nidash.org/specs/nidm-results.html" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/137" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2309,17 +2309,17 @@ nidm:NIDM_0000027 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000028 nidm:NIDM_0000028 rdf:type owl:Class ; - + rdfs:label "Finite Impulse Response Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/DesignMatrix_1stLevel-FIR.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Set of Finite impulse response (FIR) filters, with FIR the convolution kernel is represented as a set of discrete fixed-width \"impulses\" (definition adapted from [FSL wiki](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html))" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2327,15 +2327,15 @@ nidm:NIDM_0000028 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000029 nidm:NIDM_0000029 rdf:type owl:Class ; - + rdfs:label "Gamma Difference HRF" ; - + rdfs:subClassOf nidm:NIDM_0000035 ; - + obo:IAO_0000115 "'Hemodynamic Response Function' which is a difference of two gamma probability density functions." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2343,15 +2343,15 @@ nidm:NIDM_0000029 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000030 nidm:NIDM_0000030 rdf:type owl:Class ; - + rdfs:label "Gamma Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000115 "Set of gamma probability density functions." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2359,15 +2359,15 @@ nidm:NIDM_0000030 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000031 nidm:NIDM_0000031 rdf:type owl:Class ; - + rdfs:label "Gamma HRF" ; - + rdfs:subClassOf nidm:NIDM_0000035 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "'Hemodynamic Response Function' which is a gamma probability density function." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2375,17 +2375,17 @@ nidm:NIDM_0000031 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000032 nidm:NIDM_0000032 rdf:type owl:Class ; - + rdfs:label "Gaussian Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000227"^^xsd:anyURI ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000115 "A normal distribution is a continuous probability distribution described by a probability distribution function described here: http://mathworld.wolfram.com/NormalDistribution.html (Definition from STATO)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2393,17 +2393,17 @@ nidm:NIDM_0000032 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000033 nidm:NIDM_0000033 rdf:type owl:Class ; - + rdfs:label "Grand Mean Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/GrandMeanMap.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/288" ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is the mean over all observations of that element in the input maps (after any scaling of those input maps)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2411,20 +2411,20 @@ nidm:NIDM_0000033 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000034 nidm:NIDM_0000034 rdf:type owl:Class ; - + rdfs:label "Height Threshold" ; - + rdfs:subClassOf nidm:NIDM_0000162 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/HeightThreshold-FDR.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/HeightThreshold-Stat.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/HeightThreshold-Unc.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/HeightThreshold_equivThresh-FWER.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A numerical value that establishes a lower bound on statistic values and can be specified by the user in terms of FWER-corrected p-value, uncorrected p-value or minimum statistic value." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/280" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2432,15 +2432,15 @@ nidm:NIDM_0000034 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000035 nidm:NIDM_0000035 rdf:type owl:Class ; - + rdfs:label "Hemodynamic Response Function" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "'Hemodynamic Response Function' basis that can on its own be used to represent the idealised 'Hemodynamic Response Function'." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2448,15 +2448,15 @@ nidm:NIDM_0000035 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000036 nidm:NIDM_0000036 rdf:type owl:Class ; - + rdfs:label "Convolution Basis Set" ; - + rdfs:subClassOf prov:Entity ; - + rdfs:isDefinedBy "A set of functions that, when convolved with the anticipated neural responses, yield a set of regressors to model the anticipated hemodynamic responses."^^xsd:string ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000124 . @@ -2464,17 +2464,17 @@ nidm:NIDM_0000036 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000037 nidm:NIDM_0000037 rdf:type owl:Class ; - + rdfs:label "Hemodynamic Response Function Derivative" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/DesignMatrix_1stLevel_HRFBasis2_HRFBasis3-InformedBasisSet.txt"^^xsd:anyURI ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/DesignMatrix_1stLevel_HRFBasis2_HRFBasis3-InformedBasisSet.txt"^^xsd:anyURI ; + obo:IAO_0000115 "'Hemodynamic Response Function' basis which is the derivative of an 'Hemodynamic Response Function'." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2482,15 +2482,15 @@ nidm:NIDM_0000037 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000048 nidm:NIDM_0000048 rdf:type owl:Class ; - + rdfs:label "Independent Error" ; - + rdfs:subClassOf obo:STATO_0000346 ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/28" ; - + obo:IAO_0000117 "TN" ; - + obo:IAO_0000114 obo:IAO_0000423 . @@ -2498,17 +2498,17 @@ nidm:NIDM_0000048 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000049 nidm:NIDM_0000049 rdf:type owl:Class ; - + rdfs:label "Inference" ; - + rdfs:subClassOf prov:Activity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/Inference.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Statistical 'Inference' is a process of drawing conclusions following data analysis using statistical methods (statistical tests) and evaluating whether to reject or accept null hypothesis. (definition from STATO)." ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000299" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2516,17 +2516,17 @@ nidm:NIDM_0000049 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000051 nidm:NIDM_0000051 rdf:type owl:Class ; - + rdfs:label "MNI Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000075 ; - + rdfs:seeAlso "birnlex_2125" ; - + obo:IAO_0000115 "MNI 305 coordinate system or any coordinate system derived from MNI 305." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2534,9 +2534,9 @@ nidm:NIDM_0000051 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000052 nidm:NIDM_0000052 rdf:type owl:Class ; - + rdfs:label "Map" ; - + rdfs:subClassOf prov:Entity , [ rdf:type owl:Restriction ; owl:onProperty crypto:sha512 ; @@ -2558,14 +2558,14 @@ nidm:NIDM_0000052 rdf:type owl:Class ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ; owl:onDataRange xsd:string ] ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/Map_atLocation-nii.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/Map_atLocation_hasMapHeader-img.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Ordered set of values corresponding to the discrete sampling of some process (e.g. brain MRI data measured on a regular 3D lattice; or brain cortical surface data measured irregularly over the cortex)." ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/pull/149" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2573,9 +2573,9 @@ nidm:NIDM_0000052 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000053 nidm:NIDM_0000053 rdf:type owl:Class ; - + rdfs:label "Map Header" ; - + rdfs:subClassOf prov:Entity , [ rdf:type owl:Restriction ; owl:onProperty dct:format ; @@ -2597,13 +2597,13 @@ nidm:NIDM_0000053 rdf:type owl:Class ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ; owl:onDataRange xsd:string ] ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/MapHeader.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/289" ; - + obo:IAO_0000115 "A file associated with a Map to provide header information (e.g. NIfTI header file)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2611,17 +2611,17 @@ nidm:NIDM_0000053 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000054 nidm:NIDM_0000054 rdf:type owl:Class ; - + rdfs:label "Mask Map" ; - + rdfs:subClassOf nidm:NIDM_0000004 ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/258 and https://github.com/incf-nidash/nidm/issues/155" ; - + obo:IAO_0000115 "A 'Binary Map' representing the exact set of elements (e.g., pixels, voxels, vertices, and faces) in which an activity was performed (e.g. the mask map generated by the model parameter estimation activity represents the exact set of voxels in which the mass univariate model was estimated) and/or restraining the space in which an activity was performed (e.g. the mask map used by 'Inference')" ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/MaskMap.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2629,17 +2629,17 @@ nidm:NIDM_0000054 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000056 nidm:NIDM_0000056 rdf:type owl:Class ; - + rdfs:label "Model Parameters Estimation" ; - + rdfs:subClassOf prov:Activity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ModelParametersEstimation.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "the process of performing a [obo:model parameter estimation](http://purl.obolibrary.org/obo/STATO_0000119) at each element (e.g., pixel, voxel, vertex, or face) of a map" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/issues/141" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2647,15 +2647,15 @@ nidm:NIDM_0000056 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000057 nidm:NIDM_0000057 rdf:type owl:Class ; - + rdfs:label "NIDM Object Model" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Abstraction on the data model, developed for a specific application/use-case/task at hand, that specifies the components and relations necessary for use by these applications. The same object model can be reused by multiple applications (e.g., meta-analysis, Neurovault)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/137" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2663,15 +2663,15 @@ nidm:NIDM_0000057 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000058 nidm:NIDM_0000058 rdf:type owl:Class ; - + rdfs:label "Non Parametric Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000115 "Probability distribution estimated empirically on the data without assumptions on the shape of the probability distribution." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2679,13 +2679,13 @@ nidm:NIDM_0000058 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000059 nidm:NIDM_0000059 rdf:type owl:Class ; - + rdfs:label "Non Parametric Symmetric Distribution" ; - + rdfs:subClassOf obo:STATO_0000117 ; - + obo:IAO_0000115 "Probability distribution estimated empirically on the data assuming only symmetry of the probability distribution." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2693,15 +2693,15 @@ nidm:NIDM_0000059 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000060 nidm:NIDM_0000060 rdf:type owl:Class ; - + rdfs:label "One Tailed Test" ; - + rdfs:subClassOf prov:Entity ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000286"^^xsd:anyURI ; - + obo:IAO_0000116 "Re-use \"one tailed test\" from STATO." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2709,17 +2709,17 @@ nidm:NIDM_0000060 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000061 nidm:NIDM_0000061 rdf:type owl:Class ; - + rdfs:label "Parameter Estimate Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ParameterEstimateMap.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/255 and https://github.com/incf-nidash/nidm/issues/141 (see also https://github.com/ISA-tools/stato/issues/18)" ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [model parameter estimate](http://purl.obolibrary.org/obo/STATO_0000144)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2727,17 +2727,17 @@ nidm:NIDM_0000061 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000062 nidm:NIDM_0000062 rdf:type owl:Class ; - + rdfs:label "Peak" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "A map element (e.g., pixel, voxel, vertex, or face) which is a local maximum in the significant cluster and complies with the 'Peak' definition criteria." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/283" ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/Peak_ValueP.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2745,17 +2745,17 @@ nidm:NIDM_0000062 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000063 nidm:NIDM_0000063 rdf:type owl:Class ; - + rdfs:label "Peak Definition Criteria" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/PeakDefinitionCriteria_MaxPeaks.txt"^^xsd:anyURI ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/200" ; - + obo:IAO_0000115 "Set of criterion specified a priori to define the 'Peak's reported after 'Inference' (e.g. maximum number of 'Peak's within a cluster, minimum distance between 'Peak's)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2763,15 +2763,15 @@ nidm:NIDM_0000063 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000064 nidm:NIDM_0000064 rdf:type owl:Class ; - + rdfs:label "Pixel Connectivity Criterion" ; - + rdfs:subClassOf nidm:NIDM_0000012 ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "The criterion used to characterize two pixels as 'connected'. In two dimensions voxels that are connected can share an edge (4-connected) or, edge or corner (8-connected)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2779,17 +2779,17 @@ nidm:NIDM_0000064 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000065 nidm:NIDM_0000065 rdf:type owl:Class ; - + rdfs:label "Poisson Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000051"^^xsd:anyURI ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000115 "Poisson distribution is a probability distribution used to model the number of events occurring within a given time interval. It is defined by a real number (λ) and an integer k representing the number of events and a function. The expected value of a Poisson-distributed random variable is equal to λ and so is its variance. (Definition from STATO)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2797,17 +2797,17 @@ nidm:NIDM_0000065 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000066 nidm:NIDM_0000066 rdf:type owl:Class ; - + rdfs:label "Residual Mean Squares Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/255." ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [residual mean square](http://purl.obolibrary.org/obo/STATO_0000375)." ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ResidualMeanSquaresMap.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2815,15 +2815,15 @@ nidm:NIDM_0000066 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000067 nidm:NIDM_0000067 rdf:type owl:Class ; - + rdfs:label "Custom Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "Customised set of basis functions." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2831,17 +2831,17 @@ nidm:NIDM_0000067 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000068 nidm:NIDM_0000068 rdf:type owl:Class ; - + rdfs:label "Search Space Mask Map" ; - + rdfs:subClassOf nidm:NIDM_0000054 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/SearchSpaceMaskMap.txt" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/258" ; - + obo:IAO_0000115 "A 'Mask Map' representing the set of elements (e.g., pixels, voxels, vertices, or faces) in which the 'Inference' was performed" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2849,15 +2849,15 @@ nidm:NIDM_0000068 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000069 nidm:NIDM_0000069 rdf:type owl:Class ; - + rdfs:label "Fourier Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000115 "Set of Fourier basis." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2865,17 +2865,17 @@ nidm:NIDM_0000069 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000070 nidm:NIDM_0000070 rdf:type owl:Class ; - + rdfs:label "Supra-Threshold Cluster" ; - + rdfs:subClassOf obo:OBI_0000251 ; - + obo:IAO_0000115 "A cluster of map elements (e.g., pixels, voxels, vertices, and faces) that were selected by the 'Inference' activity and are contiguous according to the cluster 'Connectivity Criterion'."^^xsd:string ; - + prov:editorialNote "Discussed in https://github.com/incf-nidash/nidm/issues/71."^^xsd:string ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/SupraThresholdCluster.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2883,15 +2883,15 @@ nidm:NIDM_0000070 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000071 nidm:NIDM_0000071 rdf:type owl:Class ; - + rdfs:label "Error Parameter Map-Wise Dependence" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Map-wise dependence structure of a parameter in the 'Error Model' (i.e. variance or dependence parameter). For example, whether a temporal autocorrelation parameter is estimated at each element separately, estimated using data in a local neighbourhood, or estimated using all elements in the map." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2899,15 +2899,15 @@ nidm:NIDM_0000071 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000072 nidm:NIDM_0000072 rdf:type owl:Class ; - + rdfs:label "Constant Parameter" ; - + rdfs:subClassOf nidm:NIDM_0000071 ; - + obo:IAO_0000115 "Parameter estimated as constant over a entire set of elements considered (e.g. those in the analysis mask)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2915,15 +2915,15 @@ nidm:NIDM_0000072 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000073 nidm:NIDM_0000073 rdf:type owl:Class ; - + rdfs:label "Independent Parameter" ; - + rdfs:subClassOf nidm:NIDM_0000071 ; - + obo:IAO_0000115 "Parameter whose estimation at a given element does not depend on any other element." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2931,15 +2931,15 @@ nidm:NIDM_0000073 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000074 nidm:NIDM_0000074 rdf:type owl:Class ; - + rdfs:label "Regularized Parameter" ; - + rdfs:subClassOf nidm:NIDM_0000071 ; - + obo:IAO_0000115 "Parameter whose estimation at a given element depends on a local neighborhood of elements" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2947,17 +2947,17 @@ nidm:NIDM_0000074 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000075 nidm:NIDM_0000075 rdf:type owl:Class ; - + rdfs:label "Standardized Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000081 ; - + rdfs:comment "This is meant to be used for retrospective export when exact template is unknown." ; - + obo:IAO_0000115 "Parent of all reference spaces except \"Subject\"." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -2965,17 +2965,17 @@ nidm:NIDM_0000075 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000076 nidm:NIDM_0000076 rdf:type owl:Class ; - + rdfs:label "Statistic Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/StatisticMap_T.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/255" ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [statistic](http://purl.obolibrary.org/obo/STATO_0000039)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2983,17 +2983,17 @@ nidm:NIDM_0000076 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000077 nidm:NIDM_0000077 rdf:type owl:Class ; - + rdfs:label "Subject Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000081 ; - + obo:IAO_0000115 "Reference space corresponding to the subject brain (no spatial normalization applied)." ; - + rdfs:comment "Used in FSL and SPM un-registered data." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -3001,17 +3001,17 @@ nidm:NIDM_0000077 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000078 nidm:NIDM_0000078 rdf:type owl:Class ; - + rdfs:label "Talairach Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000075 ; - + obo:IAO_0000115 "Reference space defined by the dissected brain used for the Talairach and Tournoux atlas (cf. http://www.talairach.org/about.html)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + rdfs:seeAlso "http://www.talairach.org/" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3019,15 +3019,15 @@ nidm:NIDM_0000078 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000079 nidm:NIDM_0000079 rdf:type owl:Class ; - + rdfs:label "Two Tailed Test" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Re-use \"two tailed test\" from STATO"^^xsd:anyURI ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000287"^^xsd:anyURI ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3035,15 +3035,15 @@ nidm:NIDM_0000079 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000080 nidm:NIDM_0000080 rdf:type owl:Class ; - + rdfs:label "Voxel Connectivity Criterion" ; - + rdfs:subClassOf nidm:NIDM_0000012 ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "The criterion used to characterize two voxels as 'connected'. In three dimensions voxels that are connected can share a voxel face (6-connected), face or edge (18-connectec), or face, edge, or corner (26-connected)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3051,16 +3051,16 @@ nidm:NIDM_0000080 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000081 nidm:NIDM_0000081 rdf:type owl:Class ; - + rdfs:label "World Coordinate System" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 """Reference space on which real-world positions are expressed (cf. [Nifti-1 FAQ question 14](http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q14) and [Understanding affines on nipy](http://nipy.org/nipy/stable/devel/code_discussions/understanding_affines.html) ). A world coordinate system can be represented by an image obtained by registering an initial set of images, using a given normalization algorithm to match a target template.""" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3068,15 +3068,15 @@ nidm:NIDM_0000081 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000087 nidm:NIDM_0000087 rdf:type owl:Class ; - + rdfs:label "Drift Model" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000115 "A model used to compensate for low frequency baseline drifts when analyzing functional MRI data at the subject level." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3084,15 +3084,15 @@ nidm:NIDM_0000087 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000110 nidm:NIDM_0000110 rdf:type owl:Class ; - + rdfs:label "Gaussian HRF" ; - + rdfs:subClassOf nidm:NIDM_0000035 ; - + obo:IAO_0000115 "'Hemodynamic Response Function' which is a gaussian kernel." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3100,15 +3100,15 @@ nidm:NIDM_0000110 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000135 nidm:NIDM_0000135 rdf:type owl:Class ; - + rdfs:label "Contrast Variance Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a contrast variance (i.e. the square of a [standard error of a contrast estimate](http://purl.obolibrary.org/obo/STATO_0000385))" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/287" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3116,19 +3116,19 @@ nidm:NIDM_0000135 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000140 nidm:NIDM_0000140 rdf:type owl:Class ; - + rdfs:label "Cluster Center Of Gravity" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/257" ; - + obo:IAO_0000115 "A centre of gravity of the cluster, equivalent to the concept of Centre Of Gravity for a object with distributed mass, where intensity substitutes for mass in this case. The 'Coordinate' of the centre of gravity is the weighted average of the cluster element (e.g., pixels, voxels, vertices, or faces) 'Coordinate's, where the weighting factors are the cluster element intensities. (definition adapted from http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster)" ; - + rdfs:seeAlso "http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster" ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/FSL_ClusterCenterOfGravity.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3136,15 +3136,15 @@ nidm:NIDM_0000140 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000144 nidm:NIDM_0000144 rdf:type owl:Class ; - + rdfs:label "Resels Per Voxel Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/SPM_ReselsPerVoxelMap.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) location is the number of resels per voxel." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3152,15 +3152,15 @@ nidm:NIDM_0000144 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000150 nidm:NIDM_0000150 rdf:type owl:Class ; - + rdfs:label "Linear Spline Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "A Linear (order 1) spline, providing an estimate that is continuous over time (in contrast to a FIR basis, which is discontinuous between each time bin). This is called TENT in AFNI's 3dDeconvolve program." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3168,15 +3168,15 @@ nidm:NIDM_0000150 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000151 nidm:NIDM_0000151 rdf:type owl:Class ; - + rdfs:label "Sine Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "A set of Sine waves of differing frequencies (definition adapted from [FSL wiki](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html))." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3184,15 +3184,15 @@ nidm:NIDM_0000151 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000160 nidm:NIDM_0000160 rdf:type owl:Class ; - + rdfs:label "P-Value Uncorrected" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "A p-value reported without correction for multiple testing."^^xsd:string ; - + obo:IAO_0000116 "Discussed in [Neuroimaging terms spreadsheet](https://docs.google.com/spreadsheets/d/16pC2cDsdxlzv2CzlNMtStqt5-xHwDEsU6MjZVxWhrE4/edit?usp=sharing)"^^xsd:string ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3200,13 +3200,13 @@ nidm:NIDM_0000160 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000162 nidm:NIDM_0000162 rdf:type owl:Class ; - + rdfs:label "Threshold"^^xsd:string ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "A numerical value that establishes a bound on a set of statistic values and can be specified by the user in terms of FWER-corrected p-value, uncorrected p-value, FDR-corrected q-value or statistic value"^^xsd:string ; - + obo:IAO_0000114 obo:IAO_0000125 . @@ -3214,15 +3214,15 @@ nidm:NIDM_0000162 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000163 nidm:NIDM_0000163 rdf:type owl:Class ; - + rdfs:label "Contrast Explained Mean Square Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is the extra sum of squares divided by the 'effect Degrees of Freedom' (i.e. the numerator of an F-statistic)." ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/235" ; - + obo:IAO_0000114 obo:IAO_0000125 . @@ -3230,13 +3230,13 @@ nidm:NIDM_0000163 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000164 nidm:NIDM_0000164 rdf:type owl:Class ; - + rdfs:label "Neuroimaging Analysis Software" ; - + rdfs:subClassOf prov:SoftwareAgent ; - + obo:IAO_0000115 "Tool used to process neuroimaging data." ; - + obo:IAO_0000114 obo:IAO_0000124 . @@ -3244,13 +3244,13 @@ nidm:NIDM_0000164 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000165 nidm:NIDM_0000165 rdf:type owl:Class ; - + rdfs:label "NIDM-Results Exporter" ; - + rdfs:subClassOf prov:SoftwareAgent ; - + obo:IAO_0000115 "Tool used to export results produced by a neuroimaging software (SPM, FSL, AFNI...) into a NIDM-Results archive." ; - + obo:IAO_0000114 obo:IAO_0000124 . @@ -3258,15 +3258,15 @@ nidm:NIDM_0000165 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000166 nidm:NIDM_0000166 rdf:type owl:Class ; - + rdfs:label "NIDM-Results Export" ; - + rdfs:subClassOf prov:Activity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/Export.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "The process of exporting results created by a neuroimaging software (SPM, FSL, AFNI...) into a NIDM-Results archive." ; - + obo:IAO_0000114 obo:IAO_0000124 . @@ -3274,15 +3274,15 @@ nidm:NIDM_0000166 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000167 nidm:NIDM_0000167 rdf:type owl:Class ; - + rdfs:label "nidmfsl" ; - + rdfs:subClassOf nidm:NIDM_0000165 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ExporterSoftware-FSL.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Python library for the export of feat folders (generated by FSL) to NIDM-Results. Source available at: https://github.com/incf-nidash/nidm-results_fsl/." ; - + obo:IAO_0000114 obo:IAO_0000124 . @@ -3290,15 +3290,15 @@ nidm:NIDM_0000167 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000168 nidm:NIDM_0000168 rdf:type owl:Class ; - + rdfs:label "spm_results_nidm" ; - + rdfs:subClassOf nidm:NIDM_0000165 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/ExporterSoftware-SPM.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Matlab m file for the export of SPM results to NIDM-Results. Source available at: http://www.fil.ion.ucl.ac.uk/spm/download/toolbox/NIDM/spm_nidm.zip/." ; - + obo:IAO_0000114 obo:IAO_0000124 . @@ -3306,17 +3306,17 @@ nidm:NIDM_0000168 rdf:type owl:Class ; ### http://purl.org/nidash/spm#SPM_0000002 spm:SPM_0000002 rdf:type owl:Class ; - + rdfs:label "DCT Drift Model" ; - + rdfs:subClassOf nidm:NIDM_0000087 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/SPM_DriftModel.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000115 "A 'Drift Model' in which the drifts are modeled by a Discrete Cosine Transform basis added to regression model" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3324,17 +3324,17 @@ spm:SPM_0000002 rdf:type owl:Class ; ### http://purl.org/nidash/spm#SPM_0000005 spm:SPM_0000005 rdf:type owl:Class ; - + rdfs:label "Partial Conjunction Inference" ; - + rdfs:subClassOf nidm:NIDM_0000049 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/294" ; obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.2.0/nidm/nidm-results/terms/examples/SPM_KConjunctionInference.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "The process of testing the joint significance of multiple effects to infer that some (not necessarily all) of the respective effects are real (i.e. their null hypotheses are false). If there are K effects considered, the 'partial Conjunction Degree' u is the number non-null effects allowed as part of partial conjunction null hypothesis; if the partial conjunction null is rejected, it may be inferred that u+1 or more effects are real. The case of u=K-1 corresponds to proper \"'Conjunction Inference'\", while the case of u=0 corresponds to \"global null\" conjunction test. See [Friston et al. (2005). Conjunction revisited. NeuroImage, 25(3), 661-7.](http://dx.doi.org/10.1016/j.neuroimage.2005.01.013)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3352,13 +3352,13 @@ spm:SPM_0000005 rdf:type owl:Class ; afni:GammaHRF rdf:type nidm:NIDM_0000031 , owl:NamedIndividual ; - + rdfs:label "AFNI's Gamma HRF" ; - + obo:IAO_0000115 "'Hemodynamic Response Function' which is a fixed gamma probability density function. This is the default in AFNI (-GAM option to 3ddeconvolve, or implied via afni_proc.py)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281 and discussed in https://github.com/incf-nidash/nidm/pull/248" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3367,13 +3367,13 @@ afni:GammaHRF rdf:type nidm:NIDM_0000031 , fsl:FSL_0000001 rdf:type nidm:NIDM_0000029 , owl:NamedIndividual ; - + rdfs:label "FSL's Gamma Difference HRF" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "'Hemodynamic Response Function' which is a fixed difference of two gamma probability density functions - a standard positive function at normal lag, and a small, delayed, negated gamma probability density function, which attempts to model the late undershoot (definition adapted [FSL wiki](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html)). This is the default in FSL." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3382,13 +3382,13 @@ fsl:FSL_0000001 rdf:type nidm:NIDM_0000029 , fsl:FSL_0000003 rdf:type nidm:NIDM_0000037 , owl:NamedIndividual ; - + rdfs:label "FSL's Temporal Derivative" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "'Hemodynamic Response Function' basis that is the derivative with respect to time of the FSL's Gamma Difference heamodynamic response function." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3397,17 +3397,17 @@ fsl:FSL_0000003 rdf:type nidm:NIDM_0000037 , nidm:NIDM_0000009 rdf:type nidm:NIDM_0000075 , owl:NamedIndividual ; - + rdfs:label "Colin27 Coordinate System" ; - + obo:IAO_0000115 "Reference space defined as the stereotaxic average of 27 T1-weighted MRI scans of the same individual transformed into the Talairach stereotaxic space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres and http://neuro.debian.net/pkgs/mni-colin27-nifti.html). This is the default in SPM96 (cf. [MRC CBSU Wiki](http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach))." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + rdfs:comment "used in SPM96 (cf. http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3416,15 +3416,15 @@ nidm:NIDM_0000009 rdf:type nidm:NIDM_0000075 , nidm:NIDM_0000038 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm452 Air Coordinate System" ; - + obo:IAO_0000115 "Reference space defined as the average of 452 T1-weighted MRIs of normal young adult brains after 12 parameter AIR linear transform to the MNI 305 space (cf. http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml and http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)" ; - + rdfs:seeAlso "http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3433,15 +3433,15 @@ nidm:NIDM_0000038 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000039 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm452 Warp5 Coordinate System" ; - + rdfs:seeAlso "http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml" ; - + obo:IAO_0000115 "Reference space defined as the average of 452 T1-weighted MRIs of normal young adult brains after affine and 5 order polynomial non-linear warping to the MNI 305 space (cf. http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml and http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3450,17 +3450,17 @@ nidm:NIDM_0000039 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000040 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Linear Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin" ; - + rdfs:comment "used in SPM99 to SPM8 (cf. http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach and spm8/spm_templates.man)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Reference space which is the average of 152 T1-weighted MRI scans, linearly transformed onto the MNI 305 reference space (definition adapted from: http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin). This is the default in SPM99 to SPM8 (cf. [MRC CBSU Wiki](http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach) and spm8/spm_templates.man." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3469,15 +3469,15 @@ nidm:NIDM_0000040 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000041 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009a Asymmetric Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3486,15 +3486,15 @@ nidm:NIDM_0000041 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000042 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009a Symmetric Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to to form a symmetric model in MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3503,15 +3503,15 @@ nidm:NIDM_0000042 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000043 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009b Asymmetric Coordinate System" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans in high-resolution, non-linearly transformed to MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3520,15 +3520,15 @@ nidm:NIDM_0000043 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000044 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009b Symmetric Coordinate System" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans in high-resolution, non-linearly transformed to form a symmetric model in MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3537,17 +3537,17 @@ nidm:NIDM_0000044 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000045 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009c Asymmetric Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space using the N3 algorithm (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + rdfs:comment "Used in DARTEL toolbox in SPM12b (cf. spm12b/spm_templates.man)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3556,15 +3556,15 @@ nidm:NIDM_0000045 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000046 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009c Symmetric Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to form a symmetric model in MNI152 linear space using the N3 algorithm (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details). This is the default for DARTEL toolbox in SPM12b (cf. spm12/spm_templates.man)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3573,17 +3573,17 @@ nidm:NIDM_0000046 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000047 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear6th Generation Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6"^^xsd:anyURI ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, linearly and non-linearly (6 iterations) transformed to form a symmetric model in Talairach space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6)" ; - + rdfs:comment "Used in FSL (cf. http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3592,17 +3592,17 @@ nidm:NIDM_0000047 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000050 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Ixi549 Coordinate System" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Reference space defined by the average of the 549 subjects from the IXI dataset linearly transformed to the ICBM MNI 452 (cf. spm12/spm\\_templates.man and http://biomedic.doc.ic.ac.uk/brain-development/index.php?n=Main.Datasets). This is the default in SPM12 (cf. spm12/spm_templates.man)." ; - + rdfs:seeAlso "http://biomedic.doc.ic.ac.uk/brain-development/index.php?n=Main.Datasets" ; - + rdfs:comment "Used in SPM12b (cf. spm12b/spm_templates.man)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3611,15 +3611,15 @@ nidm:NIDM_0000050 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000055 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Mni305 Coordinate System" ; - + obo:IAO_0000115 "Reference space defined as the average of 305 T1-weighted MRI scans, linearly transformed to Talairach space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/MNI305 for more details)" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/MNI305" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3628,13 +3628,13 @@ nidm:NIDM_0000055 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000117 rdf:type nidm:NIDM_0000064 , owl:NamedIndividual ; - + rdfs:label "pixel4connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of pixels are 4-Connected if they share an edge." