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INDRA v1.23.0

23 Jul 21:00
@bgyori bgyori
1.23.0
84fd737
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What's Changed

Package structure and dependencies

Documentation

Core assembly modules

  • Add optional residue/position feature to CountScorer by @johnbachman in #1396
  • Remove mesh cycle from bio-ontology by @kkaris in #1433
  • Add version to file docstring and log message in bio ontology CLI by @kkaris in #1432

Knowledge sources

  • Handle more UP/HGNC corner cases in BioPAX by @bgyori in #1390
  • Improve BioPAX conversion processing and extend API by @bgyori in #1392
  • Fix quotes in Reach processor run command by @kwalcock in #1397
  • Propagate section information from new Reach implementation by @bgyori in #1399
  • Allow extracting all Agents from Reach entities by @bgyori in #1400
  • Db sources updates by @kkaris in #1423
  • Processor improvements by @bgyori in #1450
  • Update SIGNOR processor and FamPlex by @bgyori in #1409
  • Add coordinate info to Agent extraction endpoints from readers by @bgyori in #1412
  • Handle underscores in agent IDs for DB query by @bgyori in #1414
  • Add fix for issue with latest SIGNOR release by @bgyori in #1453
  • Fixes to input processors due to changes in sources by @haohangyan in #1454

Output assemblers

  • Implement completing source counts in HTML assembler by @bgyori in #1439

Resources and database clients

Literature clients

Other

Full Changelog: 1.22.0...1.23.0

Contributors

johnbachman, kkaris, and 5 other contributors
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INDRA v1.22.0

05 Sep 14:43
@bgyori bgyori
1.22.0
37d97fe
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INDRA v1.22.0

Package structure and dependencies

  • Protmapper and Gilda version requirements increased, PySB dependency restriction relaxed

Core assembly modules

Statement representation

Knowledge sources

Model assemblers

Model analysis

Tools

Resources and database clients

Literature clients

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INDRA v1.21.0

12 Oct 12:31
@bgyori bgyori
1.21.0
6ab6b98
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INDRA v1.21.0

Package structure and dependencies

  • Multiple modules for the world modeling use case separated out into the INDRA World package (https://github.com/indralab/indra_world). For the specific modules affected, see #1278 and #1283.
  • rdflib is no longer a requirement.
  • Increased protmapper version (0.0.22) with updated protein resources.

Core assembly modules

  • Multiple updates to the INDRA BioOntology (version incremented from 1.12 to 1.18) including adding entity types for nodes, UniProt-Entrez mappings for non-human proteins, chemical family relations from LSPCI in indra.ontology.bio.
  • Belief engine significantly refactored to allow more flexibility in statement scoring in indra.belief.
  • New belief scorer module added which learns and applies scorers using sklearn models based on curation data in indra.belief.skl.

Statement representation

Knowledge sources

Model assemblers

  • Improved hub layout generation for CX networks in indra.assemblers.cx.
  • HtmlAssembler extended to generate links out for database sources, display belief badges, and improve knowledge source badges in indra.assemblers.html.
  • IndraNet assembler extended to provide better aggregation logic for
    Statements into network edges in indra.assemblers.indranet.
  • PyBEL assembler extended to include additional annotations on edges in indra.assemblers.pybel.

Tools

Resources and database clients

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INDRA v1.20.0

27 Apr 02:31
@bgyori bgyori
1.20.0
bc0a93a
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INDRA v1.20.0

Package structure and dependencies

  • INDRA is now tested with Python 3.9 (supports 3.6-3.9).
  • Increased protmapper version (0.0.21) with updated protein resources.
  • Moved out deprecated evaluation scripts (#1283).

Core assembly modules

Statement representation

Knowledge sources

Model assemblers

Model analysis / explanation

Tools

Resources and database clients

  • Resource updates to Biomappings, ChEBI and EFO resources.
  • Many new grounding curations added to grounding resources (mappings, misgrounding, ignores).
  • Better handling for external namespaces in the OBO client indra.databases.obo_client.