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3643,13 +3643,13 @@ nidm:NIDM_0000117 rdf:type nidm:NIDM_0000064 , nidm:NIDM_0000118 rdf:type nidm:NIDM_0000064 , owl:NamedIndividual ; - + rdfs:label "pixel8connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of pixels are 8-Connected if they share an edge or corner." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3658,13 +3658,13 @@ nidm:NIDM_0000118 rdf:type nidm:NIDM_0000064 , nidm:NIDM_0000128 rdf:type nidm:NIDM_0000080 , owl:NamedIndividual ; - + rdfs:label "voxel18connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of voxels are 18-Connected if they share a face or edge." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3673,13 +3673,13 @@ nidm:NIDM_0000128 rdf:type nidm:NIDM_0000080 , nidm:NIDM_0000129 rdf:type nidm:NIDM_0000080 , owl:NamedIndividual ; - + rdfs:label "voxel26connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of voxels are 26-Connected if they share a face, edge or corner." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3688,13 +3688,13 @@ nidm:NIDM_0000129 rdf:type nidm:NIDM_0000080 , nidm:NIDM_0000130 rdf:type nidm:NIDM_0000080 , owl:NamedIndividual ; - + rdfs:label "voxel6connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of voxels are 6-Connected if they share a face." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3703,13 +3703,13 @@ nidm:NIDM_0000130 rdf:type nidm:NIDM_0000080 , spm:SPM_0000003 rdf:type nidm:NIDM_0000037 , owl:NamedIndividual ; - - rdfs:label "SPM's Dispersion Derivative" ; - + + rdfs:label "SPM's Dispersion Derivative" ; + obo:IAO_0000115 "'Hemodynamic Response Function' basis that is the derivative with respect to spatial dispersion of the SPM's Canonical heamodynamic response function." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3718,13 +3718,13 @@ spm:SPM_0000003 rdf:type nidm:NIDM_0000037 , spm:SPM_0000004 rdf:type nidm:NIDM_0000029 , owl:NamedIndividual ; - + rdfs:label "SPM's Canonical HRF" ; - + obo:IAO_0000115 "'Hemodynamic Response Function' which is a fixed difference of two gamma probability density functions and is denoted by \"canonical HRF\" in SPM. This is the default in SPM" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3733,13 +3733,13 @@ spm:SPM_0000004 rdf:type nidm:NIDM_0000029 , spm:SPM_0000006 rdf:type nidm:NIDM_0000037 , owl:NamedIndividual ; - + rdfs:label "SPM's Temporal Derivative" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "'Hemodynamic Response Function' basis that is the derivative with respect to time of the SPM's Canonical heamodynamic response function." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3763,9 +3763,9 @@ spm:SPM_0000006 rdf:type nidm:NIDM_0000037 , ### http://purl.org/dc/terms/format crypto:sha512 rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Secure Hash Algorithm 512." ; - + rdfs:comment "SHA stands for Secure Hash Algorithm. Hash algorithms compute a fixed-length digital representation (known as a message digest) of an input data sequence (the message) of any length." . ##### Imports from dc ##### . @@ -3783,9 +3783,9 @@ crypto:sha512 rdf:type owl:DatatypeProperty ; ### http://purl.org/dc/elements/1.1/description dc:description rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "An account of the resource." ; - + rdfs:comment "Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource." . @@ -3802,9 +3802,9 @@ dc:description rdf:type owl:ObjectProperty ; ### http://purl.org/dc/terms/format dct:format rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "The file format, physical medium, or dimensions of the resource." ; - + rdfs:comment "Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME]." . @@ -3821,9 +3821,9 @@ dct:format rdf:type owl:DatatypeProperty ; ### http://purl.org/dc/dcmitype/Image dctype:Image rdf:type owl:Class ; - + obo:IAO_0000115 "A visual representation other than text." ; - + rdfs:comment "Examples include images and photographs of physical objects, paintings, prints, drawings, other images and graphics, animations and moving pictures, film, diagrams, maps, musical notation. Note that Image may include both electronic and physical representations." . @@ -3836,18 +3836,18 @@ dctype:Image rdf:type owl:Class ; ##### Imports from iao ##### . rdf:type owl:Ontology ; - + dc:date "2009-07-31"^^xsd:date ; - + owl:versionInfo "2015-02-23"^^xsd:string ; - + rdfs:comment "An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at http://code.google.com/p/information-artifact-ontology/"^^xsd:string , "IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999"^^xsd:string , "IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999"^^xsd:string , "This file is based on checkout of our SVN repository revision $Revision: 717 $ "^^xsd:string ; - + protege:defaultLanguage "en"^^xsd:string ; - + dc:contributor "Adam Goldstein"@en , "Alan Ruttenberg"@en , "Albert Goldfain"@en , @@ -3883,11 +3883,11 @@ dctype:Image rdf:type owl:Class ; "William Duncan"@en , "William Hogan"@en , "Yongqun (Oliver) He"@en ; - + foaf:homepage ; - + dc:license ; - + owl:versionIRI iao:iao.owl . @@ -3907,13 +3907,13 @@ protege:defaultLanguage rdf:type owl:AnnotationProperty . ### http://purl.obolibrary.org/obo/BFO_0000179 obo:BFO_0000179 rdf:type owl:AnnotationProperty ; - + rdfs:label "BFO OWL specification label"@en ; - + obo:IAO_0000232 "Really of interest to developers only"@en ; - + obo:IAO_0000115 "Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification."@en ; - + rdfs:subPropertyOf rdfs:label . @@ -3921,15 +3921,15 @@ obo:BFO_0000179 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/BFO_0000180 obo:BFO_0000180 rdf:type owl:AnnotationProperty ; - + rdfs:label "BFO CLIF specification label"@en ; - + obo:IAO_0000119 "Person:Alan Ruttenberg" ; - + obo:IAO_0000232 "Really of interest to developers only"@en ; - + obo:IAO_0000115 "Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2"@en ; - + rdfs:subPropertyOf rdfs:label . @@ -3937,24 +3937,24 @@ obo:BFO_0000180 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000111 obo:IAO_0000111 rdf:type owl:AnnotationProperty ; - + rdfs:label "editor preferred term" , "editor preferred label"@en , "editor preferred term"@en ; - + obo:IAO_0000111 "editor preferred term" ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000115 "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)"@en ; - + obo:IAO_0000111 "editor preferred label"@en , "editor preferred term"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3962,20 +3962,20 @@ obo:IAO_0000111 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000112 obo:IAO_0000112 rdf:type owl:AnnotationProperty ; - + rdfs:label "example of usage"@en ; - + obo:IAO_0000115 "A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not"@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "example"@en , "example of usage"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3983,15 +3983,15 @@ obo:IAO_0000112 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000114 obo:IAO_0000114 rdf:type owl:AnnotationProperty ; - + rdfs:label "has curation status"@en ; - + obo:IAO_0000119 "OBI_0000281"@en ; - + obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en , "PERSON:Bill Bug"@en , "PERSON:Melanie Courtot"@en ; - + obo:IAO_0000111 "has curation status"@en . @@ -3999,27 +3999,27 @@ obo:IAO_0000114 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000115 obo:IAO_0000115 rdf:type owl:AnnotationProperty ; - + rdfs:label "definition"^^xsd:string , "textual definition"^^xsd:string , "definition" , "definition"@en ; - + obo:IAO_0000111 "definition"^^xsd:string , "textual definition"^^xsd:string , "definition" ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000115 "The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en , "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en ; - + obo:IAO_0000111 "definition"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -4027,19 +4027,19 @@ obo:IAO_0000115 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000116 obo:IAO_0000116 rdf:type owl:AnnotationProperty ; - + rdfs:label "editor note"@en ; - + obo:IAO_0000115 "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "editor note"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -4047,21 +4047,21 @@ obo:IAO_0000116 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000117 obo:IAO_0000117 rdf:type owl:AnnotationProperty ; - + rdfs:label "term editor"@en ; - + obo:IAO_0000116 "20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115."@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000115 "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "term editor"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -4069,19 +4069,19 @@ obo:IAO_0000117 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000118 obo:IAO_0000118 rdf:type owl:AnnotationProperty ; - + rdfs:label "alternative term"@en ; - + obo:IAO_0000115 "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)"@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "alternative term"@en ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:isDefinedBy . @@ -4089,20 +4089,20 @@ obo:IAO_0000118 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000119 obo:IAO_0000119 rdf:type owl:AnnotationProperty ; - + rdfs:label "definition source"@en ; - + obo:IAO_0000119 "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"^^xsd:string , "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "definition source"@en ; - + obo:IAO_0000115 "formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -4110,17 +4110,17 @@ obo:IAO_0000119 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000232 obo:IAO_0000232 rdf:type owl:AnnotationProperty ; - + rdfs:label "curator note"@en ; - + obo:IAO_0000115 "An administrative note of use for a curator but of no use for a user"@en ; - + obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en ; - + obo:IAO_0000111 "curator note"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -4128,20 +4128,20 @@ obo:IAO_0000232 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000412 obo:IAO_0000412 rdf:type owl:AnnotationProperty ; - + rdfs:label "imported from"@en ; - + obo:IAO_0000115 "For external terms/classes, the ontology from which the term was imported"@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en , "PERSON:Melanie Courtot"@en ; - + obo:IAO_0000111 "imported from"@en ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:isDefinedBy . @@ -4149,17 +4149,17 @@ obo:IAO_0000412 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000600 obo:IAO_0000600 rdf:type owl:AnnotationProperty ; - + rdfs:label "elucidation"@en ; - + obo:IAO_0000119 "Person:Barry Smith"@en ; - + obo:IAO_0000600 "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms"@en ; - + obo:IAO_0000111 "elucidation"@en ; - + obo:IAO_0000117 "person:Alan Ruttenberg"@en ; - + rdfs:isDefinedBy . @@ -4167,9 +4167,9 @@ obo:IAO_0000600 rdf:type owl:AnnotationProperty ; ### http://purl.org/dc/elements/1.1/contributor dc:contributor rdf:type owl:AnnotationProperty ; - + rdfs:label "Contributor"@en-us ; - + rdfs:isDefinedBy dc: . @@ -4177,9 +4177,9 @@ dc:contributor rdf:type owl:AnnotationProperty ; ### http://purl.org/dc/elements/1.1/date dc:date rdf:type owl:AnnotationProperty ; - + rdfs:label "Date"@en-us ; - + rdfs:isDefinedBy dc: . @@ -4220,19 +4220,19 @@ foaf:homepage rdf:type owl:AnnotationProperty . ### http://purl.obolibrary.org/obo/IAO_0000136 obo:IAO_0000136 rdf:type owl:ObjectProperty ; - + rdfs:label "is about"@en ; - + obo:IAO_0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en ; - + obo:IAO_0000112 "This document is about information artifacts and their representations"@en ; - + obo:IAO_0000115 "is_about is a (currently) primitive relation that relates an information artifact to an entity."@en ; - + obo:IAO_0000117 "person:Alan Ruttenberg"@en ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + obo:IAO_0000412 . @@ -4249,9 +4249,9 @@ obo:IAO_0000136 rdf:type owl:ObjectProperty ; ### http://usefulinc.com/ns/doap#revision doap:revision rdf:type owl:DatatypeProperty ; - + obo:IAO_0000412 ; - + rdfs:isDefinedBy ns:doap . @@ -4274,7 +4274,7 @@ doap:revision rdf:type owl:DatatypeProperty ; ### http://purl.obolibrary.org/obo/IAO_0000002 obo:IAO_0000002 rdf:type owl:NamedIndividual ; - + rdfs:label "example to be eventually removed"@en . @@ -4282,9 +4282,9 @@ obo:IAO_0000002 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000120 obo:IAO_0000120 rdf:type owl:NamedIndividual ; - + rdfs:label "metadata complete"@en ; - + obo:IAO_0000115 "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en . @@ -4292,9 +4292,9 @@ obo:IAO_0000120 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000121 obo:IAO_0000121 rdf:type owl:NamedIndividual ; - + rdfs:label "organizational term"@en ; - + obo:IAO_0000115 "term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en . @@ -4302,9 +4302,9 @@ obo:IAO_0000121 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000122 obo:IAO_0000122 rdf:type owl:NamedIndividual ; - + rdfs:label "ready for release"@en ; - + obo:IAO_0000115 "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en . @@ -4312,9 +4312,9 @@ obo:IAO_0000122 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000123 obo:IAO_0000123 rdf:type owl:NamedIndividual ; - + rdfs:label "metadata incomplete"@en ; - + obo:IAO_0000115 "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en . @@ -4322,9 +4322,9 @@ obo:IAO_0000123 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000124 obo:IAO_0000124 rdf:type owl:NamedIndividual ; - + rdfs:label "uncurated"@en ; - + obo:IAO_0000115 "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en . @@ -4332,9 +4332,9 @@ obo:IAO_0000124 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000125 obo:IAO_0000125 rdf:type owl:NamedIndividual ; - + rdfs:label "pending final vetting"@en ; - + obo:IAO_0000115 "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en . @@ -4342,13 +4342,13 @@ obo:IAO_0000125 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000423 obo:IAO_0000423 rdf:type owl:NamedIndividual ; - + rdfs:label "to be replaced with external ontology term"@en ; - + obo:IAO_0000117 "Alan Ruttenberg"@en ; - + obo:IAO_0000115 "Terms with this status should eventually replaced with a term from another ontology."@en ; - + obo:IAO_0000119 "group:OBI"@en . @@ -4356,13 +4356,13 @@ obo:IAO_0000423 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000428 obo:IAO_0000428 rdf:type owl:NamedIndividual ; - + rdfs:label "requires discussion"@en ; - + obo:IAO_0000115 "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en ; - + obo:IAO_0000117 "Alan Ruttenberg"@en ; - + obo:IAO_0000119 "group:OBI"@en . @@ -4376,14 +4376,14 @@ obo:IAO_0000428 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/iao/2015-02-23/iao.owl iao:iao.owl rdf:type owl:NamedIndividual ; - + rdfs:label "IAO Release 2015-02-23" ; - + doap:revision "SVN $Revision: 717 $" ; - + doap:file-release , iao:iao.owl ; - + rdfs:seeAlso . @@ -4439,13 +4439,13 @@ obo:IAO_0000115 rdf:type owl:AnnotationProperty . ### http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#fileName nfo:fileName rdf:type owl:DatatypeProperty ; - + rdfs:label "fileName" ; - + nrl:maxCardinality "1" ; - + obo:IAO_0000115 "Name of the file, together with the extension" ; - + rdfs:range xsd:string . @@ -4485,9 +4485,9 @@ obo:IAO_0000115 rdf:type owl:AnnotationProperty . ### http://neurolex.org/wiki/birnlex_2067 nlx:birnlex_2067 rdf:type owl:Class ; - + rdfs:label "FSL" ; - + obo:IAO_0000115 "A comprehensive library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. The tools include registration, atlases, Diffusion MRI tools for parameter reconstruction and probabilistic taractography, and a viewer. FSL runs on Apple and PCs (Linux and Windows), and is very easy to install. Most of the tools can be run both from the command line and as GUIs ('point-and-click' graphical user interfaces). Several complementary brain atlases, integrated into FSLView and Featquery, allowing viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Atlases included with FSL: * Harvard-Oxford cortical and subcortical structural atlases * Julich histological atlas * JHU DTI-based white-matter atlases * Oxford thalamic connectivity atlas * Talairach atlas * MNI structural atlas * Cerebellum atlas FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK." . @@ -4495,9 +4495,9 @@ nlx:birnlex_2067 rdf:type owl:Class ; ### http://neurolex.org/wiki/nif-0000-00343 nlx:nif-0000-00343 rdf:type owl:Class ; - + rdfs:label "SPM" ; - + obo:IAO_0000115 "Software package for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG." . @@ -4567,20 +4567,20 @@ obo:IAO_0000119 rdf:type owl:AnnotationProperty . ### http://purl.obolibrary.org/obo/OBI_0000251 obo:OBI_0000251 rdf:type owl:Class ; - + rdfs:label "cluster"@en ; - + obo:IAO_0000119 "group:OBI"^^xsd:string ; - + obo:IAO_0000115 "A data set which is a subset of data that are a similar to each other in some way."@en ; - + obo:IAO_0000112 "Cluster of the lymphocytes population."@en ; - + obo:IAO_0000111 "cluster"@en ; - + obo:IAO_0000117 "person:Allyson"@en , "person:Chris Stoeckert"@en ; - + obo:IAO_0000114 obo:IAO_0000125 . @@ -4588,9 +4588,9 @@ obo:OBI_0000251 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/OBI_0001265 obo:OBI_0001265 rdf:type owl:Class ; - + rdfs:label "FWER adjusted p-value" ; - + obo:IAO_0000115 "A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests." . @@ -4598,9 +4598,9 @@ obo:OBI_0001265 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/OBI_0001442 obo:OBI_0001442 rdf:type owl:Class ; - + rdfs:label "q-value" ; - + obo:IAO_0000115 "A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level." . @@ -4727,20 +4727,20 @@ obo:OBI_0000299 rdf:type owl:ObjectProperty . ### http://purl.obolibrary.org/obo/STATO_0000030 obo:STATO_0000030 rdf:type owl:Class ; - + rdfs:label "Chi-Squared statistic"@en ; - + rdfs:subClassOf obo:STATO_0000039 ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string , "Alejandra Gonzalez-Beltran"@en ; - + obo:IAO_0000115 "Chi-squared statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Chi-Squared distribution."@en ; - + obo:IAO_0000117 "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO"@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -4748,22 +4748,22 @@ obo:STATO_0000030 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000039 obo:STATO_0000039 rdf:type owl:Class ; - + rdfs:label "statistic"@en ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string ; - + obo:IAO_0000112 ""@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic)."@en ; - + obo:IAO_0000115 "a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data."@en ; - + obo:STATO_0000032 "statistic"@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -4771,21 +4771,21 @@ obo:STATO_0000039 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000119 obo:STATO_0000119 rdf:type owl:Class ; - + rdfs:label "model parameter estimation"@en ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string ; - + obo:IAO_0000119 ""@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000115 "model parameter estimation is a data transformation that finds parameter values (the model parameter estimates) most compatible with the data as judged by the model."@en ; - + obo:IAO_0000116 """textual definition modified following contributiong by Thomas Nichols: https://github.com/ISA-tools/stato/issues/18"""@en ; - + obo:IAO_0000114 obo:IAO_0000125 . @@ -4793,22 +4793,22 @@ https://github.com/ISA-tools/stato/issues/18"""@en ; ### http://purl.obolibrary.org/obo/STATO_0000176 obo:STATO_0000176 rdf:type owl:Class ; - + rdfs:label "t-statistic"@en ; - + rdfs:subClassOf obo:STATO_0000039 ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string ; - + obo:STATO_0000032 ""@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO"@en ; - + obo:IAO_0000115 "t-statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Student's t distribution."@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -4816,20 +4816,20 @@ obo:STATO_0000176 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000282 obo:STATO_0000282 rdf:type owl:Class ; - + rdfs:label "F-statistic"@en ; - + rdfs:subClassOf obo:STATO_0000039 ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string , "Alejandra Gonzalez-Beltran"@en ; - + obo:IAO_0000115 "F statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a F distribution. the F statistic is the ratio of two scaled sums of squares reflecting different sources of variability"@en ; - + obo:IAO_0000117 "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO"@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -4837,22 +4837,22 @@ obo:STATO_0000282 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000323 obo:STATO_0000323 rdf:type owl:Class ; - + rdfs:label "contrast weight matrix"@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Camille Maumet"@en , "Orlaith Burke"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO"@en ; - + obo:IAO_0000117 "Tom Nichols"@en ; - + obo:IAO_0000112 "[1,0,0]"@en ; - + obo:IAO_0000115 "a contrast weight matrix is a information content entity which holds a set of contrast weight, coefficient used in a weighting sum of means defining a contrast"@en ; - + obo:STATO_0000032 "contrast weights"@en . @@ -4860,19 +4860,19 @@ obo:STATO_0000323 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000346 obo:STATO_0000346 rdf:type owl:Class ; - + rdfs:label "covariance structure"@en ; - + obo:IAO_0000117 "Camille Maumet" , "Orlaith Burke" , "Tom Nichols" , "Alejandra Gonzalez-Beltran" , "Philippe Rocca-Serra" ; - + obo:IAO_0000115 "a covariance structure is a data item which is part of a regression model and which indicates a pattern in the covariance matrix. The nature of covariance structure is specified before the regression analysis and various covariance structure may be tested and evaluated using information criteria to help choose the most suitable model"@en ; - + obo:IAO_0000119 "http://www3.nd.edu/~kyuan/courses/sem/readpapers/benter.pdf" ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4880,27 +4880,27 @@ obo:STATO_0000346 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000357 obo:STATO_0000357 rdf:type owl:Class ; - + rdfs:label "Toeplitz covariance structure"@en ; - + rdfs:subClassOf obo:STATO_0000346 ; - + obo:IAO_0000117 "Orlaith Burke" ; - + obo:IAO_0000115 ""@en ; - + obo:STATO_0000041 ""@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Camille Maumet"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000118 "TOEP"@en ; - + obo:IAO_0000117 "Tom Nichols"@en ; - + obo:IAO_0000119 "http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm"@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4908,26 +4908,26 @@ obo:STATO_0000357 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000362 obo:STATO_0000362 rdf:type owl:Class ; - + rdfs:label "compound symmetry covariance structure"@en ; - + rdfs:subClassOf obo:STATO_0000346 ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en ; - + obo:IAO_0000118 "CS"@en ; - + obo:IAO_0000117 "Camille Maumet"@en , "Orlaith Burke" , "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000115 "compound symmetry covariance structure is a covariance structure which means that all the variances are equal and all the covariances are equal."@en ; - + obo:STATO_0000041 "http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corCompSymm.html"@en ; - + obo:IAO_0000119 "http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm"@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4935,25 +4935,25 @@ obo:STATO_0000362 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000370 obo:STATO_0000370 rdf:type owl:Class ; - + rdfs:label "ordinary least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000119 ; - + obo:STATO_0000032 "OLS estimation" ; - + obo:STATO_0000041 ""@en , "https://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html" ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Camille Maumet"@en , "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000119 "http://en.wikipedia.org/wiki/Ordinary_least_squares and Tom Nichols"@en ; - + obo:IAO_0000115 "the ordinary least squares estimation is a model parameter estimation for a linear regression model when the errors are uncorrelated and equal in variance. Is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption."@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4961,25 +4961,25 @@ obo:STATO_0000370 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000371 obo:STATO_0000371 rdf:type owl:Class ; - + rdfs:label "weighted least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000119 ; - + obo:STATO_0000032 "WLS estimation" ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Camille Maumet"@en , "Orlaith Burke"@en , "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000119 "http://en.wikipedia.org/wiki/Least_squares#Weighted_least_squares and Tom Nichols"@en ; - + obo:STATO_0000041 "https://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html"@en ; - + obo:IAO_0000115 "the weighted least squares estimation is a model parameter estimation for a linear regression model with errors that independent but have heterogeneous variance. Difficult to use use in practice, as weights must be set based on the variance which is usually unknown. If true variance is known, it is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption."@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -4987,22 +4987,22 @@ obo:STATO_0000371 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000372 obo:STATO_0000372 rdf:type owl:Class ; - + rdfs:label "generalized least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000119 ; - + obo:STATO_0000032 "GLS estimation" ; - + obo:IAO_0000117 "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000119 "http://en.wikipedia.org/wiki/Generalized_least_squares and Tom Nichols"@en ; - + obo:STATO_0000041 "http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/gls.html"@en ; - + obo:IAO_0000115 "the generalized least squares estimation is a model parameter estimation for a linear regression model with errors that are dependent and (possibly) have heterogeneous variance. Difficult to use use in practice, as covariance matrix of the errors must known to \"whiten\" data and model. If true covariance is known, it is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption."@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -5010,25 +5010,25 @@ obo:STATO_0000372 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000373 obo:STATO_0000373 rdf:type owl:Class ; - + rdfs:label "iteratively reweighted least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000119 ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran" , "Camille Maumet" , "Orlaith Burke" ; - + obo:STATO_0000041 ""@en ; - + obo:IAO_0000117 "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "Tom Nichols"@en ; - + obo:IAO_0000117 "Tom Nichols"@en ; - + obo:IAO_0000115 "the iteratively reweighted least squares estimation is a model parameter estimation which is a practical implementation of Weighted Least Squares, where the heterogeneous variances of the errors are estimated from the residuals of the regression model, providing an estimate for the weights. Each successive estimate of the weights improves the estimation of the regression parameters, which in turn are used to compute residuals and update the weights"@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -5036,22 +5036,22 @@ obo:STATO_0000373 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000374 obo:STATO_0000374 rdf:type owl:Class ; - + rdfs:label "feasible generalized least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000372 ; - + obo:IAO_0000115 "the feasible generalized least squares estimation is a model parameter estimation which is a practical implementation of Generalised Least Squares, where the covariance of the errors is estimated from the residuals of the regression model, providing the information needed to whiten the data and model. Each successive estimate of the whitening matrix improves the estimation of the regression parameters, which in turn are used to compute residuals and update the whitening matrix." ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Orlaith Burke"@en ; - + obo:IAO_0000119 "Tom Nichols" ; - + obo:IAO_0000117 "Camille Maumet" , "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -5059,20 +5059,20 @@ obo:STATO_0000374 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000376 obo:STATO_0000376 rdf:type owl:Class ; - + rdfs:label "Z-statistic" ; - + rdfs:subClassOf obo:STATO_0000039 ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran" , "Camille Maument" , "Philippe Rocca-Serra" , "Thomas Nichols" ; - + obo:IAO_0000119 "http://en.wikipedia.org/wiki/Z-test" ; - + obo:IAO_0000115 "Z-statistic is a statistic computed from observations and used to produce a p-value when compared to a Standard Normal Distribution in a statistical test called the Z-test." ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -5084,84 +5084,84 @@ obo:STATO_0000376 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000225 rdf:type owl:Class ; - + rdfs:label "probability distribution"@en ; - + "Orlaith Burke"^^xsd:string , "Alejandra Gonzalez-Beltran" ; - + """A probability distribution is a information content entity specifies the probability of the value of a random variable. For a discrete random variable, a mathematical formula that gives the probability of each value of the variable. For a continuous random variable, a curve described by a mathematical formula which specifies, by way of areas under the curve, the probability that the variable falls within a particular interval.""" ; - + "Philippe Rocca-Serra" ; - + . ### http://purl.obolibrary.org/obo/STATO_0000067 rdf:type owl:Class ; - + rdfs:label "continuous probability distribution"@en ; - + rdfs:subClassOf ; - + "Orlaith Burke"^^xsd:string ; - + ""@en ; - + "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + "a continuousprobability distribution is a probability distribution which is defined by a probability density function"@en ; - + """adapted from Wikipedia http://en.wikipedia.org/wiki/Probability_distribution#Continuous_probability_distribution -last accessed: +last accessed: 14/01/2014"""@en ; - + . ### http://purl.obolibrary.org/obo/STATO_0000117 rdf:type owl:Class ; - + rdfs:label "discrete probability distribution"@en ; - + rdfs:subClassOf ; - + "Orlaith Burke"^^xsd:string , "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + "a discrete probability distribution is a probability distribution which is defined by a probability mass function where the random variable can only assume a finite number of values or infinitely countable values"@en ; - + """adapted from Wikipedia http://en.wikipedia.org/wiki/Probability_distribution#Discrete_probability_distribution -last accessed: +last accessed: 14/01/2014"""@en ; - + . ### http://purl.obolibrary.org/obo/STATO_0000276 rdf:type owl:Class ; - + rdfs:label "binomial distribution"@en ; - + rdfs:subClassOf ; - + "Orlaith Burke"^^xsd:string ; - + ""@en ; - + "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + """The binomial distribution is a discrete probability distribution which describes the probability of k successes in n draws with replacement from a finite population of size N. The binomial distribution is frequently used to model the number of successes in a sample of size n drawn with replacement from a population of size N. @@ -5173,13 +5173,13 @@ notation: B(n,p) The mean is N*p The variance is N*p*q"""@en ; - + """dbinom(x, size, prob, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Binomial.html"""@en ; - + "http://en.wikipedia.org/wiki/Binomial_distribution"@en ; - + . ### http://purl.obolibrary.org/obo/STATO_0000019 @@ -5188,75 +5188,75 @@ http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Binomial.html"""@en ; ### http://purl.obolibrary.org/obo/STATO_0000227 rdf:type owl:Class ; - + rdfs:label "normal distribution"@en ; - + rdfs:subClassOf ; - + "Orlaith Burke"^^xsd:string ; - + ""@en ; - + "Alejandra Gonzalez-Beltran"@en ; - + "Gaussian distribution"@en ; - + "Philippe Rocca-Serra"@en ; - + """a normal distribution is a continuous probability distribution described by a probability distribution function described here: http://mathworld.wolfram.com/NormalDistribution.html"""@en ; - + "http://mathworld.wolfram.com/NormalDistribution.html"@en ; - + . ### http://purl.obolibrary.org/obo/STATO_0000051 rdf:type owl:Class ; - + rdfs:label "Poisson distribution"@en ; - + rdfs:subClassOf ; - + "Orlaith Burke"^^xsd:string ; - + ""@en ; - + "Alejandra Gonzalez-Beltran"@en ; - + """NIST: http://www.itl.nist.gov/div898/handbook/eda/section3/eda366j.htm """@en ; - + "Philippe Rocca-Serra"@en ; - + """Poisson distribution is a probability distribution used to model the number of events occurring within a given time interval. It is defined by a real number (λ) and an integer k representing the number of events and a function. The expected value of a Poisson-distributed random variable is equal to λ and so is its variance."""@en ; - + """dpois(x, lambda, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Poisson.html"""@en ; - + . ### http://purl.obolibrary.org/obo/STATO_0000405 rdf:type owl:Class ; - + rdfs:label "unstructured covariance structure"@en ; - + rdfs:subClassOf ; - + "Philippe Rocca-Serra" , "Alejandra Gonzalez-Beltran" , "Thomas Nichols" ; - + "A covariance structure where no restrictions are made on the covariance between any pair of measurements."@en ; - + "http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm#statug.mixed.mixedcovstruct" ; - - "Camille Maumet" . - + + "Camille Maumet" . + ##### Imports from prov ##### rdfs:comment @@ -6090,7 +6090,7 @@ prov:qualifiedEnd prov:qualifiedForm a owl:AnnotationProperty ; - rdfs:comment """This annotation property links a subproperty of prov:wasInfluencedBy with the subclass of prov:Influence and the qualifying property that are used to qualify it. + rdfs:comment """This annotation property links a subproperty of prov:wasInfluencedBy with the subclass of prov:Influence and the qualifying property that are used to qualify it. Example annotation: @@ -6103,7 +6103,7 @@ Then this unqualified assertion: can be qualified by adding: prov:entity1 prov:qualifiedGeneration prov:entity1Gen . - prov:entity1Gen + prov:entity1Gen a prov:Generation, prov:Influence; prov:activity prov:activity1; prov:customValue 1337 . @@ -6404,7 +6404,7 @@ prov:wasInfluencedBy Subproperties of prov:wasInfluencedBy may also be asserted directly without being qualified. -prov:wasInfluencedBy should not be used without also using one of its subproperties. +prov:wasInfluencedBy should not be used without also using one of its subproperties. """@en ; prov:inverse "influenced" ; prov:qualifiedForm prov:Influence, prov:qualifiedInfluence ; @@ -6491,7 +6491,7 @@ prov:wasStartedBy a owl:Ontology ; - rdfs:comment """This document is published by the Provenance Working Group (http://www.w3.org/2011/prov/wiki/Main_Page). + rdfs:comment """This document is published by the Provenance Working Group (http://www.w3.org/2011/prov/wiki/Main_Page). If you wish to make comments regarding this document, please send them to public-prov-comments@w3.org (subscribe public-prov-comments-request@w3.org, archives http://lists.w3.org/Archives/Public/public-prov-comments/). All feedback is welcome."""@en ; rdfs:label "W3C PROVenance Interchange Ontology (PROV-O)"@en ; @@ -6568,9 +6568,8 @@ If you wish to make comments regarding this document, please send them to public [] a owl:Axiom ; - rdfs:comment """Revision is a derivation (see http://www.w3.org/TR/prov-dm/#term-Revision). Moreover, according to + rdfs:comment """Revision is a derivation (see http://www.w3.org/TR/prov-dm/#term-Revision). Moreover, according to http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#term-Revision 23 April 2012 'wasRevisionOf is a strict sub-relation of wasDerivedFrom since two entities e2 and e1 may satisfy wasDerivedFrom(e2,e1) without being a variant of each other.'""" ; owl:annotatedProperty rdfs:subPropertyOf ; owl:annotatedSource prov:wasRevisionOf ; owl:annotatedTarget prov:wasDerivedFrom . - diff --git a/nidmresults/owl/nidm-results_130.owl b/nidmresults/owl/nidm-results_130.owl index f352d06..0299575 100644 --- a/nidmresults/owl/nidm-results_130.owl +++ b/nidmresults/owl/nidm-results_130.owl @@ -67,17 +67,17 @@ dc:description rdfs:range dctype:Image . ### http://purl.org/nidash/nidm#NIDM_0000088 nidm:NIDM_0000088 rdf:type owl:ObjectProperty ; - + rdfs:label "has Drift Model" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000115 "A property that associates a 'Drift Model' to a 'Design Matrix' (only used for first-level fMRI experiments)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000019 ; - + rdfs:range nidm:NIDM_0000087 . @@ -85,17 +85,17 @@ nidm:NIDM_0000088 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000089 nidm:NIDM_0000089 rdf:type owl:ObjectProperty ; - + rdfs:label "dependence Map-Wise Dependence" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000115 "Property that associates an 'Error Parameter Map-Wise Dependence' to the dependence of an 'Error Model'." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000023 ; - + rdfs:range nidm:NIDM_0000071 . @@ -103,20 +103,20 @@ nidm:NIDM_0000089 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000097 nidm:NIDM_0000097 rdf:type owl:ObjectProperty ; - + rdfs:label "has Alternative Hypothesis" ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/pull/81" ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000208" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000049 ; - + rdfs:range nidm:NIDM_0000060 , nidm:NIDM_0000079 ; - + rdfs:subPropertyOf owl:topObjectProperty . @@ -124,17 +124,17 @@ nidm:NIDM_0000097 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000098 nidm:NIDM_0000098 rdf:type owl:ObjectProperty ; - + rdfs:label "has Cluster Labels Map" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/282" ; - + obo:IAO_0000115 "A property that associates a clusters label map to the excursion set." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range nidm:NIDM_0000008 ; - + rdfs:domain nidm:NIDM_0000025 . @@ -142,17 +142,17 @@ nidm:NIDM_0000098 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000099 nidm:NIDM_0000099 rdf:type owl:ObjectProperty ; - + rdfs:label "has Connectivity Criterion" ; - + obo:IAO_0000115 "Property that associates a 'Connectivity Criterion' with a 'Cluster Definition Criteria'." ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000007 ; - + rdfs:range nidm:NIDM_0000012 . @@ -160,15 +160,15 @@ nidm:NIDM_0000099 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000100 nidm:NIDM_0000100 rdf:type owl:ObjectProperty ; - + rdfs:label "has Error Dependence" ; - + obo:IAO_0000115 "Property that associates a covariance structure representing the dependence structure of the error, used as part of model estimation with an 'Error Model'." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range obo:STATO_0000346 ; - + rdfs:domain nidm:NIDM_0000023 . @@ -176,15 +176,15 @@ nidm:NIDM_0000100 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000101 nidm:NIDM_0000101 rdf:type owl:ObjectProperty ; - + rdfs:label "has Error Distribution" ; - + obo:IAO_0000115 "Property that associates a Probability distribution used to model the error with an ErrorModel." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range obo:STATO_0000225 ; - + rdfs:domain nidm:NIDM_0000023 . @@ -192,17 +192,17 @@ nidm:NIDM_0000101 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000102 nidm:NIDM_0000102 rdf:type owl:ObjectProperty ; - + rdfs:label "has HRF Basis" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "A property that associates a set of functions that, when convolved with the anticipated neural responses, yields a set of regressors to model the anticipated hemodynamic responses in a 'Design Matrix'." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000019 ; - + rdfs:range nidm:NIDM_0000036 . @@ -210,17 +210,17 @@ nidm:NIDM_0000102 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000103 nidm:NIDM_0000103 rdf:type owl:ObjectProperty ; - + rdfs:label "has Map Header" ; - + obo:IAO_0000115 "A Property that associates an additional file containing the 'Map Header' with a map" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/289" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000052 ; - + rdfs:range nidm:NIDM_0000053 . @@ -228,17 +228,17 @@ nidm:NIDM_0000103 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000104 nidm:NIDM_0000104 rdf:type owl:ObjectProperty ; - + rdfs:label "in Coordinate Space" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/171 by NN JT CM SG KH TN." ; - + obo:IAO_0000115 "Property of a DataArray to associate a 'Coordinate Space' with a physical file." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range nidm:NIDM_0000016 ; - + rdfs:domain nidm:NIDM_0000052 . @@ -246,17 +246,17 @@ nidm:NIDM_0000104 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000105 nidm:NIDM_0000105 rdf:type owl:ObjectProperty ; - + rdfs:label "in World Coordinate System" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Property that associates a 'World Coordinate System' to the 'Coordinate Space'." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range nidm:NIDM_0000081 . @@ -264,15 +264,15 @@ nidm:NIDM_0000105 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000113 nidm:NIDM_0000113 rdf:type owl:ObjectProperty ; - + rdfs:label "object Model" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/pull/137" ; - + obo:IAO_0000114 obo:IAO_0000124 ; - + rdfs:range nidm:NIDM_0000057 ; - + rdfs:domain prov:Bundle . @@ -280,17 +280,17 @@ nidm:NIDM_0000113 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000123 nidm:NIDM_0000123 rdf:type owl:ObjectProperty ; - + rdfs:label "statistic Type" ; - + obo:IAO_0000115 "Property that associates a [stato:\"statistic\"](http://purl.obolibrary.org/obo/STATO_0000039) with a StatisticMap or a ContrastWeights entity." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/293" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range obo:STATO_0000039 ; - + rdfs:domain obo:STATO_0000323 , nidm:NIDM_0000076 . @@ -299,17 +299,17 @@ nidm:NIDM_0000123 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000126 nidm:NIDM_0000126 rdf:type owl:ObjectProperty ; - + rdfs:label "variance Map-Wise Dependence" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000115 "Property that associates an 'Error Parameter Map-Wise Dependence' to the variance of an 'Error Model'" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000023 ; - + rdfs:range nidm:NIDM_0000071 . @@ -317,17 +317,17 @@ nidm:NIDM_0000126 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000134 nidm:NIDM_0000134 rdf:type owl:ObjectProperty ; - + rdfs:label "with Estimation Method" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/293" ; - + obo:IAO_0000115 "Property that associates a [stato:\"model parameter estimation\"](http://purl.obolibrary.org/obo/STATO_0000119) method with a model parameter estimation" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range obo:STATO_0000119 ; - + rdfs:domain nidm:NIDM_0000056 . @@ -335,17 +335,17 @@ nidm:NIDM_0000134 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000138 nidm:NIDM_0000138 rdf:type owl:ObjectProperty ; - + rdfs:label "has Maximum Intensity Projection" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/293" ; - + obo:IAO_0000115 "Property that associates an image of the maximum intensity projection with an 'Excursion Set Map'." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range dctype:Image ; - + rdfs:domain nidm:NIDM_0000025 . @@ -353,17 +353,17 @@ nidm:NIDM_0000138 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000161 nidm:NIDM_0000161 rdf:type owl:ObjectProperty ; - + rdfs:label "equivalent Threshold" ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/329" ; - + obo:IAO_0000115 "Property that associates another 'Threshold' that is equivalent (e.g. if the user specified a 'Threshold' in terms of FWE-corrected p-value, this property can be used to associate the corresponding uncorrected p-value)." ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:range nidm:NIDM_0000162 ; - + rdfs:domain nidm:NIDM_0000162 . @@ -371,15 +371,15 @@ nidm:NIDM_0000161 rdf:type owl:ObjectProperty ; ### http://purl.org/nidash/nidm#NIDM_0000172 nidm:NIDM_0000172 rdf:type owl:ObjectProperty ; - + rdfs:label "has MRI Protocol" ; - + obo:IAO_0000115 "'MRI Protocol' used to acquire these 'Data'." ; - + obo:IAO_0000114 obo:IAO_0000124 ; - + rdfs:domain nidm:NIDM_0000169 ; - + rdfs:range nlx:birnlex_2177 . @@ -393,7 +393,7 @@ prv:reification_class rdfs:range owl:Class . ### http://www.w3.org/ns/prov#atLocation prov:atLocation prov:definition "The Location of any resource" ; - + obo:IAO_0000115 "The Location of any resource." . @@ -416,7 +416,7 @@ dc:description rdf:type owl:DatatypeProperty . ### http://purl.org/dc/terms/format dct:format rdf:type owl:DatatypeProperty ; - + rdfs:range xsd:string . @@ -424,17 +424,17 @@ dct:format rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/fsl#FSL_0000004 fsl:FSL_0000004 rdf:type owl:DatatypeProperty ; - + rdfs:label "drift Cutoff Period" ; - + obo:IAO_0000115 "Doubled standard deviation in seconds of the Gaussian weight function used in the running line smoother." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain fsl:FSL_0000002 ; - + rdfs:range xsd:float . @@ -442,17 +442,17 @@ fsl:FSL_0000004 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/fsl#FSL_0000005 fsl:FSL_0000005 rdf:type owl:DatatypeProperty ; - + rdfs:label "feat Version" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/291" ; - + obo:IAO_0000115 "Version of the FEAT software." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain src:SCR_002823 ; - + rdfs:range xsd:string . @@ -464,17 +464,17 @@ fsl:FSL_0000005 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000021 nidm:NIDM_0000021 rdf:type owl:DatatypeProperty ; - + rdfs:label "regressor Names" ; - + obo:IAO_0000115 "A list of abstract names associated with each column of the 'Design Matrix' (e.g. [\"motor_left\", \"motor_right\"])." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/299" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000019 ; - + rdfs:range xsd:string . @@ -482,19 +482,19 @@ nidm:NIDM_0000021 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000082 nidm:NIDM_0000082 rdf:type owl:DatatypeProperty ; - + rdfs:label "cluster Label Id" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/271" ; - + obo:IAO_0000115 "Integer value used in the cluster label map to identify the location of the cluster within the excursion set." ; - + obo:IAO_0000112 "5" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000070 ; - + rdfs:range xsd:int . @@ -506,18 +506,18 @@ nidm:NIDM_0000082 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000084 nidm:NIDM_0000084 rdf:type owl:DatatypeProperty ; - + rdfs:label "cluster Size In Voxels" ; - + obo:IAO_0000112 "18" ; - + obo:IAO_0000115 "Number of voxels that make up the cluster." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000070 ; - + rdfs:range xsd:positiveInteger . @@ -525,19 +525,19 @@ nidm:NIDM_0000084 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000085 nidm:NIDM_0000085 rdf:type owl:DatatypeProperty ; - + rdfs:label "contrast Name" ; - + obo:IAO_0000115 "Name of the contrast." ; - + obo:IAO_0000112 "\"Listening > Rest\"" ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain obo:STATO_0000323 , nidm:NIDM_0000002 , nidm:NIDM_0000076 ; - + rdfs:range xsd:string . @@ -545,19 +545,19 @@ nidm:NIDM_0000085 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000086 nidm:NIDM_0000086 rdf:type owl:DatatypeProperty ; - + rdfs:label "coordinate Vector" ; - + obo:IAO_0000112 "[-60, 32, 54]"^^xsd:string ; - + obo:IAO_0000115 "A vector with one number per dimension. The first element corresponds to the 'Coordinate' along the first dimension measured in map elements (e.g., pixels, voxels, vertices, or faces), the second element to the 'Coordinate' along the second dimension etc." ; - + obo:IAO_0000116 "Under discussion at: https://github.com/incf-nidash/nidm/pull/270 and https://github.com/incf-nidash/nidm/issues/145" ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000015 ; - + rdfs:range xsd:string . @@ -565,19 +565,19 @@ nidm:NIDM_0000086 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000090 nidm:NIDM_0000090 rdf:type owl:DatatypeProperty ; - + rdfs:label "dimensions In Voxels" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/issues/146" ; - + obo:IAO_0000115 "Number of voxels in each of the dimensions of the data array. For example, \"[91, 109, 91]\" indicates there are 91 voxels in the first dimension, 109 in the second dimension, and 91 in the third dimension." ; - + obo:IAO_0000112 "[64, 64, 20]" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:string . @@ -585,19 +585,19 @@ nidm:NIDM_0000090 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000091 nidm:NIDM_0000091 rdf:type owl:DatatypeProperty ; - + rdfs:label "effect Degrees Of Freedom" ; - + obo:IAO_0000115 "In the context of a general linear model, the effect degrees of freedom is the rank of the contrast. For example, a contrast comprising of a vector has effect degrees of freedom of 1 and can be tested with a F-test with numerator degrees of freedom of 1." ; - + obo:IAO_0000112 "1" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/issues/277" ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000076 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -610,17 +610,17 @@ nidm:NIDM_0000091 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000092 nidm:NIDM_0000092 rdf:type owl:DatatypeProperty ; - + rdfs:label "equivalent ZStatistic" ; - + obo:IAO_0000115 "Statistic value transformed into Z units; the output of a process which takes a non-normal statistic and transforms it to an equivalent z score." ; - + obo:IAO_0000112 "3.5" ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain nidm:NIDM_0000062 ; - + rdfs:range xsd:float . @@ -628,19 +628,19 @@ nidm:NIDM_0000092 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000093 nidm:NIDM_0000093 rdf:type owl:DatatypeProperty ; - + rdfs:label "error Degrees Of Freedom" ; - + obo:IAO_0000112 "72.999999" ; - + obo:IAO_0000115 "In the context of a general linear model, the error degrees of freedom are the number of observations less the rank of the 'Design Matrix'." ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/issues/277" ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000076 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -653,15 +653,15 @@ nidm:NIDM_0000093 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000094 nidm:NIDM_0000094 rdf:type owl:DatatypeProperty ; - + rdfs:label "error Variance Homogeneous" ; - + obo:IAO_0000115 "A boolean value reflecting how the variance of the error is modeled during parameter estimation; TRUE for constant variance over all observations in the model, FALSE for heterogeneous variance." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000023 ; - + rdfs:range xsd:boolean . @@ -669,19 +669,19 @@ nidm:NIDM_0000094 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000095 nidm:NIDM_0000095 rdf:type owl:DatatypeProperty ; - + rdfs:label "partial Conjunction Degree" ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/294" ; - + obo:IAO_0000115 "The number of non-null effects permitted in a partial conjunction null, as part of a 'Partial Conjunction Inference'" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain spm:SPM_0000005 ; - + rdfs:range xsd:int . @@ -689,19 +689,19 @@ nidm:NIDM_0000095 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000096 nidm:NIDM_0000096 rdf:type owl:DatatypeProperty ; - + rdfs:label "grand Mean Scaling" ; - + obo:IAO_0000115 "Binary flag defining whether the data was scaled (true for scaled). Specifically, \"grand mean scaling\" refers to multiplication of every voxel in every scan by a common (or session-specific) value." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/285" ; - + obo:IAO_0000112 "TRUE" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000169 ; - + rdfs:range xsd:boolean . @@ -709,13 +709,13 @@ nidm:NIDM_0000096 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000105 nidm:NIDM_0000105 rdf:type owl:DatatypeProperty ; - + rdfs:label "in World Coordinate System" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Property that associates a 'World Coordinate System' to the 'Coordinate Space'." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -723,17 +723,17 @@ nidm:NIDM_0000105 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000106 nidm:NIDM_0000106 rdf:type owl:DatatypeProperty ; - + rdfs:label "is User Defined" ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/pull/258" ; - + obo:IAO_0000115 "A binary flag defining whether the mask was specified by the user (true) or automatically generated during the analysis (false)" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000004 ; - + rdfs:range xsd:boolean . @@ -741,21 +741,21 @@ nidm:NIDM_0000106 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000107 nidm:NIDM_0000107 rdf:type owl:DatatypeProperty ; - + rdfs:label "masked Median" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/288, naming previously discussed at: https://github.com/incf-nidash/nidm/issues/70" ; - + obo:IAO_0000115 "Median value considering only in-mask voxels. Useful diagnostic when computed on grand mean image when grandMeanScaling is TRUE, as the median should be close to targetIntensity." ; - + rdfs:seeAlso "http://purl.obolibrary.org/obo/OBI_0200119" ; - + obo:IAO_0000112 "155.23" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000033 ; - + rdfs:range xsd:float . @@ -763,17 +763,17 @@ nidm:NIDM_0000107 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000108 nidm:NIDM_0000108 rdf:type owl:DatatypeProperty ; - + rdfs:label "max Number Of Peaks Per Cluster" ; - + obo:IAO_0000115 "Maximum number of 'Peak's to be reported after 'Inference' within a cluster." ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/200" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000063 ; - + rdfs:range xsd:int . @@ -781,17 +781,17 @@ nidm:NIDM_0000108 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000109 nidm:NIDM_0000109 rdf:type owl:DatatypeProperty ; - + rdfs:label "min Distance Between Peaks" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/200" ; - + obo:IAO_0000115 "Minimum distance between two 'Peak's to be reported after 'Inference'." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000063 ; - + rdfs:range xsd:float . @@ -799,19 +799,19 @@ nidm:NIDM_0000109 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000111 nidm:NIDM_0000111 rdf:type owl:DatatypeProperty ; - + rdfs:label "number Of Supra-Threshold Clusters" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/292" ; - + obo:IAO_0000115 "Number of 'Supra-Threshold Clusters' found by the 'Inference' activity. This is SPM's set level statistic." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000025 ; - + rdfs:range xsd:int ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -819,19 +819,19 @@ nidm:NIDM_0000111 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000112 nidm:NIDM_0000112 rdf:type owl:DatatypeProperty ; - + rdfs:label "number Of Dimensions" ; - + obo:IAO_0000115 "Number of dimensions of the data matrix (e.g. 3 for volumetric data)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/295" ; - + obo:IAO_0000112 "3" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:positiveInteger . @@ -839,23 +839,23 @@ nidm:NIDM_0000112 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000114 nidm:NIDM_0000114 rdf:type owl:DatatypeProperty ; - + rdfs:label "p Value" ; - + owl:sameAs "http://purl.obolibrary.org/obo/OBI_0000175"^^xsd:anyURI ; - + obo:IAO_0000112 "8.95E-14" ; - + rdfs:seeAlso """http://purl.obolibrary.org/obo/IAO_0000121 http://purl.obolibrary.org/obo/OBI_0000175 http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P-Value""" ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/38" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000025 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:maxInclusive "1.0"^^xsd:float @@ -870,24 +870,24 @@ http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P-Value""" ; ### http://purl.org/nidash/nidm#NIDM_0000115 nidm:NIDM_0000115 rdf:type owl:DatatypeProperty ; - + rdfs:label "p Value FWER" ; - + obo:IAO_0000112 "0.05" ; - + obo:IAO_0000115 "\"A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests\"" ; - + owl:sameAs "This definition is from OBI. Please update this note if the definition is modified." ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/38" ; - + rdfs:seeAlso "Synonym of \"nidm:pFWE\"" ; - + obo:IAO_0000114 obo:IAO_0000423 ; - + rdfs:domain nidm:NIDM_0000062 , nidm:NIDM_0000070 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:maxInclusive "1.0"^^xsd:float @@ -902,22 +902,22 @@ nidm:NIDM_0000115 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000116 nidm:NIDM_0000116 rdf:type owl:DatatypeProperty ; - + rdfs:label "p Value Uncorrected" ; - + obo:IAO_0000115 "A p-value reported without correction for multiple testing. " ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/38" ; - + obo:IAO_0000112 "0.0542" ; - + rdfs:seeAlso "http://purl.obolibrary.org/obo/IAO_0000121" ; - + obo:IAO_0000114 obo:IAO_0000423 ; - + rdfs:domain nidm:NIDM_0000062 , nidm:NIDM_0000070 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:maxInclusive "1.0"^^xsd:float @@ -932,22 +932,22 @@ nidm:NIDM_0000116 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000119 nidm:NIDM_0000119 rdf:type owl:DatatypeProperty ; - + rdfs:label "q Value FDR" ; - + obo:IAO_0000112 "0.000154" ; - + obo:IAO_0000115 "A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level (same as OBI_0001442)." ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/38" ; - + owl:sameAs "http://purl.obolibrary.org/obo/OBI_0001442" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000062 , nidm:NIDM_0000070 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:maxInclusive "1.0"^^xsd:float @@ -962,17 +962,17 @@ nidm:NIDM_0000119 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000120 nidm:NIDM_0000120 rdf:type owl:DatatypeProperty ; - + rdfs:label "random Field Stationarity" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/130" ; - + obo:IAO_0000115 "A binary flag that indicates whether Random Field Theory methods assumed smoothness that was homogeneous over the map (true), or allowed for smoothness that varies over the map (false)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:boolean . @@ -980,21 +980,21 @@ nidm:NIDM_0000120 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000121 nidm:NIDM_0000121 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume In Voxels" ; - + obo:IAO_0000112 "68656" ; - + rdfs:seeAlso "Synonyms of nidm:volumeInVoxels" ; - + obo:IAO_0000115 "Total number of voxels within the search volume." ; - + obo:IAO_0000114 obo:IAO_0000124 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1002,19 +1002,19 @@ nidm:NIDM_0000121 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000122 nidm:NIDM_0000122 rdf:type owl:DatatypeProperty ; - + rdfs:label "software Version" ; - + obo:IAO_0000112 8.6225 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/291" ; - + obo:IAO_0000115 "Name and number that specifies the software version. For SPM, this includes the main software version followed by the revision number (e.g. 8.6225 for SPM8 revision 6225)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:range xsd:string ; - + rdfs:domain prov:SoftwareAgent . @@ -1022,19 +1022,19 @@ nidm:NIDM_0000122 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000124 nidm:NIDM_0000124 rdf:type owl:DatatypeProperty ; - + rdfs:label "target Intensity" ; - + obo:IAO_0000115 "Value to which the grand mean of the Data was scaled (applies only if 'grand Mean Scaling' is true)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/285" ; - + obo:IAO_0000112 "100" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000169 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1047,24 +1047,24 @@ nidm:NIDM_0000124 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000125 nidm:NIDM_0000125 rdf:type owl:DatatypeProperty ; - + rdfs:label "user Specified Threshold Type" ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/150" ; - + obo:IAO_0000112 "nidm:pValueFWER" ; - + rdfs:comment "Range is currently string but should be limited to {'nidm:pValueFWER' not found'nidm:pValueFDR' not found'nidm:pValueUncorrected';'nidm:statistic'}?" ; - + obo:IAO_0000115 "Type of method used to define a 'Threshold' (e.g. statistic value, uncorrected P-value or corrected P-value)." ; - + obo:IAO_0000114 obo:IAO_0000428 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000034 ; - + rdfs:range xsd:string . @@ -1072,17 +1072,17 @@ nidm:NIDM_0000125 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000127 nidm:NIDM_0000127 rdf:type owl:DatatypeProperty ; - + rdfs:label "version" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/137" ; - + obo:IAO_0000115 "Version of NIDM in use in the document." ; - + obo:IAO_0000114 obo:IAO_0000124 ; - + rdfs:domain nidm:NIDM_0000057 ; - + rdfs:range xsd:string . @@ -1090,19 +1090,19 @@ nidm:NIDM_0000127 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000131 nidm:NIDM_0000131 rdf:type owl:DatatypeProperty ; - + rdfs:label "voxel Size" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/295" ; - + obo:IAO_0000115 "3D size of a voxel measured in 'voxel Units' (e.g. [2, 2, 4])" ; - + obo:IAO_0000112 "[2, 2, 4]" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:string . @@ -1110,21 +1110,21 @@ nidm:NIDM_0000131 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000132 nidm:NIDM_0000132 rdf:type owl:DatatypeProperty ; - + rdfs:label "voxel To World Mapping" ; - + obo:IAO_0000115 "Homogeneous transformation matrix to map from voxel coordinate system to 'World Coordinate System'." ; - + obo:IAO_0000116 "Range: Matrix of float." ; - + obo:IAO_0000112 "[3 0 0 0;0 3 0 0;0 0 3 0; 0 0 0 1] " ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/148" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:string . @@ -1132,21 +1132,21 @@ nidm:NIDM_0000132 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000133 nidm:NIDM_0000133 rdf:type owl:DatatypeProperty ; - + rdfs:label "voxel Units" ; - + rdfs:comment "Range: Vector of strings." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/295 and https://github.com/incf-nidash/nidm/issues/147" ; - + obo:IAO_0000112 "'[\"mm\", \"mm\", \"s\"]'" ; - + obo:IAO_0000115 "Set of units associated with the dimensions of some N-dimensional data (e.g. '[\"mm\", \"mm\", \"mm\"]')" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000016 ; - + rdfs:range xsd:string . @@ -1154,21 +1154,21 @@ nidm:NIDM_0000133 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000136 nidm:NIDM_0000136 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume In Units" ; - + obo:IAO_0000117 "Discussed at https://github.com/incf-nidash/nidm/pull/131" ; - + obo:IAO_0000116 "Context: volumeInVoxels nidm_0025. Range: Positivefloat not found." ; - + obo:IAO_0000112 "1771011" ; - + obo:IAO_0000115 "The volume of the searched region in units determined by the current 'Coordinate Space' units (e.g., mm^3 for axis units of mm in a three dimensional image, sec.Hz for a time by frequency two dimensional image)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1185,19 +1185,19 @@ nidm:NIDM_0000136 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000139 nidm:NIDM_0000139 rdf:type owl:DatatypeProperty ; - + rdfs:label "coordinate Vector In Voxels" ; - + obo:IAO_0000115 "Coordinate along the first dimension in voxels. (This definition needs to be re-worked as this term was renamed from coordinate1 to coordinate in https://github.com/incf-nidash/nidm/issues/270)" ; - + obo:IAO_0000112 "[12 51 48]" ; - + obo:IAO_0000116 "Under discussion at: https://github.com/incf-nidash/nidm/pull/270" ; - + obo:IAO_0000114 obo:IAO_0000120 ; - + rdfs:domain nidm:NIDM_0000015 ; - + rdfs:range xsd:string . @@ -1205,17 +1205,17 @@ nidm:NIDM_0000139 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000141 nidm:NIDM_0000141 rdf:type owl:DatatypeProperty ; - + rdfs:label "expected Number Of Clusters" ; - + obo:IAO_0000112 "9.51" ; - + obo:IAO_0000115 "Expected number of clusters in an excursion set under the null hypothesis." ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1232,17 +1232,17 @@ nidm:NIDM_0000141 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000143 nidm:NIDM_0000143 rdf:type owl:DatatypeProperty ; - + rdfs:label "expected Number Of Voxels Per Cluster" ; - + obo:IAO_0000115 "Expected number of voxels in a cluster under the null hypothesis." ; - + obo:IAO_0000112 "60.632" ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1255,17 +1255,17 @@ nidm:NIDM_0000143 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000145 nidm:NIDM_0000145 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise Roughness In Voxels" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/214 and https://github.com/incf-nidash/nidm/issues/275" ; - + obo:IAO_0000115 "Estimated spatial roughness of the noise process in 'voxel Units', as measured by the square-root determinant of the variance-covariance matrix of spatial derivatives of the noise process (Lambda matrix)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:float . @@ -1273,17 +1273,17 @@ nidm:NIDM_0000145 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000146 nidm:NIDM_0000146 rdf:type owl:DatatypeProperty ; - + rdfs:label "height Critical Threshold FDR 05" ; - + obo:IAO_0000112 "5.896" ; - + obo:IAO_0000115 "'Peak' statistic 'Threshold' corrected for false discovery rate at a level of alpha = 0.05. " ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:float . @@ -1291,17 +1291,17 @@ nidm:NIDM_0000146 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000147 nidm:NIDM_0000147 rdf:type owl:DatatypeProperty ; - + rdfs:label "height Critical Threshold FWE 05" ; - + obo:IAO_0000115 "'Peak' statistic 'Threshold' corrected for family-wise error at a level of alpha = 0.05. " ; - + obo:IAO_0000112 "4.913" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:float . @@ -1309,23 +1309,23 @@ nidm:NIDM_0000147 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000148 nidm:NIDM_0000148 rdf:type owl:DatatypeProperty ; - + rdfs:label "resel Size In Voxels" ; - + obo:IAO_0000112 "22.325" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/275" ; - + obo:IAO_0000115 "Size of one resel in elements (e.g., pixels, voxels or vertices)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:float ; - + rdfs:subPropertyOf owl:topDataProperty ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minExclusive "0.0"^^xsd:float @@ -1338,19 +1338,19 @@ nidm:NIDM_0000148 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000149 nidm:NIDM_0000149 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume In Resels" ; - + obo:IAO_0000112 "151.3" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/275" ; - + obo:IAO_0000115 "Size of search volume measured in resels." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1363,20 +1363,20 @@ nidm:NIDM_0000149 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000156 nidm:NIDM_0000156 rdf:type owl:DatatypeProperty ; - + rdfs:label "cluster Size In Resels" ; - + obo:IAO_0000117 "Under discussion at: https://github.com/incf-nidash/nidm/issues/127" ; - + obo:IAO_0000112 "13" ; - + obo:IAO_0000115 "Size of cluster measured in resels." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000026 , nidm:NIDM_0000070 ; - + rdfs:range [ rdf:type rdfs:Datatype ; owl:onDatatype xsd:float ; owl:withRestrictions ( [ xsd:minInclusive "0.0"^^xsd:float @@ -1389,23 +1389,23 @@ nidm:NIDM_0000156 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000157 nidm:NIDM_0000157 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Units" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + obo:IAO_0000112 "[8.87, 8.89, 7.83]" ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in world units (e.g. mm^2 or mm^3, in subject or atlas space)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1417,25 +1417,25 @@ nidm:NIDM_0000157 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000159 nidm:NIDM_0000159 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Voxels" ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in voxels." ; - + obo:IAO_0000112 "[3.7 3.7 3.1]" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + rdfs:seeAlso "Synonyms of or close match with nidm:NoiseFWHM" ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1443,15 +1443,15 @@ nidm:NIDM_0000159 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000170 nidm:NIDM_0000170 rdf:type owl:DatatypeProperty ; - + rdfs:label "group Name" ; - + obo:IAO_0000115 "Name of the group" ; - + obo:IAO_0000114 obo:IAO_0000124 ; - + rdfs:domain obo:STATO_0000193 ; - + rdfs:range xsd:string . @@ -1459,15 +1459,15 @@ nidm:NIDM_0000170 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/nidm#NIDM_0000171 nidm:NIDM_0000171 rdf:type owl:DatatypeProperty ; - + rdfs:label "number Of Subjects" ; - + obo:IAO_0000115 "Number of subjects in the group." ; - + obo:IAO_0000116 "Linked with http://purl.obolibrary.org/obo/STATO_0000088 to be discussed." ; - + rdfs:domain obo:STATO_0000193 ; - + rdfs:range xsd:int . @@ -1475,17 +1475,17 @@ nidm:NIDM_0000171 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000001 spm:SPM_0000001 rdf:type owl:DatatypeProperty ; - + rdfs:label "SPM's Drift Cut-off Period" ; - + obo:IAO_0000115 "Discrete Cosine Transform basis cut-off, specified as period length in seconds and ensures that all basis elements will have period of this duration or longer." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain spm:SPM_0000002 ; - + rdfs:range xsd:float . @@ -1493,25 +1493,25 @@ spm:SPM_0000001 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000007 spm:SPM_0000007 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Units" ; - + owl:deprecated "true"^^xsd:boolean ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + obo:IAO_0000112 "[8.87, 8.89, 7.83]" ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in world units (e.g. mm^2 or mm^3, in subject or atlas space)." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1519,23 +1519,23 @@ spm:SPM_0000007 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000008 spm:SPM_0000008 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Vertices" ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in vertices." ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + obo:IAO_0000112 "[2.95, 2.96, 2.61]" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000054 ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1543,27 +1543,27 @@ spm:SPM_0000008 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000009 spm:SPM_0000009 rdf:type owl:DatatypeProperty ; - + rdfs:label "noise FWHM In Voxels" ; - + owl:deprecated "true"^^xsd:boolean ; - + rdfs:comment "Range: Vector of positive floats." ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/214" ; - + obo:IAO_0000115 "Estimated Full Width at Half Maximum of the spatial smoothness of the noise process in voxels." ; - + obo:IAO_0000112 "[3.7 3.7 3.1]" ; - + rdfs:seeAlso "Synonyms of or close match with nidm:NoiseFWHM" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1571,25 +1571,25 @@ spm:SPM_0000009 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000010 spm:SPM_0000010 rdf:type owl:DatatypeProperty ; - + rdfs:label "search Volume Resels Geometry" ; - + obo:IAO_0000112 "[6 68.8 589.1 1475.5]" ; - + rdfs:comment "Range: Vector of 1 positive integer and 3 positive floats." ; - + rdfs:seeAlso "http://www.ncbi.nlm.nih.gov/pubmed/20408186" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000115 "Description of geometry of search volume. As per Worsley et al. [ http://www.ncbi.nlm.nih.gov/pubmed/20408186 ], for space dimension 3 the first element is the Euler Characteristic of the search volume, the second element is twice the average caliper diameter, the third element is half the surface area, and the fourth element is the volume. With the exception of the first element (which is a unitless integer) all quantities are in units of Resels." ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:string ; - + rdfs:subPropertyOf owl:topDataProperty . @@ -1605,19 +1605,19 @@ spm:SPM_0000010 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000013 spm:SPM_0000013 rdf:type owl:DatatypeProperty ; - + rdfs:label "smallest Significant Cluster Size In Voxels FDR 05" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000112 "3" ; - + obo:IAO_0000115 "Smallest cluster size in voxels that is significant at the false discovery rate of 0.05. " ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger . @@ -1625,20 +1625,20 @@ spm:SPM_0000013 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000014 spm:SPM_0000014 rdf:type owl:DatatypeProperty ; - + rdfs:label "smallest Significant Cluster Size In Voxels FWE 05" ; - - obo:IAO_0000115 """Smallest cluster size in voxels that is significant at the family-wise error corrected type I error rate (alpha value) of 0.05. + + obo:IAO_0000115 """Smallest cluster size in voxels that is significant at the family-wise error corrected type I error rate (alpha value) of 0.05. """ ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/310" ; - + obo:IAO_0000112 "1" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain nidm:NIDM_0000068 ; - + rdfs:range xsd:positiveInteger . @@ -1646,17 +1646,17 @@ spm:SPM_0000014 rdf:type owl:DatatypeProperty ; ### http://purl.org/nidash/spm#SPM_0000015 spm:SPM_0000015 rdf:type owl:DatatypeProperty ; - + rdfs:label "partial Conjunction Degree" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/294" ; - + obo:IAO_0000115 "The number of non-null effects permitted in a partial conjunction null, as part of a 'Partial Conjunction Inference'" ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:domain spm:SPM_0000005 ; - + rdfs:range xsd:int . @@ -1664,9 +1664,9 @@ spm:SPM_0000015 rdf:type owl:DatatypeProperty ; ### http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#fileName nfo:fileName rdf:type owl:DatatypeProperty ; - + obo:IAO_0000112 "con_0001.img" ; - + rdfs:range xsd:string . @@ -1683,7 +1683,7 @@ nfo:fileName rdf:type owl:DatatypeProperty ; ### http://purl.obolibrary.org/obo/OBI_0000251 obo:OBI_0000251 rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity . @@ -1691,7 +1691,7 @@ obo:OBI_0000251 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/OBI_0001265 obo:OBI_0001265 rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity . @@ -1699,7 +1699,7 @@ obo:OBI_0001265 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/OBI_0001442 obo:OBI_0001442 rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity . @@ -1719,9 +1719,9 @@ obo:STATO_0000119 rdfs:subClassOf prov:Activity . ### http://purl.obolibrary.org/obo/STATO_0000193 obo:STATO_0000193 rdf:type owl:Class ; - + rdfs:subClassOf prov:Agent ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Group.txt" . @@ -1735,9 +1735,9 @@ obo:STATO_0000225 rdfs:subClassOf prov:Entity . ### http://purl.obolibrary.org/obo/STATO_0000323 obo:STATO_0000323 rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ContrastWeights.txt" . @@ -1751,7 +1751,7 @@ obo:STATO_0000346 rdfs:subClassOf prov:Entity . ### http://purl.org/dc/dcmitype/Image dctype:Image rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity , [ rdf:type owl:Restriction ; owl:onProperty nfo:fileName ; @@ -1777,17 +1777,17 @@ dctype:Image rdf:type owl:Class ; ### http://purl.org/nidash/fsl#FSL_0000002 fsl:FSL_0000002 rdf:type owl:Class ; - + rdfs:label "Gaussian Running Line Drift Model" ; - + rdfs:subClassOf nidm:NIDM_0000087 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/FSL_DriftModel.