Literature clients

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INDRA v1.19.0

29 Dec 20:17
@bgyori bgyori
1.19.0
94075d6
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INDRA v1.19.0

Package structure and dependencies

  • Setup adjusted to require newer versions of PyBEL (0.15), PyBioPax (0.0.5), and Protmapper (0.0.19).
  • Automated testing has been migrated from Travis CI to Github Actions.

Core assembly modules

  • The statement refinement finding algorithm has been reimplemented for a speedup of multiple orders of magnitude depending on application in indra.preassembler.
  • The Preassembler now supports a series of user-supplied filter functions to speed up refinement finding in a use case-specific way in indra.preassembler.
  • The BioOntology's version has increased to 1.7 with many resource updates and new sources (e.g., Biomappings included in indra.ontology.
  • The IndraOntology no longer contains connected component labels (faster initialization and loading), in indra.ontology.
  • The grounding disambiguation code is refactored with improved prioritization in indra.preassembler.grounding_mapper.
  • Grounding disambiguation has been refactored into a separate module in indra.preassembler.grounding_mapper.disambiguate.
  • New Statement validation module for automated consistency checks of Statements, Agents, and their attributes in indra.statements.validate.
  • Improvements to WorldOntology extension during runtime in indra.ontology.world.

Knowledge sources

Model assemblers

  • New HTML look implemented (with support for old/simplified view) in the HTML Assembler in indra.assemblers.html.

Model analysis / explanation

Resources and database clients

  • indra.resources is now a proper module with helper functions to load resource files.
  • New client for interacting with identifiers.org namespaces, IDs and URLs in indra.databases.identifiers.
  • Many resources have been updated (e.g., HGNC entries, FamPlex, new grounding mappings) in indra.resources.

Literature clients

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INDRA v1.18.0

12 Sep 19:14
@bgyori bgyori
1.18.0
f9eab6b
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INDRA v1.18.0

Package structure and dependencies

  • Starting with this release, INDRA supports Python 3.6+ only.
  • The live curation service for the World Modelers use case is now in a separate repository at https://github.com/indralab/indra_wm_service.
  • New dependencies for this release include obonet, tqdm and pybiopax.
  • Pyjnius is no longer a necessary requirement for any INDRA module (though it can still be optionally used for local JAR-based reading with Eidos and Reach).

Core assembly modules

  • A major change in the current release is the introduction of the indra.ontology module which replaces the indra.preassembler.hierarchy_manager module, for more details, see #1100.
  • New BioOntology at indra.ontology.bio which implements naming, identifier mapping and hierarchical relationships among 2.1 million relevant entities (up from 250k in the previous release). The BioOntology also subsumes the old cellular component hierarchy, activity hierarchy, and modification hierarchy, which has now been removed.
  • New WorldOntology at indra.ontology.world which replaces multiple reader-specific ontologies for the WorldModelers use case.
  • New ontology web service in indra.ontology.app which allows using the IndraOntology as a service for ID mapping, isa/partof queries, name lookups, etc.
  • New VirtualOntology indra.ontology.virtual which acts as a client for the ontology web service.
  • The name standardization and grounding standardization code has been reimplemented to use the IndraOntology, and is now under the indra.ontology.standardize module with significantly extended mapping capabilities, and many new functions.
  • The Preassembler has been adapted to use the IndraOntology and is extended with new options in indra.preassembler.
  • The indra.preassembler.ontology_mapper module along with a host of other scripts for making hierarchies (all replaced by the new IndraOntology) have been deprecated and removed.
  • Improved grounding mapping and disambiguation logic when multiple texts are available for an agent in indra.preassembler.grounding_mapper.
  • Many extensions to grounding mapping resources in indra.resources.grounding.
  • Bug fixes in indra.pipeline for handling some corner cases.

Knowledge sources

Model assemblers

  • Extended support for knowledge sources and simplified support for evidence count and source count annotations in the HtmlAssembler in indra.assemblers.html. There are also several bug fixes in handling some statement types in this module, as well as improved links out to literature content.
  • Extended support for knowledge source annotations in the CX assembler in indra.assemblers.cx.
  • Handling negative modification conditions in the EnglishAssembler indra.assemblers.english.
  • Improved signed graph assembly from BEL graphs in indra.assemblers.pybel.