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A 'Drift Model' in which the drifts are modeled with a Gaussian-weighted running line smoother, fit to and subtracted from the data and each column of the 'Design Matrix'." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1795,17 +1795,17 @@ fsl:FSL_0000002 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000001 nidm:NIDM_0000001 rdf:type owl:Class ; - + rdfs:label "Contrast Estimation" ; - + rdfs:subClassOf prov:Activity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ContrastEstimation.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "The process of performing a [obo:contrast estimation](http://purl.obolibrary.org/obo/STATO_0000383) at each element (e.g., pixel, voxel, vertex, or face) of a map" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/276 and https://github.com/ISA-tools/stato/issues/23" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1813,17 +1813,17 @@ nidm:NIDM_0000001 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000002 nidm:NIDM_0000002 rdf:type owl:Class ; - + rdfs:label "Contrast Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [contrast estimate](http://purl.obolibrary.org/obo/STATO_0000384)."^^xsd:string ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ContrastMap.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/255" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1831,17 +1831,17 @@ nidm:NIDM_0000002 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000003 nidm:NIDM_0000003 rdf:type owl:Class ; - + rdfs:label "Arbitrarily Correlated Error" ; - + rdfs:subClassOf obo:STATO_0000346 ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000117 "TN" ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/28" ; - + obo:IAO_0000114 obo:IAO_0000423 . @@ -1849,15 +1849,15 @@ nidm:NIDM_0000003 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000004 nidm:NIDM_0000004 rdf:type owl:Class ; - + rdfs:label "Binary Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000115 "A map in which all values are 0, 1 or NaN. Usually, selected elements (e.g., pixels, voxels, vertices, or faces) have a value of 1 and excluded elements (i.e. the background) have a value of 0 or NaN" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/258" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1865,17 +1865,17 @@ nidm:NIDM_0000004 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000005 nidm:NIDM_0000005 rdf:type owl:Class ; - + rdfs:label "Binomial Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000276"^^xsd:anyURI ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000115 "The 'Binomial Distribution' is a discrete probability distribution which describes the probability of k successes in n draws with replacement from a finite population of size N. The 'Binomial Distribution' is frequently used to model the number of successes in a sample of size n drawn with replacement from a population of size N. The 'Binomial Distribution' gives the discrete probability distribution of obtaining exactly n successes out of N Bernoulli trials (where the result of each Bernoulli trial is true with probability p and false with probability q=1-p ) notation: B(n,p) The mean is N*p The variance is N*p*q. (Definition from STATO)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1883,17 +1883,17 @@ nidm:NIDM_0000005 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000006 nidm:NIDM_0000006 rdf:type owl:Class ; - + rdfs:label "Cluster" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "A collection of elements related by one or more criteria."^^xsd:string ; - + prov:editorialNote "Discussed in https://github.com/incf-nidash/nidm/issues/71."^^xsd:string ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1901,17 +1901,17 @@ nidm:NIDM_0000006 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000007 nidm:NIDM_0000007 rdf:type owl:Class ; - + rdfs:label "Cluster Definition Criteria" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ClusterDefinitionCriteria-06.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ClusterDefinitionCriteria-18.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ClusterDefinitionCriteria-26.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Set of criterion specified a priori to define the clusters reported after 'Inference' (e.g. pixel or voxel 'Connectivity Criterion')." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1919,17 +1919,17 @@ nidm:NIDM_0000007 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000008 nidm:NIDM_0000008 rdf:type owl:Class ; - + rdfs:label "Cluster Labels Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ClusterLabelsMap.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) denotes cluster membership within the excursion set. Each cluster is denoted by a different integer and all members of the same cluster have the same value." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/282" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1937,17 +1937,17 @@ nidm:NIDM_0000008 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000011 nidm:NIDM_0000011 rdf:type owl:Class ; - + rdfs:label "Conjunction Inference" ; - + rdfs:subClassOf nidm:NIDM_0000049 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ConjunctionInference.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Statistically testing for the joint significance of multiple effects, with emphasis on rejecting all (instead of one or more) of the respective null hypotheses." ; - + obo:IAO_0000116 "Term discussed in https://github.com/incf-nidash/nidm/pull/134" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1955,17 +1955,17 @@ nidm:NIDM_0000011 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000012 nidm:NIDM_0000012 rdf:type owl:Class ; - + rdfs:label "Connectivity Criterion" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000117 "TN, KH, CM" ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "The criterion used to characterize two voxels, pixels or vertices as 'connected'." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1973,17 +1973,17 @@ nidm:NIDM_0000012 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000013 nidm:NIDM_0000013 rdf:type owl:Class ; - + rdfs:label "Contrast Standard Error Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/255."^^xsd:anyURI ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ContrastStandardErrorMap.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [standard error of a contrast estimate](http://purl.obolibrary.org/obo/STATO_0000385)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -1991,17 +1991,17 @@ nidm:NIDM_0000013 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000015 nidm:NIDM_0000015 rdf:type owl:Class ; - + rdfs:label "Coordinate" ; - + rdfs:subClassOf prov:Entity ; - + owl:sameAs "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C44465"^^xsd:anyURI ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Coordinate.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/pull/144 and https://github.com/incf-nidash/nidm/pull/172" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2009,17 +2009,17 @@ nidm:NIDM_0000015 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000016 nidm:NIDM_0000016 rdf:type owl:Class ; - + rdfs:label "Coordinate Space" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/CoordinateSpace.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "An entity with spatial attributes (e.g., dimensions, units, and voxel-to-world mapping) that provides context to a 'Map' (e.g., a 'Statistic Map', a 'Contrast Map'...)." ; - + obo:IAO_0000116 "Under discussion at https://github.com/incf-nidash/nidm/issues/290" ; - + obo:IAO_0000114 obo:IAO_0000125 . @@ -2027,15 +2027,15 @@ nidm:NIDM_0000016 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000017 nidm:NIDM_0000017 rdf:type owl:Class ; - + rdfs:label "Custom Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000075 ; - + obo:IAO_0000115 "Custom (unknown) reference space selected by the user" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2043,17 +2043,17 @@ nidm:NIDM_0000017 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000018 nidm:NIDM_0000018 rdf:type owl:Class ; - + rdfs:label "Data Scaling" ; - + rdfs:subClassOf prov:Entity ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000115 "Scaling applied to the data before parameter estimation, including specification of the 'target Intensity'." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/285" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2061,9 +2061,9 @@ nidm:NIDM_0000018 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000019 nidm:NIDM_0000019 rdf:type owl:Class ; - + rdfs:label "Design Matrix" ; - + rdfs:subClassOf prov:Entity , [ rdf:type owl:Restriction ; owl:onProperty dc:description ; @@ -2080,16 +2080,16 @@ nidm:NIDM_0000019 rdf:type owl:Class ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ; owl:onDataRange xsd:string ] ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/DesignMatrix.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/DesignMatrix_1stLevel.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/274" ; - + obo:IAO_0000115 "A [stato:design matrix](http://purl.obolibrary.org/obo/STATO_0000289), with additional neuroimaging attributes, including HRF and drift for first-level fMRI models" ; - + rdfs:seeAlso "stato:design matrix" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2097,17 +2097,17 @@ nidm:NIDM_0000019 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000020 nidm:NIDM_0000020 rdf:type owl:Class ; - + rdfs:label "Display Mask Map" ; - + rdfs:subClassOf nidm:NIDM_0000004 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/DisplayMaskMap.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/258 and https://github.com/incf-nidash/nidm/pull/157" ; - + obo:IAO_0000115 "A 'Binary Map' used by an activity that changed the voxels displayed, but did not alter the space in which the activity was performed (e.g. at the level of 'Inference', this mask is called \"contrast masking\" in both FSL & SPM and does not alter voxel-wise corrected p-values)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2115,15 +2115,15 @@ nidm:NIDM_0000020 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000022 nidm:NIDM_0000022 rdf:type owl:Class ; - + rdfs:label "Error Distribution" ; - + rdfs:subClassOf prov:Entity ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000115 "Probability distribution used to model the error." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2131,17 +2131,17 @@ nidm:NIDM_0000022 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000023 nidm:NIDM_0000023 rdf:type owl:Class ; - + rdfs:label "Error Model" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ErrorModel-OLS.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ErrorModel-WLS.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ErrorModel-SPMnonSphericity.txt" ; - + obo:IAO_0000115 "Model used to describe the random variation of the error term as part of parameter estimation, including specification of the error probability distribution, its variance and dependence both spatially and across observations." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2149,17 +2149,17 @@ nidm:NIDM_0000023 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000024 nidm:NIDM_0000024 rdf:type owl:Class ; - + rdfs:label "Exchangeable Error" ; - + rdfs:subClassOf obo:STATO_0000346 ; - + rdfs:comment "Under gaussianity assumption this is equivalent to compound symmetry but not in general." ; - + obo:IAO_0000117 "TN" ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/28" ; - + obo:IAO_0000114 obo:IAO_0000423 . @@ -2167,22 +2167,22 @@ nidm:NIDM_0000024 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000025 nidm:NIDM_0000025 rdf:type owl:Class ; - + rdfs:label "Excursion Set Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 , [ rdf:type owl:Restriction ; owl:onProperty dc:description ; owl:onClass dctype:Image ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ] ; - + obo:IAO_0000115 "A map in which the set of elements (e.g., pixels, voxels, vertices, or faces) not selected by the 'Inference' activity is set to zero or NaN" ; - + obo:IAO_0000116 "Discussed in the Neuroimaging terms spreadsheet and in https://github.com/incf-nidash/nidm/issues/256." ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ExcursionSetMap.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2190,20 +2190,20 @@ nidm:NIDM_0000025 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000026 nidm:NIDM_0000026 rdf:type owl:Class ; - + rdfs:label "Extent Threshold" ; - + rdfs:subClassOf nidm:NIDM_0000162 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ExtentThreshold-FDR.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ExtentThreshold-Unc.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ExtentThresholdStat_clusterSizeResels.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ExtentThreshold_equivThresh-FWER.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A numerical value that establishes a lower bound on cluster-sizes and can be specified by the user in terms of FWER-corrected p-value, uncorrected p-value or minimum cluster size in voxels" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/273" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2211,17 +2211,17 @@ nidm:NIDM_0000026 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000027 nidm:NIDM_0000027 rdf:type owl:Class ; - + rdfs:label "NIDM-Results" ; - + rdfs:subClassOf nidm:NIDM_0000057 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/NIDMBundle.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/137" ; - + obo:IAO_0000115 "'NIDM Object Model' representing the results of a mass univariate neuroimaging study and targeting the application of meta-analysis. The specification is available at: http://nidm.nidash.org/specs/nidm-results.html" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2229,17 +2229,17 @@ nidm:NIDM_0000027 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000028 nidm:NIDM_0000028 rdf:type owl:Class ; - + rdfs:label "Finite Impulse Response Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/DesignMatrix_1stLevel-FIR.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Set of Finite impulse response (FIR) filters, with FIR the convolution kernel is represented as a set of discrete fixed-width \"impulses\" (definition adapted from [FSL wiki](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html))" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2247,15 +2247,15 @@ nidm:NIDM_0000028 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000029 nidm:NIDM_0000029 rdf:type owl:Class ; - + rdfs:label "Gamma Difference HRF" ; - + rdfs:subClassOf nidm:NIDM_0000035 ; - + obo:IAO_0000115 "'Hemodynamic Response Function' which is a difference of two gamma probability density functions." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2263,15 +2263,15 @@ nidm:NIDM_0000029 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000030 nidm:NIDM_0000030 rdf:type owl:Class ; - + rdfs:label "Gamma Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000115 "Set of gamma probability density functions." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2279,15 +2279,15 @@ nidm:NIDM_0000030 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000031 nidm:NIDM_0000031 rdf:type owl:Class ; - + rdfs:label "Gamma HRF" ; - + rdfs:subClassOf nidm:NIDM_0000035 ; - + obo:IAO_0000115 "'Hemodynamic Response Function' which is a gamma probability density function." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2295,17 +2295,17 @@ nidm:NIDM_0000031 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000032 nidm:NIDM_0000032 rdf:type owl:Class ; - + rdfs:label "Gaussian Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000227"^^xsd:anyURI ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000115 "A normal distribution is a continuous probability distribution described by a probability distribution function described here: http://mathworld.wolfram.com/NormalDistribution.html (Definition from STATO)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2313,17 +2313,17 @@ nidm:NIDM_0000032 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000033 nidm:NIDM_0000033 rdf:type owl:Class ; - + rdfs:label "Grand Mean Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/GrandMeanMap.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/288" ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is the mean over all observations of that element in the input maps (after any scaling of those input maps)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2331,20 +2331,20 @@ nidm:NIDM_0000033 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000034 nidm:NIDM_0000034 rdf:type owl:Class ; - + rdfs:label "Height Threshold" ; - + rdfs:subClassOf nidm:NIDM_0000162 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/HeightThreshold-FDR.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/HeightThreshold-Stat.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/HeightThreshold-Unc.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/HeightThreshold_equivThresh-FWER.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A numerical value that establishes a lower bound on statistic values and can be specified by the user in terms of FWER-corrected p-value, uncorrected p-value or minimum statistic value." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/280" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2352,15 +2352,15 @@ nidm:NIDM_0000034 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000035 nidm:NIDM_0000035 rdf:type owl:Class ; - + rdfs:label "Hemodynamic Response Function" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000115 "'Hemodynamic Response Function' basis that can on its own be used to represent the idealised 'Hemodynamic Response Function'." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2368,15 +2368,15 @@ nidm:NIDM_0000035 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000036 nidm:NIDM_0000036 rdf:type owl:Class ; - + rdfs:label "Convolution Basis Set" ; - + rdfs:subClassOf prov:Entity ; - + rdfs:isDefinedBy "A set of functions that, when convolved with the anticipated neural responses, yield a set of regressors to model the anticipated hemodynamic responses."^^xsd:string ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000124 . @@ -2384,17 +2384,17 @@ nidm:NIDM_0000036 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000037 nidm:NIDM_0000037 rdf:type owl:Class ; - + rdfs:label "Hemodynamic Response Function Derivative" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/DesignMatrix_1stLevel_HRFBasis2_HRFBasis3-InformedBasisSet.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "'Hemodynamic Response Function' basis which is the derivative of an 'Hemodynamic Response Function'." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2402,15 +2402,15 @@ nidm:NIDM_0000037 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000048 nidm:NIDM_0000048 rdf:type owl:Class ; - + rdfs:label "Independent Error" ; - + rdfs:subClassOf obo:STATO_0000346 ; - + obo:IAO_0000116 "Under discussion at https://github.com/ISA-tools/stato/issues/28" ; - + obo:IAO_0000117 "TN" ; - + obo:IAO_0000114 obo:IAO_0000423 . @@ -2418,18 +2418,18 @@ nidm:NIDM_0000048 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000049 nidm:NIDM_0000049 rdf:type owl:Class ; - + rdfs:label "Inference" ; - + rdfs:subClassOf prov:Activity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Inference-OneTailed.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Inference-TwoTailed.txt"^^xsd:anyURI ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000299" ; - + obo:IAO_0000115 "Statistical 'Inference' is a process of drawing conclusions following data analysis using statistical methods (statistical tests) and evaluating whether to reject or accept null hypothesis. (definition from STATO)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2437,17 +2437,17 @@ nidm:NIDM_0000049 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000051 nidm:NIDM_0000051 rdf:type owl:Class ; - + rdfs:label "MNI Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000075 ; - + rdfs:seeAlso "birnlex_2125" ; - + obo:IAO_0000115 "MNI 305 coordinate system or any coordinate system derived from MNI 305." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2455,9 +2455,9 @@ nidm:NIDM_0000051 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000052 nidm:NIDM_0000052 rdf:type owl:Class ; - + rdfs:label "Map" ; - + rdfs:subClassOf prov:Entity , [ rdf:type owl:Restriction ; owl:onProperty prov:atLocation ; @@ -2479,14 +2479,14 @@ nidm:NIDM_0000052 rdf:type owl:Class ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ; owl:onDataRange xsd:string ] ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Map_atLocation-nii.txt"^^xsd:anyURI , "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Map_atLocation_hasMapHeader-img.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Ordered set of values corresponding to the discrete sampling of some process (e.g. brain MRI data measured on a regular 3D lattice; or brain cortical surface data measured irregularly over the cortex)." ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/pull/149" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2494,9 +2494,9 @@ nidm:NIDM_0000052 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000053 nidm:NIDM_0000053 rdf:type owl:Class ; - + rdfs:label "Map Header" ; - + rdfs:subClassOf prov:Entity , [ rdf:type owl:Restriction ; owl:onProperty dct:format ; @@ -2518,13 +2518,13 @@ nidm:NIDM_0000053 rdf:type owl:Class ; owl:minQualifiedCardinality "0"^^xsd:nonNegativeInteger ; owl:onDataRange xsd:string ] ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/MapHeader.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/289" ; - + obo:IAO_0000115 "A file associated with a Map to provide header information (e.g. NIfTI header file)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2532,17 +2532,17 @@ nidm:NIDM_0000053 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000054 nidm:NIDM_0000054 rdf:type owl:Class ; - + rdfs:label "Mask Map" ; - + rdfs:subClassOf nidm:NIDM_0000004 ; - + obo:IAO_0000115 "A 'Binary Map' representing the exact set of elements (e.g., pixels, voxels, vertices, and faces) in which an activity was performed (e.g. the mask map generated by the model parameter estimation activity represents the exact set of voxels in which the mass univariate model was estimated) and/or restraining the space in which an activity was performed (e.g. the mask map used by 'Inference')" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/258 and https://github.com/incf-nidash/nidm/issues/155" ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/MaskMap.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2550,17 +2550,17 @@ nidm:NIDM_0000054 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000056 nidm:NIDM_0000056 rdf:type owl:Class ; - + rdfs:label "Model Parameter Estimation" ; - + rdfs:subClassOf prov:Activity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ModelParametersEstimation.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "the process of performing a [obo:model parameter estimation](http://purl.obolibrary.org/obo/STATO_0000119) at each element (e.g., pixel, voxel, vertex, or face) of a map" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/issues/141" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2568,15 +2568,15 @@ nidm:NIDM_0000056 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000057 nidm:NIDM_0000057 rdf:type owl:Class ; - + rdfs:label "NIDM Object Model" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Abstraction on the data model, developed for a specific application/use-case/task at hand, that specifies the components and relations necessary for use by these applications. The same object model can be reused by multiple applications (e.g., meta-analysis, Neurovault)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/137" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2584,15 +2584,15 @@ nidm:NIDM_0000057 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000058 nidm:NIDM_0000058 rdf:type owl:Class ; - + rdfs:label "Non Parametric Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000115 "Probability distribution estimated empirically on the data without assumptions on the shape of the probability distribution." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2600,13 +2600,13 @@ nidm:NIDM_0000058 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000059 nidm:NIDM_0000059 rdf:type owl:Class ; - + rdfs:label "Non Parametric Symmetric Distribution" ; - + rdfs:subClassOf obo:STATO_0000117 ; - + obo:IAO_0000115 "Probability distribution estimated empirically on the data assuming only symmetry of the probability distribution." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2614,15 +2614,15 @@ nidm:NIDM_0000059 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000060 nidm:NIDM_0000060 rdf:type owl:Class ; - + rdfs:label "One Tailed Test" ; - + rdfs:subClassOf prov:Entity ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000286"^^xsd:anyURI ; - + obo:IAO_0000116 "Re-use \"one tailed test\" from STATO." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2630,17 +2630,17 @@ nidm:NIDM_0000060 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000061 nidm:NIDM_0000061 rdf:type owl:Class ; - + rdfs:label "Parameter Estimate Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ParameterEstimateMap.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/255 and https://github.com/incf-nidash/nidm/issues/141 (see also https://github.com/ISA-tools/stato/issues/18)" ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [model parameter estimate](http://purl.obolibrary.org/obo/STATO_0000144)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2648,17 +2648,17 @@ nidm:NIDM_0000061 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000062 nidm:NIDM_0000062 rdf:type owl:Class ; - + rdfs:label "Peak" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/283" ; - + obo:IAO_0000115 "A map element (e.g., pixel, voxel, vertex, or face) which is a local maximum in the supra-threshold cluster and complies with the 'Peak definition criteria'." ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Peak_ValueP.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2666,17 +2666,17 @@ nidm:NIDM_0000062 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000063 nidm:NIDM_0000063 rdf:type owl:Class ; - + rdfs:label "Peak Definition Criteria" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/PeakDefinitionCriteria_MaxPeaks.txt"^^xsd:anyURI ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/200" ; - + obo:IAO_0000115 "Set of criterion specified a priori to define the 'Peak's reported after 'Inference' (e.g. maximum number of 'Peak's within a cluster, minimum distance between 'Peak's)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2684,15 +2684,15 @@ nidm:NIDM_0000063 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000064 nidm:NIDM_0000064 rdf:type owl:Class ; - + rdfs:label "Pixel Connectivity Criterion" ; - + rdfs:subClassOf nidm:NIDM_0000012 ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "The criterion used to characterize two pixels as 'connected'. In two dimensions voxels that are connected can share an edge (4-connected) or, edge or corner (8-connected)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2700,17 +2700,17 @@ nidm:NIDM_0000064 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000065 nidm:NIDM_0000065 rdf:type owl:Class ; - + rdfs:label "Poisson Distribution" ; - + rdfs:subClassOf nidm:NIDM_0000022 ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000051"^^xsd:anyURI ; - + owl:deprecated "true"^^xsd:boolean ; - + obo:IAO_0000115 "Poisson distribution is a probability distribution used to model the number of events occurring within a given time interval. It is defined by a real number (λ) and an integer k representing the number of events and a function. The expected value of a Poisson-distributed random variable is equal to λ and so is its variance. (Definition from STATO)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2718,17 +2718,17 @@ nidm:NIDM_0000065 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000066 nidm:NIDM_0000066 rdf:type owl:Class ; - + rdfs:label "Residual Mean Squares Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/255." ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [residual mean square](http://purl.obolibrary.org/obo/STATO_0000375)." ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ResidualMeanSquaresMap.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2736,15 +2736,15 @@ nidm:NIDM_0000066 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000067 nidm:NIDM_0000067 rdf:type owl:Class ; - + rdfs:label "Custom Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "Customised set of basis functions." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2752,17 +2752,17 @@ nidm:NIDM_0000067 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000068 nidm:NIDM_0000068 rdf:type owl:Class ; - + rdfs:label "Search Space Mask Map" ; - + rdfs:subClassOf nidm:NIDM_0000054 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/SearchSpaceMaskMap.txt" ; - + obo:IAO_0000115 "A 'Mask Map' representing the set of elements (e.g., pixels, voxels, vertices, or faces) in which the 'Inference' was performed" ; - + obo:IAO_0000116 "Discussed at: https://github.com/incf-nidash/nidm/pull/258" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2770,15 +2770,15 @@ nidm:NIDM_0000068 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000069 nidm:NIDM_0000069 rdf:type owl:Class ; - + rdfs:label "Fourier Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000115 "Set of Fourier basis." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2786,17 +2786,17 @@ nidm:NIDM_0000069 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000070 nidm:NIDM_0000070 rdf:type owl:Class ; - + rdfs:label "Supra-Threshold Cluster" ; - + rdfs:subClassOf obo:OBI_0000251 ; - + obo:IAO_0000115 "A cluster of map elements (e.g., pixels, voxels, vertices, and faces) that were selected by the 'Inference' activity and are contiguous according to the cluster 'Connectivity Criterion'."^^xsd:string ; - + prov:editorialNote "Discussed in https://github.com/incf-nidash/nidm/issues/71."^^xsd:string ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/SupraThresholdCluster.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2804,15 +2804,15 @@ nidm:NIDM_0000070 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000071 nidm:NIDM_0000071 rdf:type owl:Class ; - + rdfs:label "Error Parameter Map-Wise Dependence" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Map-wise dependence structure of a parameter in the 'Error Model' (i.e. variance or dependence parameter). For example, whether a temporal autocorrelation parameter is estimated at each element separately, estimated using data in a local neighbourhood, or estimated using all elements in the map." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2820,15 +2820,15 @@ nidm:NIDM_0000071 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000072 nidm:NIDM_0000072 rdf:type owl:Class ; - + rdfs:label "Constant Parameter" ; - + rdfs:subClassOf nidm:NIDM_0000071 ; - + obo:IAO_0000115 "Parameter estimated as constant over a entire set of elements considered (e.g. those in the analysis mask)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2836,15 +2836,15 @@ nidm:NIDM_0000072 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000073 nidm:NIDM_0000073 rdf:type owl:Class ; - + rdfs:label "Independent Parameter" ; - + rdfs:subClassOf nidm:NIDM_0000071 ; - + obo:IAO_0000115 "Parameter whose estimation at a given element does not depend on any other element." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2852,15 +2852,15 @@ nidm:NIDM_0000073 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000074 nidm:NIDM_0000074 rdf:type owl:Class ; - + rdfs:label "Regularized Parameter" ; - + rdfs:subClassOf nidm:NIDM_0000071 ; - + obo:IAO_0000115 "Parameter whose estimation at a given element depends on a local neighborhood of elements" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/194" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2868,17 +2868,17 @@ nidm:NIDM_0000074 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000075 nidm:NIDM_0000075 rdf:type owl:Class ; - + rdfs:label "Standardized Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000081 ; - + rdfs:comment "This is meant to be used for retrospective export when exact template is unknown." ; - + obo:IAO_0000115 "Parent of all reference spaces except \"Subject\"." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -2886,17 +2886,17 @@ nidm:NIDM_0000075 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000076 nidm:NIDM_0000076 rdf:type owl:Class ; - + rdfs:label "Statistic Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/StatisticMap-T.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/255" ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a [statistic](http://purl.obolibrary.org/obo/STATO_0000039)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2904,17 +2904,17 @@ nidm:NIDM_0000076 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000077 nidm:NIDM_0000077 rdf:type owl:Class ; - + rdfs:label "Subject Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000081 ; - + obo:IAO_0000115 "Reference space corresponding to the subject brain (no spatial normalization applied)." ; - + rdfs:comment "Used in FSL and SPM un-registered data." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -2922,17 +2922,17 @@ nidm:NIDM_0000077 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000078 nidm:NIDM_0000078 rdf:type owl:Class ; - + rdfs:label "Talairach Coordinate System" ; - + rdfs:subClassOf nidm:NIDM_0000075 ; - + obo:IAO_0000115 "Reference space defined by the dissected brain used for the Talairach and Tournoux atlas (cf. http://www.talairach.org/about.html)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + rdfs:seeAlso "http://www.talairach.org/" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2940,15 +2940,15 @@ nidm:NIDM_0000078 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000079 nidm:NIDM_0000079 rdf:type owl:Class ; - + rdfs:label "Two Tailed Test" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "Re-use \"two tailed test\" from STATO"^^xsd:anyURI ; - + owl:sameAs "http://purl.obolibrary.org/obo/STATO_0000287"^^xsd:anyURI ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2956,15 +2956,15 @@ nidm:NIDM_0000079 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000080 nidm:NIDM_0000080 rdf:type owl:Class ; - + rdfs:label "Voxel Connectivity Criterion" ; - + rdfs:subClassOf nidm:NIDM_0000012 ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "The criterion used to characterize two voxels as 'connected'. In three dimensions voxels that are connected can share a voxel face (6-connected), face or edge (18-connectec), or face, edge, or corner (26-connected)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2972,16 +2972,16 @@ nidm:NIDM_0000080 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000081 nidm:NIDM_0000081 rdf:type owl:Class ; - + rdfs:label "World Coordinate System" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 """Reference space on which real-world positions are expressed (cf. [Nifti-1 FAQ question 14](http://nifti.nimh.nih.gov/nifti-1/documentation/faq#Q14) and [Understanding affines on nipy](http://nipy.org/nipy/stable/devel/code_discussions/understanding_affines.html) ). A world coordinate system can be represented by an image obtained by registering an initial set of images, using a given normalization algorithm to match a target template.""" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -2989,15 +2989,15 @@ nidm:NIDM_0000081 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000087 nidm:NIDM_0000087 rdf:type owl:Class ; - + rdfs:label "Drift Model" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000115 "A model used to compensate for low frequency baseline drifts when analyzing functional MRI data at the subject level." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3005,15 +3005,15 @@ nidm:NIDM_0000087 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000110 nidm:NIDM_0000110 rdf:type owl:Class ; - + rdfs:label "Gaussian HRF" ; - + rdfs:subClassOf nidm:NIDM_0000035 ; - + obo:IAO_0000115 "'Hemodynamic Response Function' which is a gaussian kernel." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3021,15 +3021,15 @@ nidm:NIDM_0000110 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000135 nidm:NIDM_0000135 rdf:type owl:Class ; - + rdfs:label "Contrast Variance Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is a contrast variance (i.e. the square of a [standard error of a contrast estimate](http://purl.obolibrary.org/obo/STATO_0000385))" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/287" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3037,19 +3037,19 @@ nidm:NIDM_0000135 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000140 nidm:NIDM_0000140 rdf:type owl:Class ; - + rdfs:label "Cluster Center Of Gravity" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/pull/257" ; - + rdfs:seeAlso "http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster" ; - + obo:IAO_0000115 "A centre of gravity of the cluster, equivalent to the concept of Centre Of Gravity for a object with distributed mass, where intensity substitutes for mass in this case. The 'Coordinate' of the centre of gravity is the weighted average of the cluster element (e.g., pixels, voxels, vertices, or faces) 'Coordinate's, where the weighting factors are the cluster element intensities. (definition adapted from http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster)" ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/FSL_ClusterCenterOfGravity.txt" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3057,15 +3057,15 @@ nidm:NIDM_0000140 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000144 nidm:NIDM_0000144 rdf:type owl:Class ; - + rdfs:label "Resels Per Voxel Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/SPM_ReselsPerVoxelMap.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) location is the number of resels per voxel." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3073,15 +3073,15 @@ nidm:NIDM_0000144 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000150 nidm:NIDM_0000150 rdf:type owl:Class ; - + rdfs:label "Linear Spline Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "A Linear (order 1) spline, providing an estimate that is continuous over time (in contrast to a FIR basis, which is discontinuous between each time bin). This is called TENT in AFNI's 3dDeconvolve program." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3089,15 +3089,15 @@ nidm:NIDM_0000150 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000151 nidm:NIDM_0000151 rdf:type owl:Class ; - + rdfs:label "Sine Basis Set" ; - + rdfs:subClassOf nidm:NIDM_0000036 ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "A set of Sine waves of differing frequencies (definition adapted from [FSL wiki](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html))." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3105,15 +3105,15 @@ nidm:NIDM_0000151 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000160 nidm:NIDM_0000160 rdf:type owl:Class ; - + rdfs:label "P-Value Uncorrected" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "A p-value reported without correction for multiple testing."^^xsd:string ; - + obo:IAO_0000116 "Discussed in [Neuroimaging terms spreadsheet](https://docs.google.com/spreadsheets/d/16pC2cDsdxlzv2CzlNMtStqt5-xHwDEsU6MjZVxWhrE4/edit?usp=sharing)"^^xsd:string ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3121,13 +3121,13 @@ nidm:NIDM_0000160 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000162 nidm:NIDM_0000162 rdf:type owl:Class ; - + rdfs:label "Threshold"^^xsd:string ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000115 "A numerical value that establishes a bound on a set of statistic values and can be specified by the user in terms of FWER-corrected p-value, uncorrected p-value, FDR-corrected q-value or statistic value"^^xsd:string ; - + obo:IAO_0000114 obo:IAO_0000125 . @@ -3135,15 +3135,15 @@ nidm:NIDM_0000162 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000163 nidm:NIDM_0000163 rdf:type owl:Class ; - + rdfs:label "Contrast Explained Mean Square Map" ; - + rdfs:subClassOf nidm:NIDM_0000052 ; - + obo:IAO_0000115 "A map whose value at each element (e.g., pixel, voxel, vertex, or face) is the extra sum of squares divided by the 'effect Degrees of Freedom' (i.e. the numerator of an F-statistic)." ; - + obo:IAO_0000116 "Discussed in https://github.com/incf-nidash/nidm/issues/235" ; - + obo:IAO_0000114 obo:IAO_0000125 . @@ -3151,13 +3151,13 @@ nidm:NIDM_0000163 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000164 nidm:NIDM_0000164 rdf:type owl:Class ; - + rdfs:label "Neuroimaging Analysis Software" ; - + rdfs:subClassOf prov:SoftwareAgent ; - + obo:IAO_0000115 "Tool used to process neuroimaging data." ; - + obo:IAO_0000114 obo:IAO_0000124 . @@ -3165,13 +3165,13 @@ nidm:NIDM_0000164 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000165 nidm:NIDM_0000165 rdf:type owl:Class ; - + rdfs:label "NIDM-Results Exporter" ; - + rdfs:subClassOf prov:SoftwareAgent ; - + obo:IAO_0000115 "Tool used to export results produced by a neuroimaging software (SPM, FSL, AFNI...) into a NIDM-Results archive." ; - + obo:IAO_0000114 obo:IAO_0000124 . @@ -3179,15 +3179,15 @@ nidm:NIDM_0000165 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000166 nidm:NIDM_0000166 rdf:type owl:Class ; - + rdfs:label "NIDM-Results Export" ; - + rdfs:subClassOf prov:Activity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Export.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "The process of exporting results created by a neuroimaging software (SPM, FSL, AFNI...) into a NIDM-Results archive." ; - + obo:IAO_0000114 obo:IAO_0000124 . @@ -3195,15 +3195,15 @@ nidm:NIDM_0000166 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000167 nidm:NIDM_0000167 rdf:type owl:Class ; - + rdfs:label "nidmfsl" ; - + rdfs:subClassOf nidm:NIDM_0000165 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ExporterSoftware-FSL.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Python library for the export of feat folders (generated by FSL) to NIDM-Results. Source available at: https://github.com/incf-nidash/nidm-results_fsl/." ; - + obo:IAO_0000114 obo:IAO_0000124 . @@ -3211,15 +3211,15 @@ nidm:NIDM_0000167 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000168 nidm:NIDM_0000168 rdf:type owl:Class ; - + rdfs:label "spm_results_nidm" ; - + rdfs:subClassOf nidm:NIDM_0000165 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/ExporterSoftware-SPM.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "Matlab m file for the export of SPM results to NIDM-Results. Source available at: http://www.fil.ion.ucl.ac.uk/spm/download/toolbox/NIDM/spm_nidm.zip/." ; - + obo:IAO_0000114 obo:IAO_0000124 . @@ -3227,17 +3227,17 @@ nidm:NIDM_0000168 rdf:type owl:Class ; ### http://purl.org/nidash/nidm#NIDM_0000169 nidm:NIDM_0000169 rdf:type owl:Class ; - + rdfs:label "Data" ; - + rdfs:subClassOf prov:Entity ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/Data_wasAttributedTo.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at ..." ; - + obo:IAO_0000115 "Information about the input Data, including scaling applied to the data before parameter estimation.." ; - + obo:IAO_0000114 obo:IAO_0000124 . @@ -3245,17 +3245,17 @@ nidm:NIDM_0000169 rdf:type owl:Class ; ### http://purl.org/nidash/spm#SPM_0000002 spm:SPM_0000002 rdf:type owl:Class ; - + rdfs:label "Discrete Cosine Transform basis Drift Model" ; - + rdfs:subClassOf nidm:NIDM_0000087 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/SPM_DriftModel.txt"^^xsd:anyURI ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/298" ; - + obo:IAO_0000115 "A 'Drift Model' in which the drifts are modeled by a Discrete Cosine Transform basis added to regression model" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3263,17 +3263,17 @@ spm:SPM_0000002 rdf:type owl:Class ; ### http://purl.org/nidash/spm#SPM_0000005 spm:SPM_0000005 rdf:type owl:Class ; - + rdfs:label "Partial Conjunction Inference" ; - + rdfs:subClassOf nidm:NIDM_0000049 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/SPM_KConjunctionInference.txt"^^xsd:anyURI ; - + obo:IAO_0000115 "The process of testing the joint significance of multiple effects to infer that some (not necessarily all) of the respective effects are real (i.e. their null hypotheses are false). If there are K effects considered, the 'partial Conjunction Degree' u is the number non-null effects allowed as part of partial conjunction null hypothesis; if the partial conjunction null is rejected, it may be inferred that u+1 or more effects are real. The case of u=K-1 corresponds to proper \"'Conjunction Inference'\", while the case of u=0 corresponds to \"global null\" conjunction test. See [Friston et al. (2005). Conjunction revisited. NeuroImage, 25(3), 661-7.](http://dx.doi.org/10.1016/j.neuroimage.2005.01.013)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/294" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3281,9 +3281,9 @@ spm:SPM_0000005 rdf:type owl:Class ; ### http://scicrunch.org/resolver/SCR_002823 src:SCR_002823 rdf:type owl:Class ; - + rdfs:subClassOf nidm:NIDM_0000164 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/FSL_Software.txt"^^xsd:anyURI . @@ -3291,9 +3291,9 @@ src:SCR_002823 rdf:type owl:Class ; ### http://scicrunch.org/resolver/SCR_007037 src:SCR_007037 rdf:type owl:Class ; - + rdfs:subClassOf nidm:NIDM_0000164 ; - + obo:IAO_0000112 "https://raw.githubusercontent.com/incf-nidash/nidm/NIDM-Results_1.3.0/nidm/nidm-results/terms/examples/SPM_Software.txt"^^xsd:anyURI . @@ -3301,7 +3301,7 @@ src:SCR_007037 rdf:type owl:Class ; ### http://uri.neuinfo.org/nif/nifstd/birnlex_2094 nlx:birnlex_2094 rdf:type owl:Class ; - + rdfs:subClassOf prov:Agent . @@ -3309,7 +3309,7 @@ nlx:birnlex_2094 rdf:type owl:Class ; ### http://uri.neuinfo.org/nif/nifstd/birnlex_2177 nlx:birnlex_2177 rdf:type owl:Class ; - + rdfs:subClassOf prov:Entity . @@ -3349,13 +3349,13 @@ owl:Class rdf:type owl:Class . fsl:FSL_0000001 rdf:type nidm:NIDM_0000029 , owl:NamedIndividual ; - + rdfs:label "FSL's Gamma Difference HRF" ; - + obo:IAO_0000115 "'Hemodynamic Response Function' which is a fixed difference of two gamma probability density functions - a standard positive function at normal lag, and a small, delayed, negated gamma probability density function, which attempts to model the late undershoot (definition adapted [FSL wiki](http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html))" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3364,13 +3364,13 @@ fsl:FSL_0000001 rdf:type nidm:NIDM_0000029 , fsl:FSL_0000003 rdf:type nidm:NIDM_0000037 , owl:NamedIndividual ; - + rdfs:label "FSL's Temporal Derivative" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "'Hemodynamic Response Function' basis that is the derivative with respect to time of the FSL's Gamma Difference heamodynamic response function." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3379,11 +3379,11 @@ fsl:FSL_0000003 rdf:type nidm:NIDM_0000037 , fsl:FSL_0000006 rdf:type nidm:NIDM_0000031 , owl:NamedIndividual ; - + rdfs:label "FSL's Gamma HRF" ; - + obo:IAO_0000115 "'Hemodynamic Response Function' which is a fixed gamma probability density function. This is the default in FSL." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3392,17 +3392,17 @@ fsl:FSL_0000006 rdf:type nidm:NIDM_0000031 , nidm:NIDM_0000009 rdf:type nidm:NIDM_0000075 , owl:NamedIndividual ; - + rdfs:label "Colin27 Coordinate System" ; - + obo:IAO_0000115 "Reference space defined as the stereotaxic average of 27 T1-weighted MRI scans of the same individual transformed into the Talairach stereotaxic space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres and http://neuro.debian.net/pkgs/mni-colin27-nifti.html). This is the default in SPM96 (cf. [MRC CBSU Wiki](http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach))." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + rdfs:comment "used in SPM96 (cf. http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3411,15 +3411,15 @@ nidm:NIDM_0000009 rdf:type nidm:NIDM_0000075 , nidm:NIDM_0000038 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm452 Air Coordinate System" ; - + obo:IAO_0000115 "Reference space defined as the average of 452 T1-weighted MRIs of normal young adult brains after 12 parameter AIR linear transform to the MNI 305 space (cf. http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml and http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)" ; - + rdfs:seeAlso "http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3428,15 +3428,15 @@ nidm:NIDM_0000038 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000039 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm452 Warp5 Coordinate System" ; - + rdfs:seeAlso "http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml" ; - + obo:IAO_0000115 "Reference space defined as the average of 452 T1-weighted MRIs of normal young adult brains after affine and 5 order polynomial non-linear warping to the MNI 305 space (cf. http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml and http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3445,17 +3445,17 @@ nidm:NIDM_0000039 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000040 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Linear Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin" ; - + rdfs:comment "used in SPM99 to SPM8 (cf. http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach and spm8/spm_templates.man)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Reference space which is the average of 152 T1-weighted MRI scans, linearly transformed onto the MNI 305 reference space (definition adapted from: http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin). This is the default in SPM99 to SPM8 (cf. [MRC CBSU Wiki](http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach) and spm8/spm_templates.man." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3464,15 +3464,15 @@ nidm:NIDM_0000040 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000041 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009a Asymmetric Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3481,15 +3481,15 @@ nidm:NIDM_0000041 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000042 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009a Symmetric Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to to form a symmetric model in MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3498,15 +3498,15 @@ nidm:NIDM_0000042 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000043 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009b Asymmetric Coordinate System" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans in high-resolution, non-linearly transformed to MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3515,15 +3515,15 @@ nidm:NIDM_0000043 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000044 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009b Symmetric Coordinate System" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans in high-resolution, non-linearly transformed to form a symmetric model in MNI152 linear space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3532,17 +3532,17 @@ nidm:NIDM_0000044 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000045 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009c Asymmetric Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to MNI152 linear space using the N3 algorithm (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details)." ; - + rdfs:comment "Used in DARTEL toolbox in SPM12b (cf. spm12b/spm_templates.man)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3551,15 +3551,15 @@ nidm:NIDM_0000045 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000046 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear2009c Symmetric Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009" ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, non-linearly transformed to form a symmetric model in MNI152 linear space using the N3 algorithm (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 for more details). This is the default for DARTEL toolbox in SPM12b (cf. spm12/spm_templates.man)." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3568,17 +3568,17 @@ nidm:NIDM_0000046 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000047 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Icbm Mni152 Non Linear6th Generation Coordinate System" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6"^^xsd:anyURI ; - + obo:IAO_0000115 "Reference space defined as the average of 152 T1-weighted MRI scans, linearly and non-linearly (6 iterations) transformed to form a symmetric model in Talairach space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6)" ; - + rdfs:comment "Used in FSL (cf. http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases)" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3587,17 +3587,17 @@ nidm:NIDM_0000047 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000050 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Ixi549 Coordinate System" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000115 "Reference space defined by the average of the 549 subjects from the IXI dataset linearly transformed to the ICBM MNI 452 (cf. spm12/spm\\_templates.man and http://biomedic.doc.ic.ac.uk/brain-development/index.php?n=Main.Datasets). This is the default in SPM12 (cf. spm12/spm_templates.man)." ; - + rdfs:seeAlso "http://biomedic.doc.ic.ac.uk/brain-development/index.php?n=Main.Datasets" ; - + rdfs:comment "Used in SPM12b (cf. spm12b/spm_templates.man)" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3606,15 +3606,15 @@ nidm:NIDM_0000050 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000055 rdf:type nidm:NIDM_0000051 , owl:NamedIndividual ; - + rdfs:label "Mni305 Coordinate System" ; - + obo:IAO_0000115 "Reference space defined as the average of 305 T1-weighted MRI scans, linearly transformed to Talairach space (cf. http://www.bic.mni.mcgill.ca/ServicesAtlases/MNI305 for more details)" ; - + rdfs:seeAlso "http://www.bic.mni.mcgill.ca/ServicesAtlases/MNI305" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/284" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3623,13 +3623,13 @@ nidm:NIDM_0000055 rdf:type nidm:NIDM_0000051 , nidm:NIDM_0000117 rdf:type nidm:NIDM_0000064 , owl:NamedIndividual ; - + rdfs:label "pixel4connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of pixels are 4-Connected if they share an edge." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3638,13 +3638,13 @@ nidm:NIDM_0000117 rdf:type nidm:NIDM_0000064 , nidm:NIDM_0000118 rdf:type nidm:NIDM_0000064 , owl:NamedIndividual ; - + rdfs:label "pixel8connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of pixels are 8-Connected if they share an edge or corner." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3653,13 +3653,13 @@ nidm:NIDM_0000118 rdf:type nidm:NIDM_0000064 , nidm:NIDM_0000128 rdf:type nidm:NIDM_0000080 , owl:NamedIndividual ; - + rdfs:label "voxel18connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of voxels are 18-Connected if they share a face or edge." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3668,13 +3668,13 @@ nidm:NIDM_0000128 rdf:type nidm:NIDM_0000080 , nidm:NIDM_0000129 rdf:type nidm:NIDM_0000080 , owl:NamedIndividual ; - + rdfs:label "voxel26connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of voxels are 26-Connected if they share a face, edge or corner." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3683,13 +3683,13 @@ nidm:NIDM_0000129 rdf:type nidm:NIDM_0000080 , nidm:NIDM_0000130 rdf:type nidm:NIDM_0000080 , owl:NamedIndividual ; - + rdfs:label "voxel6connected" ; - + obo:IAO_0000117 "Discussed in https://github.com/incf-nidash/nidm/pull/201" ; - + obo:IAO_0000115 "A pair of voxels are 6-Connected if they share a face." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3697,9 +3697,9 @@ nidm:NIDM_0000130 rdf:type nidm:NIDM_0000080 , ### http://purl.org/nidash/nidm#NIDM_0000171 nidm:NIDM_0000171 rdfs:label "number Of Subjects" ; - + obo:IAO_0000115 "Number of subjects in the group." ; - + obo:IAO_0000116 "Linked with http://purl.obolibrary.org/obo/STATO_0000088 to be discussed." . @@ -3712,13 +3712,13 @@ nidm:NIDM_0000171 rdfs:label "number Of Subjects" ; spm:SPM_0000003 rdf:type nidm:NIDM_0000037 , owl:NamedIndividual ; - + rdfs:label "SPM's Dispersion Derivative" ; - + obo:IAO_0000115 "'Hemodynamic Response Function' basis that is the derivative with respect to spatial dispersion of the SPM's Canonical heamodynamic response function." ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3727,13 +3727,13 @@ spm:SPM_0000003 rdf:type nidm:NIDM_0000037 , spm:SPM_0000004 rdf:type nidm:NIDM_0000029 , owl:NamedIndividual ; - + rdfs:label "SPM's Canonical HRF" ; - + obo:IAO_0000115 "'Hemodynamic Response Function' which is a fixed difference of two gamma probability density functions and is denoted by \"canonical HRF\" in SPM. This is the default in SPM" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3742,13 +3742,13 @@ spm:SPM_0000004 rdf:type nidm:NIDM_0000029 , spm:SPM_0000006 rdf:type nidm:NIDM_0000037 , owl:NamedIndividual ; - + rdfs:label "SPM's Temporal Derivative" ; - + obo:IAO_0000116 "Discussed at https://github.com/incf-nidash/nidm/issues/281" ; - + obo:IAO_0000115 "'Hemodynamic Response Function' basis that is the derivative with respect to time of the SPM's Canonical heamodynamic response function." ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -3770,9 +3770,9 @@ spm:SPM_0000006 rdf:type nidm:NIDM_0000037 , ### http://purl.org/dc/terms/format crypto:sha512 rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "Secure Hash Algorithm 512." ; - + rdfs:comment "SHA stands for Secure Hash Algorithm. Hash algorithms compute a fixed-length digital representation (known as a message digest) of an input data sequence (the message) of any length." . ##### Imports from dc ##### . @@ -3787,9 +3787,9 @@ crypto:sha512 rdf:type owl:DatatypeProperty ; ### http://purl.org/dc/elements/1.1/description dc:description rdf:type owl:ObjectProperty ; - + obo:IAO_0000115 "An account of the resource." ; - + rdfs:comment "Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource." . @@ -3806,9 +3806,9 @@ dc:description rdf:type owl:ObjectProperty ; ### http://purl.org/dc/terms/format dct:format rdf:type owl:DatatypeProperty ; - + obo:IAO_0000115 "The file format, physical medium, or dimensions of the resource." ; - + rdfs:comment "Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME]." . @@ -3825,9 +3825,9 @@ dct:format rdf:type owl:DatatypeProperty ; ### http://purl.org/dc/dcmitype/Image dctype:Image rdf:type owl:Class ; - + obo:IAO_0000115 "A visual representation other than text." ; - + rdfs:comment "Examples include images and photographs of physical objects, paintings, prints, drawings, other images and graphics, animations and moving pictures, film, diagrams, maps, musical notation. Note that Image may include both electronic and physical representations." . @@ -3855,13 +3855,13 @@ protege:defaultLanguage rdf:type owl:AnnotationProperty . ### http://purl.obolibrary.org/obo/BFO_0000179 obo:BFO_0000179 rdf:type owl:AnnotationProperty ; - + rdfs:label "BFO OWL specification label"@en ; - + obo:IAO_0000232 "Really of interest to developers only"@en ; - + obo:IAO_0000115 "Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification."@en ; - + rdfs:subPropertyOf rdfs:label . @@ -3869,15 +3869,15 @@ obo:BFO_0000179 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/BFO_0000180 obo:BFO_0000180 rdf:type owl:AnnotationProperty ; - + rdfs:label "BFO CLIF specification label"@en ; - + obo:IAO_0000119 "Person:Alan Ruttenberg" ; - + obo:IAO_0000232 "Really of interest to developers only"@en ; - + obo:IAO_0000115 "Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2"@en ; - + rdfs:subPropertyOf rdfs:label . @@ -3885,24 +3885,24 @@ obo:BFO_0000180 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000111 obo:IAO_0000111 rdf:type owl:AnnotationProperty ; - + rdfs:label "editor preferred term" , "editor preferred label"@en , "editor preferred term"@en ; - + obo:IAO_0000111 "editor preferred term" ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000115 "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)"@en ; - + obo:IAO_0000111 "editor preferred label"@en , "editor preferred term"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3910,20 +3910,20 @@ obo:IAO_0000111 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000112 obo:IAO_0000112 rdf:type owl:AnnotationProperty ; - + rdfs:label "example of usage"@en ; - + obo:IAO_0000115 "A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not"@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "example"@en , "example of usage"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3931,15 +3931,15 @@ obo:IAO_0000112 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000114 obo:IAO_0000114 rdf:type owl:AnnotationProperty ; - + rdfs:label "has curation status"@en ; - + obo:IAO_0000119 "OBI_0000281"@en ; - + obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en , "PERSON:Bill Bug"@en , "PERSON:Melanie Courtot"@en ; - + obo:IAO_0000111 "has curation status"@en . @@ -3947,27 +3947,27 @@ obo:IAO_0000114 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000115 obo:IAO_0000115 rdf:type owl:AnnotationProperty ; - + rdfs:label "definition"^^xsd:string , "textual definition"^^xsd:string , "definition" , "definition"@en ; - + obo:IAO_0000111 "definition"^^xsd:string , "textual definition"^^xsd:string , "definition" ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000115 "The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en , "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en ; - + obo:IAO_0000111 "definition"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3975,19 +3975,19 @@ obo:IAO_0000115 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000116 obo:IAO_0000116 rdf:type owl:AnnotationProperty ; - + rdfs:label "editor note"@en ; - + obo:IAO_0000115 "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "editor note"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -3995,21 +3995,21 @@ obo:IAO_0000116 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000117 obo:IAO_0000117 rdf:type owl:AnnotationProperty ; - + rdfs:label "term editor"@en ; - + obo:IAO_0000116 "20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115."@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000115 "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "term editor"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -4017,19 +4017,19 @@ obo:IAO_0000117 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000118 obo:IAO_0000118 rdf:type owl:AnnotationProperty ; - + rdfs:label "alternative term"@en ; - + obo:IAO_0000115 "An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)"@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "alternative term"@en ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:isDefinedBy . @@ -4037,20 +4037,20 @@ obo:IAO_0000118 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000119 obo:IAO_0000119 rdf:type owl:AnnotationProperty ; - + rdfs:label "definition source"@en ; - + obo:IAO_0000119 "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"^^xsd:string , "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Daniel Schober"@en ; - + obo:IAO_0000111 "definition source"@en ; - + obo:IAO_0000115 "formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -4058,17 +4058,17 @@ obo:IAO_0000119 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000232 obo:IAO_0000232 rdf:type owl:AnnotationProperty ; - + rdfs:label "curator note"@en ; - + obo:IAO_0000115 "An administrative note of use for a curator but of no use for a user"@en ; - + obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en ; - + obo:IAO_0000111 "curator note"@en ; - + obo:IAO_0000114 obo:IAO_0000122 ; - + rdfs:isDefinedBy . @@ -4076,20 +4076,20 @@ obo:IAO_0000232 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000412 obo:IAO_0000412 rdf:type owl:AnnotationProperty ; - + rdfs:label "imported from"@en ; - + obo:IAO_0000115 "For external terms/classes, the ontology from which the term was imported"@en ; - + obo:IAO_0000119 "GROUP:OBI:"@en ; - + obo:IAO_0000117 "PERSON:Alan Ruttenberg"@en , "PERSON:Melanie Courtot"@en ; - + obo:IAO_0000111 "imported from"@en ; - + obo:IAO_0000114 obo:IAO_0000125 ; - + rdfs:isDefinedBy . @@ -4097,17 +4097,17 @@ obo:IAO_0000412 rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000600 obo:IAO_0000600 rdf:type owl:AnnotationProperty ; - + rdfs:label "elucidation"@en ; - + obo:IAO_0000119 "Person:Barry Smith"@en ; - + obo:IAO_0000600 "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms"@en ; - + obo:IAO_0000111 "elucidation"@en ; - + obo:IAO_0000117 "person:Alan Ruttenberg"@en ; - + rdfs:isDefinedBy . @@ -4115,9 +4115,9 @@ obo:IAO_0000600 rdf:type owl:AnnotationProperty ; ### http://purl.org/dc/elements/1.1/contributor dc:contributor rdf:type owl:AnnotationProperty ; - + rdfs:label "Contributor"@en-us ; - + rdfs:isDefinedBy dc: . @@ -4125,9 +4125,9 @@ dc:contributor rdf:type owl:AnnotationProperty ; ### http://purl.org/dc/elements/1.1/date dc:date rdf:type owl:AnnotationProperty ; - + rdfs:label "Date"@en-us ; - + rdfs:isDefinedBy dc: . @@ -4181,7 +4181,7 @@ foaf:homepage rdf:type owl:AnnotationProperty . ### http://usefulinc.com/ns/doap#revision doap:revision rdf:type owl:AnnotationProperty ; - + obo:IAO_0000412 . @@ -4204,7 +4204,7 @@ doap:revision rdf:type owl:AnnotationProperty ; ### http://purl.obolibrary.org/obo/IAO_0000002 obo:IAO_0000002 rdf:type owl:NamedIndividual ; - + rdfs:label "example to be eventually removed"@en . @@ -4212,9 +4212,9 @@ obo:IAO_0000002 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000120 obo:IAO_0000120 rdf:type owl:NamedIndividual ; - + rdfs:label "metadata complete"@en ; - + obo:IAO_0000115 "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en . @@ -4222,9 +4222,9 @@ obo:IAO_0000120 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000121 obo:IAO_0000121 rdf:type owl:NamedIndividual ; - + rdfs:label "organizational term"@en ; - + obo:IAO_0000115 "term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en . @@ -4232,9 +4232,9 @@ obo:IAO_0000121 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000122 obo:IAO_0000122 rdf:type owl:NamedIndividual ; - + rdfs:label "ready for release"@en ; - + obo:IAO_0000115 "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en . @@ -4242,9 +4242,9 @@ obo:IAO_0000122 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000123 obo:IAO_0000123 rdf:type owl:NamedIndividual ; - + rdfs:label "metadata incomplete"@en ; - + obo:IAO_0000115 "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en . @@ -4252,9 +4252,9 @@ obo:IAO_0000123 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000124 obo:IAO_0000124 rdf:type owl:NamedIndividual ; - + rdfs:label "uncurated"@en ; - + obo:IAO_0000115 "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en . @@ -4262,9 +4262,9 @@ obo:IAO_0000124 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000125 obo:IAO_0000125 rdf:type owl:NamedIndividual ; - + rdfs:label "pending final vetting"@en ; - + obo:IAO_0000115 "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en . @@ -4272,13 +4272,13 @@ obo:IAO_0000125 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000423 obo:IAO_0000423 rdf:type owl:NamedIndividual ; - + rdfs:label "to be replaced with external ontology term"@en ; - + obo:IAO_0000117 "Alan Ruttenberg"@en ; - + obo:IAO_0000115 "Terms with this status should eventually replaced with a term from another ontology."@en ; - + obo:IAO_0000119 "group:OBI"@en . @@ -4286,13 +4286,13 @@ obo:IAO_0000423 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/IAO_0000428 obo:IAO_0000428 rdf:type owl:NamedIndividual ; - + rdfs:label "requires discussion"@en ; - + obo:IAO_0000115 "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en ; - + obo:IAO_0000117 "Alan Ruttenberg"@en ; - + obo:IAO_0000119 "group:OBI"@en . @@ -4306,14 +4306,14 @@ obo:IAO_0000428 rdf:type owl:NamedIndividual ; ### http://purl.obolibrary.org/obo/iao/2015-02-23/iao.owl iao:iao.owl rdf:type owl:NamedIndividual ; - + rdfs:label "IAO Release 2015-02-23" ; - + doap:revision "SVN $Revision: 717 $" ; - + doap:file-release , iao:iao.owl ; - + rdfs:seeAlso . @@ -4359,13 +4359,13 @@ obo:IAO_0000115 rdf:type owl:AnnotationProperty . ### http://www.semanticdesktop.org/ontologies/2007/03/22/nfo#fileName nfo:fileName rdf:type owl:DatatypeProperty ; - + rdfs:label "fileName" ; - + nrl:maxCardinality "1" ; - + obo:IAO_0000115 "Name of the file, together with the extension" ; - + rdfs:range xsd:string . @@ -4403,9 +4403,9 @@ obo:IAO_0000115 rdf:type owl:AnnotationProperty . ### http://neurolex.org/wiki/birnlex_2067 src:SCR_002823 rdf:type owl:Class ; - + rdfs:label "FSL" ; - + obo:IAO_0000115 "A comprehensive library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. The tools include registration, atlases, Diffusion MRI tools for parameter reconstruction and probabilistic taractography, and a viewer. FSL runs on Apple and PCs (Linux and Windows), and is very easy to install. Most of the tools can be run both from the command line and as GUIs ('point-and-click' graphical user interfaces). Several complementary brain atlases, integrated into FSLView and Featquery, allowing viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Atlases included with FSL: * Harvard-Oxford cortical and subcortical structural atlases * Julich histological atlas * JHU DTI-based white-matter atlases * Oxford thalamic connectivity atlas * Talairach atlas * MNI structural atlas * Cerebellum atlas FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK." . @@ -4413,121 +4413,121 @@ src:SCR_002823 rdf:type owl:Class ; ### http://neurolex.org/wiki/nif-0000-00343 src:SCR_007037 rdf:type owl:Class ; - + rdfs:label "SPM" ; - + obo:IAO_0000115 "Software package for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG." . nlx:birnlex_2177 rdf:type owl:Class ; - + rdfs:label "MRI protocol"^^xsd:string ; - + core:definition """* MRI uses radiofrequency waves and a strong magnetic field rather than x-rays to provide amazingly clear and detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders. (NCI) * Non-invasive method of demonstrating internal anatomy based on the principle that atomic nuclei in a strong magnetic field absorb pulses of radiofrequency energy and emit them as radiowaves which can be reconstructed into computerized images. The concept includes proton spin tomographic techniques. (MSH) * non-invasive method of demonstrating internal anatomy based on the principle that atomic nuclei in a strong magnetic field absorb pulses of radiofrequency energy and emit them as radiowaves which can be reconstructed into computerized images; concept includes proton spin tomographic techniques. (CSP)"""^^xsd:string ; - + obo_annot:createdDate "2007-03-07"^^xsd:string ; - + obo_annot:modifiedDate "2008-05-01"^^xsd:string ; - + obo_annot:tempDefinition "An imaging protocol where images are acquired using a Magnetic Resonance Imaging device."^^xsd:string ; - + obo_annot:UmlsCui "C0024485"^^xsd:string ; - + obo_annot:synonym "MRI"^^xsd:string ; - + core:prefLabel "MRI protocol"^^xsd:string ; - + obo_annot:nifID "_7_2.2"^^xsd:string ; - + birn_annot:hasBirnlexCurator "http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug"^^xsd:string , "http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Jessica_Turner"^^xsd:string ; - + birn_annot:hasCurationStatus "http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated"^^xsd:string ; - - obo_annot:hasDefinitionSource "http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS_defSource"^^xsd:string . + + obo_annot:hasDefinitionSource "http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS_defSource"^^xsd:string . ### http://uri.interlex.org/base/ixl_0050004 nlx:ixl_0050004 rdf:type owl:Class ; - + rdfs:label "Anatomical MRI protocol"^^xsd:string ; - + rdfs:subClassOf nlx:birnlex_2251 ; - + core:definition ""^^xsd:string , """ An anatomical MRI protocol is a structural MRI protocol that can be used to delineate the anatomy, for example by the way of a segmentation or parcellation. """^^xsd:string ; - + obo_annot:createdDate "2016-02-15"^^xsd:string ; - - obo_annot:hasDefinitionSource "http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS_defSource"^^xsd:string . - + + obo_annot:hasDefinitionSource "http://ontology.neuinfo.org/NIF/Backend/OBO_annotation_properties.owl#UMLS_defSource"^^xsd:string . + nlx:birnlex_2250 rdf:type owl:Class ; - + rdfs:label "Functional MRI protocol"^^xsd:string ; - + rdfs:subClassOf nlx:birnlex_2177 ; - + owl:disjointWith nlx:birnlex_2251 ; - + obo_annot:createdDate "2007-10-09"^^xsd:string ; - + obo_annot:modifiedDate "2007-10-09"^^xsd:string ; - + core:prefLabel "Functional MRI protocol"^^xsd:string ; - + obo_annot:nifID "_7_2.2.2"^^xsd:string ; - + obo_annot:synonym "fMRI"^^xsd:string ; - + birn_annot:hasBirnlexCurator "http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug"^^xsd:string ; - - birn_annot:hasCurationStatus "http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated"^^xsd:string . + + birn_annot:hasCurationStatus "http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated"^^xsd:string . ### http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#nlx_inv_20090249 nlx:nlx_inv_20090249 rdf:type owl:Class ; - + rdfs:label "Diffusion-weighted imaging protocol"^^xsd:string ; - + rdfs:subClassOf nlx:birnlex_2251 ; - + core:definition "A magnetic resonance imaging protocol that is sensitive to the diffusion of water molecules."^^xsd:string ; - + core:prefLabel "Diffusion-weighted imaging protocol"^^xsd:string ; - + obo_annot:createdDate "February 9, 2009"^^xsd:string ; - - obo_annot:externalSourceId "UMLS, C1136216"^^xsd:string . + + obo_annot:externalSourceId "UMLS, C1136216"^^xsd:string . ### http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2251 nlx:birnlex_2251 rdf:type owl:Class ; - + rdfs:label "Structural MRI protocol"^^xsd:string ; - + rdfs:subClassOf nlx:birnlex_2177 ; - + obo_annot:modifiedDate "2007-10-09"^^xsd:string ; - + obo_annot:createdDate "2007-10-09"^^xsd:string ; - + core:definition "A structural MRI protocol is an MRI protocol that provides information to qualitatively and quantitatively describe the shape, size, and integrity of gray and white matter structures in the brain."^^xsd:string ; - + obo_annot:synonym "MRI"^^xsd:string ; - + core:prefLabel "Structural MRI protocol"^^xsd:string ; - + obo_annot:nifID "_7_2.2.1"^^xsd:string ; - + obo_annot:definingCitationURI "http://fmri.ucsd.edu/Research/whatisfmri.html"^^xsd:string ; - + birn_annot:hasBirnlexCurator "http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#Bill_Bug"^^xsd:string ; - - birn_annot:hasCurationStatus "http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated"^^xsd:string . - + + birn_annot:hasCurationStatus "http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated"^^xsd:string . + ### Generated by the OWL API (version 3.5.0) http://owlapi.sourceforge.net @@ -4536,109 +4536,109 @@ nlx:birnlex_2251 rdf:type owl:Class ; ### http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2100 nlx:birnlex_2100 rdf:type owl:Class ; - + rdfs:label "Magnetic resonance imaging scanner"^^xsd:string ; - + rdfs:subClassOf nlx:birnlex_2094 ; - + obo_annot:createdDate "2006-05-15"^^xsd:string ; - + obo_annot:modifiedDate "2006-10-11"^^xsd:string ; - + obo_annot:synonym "MRI scanner"^^xsd:string ; - + core:prefLabel "Magnetic resonance imaging scanner"^^xsd:string ; - + birn_annot:hasBirnlexCurator "http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF"^^xsd:string ; - + birn_annot:hasCurationStatus "http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated"^^xsd:string . ### http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_2094 nlx:birnlex_2094 rdf:type owl:Class ; - + rdfs:label "Imaging instrument"^^xsd:string ; - + obo_annot:createdDate "2006-05-15"^^xsd:string ; - + obo_annot:modifiedDate "2006-10-11"^^xsd:string ; - + core:prefLabel "Imaging instrument"^^xsd:string ; - + birn_annot:hasBirnlexCurator "http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#BIRN_OTF"^^xsd:string ; - - birn_annot:hasCurationStatus "http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated"^^xsd:string . + + birn_annot:hasCurationStatus "http://ontology.neuinfo.org/NIF/Backend/BIRNLex_annotation_properties.owl#uncurated"^^xsd:string . ### http://uri.interlex.org/base/ixl_0050000 nlx:ixl_0050000 rdf:type owl:Class ; - + rdfs:label "Positron emission tomography scanner"^^xsd:string ; - + rdfs:subClassOf nlx:birnlex_2094 ; - + obo_annot:createdDate "2016-02-12"^^xsd:string ; - + core:definition "A Positron emission tomography scanner is a device used in a nuclear medicine to observe metabolic processes in the body."^^xsd:string ; - + obo_annot:synonym "PET scanner"^^xsd:string ; - + core:prefLabel "Positron emission tomography scanner"^^xsd:string ; - + obo_annot:definingCitationURI "https://en.wikipedia.org/wiki/Positron_emission_tomography"^^xsd:string . ### http://uri.interlex.org/base/ixl_0050001 nlx:ixl_0050001 rdf:type owl:Class ; - + rdfs:label "Single-photon emission computed tomography scanner"^^xsd:string ; - + rdfs:subClassOf nlx:birnlex_2094 ; - + obo_annot:createdDate "2016-02-12"^^xsd:string ; - + core:definition "A Single-photon emission computed tomography scanner is a device used in nuclear medicine tomographic imaging to measure perfusion in the body using gamma rays."^^xsd:string ; - + obo_annot:synonym "SPECT scanner"^^xsd:string ; - + core:prefLabel "Single-photon emission computed tomography scanner"^^xsd:string ; - + obo_annot:definingCitationURI "https://en.wikipedia.org/wiki/Single-photon_emission_computed_tomography"^^xsd:string . ### http://uri.interlex.org/base/ixl_0050003 nlx:ixl_0050003 rdf:type owl:Class ; - + rdfs:label "Electroencephalography machine"^^xsd:string ; - + rdfs:subClassOf nlx:birnlex_2094 ; - + obo_annot:createdDate "2016-02-12"^^xsd:string ; - + core:definition "A Electroencephalography machine is a device used in electrophysiology to record electrical activity of the brain.."^^xsd:string ; - + obo_annot:synonym "EEG machine"^^xsd:string ; - + core:prefLabel "Electroencephalography machine"^^xsd:string ; - + obo_annot:definingCitationURI "https://en.wikipedia.org/wiki/Electroencephalography"^^xsd:string . ### http://ontology.neuinfo.org/NIF/DigitalEntities/NIF-Investigation.owl#birnlex_XXX_MEG_machine nlx:ixl_0050002 rdf:type owl:Class ; - + rdfs:label "Magnetoencephalography machine"^^xsd:string ; - + rdfs:subClassOf nlx:birnlex_2094 ; - + obo_annot:createdDate "2016-02-12"^^xsd:string ; - + core:definition "A Magnetoencephalography machine is a device used in functional neuroimaging for mapping brain activity by recording magnetic fields produced by electrical currents occurring naturally in the brain, using very sensitive magnetometers.."^^xsd:string ; - + obo_annot:synonym "MEG machine"^^xsd:string ; - + core:prefLabel "Magnetoencephalography machine"^^xsd:string ; - + obo_annot:definingCitationURI "https://en.wikipedia.org/wiki/Magnetoencephalography"^^xsd:string . @@ -4699,20 +4699,20 @@ obo:IAO_0000119 rdf:type owl:AnnotationProperty . ### http://purl.obolibrary.org/obo/OBI_0000251 obo:OBI_0000251 rdf:type owl:Class ; - + rdfs:label "cluster"@en ; - + obo:IAO_0000119 "group:OBI"^^xsd:string ; - + obo:IAO_0000115 "A data set which is a subset of data that are a similar to each other in some way."@en ; - + obo:IAO_0000112 "Cluster of the lymphocytes population."@en ; - + obo:IAO_0000111 "cluster"@en ; - + obo:IAO_0000117 "person:Allyson"@en , "person:Chris Stoeckert"@en ; - + obo:IAO_0000114 obo:IAO_0000125 . @@ -4720,9 +4720,9 @@ obo:OBI_0000251 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/OBI_0001265 obo:OBI_0001265 rdf:type owl:Class ; - + rdfs:label "FWER adjusted p-value" ; - + obo:IAO_0000115 "A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests." . @@ -4730,9 +4730,9 @@ obo:OBI_0001265 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/OBI_0001442 obo:OBI_0001442 rdf:type owl:Class ; - + rdfs:label "q-value" ; - + obo:IAO_0000115 "A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level." . @@ -4754,19 +4754,19 @@ obo:OBI_0001442 rdf:type owl:Class ; ### http://purl.org/dc/elements/1.1/creator dc:creator rdfs:label "Creator"@en ; - + "1999-07-02"^^xsd:date ; - + "2008-01-14"^^xsd:date ; - + "A second property with the same name as this property has been declared in the dcterms: namespace (http://purl.org/dc/terms/). See the Introduction to the document \"DCMI Metadata Terms\" (http://dublincore.org/documents/dcmi-terms/) for an explanation."@en ; - + rdfs:comment "An entity primarily responsible for making the resource."@en ; - + "Examples of a Creator include a person, an organization, or a service. Typically, the name of a Creator should be used to indicate the entity."@en ; - + ; - + rdfs:isDefinedBy dc: . @@ -4774,19 +4774,19 @@ dc:creator rdfs:label "Creator"@en ; ### http://purl.org/dc/elements/1.1/date dc:date rdfs:label "Date"@en ; - + "1999-07-02"^^xsd:date ; - + "2008-01-14"^^xsd:date ; - + rdfs:comment "A point or period of time associated with an event in the lifecycle of the resource."@en ; - + "A second property with the same name as this property has been declared in the dcterms: namespace (http://purl.org/dc/terms/). See the Introduction to the document \"DCMI Metadata Terms\" (http://dublincore.org/documents/dcmi-terms/) for an explanation."@en ; - + "Date may be used to express temporal information at any level of granularity. Recommended best practice is to use an encoding scheme, such as the W3CDTF profile of ISO 8601 [W3CDTF]."@en ; - + ; - + rdfs:isDefinedBy dc: . @@ -4794,19 +4794,19 @@ dc:date rdfs:label "Date"@en ; ### http://purl.org/dc/elements/1.1/description dc:description rdfs:label "Description"@en ; - + "1999-07-02"^^xsd:date ; - + "2008-01-14"^^xsd:date ; - + "A second property with the same name as this property has been declared in the dcterms: namespace (http://purl.org/dc/terms/). See the Introduction to the document \"DCMI Metadata Terms\" (http://dublincore.org/documents/dcmi-terms/) for an explanation."@en ; - + rdfs:comment "An account of the resource."@en ; - + "Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource."@en ; - + ; - + rdfs:isDefinedBy dc: . @@ -4814,17 +4814,17 @@ dc:description rdfs:label "Description"@en ; ### http://purl.org/dc/elements/1.1/title dc:title rdfs:label "Title"@en ; - + "1999-07-02"^^xsd:date ; - + "2008-01-14"^^xsd:date ; - + rdfs:comment "A name given to the resource."@en ; - + "A second property with the same name as this property has been declared in the dcterms: namespace (http://purl.org/dc/terms/). See the Introduction to the document \"DCMI Metadata Terms\" (http://dublincore.org/documents/dcmi-terms/) for an explanation."@en ; - + ; - + rdfs:isDefinedBy dc: . @@ -4898,17 +4898,17 @@ xsd:date rdf:type rdfs:Datatype . ### http://purl.org/ontology/prv/core#object_property prv:object_property rdf:type owl:ObjectProperty ; - + rdfs:label "has object property"@en ; - + rdfs:comment "Relates to the property of the reification class, which relates to the object of the \"shortcut relation\"."@en ; - + status:term_status "testing"@en ; - + rdfs:isDefinedBy ; - + rdfs:domain prv:PropertyReification ; - + rdfs:range rdf:Property . @@ -4916,34 +4916,34 @@ prv:object_property rdf:type owl:ObjectProperty ; ### http://purl.org/ontology/prv/core#reification_class prv:reification_class rdf:type owl:ObjectProperty ; - + rdfs:label "has reification class"@en ; - - rdfs:comment """Relates to the reification class, which can be related to the object and subject property to be able to associate the -object and subject of the \"shortcut relation\". The reification class should provide detailed descriptions of the relationship that is + + rdfs:comment """Relates to the reification class, which can be related to the object and subject property to be able to associate the +object and subject of the \"shortcut relation\". The reification class should provide detailed descriptions of the relationship that is described in a simple form by the \"shortcut relation\"."""@en ; - + status:term_status "testing"@en ; - + rdfs:isDefinedBy ; - + rdfs:domain prv:PropertyReification . ### http://purl.org/ontology/prv/core#shortcut prv:shortcut rdf:type owl:ObjectProperty ; - + rdfs:label "has shortcut"@en ; - + rdfs:comment "Relates to the property of the \"shortcut relation\" (its predicate)."@en ; - + status:term_status "testing"@en ; - + rdfs:isDefinedBy ; - + rdfs:domain prv:PropertyReification ; - + rdfs:range rdf:Property . @@ -4951,19 +4951,19 @@ prv:shortcut rdf:type owl:ObjectProperty ; ### http://purl.org/ontology/prv/core#shortcut_property prv:shortcut_property rdf:type owl:ObjectProperty ; - + rdfs:label "has shortcut property"@en ; - - rdfs:comment """Relates to the property of the reification class, which relates to the predicate of the \"shortcut relation\". So -that the specific property reification can be \"verified\" (the property of the prv:shortcut relation and this one associated by the + + rdfs:comment """Relates to the property of the reification class, which relates to the predicate of the \"shortcut relation\". So +that the specific property reification can be \"verified\" (the property of the prv:shortcut relation and this one associated by the referred shortcut property should be equal)."""@en ; - + status:term_status "testing"@en ; - + rdfs:isDefinedBy ; - + rdfs:domain prv:PropertyReification ; - + rdfs:range rdf:Property . @@ -4971,17 +4971,17 @@ referred shortcut property should be equal)."""@en ; ### http://purl.org/ontology/prv/core#subject_property prv:subject_property rdf:type owl:ObjectProperty ; - + rdfs:label "has subject property"@en ; - + rdfs:comment "Relates to the property of the reification class, which relates to the subject of the \"shortcut relation\"."@en ; - + status:term_status "testing"@en ; - + rdfs:isDefinedBy ; - + rdfs:domain prv:PropertyReification ; - + rdfs:range rdf:Property . @@ -4998,14 +4998,14 @@ prv:subject_property rdf:type owl:ObjectProperty ; ### http://purl.org/ontology/prv/core#PropertyReification prv:PropertyReification rdf:type owl:Class ; - + rdfs:label "Property Reification"@en ; - - rdfs:comment """The class, which describes the relations of a property reification. That means, its \"shortcut relation\", its + + rdfs:comment """The class, which describes the relations of a property reification. That means, its \"shortcut relation\", its reification class, and the properties that are relating to the subject and object of the \"shortcut relation\"."""@en ; - + status:term_status "testing"@en ; - + rdfs:isDefinedBy . @@ -5029,19 +5029,19 @@ rdf:Property rdf:type owl:Class . ### http://purl.obolibrary.org/obo/STATO_0000193 obo:STATO_0000193 rdf:type owl:Class ; - + rdfs:label "study group population" ; - + "Alejandra Gonzalez-Beltran"@en , "Orlaith Burke" , "Philippe Rocca-Serra" ; - + "STATO"@en ; - + "is a population whose individual members realize (may be expressed as) a combination of inclusion rule values specifications or resulting from a sampling process (e.g. recruitment followed by randomization to group) on which a number of measurements will be carried out, which may be used as input to statistical tests and statistical inference." ; - + "statistical sample"@en ; - + . ### http://purl.obolibrary.org/obo/IAO_0000112 @@ -5121,20 +5121,20 @@ obo:STATO_0000041 rdf:type owl:AnnotationProperty . ### http://purl.obolibrary.org/obo/STATO_0000030 obo:STATO_0000030 rdf:type owl:Class ; - + rdfs:label "Chi-Squared statistic"@en ; - + rdfs:subClassOf obo:STATO_0000039 ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string , "Alejandra Gonzalez-Beltran"@en ; - + obo:IAO_0000115 "Chi-squared statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Chi-Squared distribution."@en ; - + obo:IAO_0000117 "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO"@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -5142,22 +5142,22 @@ obo:STATO_0000030 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000039 obo:STATO_0000039 rdf:type owl:Class ; - + rdfs:label "statistic"@en ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string ; - + obo:IAO_0000112 ""@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic)."@en ; - + obo:IAO_0000115 "a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data."@en ; - + obo:STATO_0000032 "statistic"@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -5165,21 +5165,21 @@ obo:STATO_0000039 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000119 obo:STATO_0000119 rdf:type owl:Class ; - + rdfs:label "model parameter estimation"@en ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string ; - + obo:IAO_0000119 ""@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000115 "model parameter estimation is a data transformation that finds parameter values (the model parameter estimates) most compatible with the data as judged by the model."@en ; - + obo:IAO_0000116 """textual definition modified following contributiong by Thomas Nichols: https://github.com/ISA-tools/stato/issues/18"""@en ; - + obo:IAO_0000114 obo:IAO_0000125 . @@ -5187,22 +5187,22 @@ https://github.com/ISA-tools/stato/issues/18"""@en ; ### http://purl.obolibrary.org/obo/STATO_0000176 obo:STATO_0000176 rdf:type owl:Class ; - + rdfs:label "t-statistic"@en ; - + rdfs:subClassOf obo:STATO_0000039 ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string ; - + obo:STATO_0000032 ""@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO"@en ; - + obo:IAO_0000115 "t-statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Student's t distribution."@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -5210,20 +5210,20 @@ obo:STATO_0000176 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000282 obo:STATO_0000282 rdf:type owl:Class ; - + rdfs:label "F-statistic"@en ; - + rdfs:subClassOf obo:STATO_0000039 ; - + obo:IAO_0000117 "Orlaith Burke"^^xsd:string , "Alejandra Gonzalez-Beltran"@en ; - + obo:IAO_0000115 "F statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a F distribution. the F statistic is the ratio of two scaled sums of squares reflecting different sources of variability"@en ; - + obo:IAO_0000117 "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO"@en ; - + obo:IAO_0000114 obo:IAO_0000122 . @@ -5231,22 +5231,22 @@ obo:STATO_0000282 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000323 obo:STATO_0000323 rdf:type owl:Class ; - + rdfs:label "contrast weight matrix"@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Camille Maumet"@en , "Orlaith Burke"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "STATO"@en ; - + obo:IAO_0000117 "Tom Nichols"@en ; - + obo:IAO_0000112 "[1,0,0]"@en ; - + obo:IAO_0000115 "a contrast weight matrix is a information content entity which holds a set of contrast weight, coefficient used in a weighting sum of means defining a contrast"@en ; - + obo:STATO_0000032 "contrast weights"@en . @@ -5254,19 +5254,19 @@ obo:STATO_0000323 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000346 obo:STATO_0000346 rdf:type owl:Class ; - + rdfs:label "covariance structure"@en ; - + obo:IAO_0000117 "Camille Maumet" , "Orlaith Burke" , "Tom Nichols" , "Alejandra Gonzalez-Beltran" , "Philippe Rocca-Serra" ; - + obo:IAO_0000115 "a covariance structure is a data item which is part of a regression model and which indicates a pattern in the covariance matrix. The nature of covariance structure is specified before the regression analysis and various covariance structure may be tested and evaluated using information criteria to help choose the most suitable model"@en ; - + obo:IAO_0000119 "http://www3.nd.edu/~kyuan/courses/sem/readpapers/benter.pdf" ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -5274,27 +5274,27 @@ obo:STATO_0000346 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000357 obo:STATO_0000357 rdf:type owl:Class ; - + rdfs:label "Toeplitz covariance structure"@en ; - + rdfs:subClassOf obo:STATO_0000346 ; - + obo:IAO_0000117 "Orlaith Burke" ; - + obo:IAO_0000115 ""@en ; - + obo:STATO_0000041 ""@en ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Camille Maumet"@en , "Philippe Rocca-Serra"@en ; - + obo:IAO_0000118 "TOEP"@en ; - + obo:IAO_0000117 "Tom Nichols"@en ; - + obo:IAO_0000119 "http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm"@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -5302,26 +5302,26 @@ obo:STATO_0000357 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000362 obo:STATO_0000362 rdf:type owl:Class ; - + rdfs:label "compound symmetry covariance structure"@en ; - + rdfs:subClassOf obo:STATO_0000346 ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en ; - + obo:IAO_0000118 "CS"@en ; - + obo:IAO_0000117 "Camille Maumet"@en , "Orlaith Burke" , "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000115 "compound symmetry covariance structure is a covariance structure which means that all the variances are equal and all the covariances are equal."@en ; - + obo:STATO_0000041 "http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corCompSymm.html"@en ; - + obo:IAO_0000119 "http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm"@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -5329,25 +5329,25 @@ obo:STATO_0000362 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000370 obo:STATO_0000370 rdf:type owl:Class ; - + rdfs:label "ordinary least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000119 ; - + obo:STATO_0000032 "OLS estimation" ; - + obo:STATO_0000041 ""@en , "https://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html" ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Camille Maumet"@en , "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000119 "http://en.wikipedia.org/wiki/Ordinary_least_squares and Tom Nichols"@en ; - + obo:IAO_0000115 "the ordinary least squares estimation is a model parameter estimation for a linear regression model when the errors are uncorrelated and equal in variance. Is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption."@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -5355,25 +5355,25 @@ obo:STATO_0000370 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000371 obo:STATO_0000371 rdf:type owl:Class ; - + rdfs:label "weighted least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000119 ; - + obo:STATO_0000032 "WLS estimation" ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Camille Maumet"@en , "Orlaith Burke"@en , "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000119 "http://en.wikipedia.org/wiki/Least_squares#Weighted_least_squares and Tom Nichols"@en ; - + obo:STATO_0000041 "https://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html"@en ; - + obo:IAO_0000115 "the weighted least squares estimation is a model parameter estimation for a linear regression model with errors that independent but have heterogeneous variance. Difficult to use use in practice, as weights must be set based on the variance which is usually unknown. If true variance is known, it is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption."@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -5381,22 +5381,22 @@ obo:STATO_0000371 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000372 obo:STATO_0000372 rdf:type owl:Class ; - + rdfs:label "generalized least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000119 ; - + obo:STATO_0000032 "GLS estimation" ; - + obo:IAO_0000117 "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000119 "http://en.wikipedia.org/wiki/Generalized_least_squares and Tom Nichols"@en ; - + obo:STATO_0000041 "http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/gls.html"@en ; - + obo:IAO_0000115 "the generalized least squares estimation is a model parameter estimation for a linear regression model with errors that are dependent and (possibly) have heterogeneous variance. Difficult to use use in practice, as covariance matrix of the errors must known to \"whiten\" data and model. If true covariance is known, it is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption."@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -5404,25 +5404,25 @@ obo:STATO_0000372 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000373 obo:STATO_0000373 rdf:type owl:Class ; - + rdfs:label "iteratively reweighted least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000119 ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran" , "Camille Maumet" , "Orlaith Burke" ; - + obo:STATO_0000041 ""@en ; - + obo:IAO_0000117 "Philippe Rocca-Serra"@en ; - + obo:IAO_0000119 "Tom Nichols"@en ; - + obo:IAO_0000117 "Tom Nichols"@en ; - + obo:IAO_0000115 "the iteratively reweighted least squares estimation is a model parameter estimation which is a practical implementation of Weighted Least Squares, where the heterogeneous variances of the errors are estimated from the residuals of the regression model, providing an estimate for the weights. Each successive estimate of the weights improves the estimation of the regression parameters, which in turn are used to compute residuals and update the weights"@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -5430,22 +5430,22 @@ obo:STATO_0000373 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000374 obo:STATO_0000374 rdf:type owl:Class ; - + rdfs:label "feasible generalized least squares estimation"@en ; - + rdfs:subClassOf obo:STATO_0000372 ; - + obo:IAO_0000115 "the feasible generalized least squares estimation is a model parameter estimation which is a practical implementation of Generalised Least Squares, where the covariance of the errors is estimated from the residuals of the regression model, providing the information needed to whiten the data and model. Each successive estimate of the whitening matrix improves the estimation of the regression parameters, which in turn are used to compute residuals and update the whitening matrix." ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran"@en , "Orlaith Burke"@en ; - + obo:IAO_0000119 "Tom Nichols" ; - + obo:IAO_0000117 "Camille Maumet" , "Philippe Rocca-Serra"@en , "Tom Nichols"@en ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -5453,20 +5453,20 @@ obo:STATO_0000374 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000376 obo:STATO_0000376 rdf:type owl:Class ; - + rdfs:label "Z-statistic" ; - + rdfs:subClassOf obo:STATO_0000039 ; - + obo:IAO_0000117 "Alejandra Gonzalez-Beltran" , "Camille Maument" , "Philippe Rocca-Serra" , "Thomas Nichols" ; - + obo:IAO_0000119 "http://en.wikipedia.org/wiki/Z-test" ; - + obo:IAO_0000115 "Z-statistic is a statistic computed from observations and used to produce a p-value when compared to a Standard Normal Distribution in a statistical test called the Z-test." ; - + obo:IAO_0000114 obo:IAO_0000120 . @@ -5478,84 +5478,84 @@ obo:STATO_0000376 rdf:type owl:Class ; ### http://purl.obolibrary.org/obo/STATO_0000225 rdf:type owl:Class ; - + rdfs:label "probability distribution"@en ; - + "Orlaith Burke"^^xsd:string , "Alejandra Gonzalez-Beltran" ; - + """A probability distribution is a information content entity specifies the probability of the value of a random variable. For a discrete random variable, a mathematical formula that gives the probability of each value of the variable. For a continuous random variable, a curve described by a mathematical formula which specifies, by way of areas under the curve, the probability that the variable falls within a particular interval.""" ; - + "Philippe Rocca-Serra" ; - + . ### http://purl.obolibrary.org/obo/STATO_0000067 rdf:type owl:Class ; - + rdfs:label "continuous probability distribution"@en ; - + rdfs:subClassOf ; - + "Orlaith Burke"^^xsd:string ; - + ""@en ; - + "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + "a continuousprobability distribution is a probability distribution which is defined by a probability density function"@en ; - + """adapted from Wikipedia http://en.wikipedia.org/wiki/Probability_distribution#Continuous_probability_distribution -last accessed: +last accessed: 14/01/2014"""@en ; - + . ### http://purl.obolibrary.org/obo/STATO_0000117 rdf:type owl:Class ; - + rdfs:label "discrete probability distribution"@en ; - + rdfs:subClassOf ; - + "Orlaith Burke"^^xsd:string , "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + "a discrete probability distribution is a probability distribution which is defined by a probability mass function where the random variable can only assume a finite number of values or infinitely countable values"@en ; - + """adapted from Wikipedia http://en.wikipedia.org/wiki/Probability_distribution#Discrete_probability_distribution -last accessed: +last accessed: 14/01/2014"""@en ; - + . ### http://purl.obolibrary.org/obo/STATO_0000276 rdf:type owl:Class ; - + rdfs:label "binomial distribution"@en ; - + rdfs:subClassOf ; - + "Orlaith Burke"^^xsd:string ; - + ""@en ; - + "Alejandra Gonzalez-Beltran"@en , "Philippe Rocca-Serra"@en ; - + """The binomial distribution is a discrete probability distribution which describes the probability of k successes in n draws with replacement from a finite population of size N. The binomial distribution is frequently used to model the number of successes in a sample of size n drawn with replacement from a population of size N. @@ -5567,13 +5567,13 @@ notation: B(n,p) The mean is N*p The variance is N*p*q"""@en ; - + """dbinom(x, size, prob, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Binomial.html"""@en ; - + "http://en.wikipedia.org/wiki/Binomial_distribution"@en ; - + . ### http://purl.obolibrary.org/obo/STATO_0000019 @@ -5582,79 +5582,79 @@ http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Binomial.html"""@en ; ### http://purl.obolibrary.org/obo/STATO_0000227 rdf:type owl:Class ; - + rdfs:label "normal distribution"@en ; - + rdfs:subClassOf ; - + "Orlaith Burke"^^xsd:string ; - + ""@en ; - + "Alejandra Gonzalez-Beltran"@en ; - + "Gaussian distribution"@en ; - + "Philippe Rocca-Serra"@en ; - + """a normal distribution is a continuous probability distribution described by a probability distribution function described here: http://mathworld.wolfram.com/NormalDistribution.html"""@en ; - + "http://mathworld.wolfram.com/NormalDistribution.html"@en ; - + . ### http://purl.obolibrary.org/obo/STATO_0000051 rdf:type owl:Class ; - + rdfs:label "Poisson distribution"@en ; - + rdfs:subClassOf ; - + "Orlaith Burke"^^xsd:string ; - + ""@en ; - + "Alejandra Gonzalez-Beltran"@en ; - + """NIST: http://www.itl.nist.gov/div898/handbook/eda/section3/eda366j.htm """@en ; - + "Philippe Rocca-Serra"@en ; - + """Poisson distribution is a probability distribution used to model the number of events occurring within a given time interval. It is defined by a real number (λ) and an integer k representing the number of events and a function. The expected value of a Poisson-distributed random variable is equal to λ and so is its variance."""@en ; - + """dpois(x, lambda, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Poisson.html"""@en ; - + . ### http://purl.obolibrary.org/obo/STATO_0000405 rdf:type owl:Class ; - + rdfs:label "unstructured covariance structure"@en ; - + rdfs:subClassOf ; - + "Philippe Rocca-Serra" , "Alejandra Gonzalez-Beltran" , "Thomas Nichols" ; - + "A covariance structure where no restrictions are made on the covariance between any pair of measurements."@en ; - + "http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm#statug.mixed.mixedcovstruct" ; - - "Camille Maumet" . - - + "Camille Maumet" . + + + + - ##### Imports from prov ##### rdfs:comment @@ -6488,7 +6488,7 @@ prov:qualifiedEnd prov:qualifiedForm a owl:AnnotationProperty ; - rdfs:comment """This annotation property links a subproperty of prov:wasInfluencedBy with the subclass of prov:Influence and the qualifying property that are used to qualify it. + rdfs:comment """This annotation property links a subproperty of prov:wasInfluencedBy with the subclass of prov:Influence and the qualifying property that are used to qualify it. Example annotation: @@ -6501,7 +6501,7 @@ Then this unqualified assertion: can be qualified by adding: prov:entity1 prov:qualifiedGeneration prov:entity1Gen . - prov:entity1Gen + prov:entity1Gen a prov:Generation, prov:Influence; prov:activity prov:activity1; prov:customValue 1337 . @@ -6802,7 +6802,7 @@ prov:wasInfluencedBy Subproperties of prov:wasInfluencedBy may also be asserted directly without being qualified. -prov:wasInfluencedBy should not be used without also using one of its subproperties. +prov:wasInfluencedBy should not be used without also using one of its subproperties. """@en ; prov:inverse "influenced" ; prov:qualifiedForm prov:Influence, prov:qualifiedInfluence ; @@ -6889,7 +6889,7 @@ prov:wasStartedBy a owl:Ontology ; - rdfs:comment """This document is published by the Provenance Working Group (http://www.w3.org/2011/prov/wiki/Main_Page). + rdfs:comment """This document is published by the Provenance Working Group (http://www.w3.org/2011/prov/wiki/Main_Page). If you wish to make comments regarding this document, please send them to public-prov-comments@w3.org (subscribe public-prov-comments-request@w3.org, archives http://lists.w3.org/Archives/Public/public-prov-comments/). All feedback is welcome."""@en ; rdfs:label "W3C PROVenance Interchange Ontology (PROV-O)"@en ; @@ -6966,9 +6966,8 @@ If you wish to make comments regarding this document, please send them to public [] a owl:Axiom ; - rdfs:comment """Revision is a derivation (see http://www.w3.org/TR/prov-dm/#term-Revision). Moreover, according to + rdfs:comment """Revision is a derivation (see http://www.w3.org/TR/prov-dm/#term-Revision). Moreover, according to http://www.w3.org/TR/2013/REC-prov-constraints-20130430/#term-Revision 23 April 2012 'wasRevisionOf is a strict sub-relation of wasDerivedFrom since two entities e2 and e1 may satisfy wasDerivedFrom(e2,e1) without being a variant of each other.'""" ; owl:annotatedProperty rdfs:subPropertyOf ; owl:annotatedSource prov:wasRevisionOf ; owl:annotatedTarget prov:wasDerivedFrom . - diff --git a/nidmresults/owl/owl_reader.py b/nidmresults/owl/owl_reader.py index 50345b5..fbe001e 100644 --- a/nidmresults/owl/owl_reader.py +++ b/nidmresults/owl/owl_reader.py @@ -1,36 +1,38 @@ #!/usr/bin/env python -'''Read an owl file and extract interesting information +"""Read an owl file and extract interesting information. @author: Camille Maumet @copyright: University of Warwick 2014 -''' +""" + +import collections +import csv +import logging -import warnings # import vcr import os -import logging -import csv -import collections import re import warnings + +from future.standard_library import hooks from rdflib import RDF, term from rdflib.graph import Graph from rdflib.term import Literal + from nidmresults.objects.constants_rdflib import * from nidmresults.objects.constants_rdflib import namespaces as namespace_names -from future.standard_library import hooks with hooks(): - from urllib.request import urlopen, Request + from urllib.request import urlopen RELPATH = os.path.dirname(os.path.abspath(__file__)) NIDM_PATH = os.path.dirname(RELPATH) -logging.basicConfig(filename='debug.log', level=logging.DEBUG, filemode='w') +logging.basicConfig(filename="debug.log", level=logging.DEBUG, filemode="w") logger = logging.getLogger(__name__) -class OwlReader(): +class OwlReader: def __init__(self, owl_file, import_owl_files=None): self.file = owl_file @@ -43,21 +45,26 @@ def __init__(self, owl_file, import_owl_files=None): self.individuals = self.get_individuals() # For each class find out attribute list as defined by domain in # attributes - self.attributes, self.ranges, \ - self.type_restrictions, self.parent_ranges = self.get_attributes() - - labels = self.graph.subject_objects(RDFS['label']) + ( + self.attributes, + self.ranges, + self.type_restrictions, + self.parent_ranges, + ) = self.get_attributes() + + labels = self.graph.subject_objects(RDFS["label"]) # Ignore deprecated self.labels = collections.OrderedDict( - (key, value) for (value, key) in labels - if not self.is_deprecated(value)) + (key, value) + for (value, key) in labels + if not self.is_deprecated(value) + ) def get_class_names(self): # Add PROV sub-types - sub_types = set([PROV['Bundle'], PROV['Location'], - PROV['Collection']]) + sub_types = {PROV["Bundle"], PROV["Location"], PROV["Collection"]} - for class_name in self.graph.subjects(RDF['type'], OWL['Class']): + for class_name in self.graph.subjects(RDF["type"], OWL["Class"]): if not isinstance(class_name, term.BNode): sub_types.add(class_name) @@ -67,7 +74,7 @@ def get_direct_children(self, term): # Find all direct children of 'term' children = set() - for class_name in self.graph.subjects(RDFS['subClassOf'], term): + for class_name in self.graph.subjects(RDFS["subClassOf"], term): if not self.is_deprecated(class_name): children.add(class_name) @@ -77,7 +84,7 @@ def get_direct_parents(self, term): # Find all direct parents of 'term' parents = set() - for parent_name in self.graph.objects(term, RDFS['subClassOf']): + for parent_name in self.graph.objects(term, RDFS["subClassOf"]): parents.add(parent_name) return parents @@ -93,19 +100,23 @@ def get_nidm_parent(self, term): return None def is_class(self, uri): - return (uri, RDF['type'], OWL['Class']) in self.graph + return (uri, RDF["type"], OWL["Class"]) in self.graph def is_named_individual(self, uri): - return (uri, RDF['type'], OWL['NamedIndividual']) in self.graph - - def all_of_rdf_type(self, rdf_type, prefix=None, but=set(), - but_type=OWL['AnnotationProperty']): - classes = self.graph.subjects(RDF['type'], rdf_type) - - deprecated = self.graph.subjects( - OWL['deprecated'], term.Literal(True)) + return (uri, RDF["type"], OWL["NamedIndividual"]) in self.graph + + def all_of_rdf_type( + self, + rdf_type, + prefix=None, + but=set(), + but_type=OWL["AnnotationProperty"], + ): + classes = self.graph.subjects(RDF["type"], rdf_type) + + deprecated = self.graph.subjects(OWL["deprecated"], term.Literal(True)) but = set(but).union(set(deprecated)) - annotations = self.graph.subjects(RDF['type'], but_type) + annotations = self.graph.subjects(RDF["type"], but_type) but = but.union(set(annotations)) # FIXME: Is there a more efficient way? @@ -122,7 +133,7 @@ def all_of_rdf_type(self, rdf_type, prefix=None, but=set(), return classes def get_classes(self, prefix=None, but=None): - return self.all_of_rdf_type(OWL['Class'], prefix, but) + return self.all_of_rdf_type(OWL["Class"], prefix, but) def get_by_namespaces(self, term_list, but=None): by_nsp = dict() @@ -137,8 +148,9 @@ def get_by_namespaces(self, term_list, but=None): qname = None nsp = None - if (str(nsp) not in but) and \ - ((qname is None) or (not qname.startswith(but))): + if (str(nsp) not in but) and ( + (qname is None) or (not qname.startswith(but)) + ): by_nsp.setdefault(nsp, list()).append(uri) else: ignored.append(uri) @@ -149,13 +161,28 @@ def get_by_namespaces(self, term_list, but=None): return by_nsp def count_by_namespaces(self): - owl_types = list([OWL['Class'], OWL['DatatypeProperty'], - OWL['ObjectProperty'], OWL['NamedIndividual']]) + owl_types = list( + [ + OWL["Class"], + OWL["DatatypeProperty"], + OWL["ObjectProperty"], + OWL["NamedIndividual"], + ] + ) # Ignore the following namespaces/terms (not part of the model) from # the count - but = ("owl", "rdf", "prv", "protege", "xsd", "obo:IAO_", "iao", - "obo:iao.owl", "prov") + but = ( + "owl", + "rdf", + "prv", + "protege", + "xsd", + "obo:IAO_", + "iao", + "obo:iao.owl", + "prov", + ) counter_dict = dict() @@ -166,12 +193,15 @@ def count_by_namespaces(self): terms = self.get_by_namespaces(self.all_of_rdf_type(owl_type), but) keys = set(all_terms).union(terms) no = [] - all_terms = dict( - (k, all_terms.get(k, no) + terms.get(k, no)) for k in keys) + all_terms = { + k: all_terms.get(k, no) + terms.get(k, no) for k in keys + } len_dict = { - key: (len(value), terms) for (key, value) in - list(terms.items()) if key is not None} + key: (len(value), terms) + for (key, value) in list(terms.items()) + if key is not None + } num = sum([x[0] for x in list(len_dict.values())]) type_id = self.graph.qname(owl_type).split(":")[1] counter = counter + num @@ -180,34 +210,49 @@ def count_by_namespaces(self): counter_dict[type_id] = (num, len_dict) - num_attributes = counter_dict['DatatypeProperty'][0] + \ - counter_dict['ObjectProperty'][0] - num_classes = counter_dict['Class'][0] + \ - counter_dict['NamedIndividual'][0] + num_attributes = ( + counter_dict["DatatypeProperty"][0] + + counter_dict["ObjectProperty"][0] + ) + num_classes = ( + counter_dict["Class"][0] + counter_dict["NamedIndividual"][0] + ) num_terms = num_attributes + num_classes - all_terms_len = {key: (len(value), value) for (key, value) in - list(all_terms.items()) if key is not None} - - num_defined = all_terms_len['nidm'][0] + all_terms_len['spm'][0] + \ - all_terms_len['fsl'][0] + all_terms_len = { + key: (len(value), value) + for (key, value) in list(all_terms.items()) + if key is not None + } + + num_defined = ( + all_terms_len["nidm"][0] + + all_terms_len["spm"][0] + + all_terms_len["fsl"][0] + ) num_reused = num_terms - num_defined # Sanity check num_terms_from_all = sum([x[0] for x in list(all_terms_len.values())]) if not num_terms_from_all == num_terms: - raise Exception('Error: number of terms from all is inconsistent.') - - return (num_terms, num_classes, num_attributes, num_reused, - all_terms_len) - - def get_class_names_by_prov_type(self, classes=None, prefix=None, - but=None): + raise Exception("Error: number of terms from all is inconsistent.") + + return ( + num_terms, + num_classes, + num_attributes, + num_reused, + all_terms_len, + ) + + def get_class_names_by_prov_type( + self, classes=None, prefix=None, but=None + ): class_names = dict() # We at least want to have an output for Entity, Activity and Agent - class_names[PROV['Entity']] = list() - class_names[PROV['Activity']] = list() - class_names[PROV['Agent']] = list() + class_names[PROV["Entity"]] = list() + class_names[PROV["Activity"]] = list() + class_names[PROV["Agent"]] = list() class_names[None] = list() @@ -216,45 +261,52 @@ def get_class_names_by_prov_type(self, classes=None, prefix=None, for class_name in classes: if not self.is_class(class_name): - warnings.warn('Class '+str(class_name)+' does not exist.') + warnings.warn("Class " + str(class_name) + " does not exist.") if not isinstance(class_name, term.BNode): prov_type = self.get_prov_class(class_name) if prov_type: - class_names.setdefault(prov_type, list())\ - .append(class_name) + class_names.setdefault(prov_type, list()).append( + class_name + ) else: prov_type_found = False parent_classes = self.get_direct_parents(class_name) for parent_class in parent_classes: - prov_type = self.get_prov_class(parent_class, - recursive=6) + prov_type = self.get_prov_class( + parent_class, recursive=6 + ) if prov_type: - class_names.setdefault(prov_type, list())\ - .append(class_name) + class_names.setdefault(prov_type, list()).append( + class_name + ) prov_type_found = True if not prov_type_found: - warnings.warn('No PROV type for class: ' + - self.graph.qname(class_name)) + warnings.warn( + "No PROV type for class: " + + self.graph.qname(class_name) + ) class_names.setdefault(None, list()).append(class_name) return class_names def is_deprecated(self, term): deprecated = False - if (term, OWL['deprecated'], Literal(True)) in self.graph: + if (term, OWL["deprecated"], Literal(True)) in self.graph: deprecated = True return deprecated def get_property_names(self): properties = set() for class_name in self.graph.subjects( - RDF['type'], OWL['DatatypeProperty']): + RDF["type"], OWL["DatatypeProperty"] + ): if not self.is_deprecated(class_name): properties.add(class_name) for class_name in self.graph.subjects( - RDF['type'], OWL['ObjectProperty']): + RDF["type"], OWL["ObjectProperty"] + ): if not self.is_deprecated(class_name): properties.add(class_name) return properties @@ -264,10 +316,10 @@ def get_individuals(self, uri=None): if uri is None: individuals = self.graph.subjects( - RDF['type'], OWL['NamedIndividual']) + RDF["type"], OWL["NamedIndividual"] + ) else: - individuals = self.graph.subjects( - RDF['type'], uri) + individuals = self.graph.subjects(RDF["type"], uri) return list(individuals) @@ -281,83 +333,101 @@ def get_attributes(self): restrictions = dict() # Check owl restrictions on classes - for class_name in self.graph.subjects(RDF['type'], OWL['Class']): + for class_name in self.graph.subjects(RDF["type"], OWL["Class"]): if not self.is_deprecated(class_name): for class_restr in self.graph.objects( - class_name, RDFS['subClassOf']): + class_name, RDFS["subClassOf"] + ): if isinstance(class_restr, term.BNode): for prp in self.graph.objects( - class_restr, OWL['onProperty']): + class_restr, OWL["onProperty"] + ): attributes.setdefault(class_name, set()).add(prp) for child_class in self.graph.transitive_subjects( - RDFS['subClassOf'], class_name): + RDFS["subClassOf"], class_name + ): if not self.is_deprecated(child_class): attributes.setdefault( - child_class, set()).add(prp) + child_class, set() + ).add(prp) # Attributes that can be found in all classes - for prp, p, o in self.graph.triples((None, RDF['type'], None)): + for prp, p, o in self.graph.triples((None, RDF["type"], None)): if not self.is_deprecated(prp): - if o == OWL['DatatypeProperty'] or o == OWL['ObjectProperty']: - for class_name in self.graph.objects(prp, RDFS['domain']): + if o == OWL["DatatypeProperty"] or o == OWL["ObjectProperty"]: + for class_name in self.graph.objects(prp, RDFS["domain"]): if not self.is_deprecated(class_name): # Add attribute to current class attributes.setdefault(class_name, set()).add(prp) # Add attribute to children of current class for child_class in self.graph.transitive_subjects( - RDFS['subClassOf'], class_name): + RDFS["subClassOf"], class_name + ): if not self.is_deprecated(child_class): # Add attribute to current class - attributes.setdefault( - child_class, set()).add(prp) + attributes.setdefault(child_class, set()).add( + prp + ) - for range_name in self.graph.objects(prp, RDFS['range']): + for range_name in self.graph.objects(prp, RDFS["range"]): # More complex type including restrictions if isinstance(range_name, term.BNode): for restriction_node in self.graph.objects( - range_name, OWL['withRestrictions']): + range_name, OWL["withRestrictions"] + ): for first_restriction in self.graph.objects( - restriction_node, RDF['first']): - xsd_restrictions = set( - ['minInclusive', 'minExclusive', - 'maxInclusive', 'maxExclusive']) + restriction_node, RDF["first"] + ): + xsd_restrictions = { + "minInclusive", + "minExclusive", + "maxInclusive", + "maxExclusive", + } for rct in xsd_restrictions: for min_incl in self.graph.objects( - first_restriction, - XSD[rct]): - if (prp in restrictions): - if (rct in restrictions[prp]): + first_restriction, XSD[rct] + ): + if prp in restrictions: + if rct in restrictions[prp]: restrictions[prp] = max( restrictions[prp][rct], - min_incl) + min_incl, + ) else: restrictions[prp] = { - rct: min_incl} + rct: min_incl + } else: restrictions[prp] = { - rct: min_incl} + rct: min_incl + } for sub_range_name in self.graph.objects( - range_name, OWL['onDatatype']): + range_name, OWL["onDatatype"] + ): range_name = sub_range_name parent_ranges.setdefault(prp, set()).add(range_name) # Is XSD:float is requested, also accept XSD:double # (linked to the fact that python floats are more # doubles) - if range_name == XSD['float']: - parent_ranges.setdefault( - prp, set()).add(XSD['double']) + if range_name == XSD["float"]: + parent_ranges.setdefault(prp, set()).add( + XSD["double"] + ) # Add child_class to range (for ObjectProperty) for child in self.graph.transitive_subjects( - RDFS['subClassOf'], range_name): + RDFS["subClassOf"], range_name + ): if not self.is_deprecated(child): ranges.setdefault(prp, set()).add(child) - if child == XSD['float']: - ranges.setdefault( - prp, set()).add(XSD['double']) + if child == XSD["float"]: + ranges.setdefault(prp, set()).add( + XSD["double"] + ) return list((attributes, ranges, restrictions, parent_ranges)) @@ -368,7 +438,7 @@ def get_graph(self): # owl_txt = urllib2.urlopen(self.file).read() # else: # owl_txt = open(self.file, 'r').read() - owl_graph.parse(self.file, format='turtle') + owl_graph.parse(self.file, format="turtle") # owl_graph.parse(data=owl_txt, format='turtle') if self.import_files: @@ -384,7 +454,7 @@ def get_graph(self): # as described in https://github.com/RDFLib/rdflib/issues/379, # When the fix is introduced in rdflib these 2 lines will be # replaced by: - import_graph.parse(import_file, format='turtle') + import_graph.parse(import_file, format="turtle") # import_txt = import_txt.replace( # "http://www.w3.org/2002/07/owl#", # "http://www.w3.org/2002/07/owl") @@ -399,12 +469,14 @@ def get_graph(self): return owl_graph def get_prov_class(self, owl_term, recursive=3): - if not isinstance(owl_term, term.BNode) and \ - self.graph.qname(owl_term).startswith("prov:"): + if not isinstance(owl_term, term.BNode) and self.graph.qname( + owl_term + ).startswith("prov:"): prov_class = owl_term else: - parent_classes = list(self.graph.objects( - owl_term, RDFS['subClassOf'])) + parent_classes = list( + self.graph.objects(owl_term, RDFS["subClassOf"]) + ) prov_class = None for parent_class in parent_classes: @@ -419,62 +491,87 @@ def get_prov_class(self, owl_term, recursive=3): for parent_class_super in parent_classes_super: if not isinstance(parent_class_super, term.BNode): prov_class = self.get_prov_class( - parent_class_super, recursive=recursive-1) + parent_class_super, recursive=recursive - 1 + ) if prov_class is not None: break # Get more generic PROV types - if prov_class in set([PROV['SoftwareAgent'], PROV['Organization'], - PROV['Person']]): - prov_class = PROV['Agent'] - if prov_class in set([PROV['Collection'], PROV['Location'], - PROV['Bundle'], PROV['Plan'], - PROV['EmptyCollection']]): - prov_class = PROV['Entity'] - if prov_class in set([ - PROV['Usage'], PROV['AgentInfluence'], - PROV['Derivation'], PROV['PrimarySource'], - PROV['ActivityInfluence'], PROV['Delegation'], - PROV['Start'], PROV['EntityInfluence'], PROV['Quotation'], - PROV['End'], PROV['Attribution'], PROV['Association'], - PROV['Revision'], PROV['Communication'], - PROV['Generation']]): - prov_class = PROV['Influence'] - if prov_class == PROV['Invalidation']: - prov_class = PROV['InstantaneousEvent'] + if prov_class in { + PROV["SoftwareAgent"], + PROV["Organization"], + PROV["Person"], + }: + prov_class = PROV["Agent"] + if prov_class in { + PROV["Collection"], + PROV["Location"], + PROV["Bundle"], + PROV["Plan"], + PROV["EmptyCollection"], + }: + prov_class = PROV["Entity"] + if prov_class in { + PROV["Usage"], + PROV["AgentInfluence"], + PROV["Derivation"], + PROV["PrimarySource"], + PROV["ActivityInfluence"], + PROV["Delegation"], + PROV["Start"], + PROV["EntityInfluence"], + PROV["Quotation"], + PROV["End"], + PROV["Attribution"], + PROV["Association"], + PROV["Revision"], + PROV["Communication"], + PROV["Generation"], + }: + prov_class = PROV["Influence"] + if prov_class == PROV["Invalidation"]: + prov_class = PROV["InstantaneousEvent"] return prov_class def get_definition(self, owl_term, add_links=True): definition = list(self.graph.objects(owl_term, OBO_DEFINITION)) - definition = definition + \ - list(self.graph.objects(owl_term, SKOS_DEFINITION)) + definition = definition + list( + self.graph.objects(owl_term, SKOS_DEFINITION) + ) if definition: if len(definition) > 1: - warnings.warn('Multiple definitions for ' - + self.get_label(owl_term) + ': ' - + ",".join(definition)) - definition = definition[0].encode('utf-8') + warnings.warn( + "Multiple definitions for " + + self.get_label(owl_term) + + ": " + + ",".join(definition) + ) + definition = definition[0].encode("utf-8") else: definition = "" # Add link to term in document if the definition refer to a term if add_links: # definition = re.sub( - # "("+"|".join(self.labels.keys())+")", "[\\1]", definition) - terms = re.findall(r'\'.*?\'', definition) + # "("+"|".join(self.labels.keys())+")", "[\\1]", definition) + terms = re.findall(r"\'.*?\'", definition) for mterm in sorted(set(terms), key=len, reverse=True): literal = Literal(mterm.replace("'", "")) if str(literal) in self.labels: purl = self.labels[str(literal)] - if "#" in purl and \ - not self.is_deprecated(term.URIRef(mterm)): + if "#" in purl and not self.is_deprecated( + term.URIRef(mterm) + ): definition = definition.replace( mterm, - "" + - mterm.replace("[", "").replace("]", "")+"") + "" + + mterm.replace("[", "").replace("]", "") + + "", + ) # Remove final dot if present if definition: @@ -484,9 +581,9 @@ def get_definition(self, owl_term, add_links=True): return definition def get_individual_type(self, owl_term): - indiv_type = list(self.graph.objects(owl_term, RDF['type'])) - if OWL['NamedIndividual'] in indiv_type: - indiv_type.remove(OWL['NamedIndividual']) + indiv_type = list(self.graph.objects(owl_term, RDF["type"])) + if OWL["NamedIndividual"] in indiv_type: + indiv_type.remove(OWL["NamedIndividual"]) if indiv_type: indiv_type = ", ".join(map(self.graph.qname, indiv_type)) @@ -495,7 +592,7 @@ def get_individual_type(self, owl_term): return indiv_type def get_same_as(self, owl_term): - same_as = list(self.graph.objects(owl_term, OWL['sameAs'])) + same_as = list(self.graph.objects(owl_term, OWL["sameAs"])) if same_as: same_as = ", ".join(same_as) else: @@ -503,12 +600,13 @@ def get_same_as(self, owl_term): return same_as def get_used_by(self, owl_term): - used_by = list(self.graph.objects(owl_term, PROV['used'])) + used_by = list(self.graph.objects(owl_term, PROV["used"])) return used_by def get_generated_by(self, owl_term): - generated_by = list(self.graph.objects( - owl_term, PROV['wasGeneratedBy'])) + generated_by = list( + self.graph.objects(owl_term, PROV["wasGeneratedBy"]) + ) return generated_by def get_example(self, owl_term, base_repository=None): @@ -517,22 +615,24 @@ def get_example(self, owl_term, base_repository=None): examples = list(self.graph.objects(owl_term, OBO_EXAMPLE)) for example in examples: - if (base_repository is not None) and \ - example.startswith(base_repository): + if (base_repository is not None) and example.startswith( + base_repository + ): local_path = example.replace(base_repository, "./") fid_ex = open(local_path) example = fid_ex.read() fid_ex.close() elif example.startswith("http"): with vcr.use_cassette( - os.path.join(NIDM_PATH, 'vcr_cassettes/synopsis.yaml'), - record_mode='new_episodes'): + os.path.join(NIDM_PATH, "vcr_cassettes/synopsis.yaml"), + record_mode="new_episodes", + ): # Read file from url example = urlopen(example).read() title = "" if example.startswith("#"): - title = (example.split('\n', 1)[0]).replace("#", "") + title = (example.split("\n", 1)[0]).replace("#", "") example = example.replace("#" + title, "") example_list.append([title, example]) @@ -540,38 +640,42 @@ def get_example(self, owl_term, base_repository=None): return sorted(example_list) def get_range(self, owl_term): - ranges = list(self.graph.objects(owl_term, RDFS['range'])) + ranges = list(self.graph.objects(owl_term, RDFS["range"])) range_display = "" for range_value in ranges: if not isinstance(range_value, term.BNode): if isinstance(range_value, term.URIRef): - range_display += str(self.graph.qname(range_value))+" " + range_display += str(self.graph.qname(range_value)) + " " else: range_display += str(range_value) return range_display def get_domain(self, owl_term): - domains = list(self.graph.objects(owl_term, RDFS['domain'])) + domains = list(self.graph.objects(owl_term, RDFS["domain"])) domain_display = "" for domain_value in sorted(domains): if isinstance(domain_value, term.URIRef): - domain_display += str(self.graph.qname(domain_value))+" " + domain_display += str(self.graph.qname(domain_value)) + " " else: domain_display += str(domain_value) return domain_display def get_curation_status(self, owl_term): - curation_status = list(self.graph.objects( - owl_term, HAS_CURATION_STATUS)) + curation_status = list( + self.graph.objects(owl_term, HAS_CURATION_STATUS) + ) if curation_status: if len(curation_status) > 1: - warnings.warn('Multiple curation status for ' - + self.get_label(owl_term) + ': ' - + ",".join(curation_status)) + warnings.warn( + "Multiple curation status for " + + self.get_label(owl_term) + + ": " + + ",".join(curation_status) + ) curation_status = curation_status[0] else: # By default consider that term is "uncurated" @@ -582,10 +686,13 @@ def get_editor(self, owl_term): editor = list(self.graph.objects(owl_term, OBO_TERM_EDITOR)) if editor: if len(editor) > 1: - warnings.warn('Multiple editors for ' - + self.get_label(owl_term) + ': ' - + ",".join(editor)) - editor = " (editor: "+editor[0]+")" + warnings.warn( + "Multiple editors for " + + self.get_label(owl_term) + + ": " + + ",".join(editor) + ) + editor = " (editor: " + editor[0] + ")" else: editor = "" return editor @@ -594,9 +701,12 @@ def get_editor_note(self, owl_term): editor_note = list(self.graph.objects(owl_term, OBO_EDITOR_NOTE)) if editor_note: if len(editor_note) > 1: - warnings.warn('Multiple editor notes for ' - + self.get_label(owl_term) + ': ' - + ",".join(editor_note)) + warnings.warn( + "Multiple editor notes for " + + self.get_label(owl_term) + + ": " + + ",".join(editor_note) + ) editor_note = editor_note[0] else: editor_note = "" @@ -605,7 +715,7 @@ def get_editor_note(self, owl_term): def get_sub_class_names(self): sub_types = set() - prov_types = set([PROV['Entity'], PROV['Activity'], PROV['Agent']]) + prov_types = {PROV["Entity"], PROV["Activity"], PROV["Agent"]} for prov_type in prov_types: for instance_id in self.graph.subjects(RDF.type, prov_type): for class_name in self.graph.objects(instance_id, RDF.type): @@ -629,13 +739,14 @@ def check_class_names(self, ex_graph, ex_name, raise_now=False): for unrecognised_class in unrecognised_classes: if not unrecognised_class.startswith(str(PROV)): # key = ex_graph.qname(not_recognised_sub_type) - key = "\n Unrecognised sub-type: " + \ - ex_graph.qname(unrecognised_class) + key = "\n Unrecognised sub-type: " + ex_graph.qname( + unrecognised_class + ) error_msg += key if key in my_exception: my_exception[key].add(ex_name) else: - my_exception[key] = set([ex_name]) + my_exception[key] = {ex_name} if raise_now: if error_msg: @@ -644,18 +755,21 @@ def check_class_names(self, ex_graph, ex_name, raise_now=False): return my_exception def check_attributes(self, ex_graph, ex_name, raise_now=False): - ignored_attributes = set([ - RDFS['label'], - RDF['type'], - PROV['value'], PROV['atTime'], PROV['used'], - PROV['wasAssociatedWith'], - PROV['qualifiedGeneration'], PROV['wasGeneratedBy'], - PROV['atLocation'], - PROV['wasAttributedTo'], - PROV['activity'], - PROV['wasDerivedFrom'], - CRYPTO['sha512'] - ]) + ignored_attributes = { + RDFS["label"], + RDF["type"], + PROV["value"], + PROV["atTime"], + PROV["used"], + PROV["wasAssociatedWith"], + PROV["qualifiedGeneration"], + PROV["wasGeneratedBy"], + PROV["atLocation"], + PROV["wasAttributedTo"], + PROV["activity"], + PROV["wasDerivedFrom"], + CRYPTO["sha512"], + } my_exception = dict() my_range_exception = dict() @@ -674,8 +788,7 @@ def check_attributes(self, ex_graph, ex_name, raise_now=False): # Get all defined types of current object found_attributes = False class_names = "" - for class_name in sorted(ex_graph.objects( - s, RDF['type'])): + for class_name in sorted(ex_graph.objects(s, RDF["type"])): attributes = owl_attributes.get(class_name) # If the current class was defined in the owl file check if @@ -684,19 +797,29 @@ def check_attributes(self, ex_graph, ex_name, raise_now=False): if p in attributes: found_attributes = True - class_names += ", "+ex_graph.qname(class_name) + \ - " (i.e. " + self.get_label(class_name) + ")" + class_names += ( + ", " + + ex_graph.qname(class_name) + + " (i.e. " + + self.get_label(class_name) + + ")" + ) # if not found_attributes: - # if attributes: - # if not (p in attributes): + # if attributes: + # if not (p in attributes): if not found_attributes: - key = "\n Unrecognised attribute: " + \ - ex_graph.qname(p) + \ - " (i.e. " + self.get_label(p) + ")" + \ - " in "+class_names[2:] + key = ( + "\n Unrecognised attribute: " + + ex_graph.qname(p) + + " (i.e. " + + self.get_label(p) + + ")" + + " in " + + class_names[2:] + ) if key not in my_exception: - my_exception[key] = set([ex_name]) + my_exception[key] = {ex_name} else: my_exception[key].add(ex_name) @@ -704,20 +827,22 @@ def check_attributes(self, ex_graph, ex_name, raise_now=False): if isinstance(o, term.URIRef): # An ObjectProperty can point to an instance, then we look # for its type: - found_range = set(ex_graph.objects(o, RDF['type'])) + found_range = set(ex_graph.objects(o, RDF["type"])) # An ObjectProperty can point to a term if not found_range: - found_range = set([o]) + found_range = {o} # If the term is an individual, look for its type - if OWL['NamedIndividual'] in \ - set(self.graph.objects(o, RDF['type'])): + if OWL["NamedIndividual"] in set( + self.graph.objects(o, RDF["type"]) + ): found_range = set( - self.graph.objects(o, RDF['type'])) + self.graph.objects(o, RDF["type"]) + ) elif isinstance(o, term.Literal): - found_range = set([o.datatype]) + found_range = {o.datatype} correct_range = False if p in owl_ranges: @@ -736,29 +861,34 @@ def check_attributes(self, ex_graph, ex_name, raise_now=False): # FIXME: we should be able to do better than # that to check that XSD['positiveInteger'] is # in owl_ranges[p] - if (XSD['positiveInteger'] == owl_range) \ - and (next(iter(found_range)) == - XSD['int']) \ - and (o.value >= 0): + if ( + (XSD["positiveInteger"] == owl_range) + and (next(iter(found_range)) == XSD["int"]) + and (o.value >= 0) + ): correct_range = True if not correct_range: found_range_line = "" # FIXME: This should be better handled to be able to do # "if found_range" if None not in found_range: - found_range_line = ', '.join( - map(self.get_name_label, sorted(found_range))) + found_range_line = ", ".join( + map(self.get_name_label, sorted(found_range)) + ) owl_range_line = "" if p in owl_ranges: - owl_range_line = ', '.join( + owl_range_line = ", ".join( map(self.get_name_label, sorted(owl_ranges[p])) - ) - - key = "\n Unrecognised range: " + \ - found_range_line + \ - ' for '+self.get_name_label(p) + \ - ' should be ' + \ - owl_range_line + ) + + key = ( + "\n Unrecognised range: " + + found_range_line + + " for " + + self.get_name_label(p) + + " should be " + + owl_range_line + ) else: # No range found for current attribute correct_range = False @@ -766,33 +896,41 @@ def check_attributes(self, ex_graph, ex_name, raise_now=False): if not correct_range: if key not in my_range_exception: - my_range_exception[key] = set([ex_name]) + my_range_exception[key] = {ex_name} else: my_range_exception[key].add(ex_name) if p in owl_restrictions: restrictions_ok = True - if 'minInclusive' in owl_restrictions[p]: - if o.value < owl_restrictions[p]['minInclusive'].value: + if "minInclusive" in owl_restrictions[p]: + if o.value < owl_restrictions[p]["minInclusive"].value: restrictions_ok = False - if 'minExclusive' in owl_restrictions[p]: - if o.value <= \ - owl_restrictions[p]['minExclusive'].value: + if "minExclusive" in owl_restrictions[p]: + if ( + o.value + <= owl_restrictions[p]["minExclusive"].value + ): restrictions_ok = False - if 'maxInclusive' in owl_restrictions[p]: - if o.value > owl_restrictions[p]['maxInclusive'].value: + if "maxInclusive" in owl_restrictions[p]: + if o.value > owl_restrictions[p]["maxInclusive"].value: restrictions_ok = False - if 'maxExclusive' in owl_restrictions[p]: - if o.value >= \ - owl_restrictions[p]['maxExclusive'].value: + if "maxExclusive" in owl_restrictions[p]: + if ( + o.value + >= owl_restrictions[p]["maxExclusive"].value + ): restrictions_ok = False if not restrictions_ok: - key = "\n Constraints: value "+str(o.value) + \ - ' for '+ex_graph.qname(p) + \ - ' does not observe constraints ' + \ - ', '.join(sorted(owl_restrictions[p])) + key = ( + "\n Constraints: value " + + str(o.value) + + " for " + + ex_graph.qname(p) + + " does not observe constraints " + + ", ".join(sorted(owl_restrictions[p])) + ) if key not in my_restriction_exception: - my_restriction_exception[key] = set([ex_name]) + my_restriction_exception[key] = {ex_name} else: my_restriction_exception[key].add(ex_name) @@ -808,8 +946,9 @@ def check_attributes(self, ex_graph, ex_name, raise_now=False): if error_msg: raise Exception(error_msg) - return list((my_exception, my_range_exception, - my_restriction_exception)) + return list( + (my_exception, my_range_exception, my_restriction_exception) + ) def get_label(self, uri): if not isinstance(uri, term.BNode): @@ -822,20 +961,24 @@ def get_label(self, uri): name = uri # If a label is available, use the namespace:label, otherwise qname - label = list(self.graph.objects(uri, RDFS['label'])) + label = list(self.graph.objects(uri, RDFS["label"])) if label: if len(label) > 1 and not self.is_external_namespace(uri): - warnings.warn('Multiple labels for '+name+': '+",".join(label)) + warnings.warn( + "Multiple labels for " + name + ": " + ",".join(label) + ) label = sorted(label)[0] - name = name.split(":")[0]+":'"+label+"'" + name = name.split(":")[0] + ":'" + label + "'" return name def is_external_namespace(self, term_uri): - return not (term_uri.startswith(NIDM) - or term_uri.startswith(FSL) - or term_uri.startswith(SPM) - or term_uri.startswith(AFNI)) + return not ( + term_uri.startswith(NIDM) + or term_uri.startswith(FSL) + or term_uri.startswith(SPM) + or term_uri.startswith(AFNI) + ) def is_prov(self, term_uri): term_label = self.get_label(term_uri) @@ -862,50 +1005,55 @@ def get_preferred_prefix(self, uri): else: label = self.get_label(uri).replace("'", "") - prefix, words = label.split(':') + prefix, words = label.split(":") label_words = re.findall(r"[\w']+", words) # Camel case terms that come from external ontologies if self.is_external_namespace(uri): if len(label_words) > 1: - words = '' + words = "" for word in label_words: if len(word) > 1: words += word[0].upper() + word[1:] else: words += word[0].upper() - if (not self.is_class(uri) and - not self.is_named_individual(uri)): + if not self.is_class(uri) and not self.is_named_individual( + uri + ): # avoid lowercaseing acronyms - if not words[1].istitle() and words not in ('nidm', 'spm'): + if not words[1].istitle() and words not in ("nidm", "spm"): words = words[0].lower() + words[1:] else: # avoid lowercaseing software names if words not in ( - 'nidmfsl', 'spm_results_nidm', 'Legendre'): + "nidmfsl", + "spm_results_nidm", + "Legendre", + ): words = words[0].upper() + words[1:] - prefix_name = prefix + '_' + words + prefix_name = prefix + "_" + words else: - prefix_name = prefix + '_' + "".join(label_words) + prefix_name = prefix + "_" + "".join(label_words) return prefix_name def sorted_by_labels(self, term_list): class_labels = list(map(self.get_label, term_list)) - sorted_term_list = [x for (y, x) in - sorted(zip(class_labels, term_list))] + sorted_term_list = [ + x for (y, x) in sorted(zip(class_labels, term_list)) + ] return sorted_term_list def prefixes_as_csv(self, csvfile): - with open(csvfile, 'wb') as fid: + with open(csvfile, "wb") as fid: writer = csv.writer(fid) writer.writerow(["qname", "Preferred prefix", "URI"]) # For anything that has a label - for s, o in sorted(self.graph.subject_objects(RDFS['label'])): + for s, o in sorted(self.graph.subject_objects(RDFS["label"])): try: self.graph.qname(s) except Exception: diff --git a/nidmresults/test/check_consistency.py b/nidmresults/test/check_consistency.py index 6144fa4..4af8f12 100644 --- a/nidmresults/test/check_consistency.py +++ b/nidmresults/test/check_consistency.py @@ -1,28 +1,33 @@ #!/usr/bin/env python -'''Check that a given provn file is consistent with nidm-results.owl +"""Check that a given provn file is consistent with nidm-results.owl. @author: Camille Maumet @copyright: University of Warwick 2014 -''' +""" -from rdflib import RDF, term -# from rdflib.graph import Graph -import sys, os +import os +import sys + +from rdflib import RDF + +from nidmresults.objects.constants import * RELPATH = os.path.dirname(os.path.abspath(__file__)) # Append parent script directory to path -sys.path.append(os.path.join(RELPATH, os.pardir, os.pardir, os.pardir, "scripts")) -from nidmresults.objects.constants import * +sys.path.append( + os.path.join(RELPATH, os.pardir, os.pardir, os.pardir, "scripts") +) -# ignored_attributes = set([ -# RDFS['label'], -# RDF['type'], -# PROV['value'], PROV['atTime'], PROV['used'], PROV['wasAssociatedWith'], -# PROV['qualifiedGeneration'], PROV['wasGeneratedBy'], PROV['atLocation'], -# PROV['wasDerivedFrom'], -# CRYPTO['sha512'] -# ]) + +# ignored_attributes = set([ +# RDFS['label'], +# RDF['type'], +# PROV['value'], PROV['atTime'], PROV['used'], PROV['wasAssociatedWith'], +# PROV['qualifiedGeneration'], PROV['wasGeneratedBy'], PROV['atLocation'], +# PROV['wasDerivedFrom'], +# CRYPTO['sha512'] +# ]) # def get_sub_class_names(my_graph): # sub_types = set() @@ -45,14 +50,20 @@ # return sub_types + def get_property_names_in_owl(my_owl_graph): - properties = set(); - for class_name in my_owl_graph.subjects(RDF['type'], OWL['DatatypeProperty']): + properties = set() + for class_name in my_owl_graph.subjects( + RDF["type"], OWL["DatatypeProperty"] + ): properties.add(class_name) - for class_name in my_owl_graph.subjects(RDF['type'], OWL['ObjectProperty']): + for class_name in my_owl_graph.subjects( + RDF["type"], OWL["ObjectProperty"] + ): properties.add(class_name) return properties + # def get_attributes_from_owl(my_owl_graph): # attributes = dict() # # For each ObjectProperty found out corresponding range @@ -61,164 +72,232 @@ def get_property_names_in_owl(my_owl_graph): # restrictions = dict() # # Check owl restrictions on classes -# for class_name in my_owl_graph.subjects(RDF['type'], OWL['Class']): -# for class_restr in my_owl_graph.objects(class_name, RDFS['subClassOf']): +# for class_name in my_owl_graph.subjects(RDF["type"], OWL["Class"]): +# for class_restr in my_owl_graph.objects( +# class_name, RDFS["subClassOf"] +# ): # if isinstance(class_restr, term.BNode): -# for prop in my_owl_graph.objects(class_restr,OWL['onProperty']): -# attributes.setdefault(class_name, set([prop])).add(prop) -# for child_class in my_owl_graph.subjects(RDFS['subClassOf'], class_name): -# attributes.setdefault(child_class, set([prop])).add(prop) +# for prop in my_owl_graph.objects( +# class_restr, OWL["onProperty"] +# ): +# attributes.setdefault(class_name, {prop}).add(prop) +# for child_class in my_owl_graph.subjects( +# RDFS["subClassOf"], class_name +# ): +# attributes.setdefault(child_class, {prop}).add(prop) # # Attributes that can be found in all classes -# for prop,p,o in my_owl_graph.triples((None, RDF['type'], None)): -# if o == OWL['DatatypeProperty'] or o == OWL['ObjectProperty']: +# for prop, p, o in my_owl_graph.triples((None, RDF["type"], None)): +# if o == OWL["DatatypeProperty"] or o == OWL["ObjectProperty"]: # # Check property domain -# for class_name in my_owl_graph.objects(prop, RDFS['domain']): +# for class_name in my_owl_graph.objects(prop, RDFS["domain"]): # # Add attribute to current class # if class_name in attributes: # attributes[class_name].add(prop) # else: -# attributes[class_name] = set([prop]) - +# attributes[class_name] = {prop} + # # Add attribute to children of current class -# for child_class in my_owl_graph.subjects(RDFS['subClassOf'], class_name): +# for child_class in my_owl_graph.subjects( +# RDFS["subClassOf"], class_name +# ): # # Add attribute to current class # if child_class in attributes: # attributes[child_class].add(prop) # else: -# attributes[child_class] = set([prop]) +# attributes[child_class] = {prop} # class_name = child_class -# for range_name in my_owl_graph.objects(prop, RDFS['range']): +# for range_name in my_owl_graph.objects(prop, RDFS["range"]): # # More complex type including restrictions # if isinstance(range_name, term.BNode): -# for restriction_node in my_owl_graph.objects(range_name, OWL['withRestrictions']): -# for first_restriction in my_owl_graph.objects(restriction_node, RDF['first']): -# xsd_restrictions = set(['minInclusive', 'minExclusive', 'maxInclusive', 'maxExclusive']) +# for restriction_node in my_owl_graph.objects( +# range_name, OWL["withRestrictions"] +# ): +# for first_restriction in my_owl_graph.objects( +# restriction_node, RDF["first"] +# ): +# xsd_restrictions = { +# "minInclusive", +# "minExclusive", +# "maxInclusive", +# "maxExclusive", +# } # for xsd_restriction in xsd_restrictions: -# for min_incl in my_owl_graph.objects(first_restriction, XSD[xsd_restriction]): -# if (prop in restrictions): -# if (xsd_restriction in restrictions[prop]): -# restrictions[prop] = max(restrictions[prop][xsd_restriction], min_incl) +# for min_incl in my_owl_graph.objects( +# first_restriction, XSD[xsd_restriction] +# ): +# if prop in restrictions: +# if ( +# xsd_restriction +# in restrictions[prop] +# ): +# restrictions[prop] = max( +# restrictions[prop][ +# xsd_restriction +# ], +# min_incl, +# ) # else: -# restrictions[prop] = { xsd_restriction: min_incl} +# restrictions[prop] = { +# xsd_restriction: min_incl +# } # else: -# restrictions[prop] = { xsd_restriction: min_incl} +# restrictions[prop] = { +# xsd_restriction: min_incl +# } -# for sub_range_name in my_owl_graph.objects(range_name, OWL['onDatatype']): +# for sub_range_name in my_owl_graph.objects( +# range_name, OWL["onDatatype"] +# ): # range_name = sub_range_name # if prop in ranges: # ranges[prop].add(range_name) # else: -# ranges[prop] = set([range_name]) +# ranges[prop] = {range_name} # # FIXME: more elegant? # # Add child_class to range (for ObjectProperty) -# for child_class in my_owl_graph.subjects(RDFS['subClassOf'], range_name): +# for child_class in my_owl_graph.subjects( +# RDFS["subClassOf"], range_name +# ): # # Add range to current class # if prop in ranges: # ranges[prop].add(child_class) # else: -# ranges[prop] = set([child_class]) +# ranges[prop] = {child_class} # range_name = child_class -# for child_class in my_owl_graph.subjects(RDFS['subClassOf'], range_name): +# for child_class in my_owl_graph.subjects( +# RDFS["subClassOf"], range_name +# ): # # Add attribute to current class # if prop in ranges: # ranges[prop].add(child_class) # else: -# ranges[prop] = set([child_class]) +# ranges[prop] = {child_class} # range_name = child_class -# for child_class in my_owl_graph.subjects(RDFS['subClassOf'], range_name): +# for child_class in my_owl_graph.subjects( +# RDFS["subClassOf"], range_name +# ): # # Add attribute to current class # if prop in ranges: # ranges[prop].add(child_class) # else: -# ranges[prop] = set([child_class]) +# ranges[prop] = {child_class} # range_name = child_class -# for child_class in my_owl_graph.subjects(RDFS['subClassOf'], range_name): +# for child_class in my_owl_graph.subjects( +# RDFS["subClassOf"], range_name +# ): # # Add attribute to current class # if prop in ranges: # ranges[prop].add(child_class) # else: -# ranges[prop] = set([child_class]) +# ranges[prop] = {child_class} # range_name = child_class - + # return list((attributes, ranges, restrictions)) + # def get_owl_graph(owl_file, import_files=None): # # Read owl (turtle) file # owl_graph = Graph() -# # This is a workaround to avoid issue with "#" in base prefix as +# # This is a workaround to avoid issue with "#" in base prefix as # # described in https://github.com/RDFLib/rdflib/issues/379, # # When the fix is introduced in rdflib these 2 lines will be replaced by: # # self.owl.parse(owl_file, format='turtle') -# owl_txt = open(owl_file, 'r').read().replace("http://www.w3.org/2002/07/owl#", -# "http://www.w3.org/2002/07/owl") -# owl_graph.parse(data=owl_txt, format='turtle') +# owl_txt = ( +# open(owl_file) +# .read() +# .replace( +# "http://www.w3.org/2002/07/owl#", "http://www.w3.org/2002/07/owl" +# ) +# ) +# owl_graph.parse(data=owl_txt, format="turtle") # if import_files is not None: # for import_file in import_files: # # Read owl (turtle) file # import_graph = Graph() -# import_txt = open(import_file, 'r').read() +# import_txt = open(import_file).read() -# # This is a workaround to avoid issue with "#" in base prefix as +# # This is a workaround to avoid issue with "#" in base prefix as # # described in https://github.com/RDFLib/rdflib/issues/379, -# # When the fix is introduced in rdflib these 2 lines will be replaced by: +# # When the fix is introduced in rdflib these 2 lines +# # will be replaced by: # # self.owl.parse(owl_file, format='turtle') -# import_txt = import_txt.replace("http://www.w3.org/2002/07/owl#", -# "http://www.w3.org/2002/07/owl") -# import_graph.parse(data=import_txt, format='turtle') +# import_txt = import_txt.replace( +# "http://www.w3.org/2002/07/owl#", +# "http://www.w3.org/2002/07/owl", +# ) +# import_graph.parse(data=import_txt, format="turtle") # owl_graph = owl_graph + import_graph # return owl_graph -# def check_class_names(example_graph, example_name, class_names=None, -# owl_file=None, owl_imports=None): +# def check_class_names( +# example_graph, +# example_name, +# class_names=None, +# owl_file=None, +# owl_imports=None, +# ): # my_exception = dict() # if not class_names: # if owl_file is None: -# raise Exception("One of class_names or owl_file must be not None.") +# raise Exception( +# "One of class_names or owl_file must be not None.") # else: # owl_graph = get_owl_graph(owl_file) # class_names = get_class_names_in_owl(owl_graph) # sub_types = get_sub_class_names(example_graph) -# for not_recognised_sub_type in (sub_types - class_names): +# for not_recognised_sub_type in sub_types - class_names: # if not not_recognised_sub_type.startswith(str(PROV)): # # key = example_graph.qname(not_recognised_sub_type) -# key = "\n Unrecognised sub-type: "+example_graph.qname(not_recognised_sub_type) +# key = "\n Unrecognised sub-type: " + example_graph.qname( +# not_recognised_sub_type +# ) # if key in my_exception: # my_exception[key].add(example_name) # else: -# my_exception[key] = set([example_name]) +# my_exception[key] = {example_name} # return my_exception -# def check_attributes(example_graph, example_name, owl_attributes=None, owl_ranges=None, -# owl_restrictions=None, owl_graph=None, owl_file=None, owl_imports=None): + +# def check_attributes( +# example_graph, +# example_name, +# owl_attributes=None, +# owl_ranges=None, +# owl_restrictions=None, +# owl_graph=None, +# owl_file=None, +# owl_imports=None, +# ): # my_exception = dict() # my_range_exception = dict() # my_restriction_exception = dict() # if not owl_attributes or not owl_ranges: # if owl_file is None: -# raise Exception("One of class_names or owl_file must be not None.") +# raise Exception( +# "One of class_names or owl_file must be not None.") # else: # owl_graph = get_owl_graph(owl_file, owl_imports) # attributes_ranges = get_attributes_from_owl(owl_graph) # owl_attributes = attributes_ranges[0] -# owl_ranges = attributes_ranges[1] +# owl_ranges = attributes_ranges[1] # owl_restrictions = attributes_ranges[2] # # Find all attributes -# for s,p,o in example_graph.triples((None, None, None)): +# for s, p, o in example_graph.triples((None, None, None)): # # To be a DataTypeProperty then o must be a literal # # if isinstance(o, rdflib.term.Literal): # if p not in ignored_attributes: @@ -226,109 +305,133 @@ def get_property_names_in_owl(my_owl_graph): # # Get all defined types of current object # found_attributes = False # class_names = "" -# for class_name in sorted(example_graph.objects(s, RDF['type'])): +# for class_name in sorted(example_graph.objects(s, RDF["type"])): # attributes = owl_attributes.get(class_name) -# # If the current class was defined in the owl file check if current -# # attribute was also defined. +# # If the current class was defined in the owl file check +# # if current attribute was also defined. # if attributes: # if p in attributes: # found_attributes = True -# class_names += ", "+example_graph.qname(class_name) +# class_names += ", " + example_graph.qname(class_name) # # if not found_attributes: -# # if attributes: -# # if not (p in attributes): +# # if attributes: +# # if not (p in attributes): # if not found_attributes: -# key = "\n Unrecognised attribute: "+example_graph.qname(p)+\ -# " in "+class_names[2:] -# if not key in my_exception: -# my_exception[key] = set([example_name]) +# key = ( +# "\n Unrecognised attribute: " +# + example_graph.qname(p) +# + " in " +# + class_names[2:] +# ) +# if key not in my_exception: +# my_exception[key] = {example_name} # else: # my_exception[key].add(example_name) - # # *** Check range for ObjectProperties and DataProperties # if isinstance(o, term.URIRef): -# # An ObjectProperty can point to an instance, then we look for its type: -# found_range = set(example_graph.objects(o, RDF['type'])) +# # An ObjectProperty can point to an instance, +# # then we look for its type: +# found_range = set(example_graph.objects(o, RDF["type"])) # # An ObjectProperty can point to a term # if not found_range: -# found_range = set([o]) +# found_range = {o} # # If the term is an individual, look for its type -# if OWL['NamedIndividual'] in \ -# set(owl_graph.objects(o, RDF['type'])): -# found_range = set(owl_graph.objects(o, RDF['type'])) +# if OWL["NamedIndividual"] in set( +# owl_graph.objects(o, RDF["type"]) +# ): +# found_range = set(owl_graph.objects(o, RDF["type"])) # elif isinstance(o, term.Literal): -# found_range = set([o.datatype]) +# found_range = {o.datatype} # correct_range = False # if p in owl_ranges: -# # If none of the class found for current ObjectProperty value is part of the range +# # If none of the class found for current ObjectProperty value +# # is part of the range # # throw an error -# # If the type of current value is within the authorised ranges +# # If the type of current value +# # is within the authorised ranges # if found_range.intersection(owl_ranges[p]): # correct_range = True # else: # if p in owl_ranges: -# # A bit more complicated to deal with "positiveInteger" +# # A bit more complicated to deal +# # with "positiveInteger" # for owl_range in owl_ranges[p]: -# # FIXME: we should be able to do better than that to check that XSD['positiveInteger'] is -# # in owl_ranges[p] -# if (XSD['positiveInteger'] == owl_range) and\ -# (next(iter(found_range)) == XSD['int']) and\ -# (o.value >= 0): -# correct_range = True +# # FIXME: we should be able to do better +# # than that to check that XSD['positiveInteger'] +# # is in owl_ranges[p] +# if ( +# (XSD["positiveInteger"] == owl_range) +# and (next(iter(found_range)) == XSD["int"]) +# and (o.value >= 0) +# ): +# correct_range = True # if not correct_range: # found_range_line = "" -# # FIXME: This should be better handled to be able to do "if found_range" -# if not None in found_range: -# found_range_line = ', '.join(map(example_graph.qname, sorted(found_range))) +# # FIXME: This should be better handled to be able +# # to do "if found_range" +# if None not in found_range: +# found_range_line = ", ".join( +# map(example_graph.qname, sorted(found_range)) +# ) # owl_range_line = "" # if p in owl_ranges: -# owl_range_line = ', '.join(map(example_graph.qname, sorted(owl_ranges[p]))) - -# key = "\n Unrecognised range: "+\ -# found_range_line+\ -# ' for '+example_graph.qname(p)+' should be '+\ -# owl_range_line +# owl_range_line = ", ".join( +# map(example_graph.qname, sorted(owl_ranges[p])) +# ) + +# key = ( +# "\n Unrecognised range: " +# + found_range_line +# + " for " +# + example_graph.qname(p) +# + " should be " +# + owl_range_line +# ) # else: # # No range found for current attribute # correct_range = False -# key = "\n No range defined for: "+\ -# example_graph.qname(p) +# key = "\n No range defined for: " + example_graph.qname(p) # if not correct_range: -# if not key in my_range_exception: -# my_range_exception[key] = set([example_name]) +# if key not in my_range_exception: +# my_range_exception[key] = {example_name} # else: # my_range_exception[key].add(example_name) # if p in owl_restrictions: # restrictions_ok = True -# if 'minInclusive' in owl_restrictions[p]: -# if o.value < owl_restrictions[p]['minInclusive'].value: +# if "minInclusive" in owl_restrictions[p]: +# if o.value < owl_restrictions[p]["minInclusive"].value: # restrictions_ok = False -# if 'minExclusive' in owl_restrictions[p]: -# if o.value <= owl_restrictions[p]['minExclusive'].value: +# if "minExclusive" in owl_restrictions[p]: +# if o.value <= owl_restrictions[p]["minExclusive"].value: # restrictions_ok = False -# if 'maxInclusive' in owl_restrictions[p]: -# if o.value > owl_restrictions[p]['maxInclusive'].value: +# if "maxInclusive" in owl_restrictions[p]: +# if o.value > owl_restrictions[p]["maxInclusive"].value: # restrictions_ok = False -# if 'maxExclusive' in owl_restrictions[p]: -# if o.value >= owl_restrictions[p]['maxExclusive'].value: +# if "maxExclusive" in owl_restrictions[p]: +# if o.value >= owl_restrictions[p]["maxExclusive"].value: # restrictions_ok = False # if not restrictions_ok: -# key = "\n Constraints: value "+str(o.value)+\ -# ' for '+example_graph.qname(p)+' does not observe constraints '+\ -# ', '.join(sorted(owl_restrictions[p])) -# if not key in my_restriction_exception: -# my_restriction_exception[key] = set([example_name]) +# key = ( +# "\n Constraints: value " +# + str(o.value) +# + " for " +# + example_graph.qname(p) +# + " does not observe constraints " +# + ", ".join(sorted(owl_restrictions[p])) +# ) +# if key not in my_restriction_exception: +# my_restriction_exception[key] = {example_name} # else: # my_restriction_exception[key].add(example_name) diff --git a/nidmresults/test/test_commons.py b/nidmresults/test/test_commons.py index 201977e..e997c92 100644 --- a/nidmresults/test/test_commons.py +++ b/nidmresults/test/test_commons.py @@ -1,28 +1,35 @@ #!/usr/bin/env python -'''Common functions for test procedures +"""Common functions for test procedures. @author: Camille Maumet , Satrajit Ghosh @copyright: University of Warwick 2014 -''' +""" import os -import sys import re -import vcr +import sys +import vcr from future.standard_library import hooks + with hooks(): from urllib.request import urlopen, Request from urllib.error import URLError -import rdflib -from rdflib.graph import Graph -from rdflib.compare import * +import glob import logging import signal import socket import ssl -import glob + +import rdflib +from rdflib.compare import * +from rdflib.graph import Graph + +from nidmresults.objects.constants import ( + FSL_FEAT_VERSION, + NIDM_SOFTWARE_VERSION, +) RELPATH = os.path.dirname(os.path.abspath(__file__)) @@ -31,127 +38,163 @@ # Append parent script directory to path sys.path.append(os.path.join(NIDM_PATH, "scripts")) -from nidmresults.objects.constants import \ - NIDM_SOFTWARE_VERSION, FSL_FEAT_VERSION # Save debug info in a log file (debug.log) -logging.basicConfig(filename='debug.log', level=logging.DEBUG, filemode='w') +logging.basicConfig(filename="debug.log", level=logging.DEBUG, filemode="w") logger = logging.getLogger(__name__) -logger.info(' ---------- Debug log ----------') +logger.info(" ---------- Debug log ----------") # Complete examples (used for test queries) import_test_filenames = set( - glob.glob(os.path.join(NIDM_RESULTS_PATH, 'spm', '*.ttl')) + - glob.glob(os.path.join(NIDM_RESULTS_PATH, 'spm', '*', '*.ttl')) + - glob.glob(os.path.join(NIDM_RESULTS_PATH, 'fsl', '*', '*.ttl')) + - glob.glob(os.path.join(NIDM_RESULTS_PATH, 'fsl', '*.ttl')) + - glob.glob(os.path.join(NIDM_RESULTS_PATH, 'afni', '*', '*.ttl'))) + glob.glob(os.path.join(NIDM_RESULTS_PATH, "spm", "*.ttl")) + + glob.glob(os.path.join(NIDM_RESULTS_PATH, "spm", "*", "*.ttl")) + + glob.glob(os.path.join(NIDM_RESULTS_PATH, "fsl", "*", "*.ttl")) + + glob.glob(os.path.join(NIDM_RESULTS_PATH, "fsl", "*.ttl")) + + glob.glob(os.path.join(NIDM_RESULTS_PATH, "afni", "*", "*.ttl")) +) # All examples -example_filenames = import_test_filenames.union(set(glob.glob( - os.path.join(NIDM_RESULTS_PATH, 'test', 'ground_truth', '*', '*.ttl')))) - -# If True turtle file will be downloaded from the prov store using the address specified in the README. -# If False the turtle version will be retrieved on the fly using the prov translator. By default set to True -# to check as README should be up to date but setting to False can be useful for local testing. +example_filenames = import_test_filenames.union( + set( + glob.glob( + os.path.join( + NIDM_RESULTS_PATH, "test", "ground_truth", "*", "*.ttl" + ) + ) + ) +) + +""" +If True turtle file will be downloaded +from the prov store using the address specified in the README. +If False the turtle version will be retrieved +on the fly using the prov translator. +By default set to True to check as README should be up to date +but setting to False can be useful for local testing. +""" ttl_from_readme = False def get_turtle(provn_file): if ttl_from_readme: # Get URL of turtle from README file - readme_file = os.path.join(os.path.dirname(provn_file), 'README') - readme_file = open(readme_file, 'r') + readme_file = os.path.join(os.path.dirname(provn_file), "README") + readme_file = open(readme_file) readme_txt = readme_file.read() - turtle_search = re.compile(r'.*turtle: (?P.*\.ttl).*') - extracted_data = turtle_search.search(readme_txt) - ttl_file_url = extracted_data.group('ttl_file'); + turtle_search = re.compile(r".*turtle: (?P.*\.ttl).*") + extracted_data = turtle_search.search(readme_txt) + ttl_file_url = extracted_data.group("ttl_file") else: # Open corresponding provn file - logger.info(' Converting '+provn_file) - provn_file = open(provn_file, 'r') + logger.info(" Converting " + provn_file) + provn_file = open(provn_file) ex_provn = provn_file.read() # Convert to turtle using Prov Translator APIs url = "https://provenance.ecs.soton.ac.uk/validator/provapi/documents/" - headers = { 'Content-type' : "text/provenance-notation", - 'Accept' : "text/turtle" } + headers = { + "Content-type": "text/provenance-notation", + "Accept": "text/turtle", + } req = Request(url, ex_provn, headers) MAX_RETRY = 15 retry = 0 while retry <= MAX_RETRY: try: - logger.info(' urllib2 open ') + logger.info(" urllib2 open ") with vcr.use_cassette( - os.path.join(NIDM_PATH, 'vcr_cassettes/synopsis.yaml'), - record_mode='new_episodes', - match_on=['method', 'scheme', 'host', 'port', 'path', - 'query', 'body']): + os.path.join(NIDM_PATH, "vcr_cassettes/synopsis.yaml"), + record_mode="new_episodes", + match_on=[ + "method", + "scheme", + "host", + "port", + "path", + "query", + "body", + ], + ): response = urlopen(req, timeout=10) except (socket.timeout, URLError, ssl.SSLError): # On timeout retry - retry = retry + 1 - logger.info('Retry #'+str(retry)) + retry = retry + 1 + logger.info("Retry #" + str(retry)) continue break if retry > MAX_RETRY: - raise Exception("Too many retry ("+str(retry)+")") + raise Exception("Too many retry (" + str(retry) + ")") ttl_file_url = response.geturl() - logger.info(' Loading turtle file '+ttl_file_url) + logger.info(" Loading turtle file " + ttl_file_url) return ttl_file_url + def merge_exception_dict(excep_dict, other_except_dict): - merged_dict = dict(list(excep_dict.items()) + list(other_except_dict.items())) + merged_dict = dict( + list(excep_dict.items()) + list(other_except_dict.items()) + ) # When key is in both dictionaries, we need to merge the set manually for key in list(set(excep_dict.keys()) & set(other_except_dict.keys())): merged_dict[key] = excep_dict[key].union(other_except_dict[key]) return merged_dict + def display_graph(diff_graph, prefix_msg="Difference in:"): found_difference = False - for s,p,o in diff_graph.triples((None,None,None)): - # workaround to avoid issue with "5853" being a string - prefix, namespace, name = diff_graph.compute_qname(p) - if p != NIDM_SOFTWARE_VERSION: - if p != FSL_FEAT_VERSION: - o_name = "" - if isinstance(o, rdflib.URIRef): - unused, unused, o_name = diff_graph.compute_qname(o) - # Ignore prov:Location not specified explicitly - if o_name != 'Location': - found_difference = True - - s_str = str(s) - if isinstance(s, rdflib.term.URIRef) \ - and not isinstance(s, rdflib.term.BNode): - s_str = diff_graph.qname(s) - elif isinstance(s, rdflib.term.Literal): - s_str = s_str+" ("+str(s.datatype)+")" - p_str = str(p) - if isinstance(p, rdflib.term.URIRef) \ - and not isinstance(p, rdflib.term.BNode): - p_str = diff_graph.qname(p) - elif isinstance(p, rdflib.term.Literal): - p_str = p_str+" ("+str(p.datatype)+")" - o_str = str(o) - if isinstance(o, rdflib.term.URIRef) \ - and not isinstance(o, rdflib.term.BNode): - o_str = diff_graph.qname(o) - elif isinstance(o, rdflib.term.Literal): - o_str = o_str+" ("+str(o.datatype)+")" - - logger.debug("\t"+prefix_msg+' s='+s_str+\ - ", p="+p_str+\ - ", o="+o_str) + for s, p, o in diff_graph.triples((None, None, None)): + # workaround to avoid issue with "5853" being a string + prefix, namespace, name = diff_graph.compute_qname(p) + if p != NIDM_SOFTWARE_VERSION: + if p != FSL_FEAT_VERSION: + o_name = "" + if isinstance(o, rdflib.URIRef): + unused, unused, o_name = diff_graph.compute_qname(o) + # Ignore prov:Location not specified explicitly + if o_name != "Location": + found_difference = True + + s_str = str(s) + if isinstance(s, rdflib.term.URIRef) and not isinstance( + s, rdflib.term.BNode + ): + s_str = diff_graph.qname(s) + elif isinstance(s, rdflib.term.Literal): + s_str = s_str + " (" + str(s.datatype) + ")" + p_str = str(p) + if isinstance(p, rdflib.term.URIRef) and not isinstance( + p, rdflib.term.BNode + ): + p_str = diff_graph.qname(p) + elif isinstance(p, rdflib.term.Literal): + p_str = p_str + " (" + str(p.datatype) + ")" + o_str = str(o) + if isinstance(o, rdflib.term.URIRef) and not isinstance( + o, rdflib.term.BNode + ): + o_str = diff_graph.qname(o) + elif isinstance(o, rdflib.term.Literal): + o_str = o_str + " (" + str(o.datatype) + ")" + + logger.debug( + "\t" + + prefix_msg + + " s=" + + s_str + + ", p=" + + p_str + + ", o=" + + o_str + ) return found_difference + def compare_graphs(graph_doc1, graph_doc2): # Use isomorphic to ignore BNode iso1 = to_isomorphic(graph_doc1) @@ -166,21 +209,24 @@ def compare_graphs(graph_doc1, graph_doc2): found_difference_1 = display_graph(in_first, "\t In first: ") found_difference_2 = display_graph(in_second, "\t In second: ") found_difference = found_difference_1 or found_difference_2 - - # break; + + # break; return found_difference + class TimeoutError(Exception): """Base class for timeout exceptions in this module.""" + pass + def _get_ttl_doc_content(doc): - logger.info(' Opening '+doc) + logger.info(" Opening " + doc) def _raise_timeout(*args): raise TimeoutError("end of time") - if doc.startswith("http"): + if doc.startswith("http"): # Number of retry MAX_RETRY = 15 # Timeout after 5s @@ -189,37 +235,38 @@ def _raise_timeout(*args): retry = 0 while retry <= MAX_RETRY: try: - logger.info(' urllib2 open ') + logger.info(" urllib2 open ") with vcr.use_cassette( - os.path.join(NIDM_PATH, 'vcr_cassettes/synopsis.yaml'), - record_mode='new_episodes'): + os.path.join(NIDM_PATH, "vcr_cassettes/synopsis.yaml"), + record_mode="new_episodes", + ): ttl_doc_req = urlopen(doc, timeout=TIMEOUT) - # There is no mechanism to handle timeout on read() in urllib2, + # There is no mechanism to handle timeout on read() in urllib2, # so we need to use a timer - signal.signal(signal.SIGALRM, _raise_timeout) + signal.signal(signal.SIGALRM, _raise_timeout) signal.alarm(TIMEOUT) - logger.info(' urllib2 read ') + logger.info(" urllib2 read ") doc_content = ttl_doc_req.read() signal.alarm(0) except (socket.timeout, TimeoutError, URLError): # On timeout retry - retry = retry + 1 - logger.info(' Retry #'+str(retry)) + retry = retry + 1 + logger.info(" Retry #" + str(retry)) continue break if retry > MAX_RETRY: - raise Exception("Too many retry ("+str(retry)+")") + raise Exception("Too many retry (" + str(retry) + ")") else: # Document locally on disk - logger.info(' file read ') + logger.info(" file read ") fid = open(doc) doc_content = fid.read() - logger.info('*** ------- > read') + logger.info("*** ------- > read") return doc_content @@ -227,11 +274,11 @@ def compare_ttl_documents(ttl_doc1, ttl_doc2): # Check whether most recent document is identical to current version doc_graph = Graph() doc1 = _get_ttl_doc_content(ttl_doc1) - doc_graph.parse(data=doc1, format='turtle') - + doc_graph.parse(data=doc1, format="turtle") + same_doc_graph = Graph() doc2 = _get_ttl_doc_content(ttl_doc2) - same_doc_graph.parse(data=doc2, format='turtle') + same_doc_graph.parse(data=doc2, format="turtle") found_difference = compare_graphs(same_doc_graph, doc_graph) @@ -248,6 +295,6 @@ def compare_ttl_documents(ttl_doc1, ttl_doc2): # found_difference_1 = display_graph(in_first, "\t In first: ") # found_difference_2 = display_graph(in_second, "\t In second: ") # found_difference = found_difference_1 or found_difference_2 - + # # break; - return found_difference \ No newline at end of file + return found_difference diff --git a/nidmresults/test/test_results_doc.py b/nidmresults/test/test_results_doc.py index 1da100f..801682b 100644 --- a/nidmresults/test/test_results_doc.py +++ b/nidmresults/test/test_results_doc.py @@ -1,23 +1,25 @@ #!/usr/bin/env python -'''Common tests across-software for NI-DM export. +"""Common tests across-software for NI-DM export. + The software-specific test classes must inherit from this class. @author: Camille Maumet , Satrajit Ghosh @copyright: University of Warwick 2014 -''' -from nidmresults.objects.constants_rdflib import * -from nidmresults.owl.owl_reader import OwlReader -from rdflib.namespace import RDF -from rdflib.graph import Graph -from rdflib.compare import graph_diff +""" +import glob +import json +import logging import os -import rdflib import re + import numpy as np -import json -import glob +import rdflib +from rdflib.compare import graph_diff +from rdflib.graph import Graph +from rdflib.namespace import RDF -import logging +from nidmresults.objects.constants_rdflib import * +from nidmresults.owl.owl_reader import OwlReader # Append parent script directory to path RELPATH = os.path.dirname(os.path.abspath(__file__)) @@ -25,14 +27,14 @@ logger = logging.getLogger(__name__) -class TestResultDataModel(object): +class TestResultDataModel: def get_readable_name(self, owl, graph, item): if isinstance(item, rdflib.term.Literal): if item.datatype: typeStr = graph.qname(item.datatype) else: - typeStr = '' + typeStr = "" if typeStr: typeStr = "(" + typeStr + ")" name = "'" + item + "'" + typeStr @@ -47,11 +49,10 @@ def get_readable_name(self, owl, graph, item): name = graph.qname(item) if not name.startswith("niiri"): - m = re.search(r'\d\d\d\d$', name) + m = re.search(r"\d\d\d\d$", name) # alphanumeric identifier if m is not None: - name += " (i.e. " + \ - owl.get_label(item).split(":")[1] + ")" + name += " (i.e. " + owl.get_label(item).split(":")[1] + ")" else: name = "unsupported type: " + item return name @@ -59,10 +60,14 @@ def get_readable_name(self, owl, graph, item): def get_alternatives(self, owl, graph, s=None, p=None, o=None): found = "" - for (s_in, p_in, o_in) in graph.triples((s, p, o)): + for s_in, p_in, o_in in graph.triples((s, p, o)): if not o: if not o_in.startswith(str(PROV)): - found += "; " + self.get_readable_name(owl, graph, o_in,) + found += "; " + self.get_readable_name( + owl, + graph, + o_in, + ) if not p: if not p_in.startswith(str(PROV)): found += "; " + self.get_readable_name(owl, graph, p_in) @@ -70,19 +75,19 @@ def get_alternatives(self, owl, graph, s=None, p=None, o=None): if not s_in.startswith(str(PROV)): found += "; " + self.get_readable_name(owl, graph, s_in) if len(found) > 200: - found = '' + found = "" else: found = found[2:] return found # FIXME: Extend tests to more than one dataset (group analysis, ...) - '''Tests based on the analysis of single-subject auditory data based on + """Tests based on the analysis of single-subject auditory data based on test01_spm_batch.m using SPM12b r5918. @author: Camille Maumet , Satrajit Ghosh @copyright: University of Warwick 2014 - ''' + """ def setUp(self, parent_gt_dir=None): self.my_execption = "" @@ -94,22 +99,26 @@ def load_graph(self, ttl_name): ttl = ttl_name test_dir = os.path.dirname(ttl) - configfile = os.path.join(test_dir, 'config.json') + configfile = os.path.join(test_dir, "config.json") if not os.path.isfile(configfile): configfile = os.path.join( - os.path.abspath( - os.path.join(test_dir, os.pardir)), 'config.json') + os.path.abspath(os.path.join(test_dir, os.pardir)), + "config.json", + ) with open(configfile) as data_file: metadata = json.load(data_file) try: - gt_file = [os.path.join(self.gt_dir, metadata["version"], x) - for x in metadata["ground_truth"]] + gt_file = [ + os.path.join(self.gt_dir, metadata["version"], x) + for x in metadata["ground_truth"] + ] except Exception: # This part should be removed once SPM can modify json files - gt_file = [os.path.join(self.gt_dir, metadata["versions"][0], - x) - for x in metadata["ground_truth"]] + gt_file = [ + os.path.join(self.gt_dir, metadata["versions"][0], x) + for x in metadata["ground_truth"] + ] inclusive = metadata["inclusive"] if "version" in metadata: version = metadata["version"] @@ -119,7 +128,8 @@ def load_graph(self, ttl_name): name = ttl.replace(test_dir, "") self.ex_graphs[ttl_name] = ExampleGraph( - name, ttl, gt_file, inclusive, version) + name, ttl, gt_file, inclusive, version + ) return self.ex_graphs[ttl_name] @@ -128,22 +138,22 @@ def load_graph(self, ttl_name): # inspect.getfile(inspect.currentframe()))) def print_results(self, res): - '''Print the results query 'res' to the console''' + """Print the results query 'res' to the console.""" for idx, row in enumerate(res.bindings): rowfmt = [] print("Item %d" % idx) for key, val in sorted(row.items()): - rowfmt.append('%s-->%s' % (key, val.decode())) - print('\n'.join(rowfmt)) + rowfmt.append(f"{key}-->{val.decode()}") + print("\n".join(rowfmt)) def successful_retreive(self, res, info_str=""): - '''Check if the results query 'res' contains a value for each field''' + """Check if the results query 'res' contains a value for each field.""" if not res.bindings: self.my_execption = info_str + """: Empty query results""" return False for idx, row in enumerate(res.bindings): for key, val in sorted(row.items()): - logging.debug('%s-->%s' % (key, val.decode())) + logging.debug(f"{key}-->{val.decode()}") if not val.decode(): self.my_execption += "\nMissing: \t %s" % (key) return False @@ -154,10 +164,8 @@ def successful_retreive(self, res, info_str=""): # raise Exception(self.my_execption) def _replace_match(self, graph1, graph2, rdf_type): - """ - Match classes of type 'rdf_type' across documents based on attributes. - """ - + """Match classes of type 'rdf_type' across documents \ + based on attributes.""" # Retrieve objects of type 'rdf_type' (e.g. prov:Entities) g1_terms = set(graph1.subjects(RDF.type, rdf_type)) g2_terms = set(graph2.subjects(RDF.type, rdf_type)) @@ -170,24 +178,30 @@ def _replace_match(self, graph1, graph2, rdf_type): # inCoordinateSpace might be the same for all) MIN_MAP_MATCHING = 4 - if rdf_type == PROV['Activity']: + if rdf_type == PROV["Activity"]: activity = True - elif rdf_type == PROV['Entity']: + elif rdf_type == PROV["Entity"]: # FIXME: This would be more efficiently done using the prov owl # file - g1_terms = g1_terms.union(set( - graph1.subjects(RDF.type, PROV['Bundles']))) - g1_terms = g1_terms.union(set( - graph1.subjects(RDF.type, PROV['Coordinate']))) - g1_terms = g1_terms.union(set( - graph1.subjects(RDF.type, PROV['Person']))) - g2_terms = g2_terms.union(set( - graph2.subjects(RDF.type, PROV['Bundles']))) + g1_terms = g1_terms.union( + set(graph1.subjects(RDF.type, PROV["Bundles"])) + ) + g1_terms = g1_terms.union( + set(graph1.subjects(RDF.type, PROV["Coordinate"])) + ) + g1_terms = g1_terms.union( + set(graph1.subjects(RDF.type, PROV["Person"])) + ) g2_terms = g2_terms.union( - set(graph2.subjects(RDF.type, PROV['Coordinate']))) + set(graph2.subjects(RDF.type, PROV["Bundles"])) + ) g2_terms = g2_terms.union( - set(graph2.subjects(RDF.type, PROV['Person']))) - elif rdf_type == PROV['Agent']: + set(graph2.subjects(RDF.type, PROV["Coordinate"])) + ) + g2_terms = g2_terms.union( + set(graph2.subjects(RDF.type, PROV["Person"])) + ) + elif rdf_type == PROV["Agent"]: agent = True for g1_term in g1_terms: @@ -199,14 +213,18 @@ def _replace_match(self, graph1, graph2, rdf_type): format_found = False for p, o in graph1.predicate_objects(g1_term): - logging.debug("Trying to find a match for " + - str(graph1.qname(g1_term)) + " " + - str(graph1.qname(p)) + " " + - str(o)) + logging.debug( + "Trying to find a match for " + + str(graph1.qname(g1_term)) + + " " + + str(graph1.qname(p)) + + " " + + str(o) + ) if p == NIDM_IN_COORDINATE_SPACE: coord_space_found = True - if p == DCT['format']: + if p == DCT["format"]: format_found = True if coord_space_found and format_found: min_matching = MIN_MAP_MATCHING @@ -216,27 +234,32 @@ def _replace_match(self, graph1, graph2, rdf_type): # if activity or \ # (isinstance(o, rdflib.term.Literal) or p == RDF.type): # if graph2.subjects(p, o): - for g2_term in \ - (x for x in graph2.subjects(p, o) if x in g2_match): + for g2_term in ( + x for x in graph2.subjects(p, o) if x in g2_match + ): g2_match[g2_term] += 1 logging.debug( - "Match found with " + str(graph1.qname(g2_term))) + "Match found with " + str(graph1.qname(g2_term)) + ) # else: # print(sum(g2_match.values())) - # logging.debug("NO --- Match found") + # logging.debug("NO --- Match found") # If o is a string that is likely to be json check if we have # an equivalent json string same_json_array = False close_float = False - if hasattr(o, 'datatype') and o.datatype == XSD['string']: + if hasattr(o, "datatype") and o.datatype == XSD["string"]: for g2_term, g2_o in graph2.subject_objects(p): - same_json_array, close_float, same_str = \ + same_json_array, close_float, same_str = ( self._same_json_or_float(o, g2_o) + ) if same_json_array or close_float or same_str: g2_match[g2_term] += 1 - logging.debug("Match found with " + - str(graph1.qname(g2_term))) + logging.debug( + "Match found with " + + str(graph1.qname(g2_term)) + ) if activity or agent: for s, p in graph1.subject_predicates(g1_term): @@ -249,20 +272,25 @@ def _replace_match(self, graph1, graph2, rdf_type): g2_matched = set() for g2_term, match_index in list(g2_match.items()): if max(g2_match.values()) >= min_matching: - if (match_index == max(g2_match.values())) \ - and g2_term not in g2_matched: + if ( + match_index == max(g2_match.values()) + ) and g2_term not in g2_matched: # Found matching term g2_matched.add(g2_term) if not g1_term == g2_term: g2_name = graph2.qname(g2_term).split(":")[-1] - new_id = g1_term + '_' + g2_name - logging.debug(graph1.qname(g1_term) + - " is matched to " + - graph2.qname(g2_term) + - " and replaced by " + - graph2.qname(new_id) + - " (match=" + str(match_index) + ")") + new_id = g1_term + "_" + g2_name + logging.debug( + graph1.qname(g1_term) + + " is matched to " + + graph2.qname(g2_term) + + " and replaced by " + + graph2.qname(new_id) + + " (match=" + + str(match_index) + + ")" + ) for p, o in graph1.predicate_objects(g1_term): graph1.remove((g1_term, p, o)) @@ -280,10 +308,14 @@ def _replace_match(self, graph1, graph2, rdf_type): g2_terms.remove(g2_term) g2_terms.add(new_id) else: - logging.debug(graph1.qname(g1_term) + - " is matched to " + - graph2.qname(g2_term) + - " (match=" + str(match_index) + ")") + logging.debug( + graph1.qname(g1_term) + + " is matched to " + + graph2.qname(g2_term) + + " (match=" + + str(match_index) + + ")" + ) match_found = True break @@ -294,11 +326,8 @@ def _replace_match(self, graph1, graph2, rdf_type): return list([graph1, graph2]) def _reconcile_graphs(self, graph1, graph2, recursive=10): - """ - Reconcile: if two entities have exactly the same attributes: they - are considered to be the same (set the same id for both) - """ - + """Reconcile: if two entities have exactly the same attributes: \ + they are considered to be the same (set the same id for both).""" # FIXME: reconcile entities+agents first (ignoring non attributes) # then reconcile activities based on everything # for each item select the closest match in the other graph (instead of @@ -308,21 +337,30 @@ def _reconcile_graphs(self, graph1, graph2, recursive=10): # We reconcile first entities and agents (based on data properties) and # then activities (based on all relations) - graph1, graph2 = self._replace_match(graph1, graph2, PROV['Entity']) - graph1, graph2 = self._replace_match(graph1, graph2, PROV['Agent']) - graph1, graph2 = self._replace_match(graph1, graph2, PROV['Activity']) + graph1, graph2 = self._replace_match(graph1, graph2, PROV["Entity"]) + graph1, graph2 = self._replace_match(graph1, graph2, PROV["Agent"]) + graph1, graph2 = self._replace_match(graph1, graph2, PROV["Activity"]) return list([graph1, graph2]) - def compare_full_graphs(self, gt_graph, other_graph, owl, include=False, - raise_now=False, reconcile=True, to_ignore=None): - ''' Compare gt_graph and other_graph ''' + def compare_full_graphs( + self, + gt_graph, + other_graph, + owl, + include=False, + raise_now=False, + reconcile=True, + to_ignore=None, + ): + """Compare gt_graph and other_graph.""" my_exception = "" # We reconcile gt_graph with other_graph if reconcile: gt_graph, other_graph = self._reconcile_graphs( - gt_graph, other_graph) + gt_graph, other_graph + ) in_both, in_gt, in_other = graph_diff(gt_graph, other_graph) @@ -331,22 +369,24 @@ def compare_full_graphs(self, gt_graph, other_graph, owl, include=False, for s, p, o in in_gt: # If there is a corresponding s,p check if # there is an equivalent o - for o_other in in_other.objects(s, p): - same_json_array, close_float, same_str = \ - self._same_json_or_float(o, o_other) + for o_other in in_other.objects(s, p): + same_json_array, close_float, same_str = ( + self._same_json_or_float(o, o_other) + ) if same_json_array or close_float or same_str: # Remove equivalent o from other as well in_other.remove((s, p, o_other)) break else: - if (p not in to_ignore): + if p not in to_ignore: exc_missing.append( "\nMissing :\t '%s %s %s'" % ( self.get_readable_name(owl, gt_graph, s), self.get_readable_name(owl, gt_graph, p), - self.get_readable_name(owl, gt_graph, o) - )) + self.get_readable_name(owl, gt_graph, o), + ) + ) exc_added = list() if not include: @@ -357,8 +397,9 @@ def compare_full_graphs(self, gt_graph, other_graph, owl, include=False, % ( self.get_readable_name(owl, other_graph, s), self.get_readable_name(owl, other_graph, p), - self.get_readable_name(owl, other_graph, o) - )) + self.get_readable_name(owl, other_graph, o), + ) + ) my_exception += "".join(sorted(exc_missing) + sorted(exc_added)) @@ -380,7 +421,8 @@ def _same_json_or_float(self, o, o_other): same_str = False if isinstance(o, rdflib.term.Literal) and isinstance( - o_other, rdflib.term.Literal): + o_other, rdflib.term.Literal + ): if o.startswith("[") and o.endswith("]"): try: if json.loads(o) == json.loads(o_other): @@ -409,12 +451,13 @@ def _same_json_or_float(self, o, o_other): return (same_json_array, close_float, same_str) -class ExampleGraph(object): - '''Class representing a NIDM-Results examples graph to be compared to some - ground truth graph''' +class ExampleGraph: + """Class representing a NIDM-Results examples graph \ + to be compared to some ground truth graph.""" - def __init__(self, name, ttl_file, gt_ttl_files, - exact_comparison, version): + def __init__( + self, name, ttl_file, gt_ttl_files, exact_comparison, version + ): self.name = name self.ttl_file = ttl_file @@ -424,27 +467,38 @@ def __init__(self, name, ttl_file, gt_ttl_files, print(ttl_file) - self.graph.parse(ttl_file, format='turtle') + self.graph.parse(ttl_file, format="turtle") # Get NIDM-Results version for each example self.version = version if self.version != "dev": self.gt_ttl_files = [ - x.replace(os.path.join("nidm", "nidm"), - os.path.join("nidm_releases", self.version, "nidm")) - for x in self.gt_ttl_files] + x.replace( + os.path.join("nidm", "nidm"), + os.path.join("nidm_releases", self.version, "nidm"), + ) + for x in self.gt_ttl_files + ] # Owl file corresponding to version owl_file = os.path.join( - os.path.dirname(os.path.dirname(__file__)), 'owl', - "nidm-results_" + version.replace(".", "") + ".owl") + os.path.dirname(os.path.dirname(__file__)), + "owl", + "nidm-results_" + version.replace(".", "") + ".owl", + ) self.owl_file = owl_file owl_imports = None if self.version == "dev": owl_imports = glob.glob( - os.path.join(os.path.dirname(owl_file), - os.pardir, os.pardir, "imports", '*.ttl')) + os.path.join( + os.path.dirname(owl_file), + os.pardir, + os.pardir, + "imports", + "*.ttl", + ) + ) self.owl = OwlReader(self.owl_file, owl_imports) diff --git a/pyproject.toml b/pyproject.toml index 865150f..5fc3ae8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -55,6 +55,9 @@ nidmresults = "nidmresults.cli.nidmresults:main" [project.urls] Development = "https://github.com/incf-nidash/nidmresults" +[tool.black] +line-length = 79 + [tool.codespell] ignore-words-list = "fwe,re-use,nd" skip = ".git,*.pdf,*.svg" @@ -67,3 +70,16 @@ packages = ["nidmresults"] [tool.hatch.version] source = "vcs" + +[tool.isort] +combine_as_imports = true +line_length = 79 +profile = "black" +skip_gitignore = true + +[tool.pytest.ini_options] +addopts = "-ra --strict-config --strict-markers --doctest-modules --showlocals -s -vv --durations=0" +doctest_optionflags = "NORMALIZE_WHITESPACE ELLIPSIS" +junit_family = "xunit2" +minversion = "6.0" +xfail_strict = true diff --git a/test/test_data.json b/test/test_data.json index 1f5e3c1..c9f3587 100644 --- a/test/test_data.json +++ b/test/test_data.json @@ -1 +1 @@ -{"location":""} \ No newline at end of file +{"location":""} diff --git a/test/test_reader.py b/test/test_reader.py index 933c5b1..24a0e82 100644 --- a/test/test_reader.py +++ b/test/test_reader.py @@ -1,27 +1,26 @@ #!/usr/bin/env python -""" -Test NIDM FSL export tool installation - +"""Test NIDM FSL export tool installation. @author: Camille Maumet @copyright: University of Warwick 2013-2015 """ -from nidmresults.owl.owl_reader import OwlReader -import unittest -from nidmresults.graph import * -from nidmresults.test.test_results_doc import TestResultDataModel -from future.standard_library import hooks -import zipfile +import glob +import inspect import json + # from ddt import ddt, data, unpack import os -import inspect -import glob import shutil -from rdflib.compare import isomorphic, graph_diff -import os +import unittest + +from future.standard_library import hooks + +from nidmresults.graph import * +from nidmresults.owl.owl_reader import OwlReader +from nidmresults.test.test_results_doc import TestResultDataModel + with hooks(): - from urllib.request import urlopen, Request + from urllib.request import Request, urlopen # @ddt @@ -30,29 +29,32 @@ class TestReader(unittest.TestCase, TestResultDataModel): def setUp(self): self.my_execption = "" - owl_file = os.path.join(os.path.dirname( - os.path.dirname( - os.path.realpath(__file__))), - 'nidmresults', 'owl', - 'nidm-results_130.owl') + owl_file = os.path.join( + os.path.dirname(os.path.dirname(os.path.realpath(__file__))), + "nidmresults", + "owl", + "nidm-results_130.owl", + ) self.owl = OwlReader(owl_file) pwd = os.path.dirname( - os.path.abspath(inspect.getfile(inspect.currentframe()))) + os.path.abspath(inspect.getfile(inspect.currentframe())) + ) # Store test data in a 'data' folder until 'test' - data_dir = os.path.join(pwd, 'data') + data_dir = os.path.join(pwd, "data") if not os.path.exists(data_dir): os.makedirs(data_dir) # Collection containing examples of NIDM-Results packs (1.3.0) req = Request( - "http://neurovault.org/api/collections/2210/nidm_results") + "http://neurovault.org/api/collections/2210/nidm_results" + ) rep = urlopen(req) response = rep.read() - data = json.loads(response.decode('utf-8')) + data = json.loads(response.decode("utf-8")) # Download the NIDM-Results packs from NeuroVault if not available # locally @@ -69,8 +71,8 @@ def setUp(self): local_file.write(f.read()) self.packs.append(nidmpack) - self.packs = glob.glob(os.path.join(data_dir, '*.nidm.zip')) - self.out_dir = os.path.join(data_dir, 'recomputed') + self.packs = glob.glob(os.path.join(data_dir, "*.nidm.zip")) + self.out_dir = os.path.join(data_dir, "recomputed") if os.path.isdir(self.out_dir): shutil.rmtree(self.out_dir) @@ -78,9 +80,10 @@ def setUp(self): os.mkdir(self.out_dir) def test_read_object(self): - """ - Round-trip test. Check that we can read all NIDM packs, rewrite them - and get the same pack again + """Round-trip test. + + Check that we can read all NIDM packs, + rewrite them and get the same pack again """ all_excs = "" for nidmpack in self.packs: @@ -88,9 +91,9 @@ def test_read_object(self): # Known issues in the NIDM packs to_replace = { - ' \\ntask': '\\\\n task', - ';\n nidm_coordinateVectorInVoxels: "null"^^xsd:string .': - '.'} + " \\ntask": "\\\\n task", + ';\n nidm_coordinateVectorInVoxels: "null"^^xsd:string .': ".", + } # Read the NIDM pack nidmres = NIDMResults(nidm_zip=nidmpack, to_replace=to_replace) @@ -98,7 +101,7 @@ def test_read_object(self): # Rewrite the NIDM pack new_name = os.path.join(self.out_dir, os.path.basename(nidmpack)) nidmres.serialize(new_name) - print('Serialised to ' + new_name) + print("Serialised to " + new_name) print("----") # Read the rewritten pack @@ -106,8 +109,13 @@ def test_read_object(self): # Check equivalence between the two packs (original vs rewritten) exc = self.compare_full_graphs( - nidmres.graph, new_nidmres.graph, self.owl, - include=False, raise_now=False, reconcile=False) + nidmres.graph, + new_nidmres.graph, + self.owl, + include=False, + raise_now=False, + reconcile=False, + ) all_excs = all_excs + exc @@ -115,5 +123,5 @@ def test_read_object(self): raise Exception(all_excs) -if __name__ == '__main__': +if __name__ == "__main__": unittest.main() diff --git a/tox.ini b/tox.ini index 1f02de4..a1a9dc5 100644 --- a/tox.ini +++ b/tox.ini @@ -3,11 +3,34 @@ requires = tox>=4 ; run lint by default when just calling "tox" -env_list = tests +env_list = lint +; ENVIRONMENTS +; ------------ +[style] +description = common environment for style checkers (rely on pre-commit hooks) +skip_install = true +deps = + pre-commit ; COMMANDS ; -------- +[testenv:lint] +description = run all linters and formatters +skip_install = true +deps = + {[style]deps} +commands = + pre-commit run --all-files --show-diff-on-failure {posargs:} + +[testenv:flake8] +description = run flake8 +skip_install = true +deps = + {[style]deps} +commands = + pre-commit run --all-files --show-diff-on-failure flake8 + [testenv:tests] description = run tests extras = test