Model analysis / explanation

Resources and database clients

Literature clients

REST API

  • The INDRA REST API has been completely reimplemented in a new framework, and has been extended significantly in its functionalities. It also comes with improved Swagger documentation with a public instance
    running at http://api.indra.bio:8000.
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INDRA v1.17.0

19 May 14:21
@bgyori bgyori
1.17.0
13918aa
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INDRA v1.17.0

Package structure and dependencies

  • The high-throughput reading tools in indra.tools.reading have been
    moved into an independent repository at
    https://github.com/indralab/indra_reading.
  • The obonet package is now a required dependency.

Input processors

  • New VirHostNet API and processor in indra.sources.virhostnet.
  • New Hypothes.is API and processor allowing processing
    annotations into INDRA Statements in indra.sources.hypothesis.
  • Integrated new version of Sparser reader with improved and adapted
    processor in indra.sources.sparser.
  • Refactored Eidos API into separate reader, client and server with
    significantly extended usage instructions in indra.sources.eidos.
  • New endpoints in Eidos API implementing biology-oriented processing, as
    well as regrounding with respect to a user-supplied ontology in
    indra.sources.eidos.
  • Overhauled Reach API supporting the latest Reach version and prioritizing
    using Reach as a (local) web service over JAR-based reading
    in indra.sources.reach, also with significantly extended usage
    instructions.
  • Support for extracting Conversion statements from Reach output in
    indra.sources.reach.
  • ISI reader processor in indra.sources.isi no longer requires a Python 2
    runtime and the separate nxml2text tool.
  • Updated RLIMS-P API in indra.sources.rlimsp to work with latest web service at
    https://research.bioinformatics.udel.edu/itextmine/api/data/rlims/.

Resources and clients

  • Overhauled GO resources and client to be based on OBO in
    indra.databases.go_client.
  • MeSH tree numbers, isa relationships and determination of
    subtree implemented in indra.databases.mesh_client.
  • Extended mappings added between MeSH and GO, ChEBI, EFO, DOID, HP.
  • All resource files updated to latest version in indra.resources.

Core assembly modules

  • New Pipeline module in indra.pipeline allowing building
    and running custom assembly pipelines programmatically or from a JSON file.
  • UniProt protein features and EFO, DOID, HP ontologies
    integrated with name/grounding standardization.
  • Overhauled integration of Gilda (https://github.com/indralab/gilda) with
    indra.preassembler.grounding_mapper allowing selective re-grounding
    of statements as well as disambiguation.
  • New one-statement-per-line JSON output mode in indra.statements.io to
    support streaming large INDRA Statement JSONs.

Literature

  • New bioRxiv/medRxiv client to monitor collections and download PDF/XML/text
    content in indra.literature.biorxiv_client.
  • Significantly improved text extraction from PMC NXML in
    indra.literature.pmc_client.

Output assemblers

  • Refactoried English assembler to allow keeping track of
    entity coordinates within each assembled sentence in
    indra.assemblers.english.
  • Improved construction of entity links in HTML assembler
    in indra.assemblers.html.
  • More annotations propagated into PyBEL graph in
    indra.assemblers.pybel.
  • Made the upload and update of CX networks more robust in
    indra.assemblers.cx.

Explanation

  • Improvements to finding all paths of a given length in
    indra.explanation.

Tools

  • Refactored LiveCuration service into a separate module in
    indra.tools.live_curation.
  • Updated outdated assembly approach in GeneNetwork tool in
    indra.tools.gene_network.

Other

  • Updated and extended README, usage examples and tutorials.
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INDRA v1.16.0

04 Feb 19:30
@bgyori bgyori
1.16.0
38a53c9
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INDRA v1.16.0

Input processors

  • New PhosphoELM API and processor in indra.sources.phosphoelm.
  • PyBEL API and processor updated for PyBEL 0.14 compatibility in indra.sources.bel.
  • Improvements in regrounding approach with Eidos in indra.sources.eidos.
  • Bug fixes to offline reading via the REACH API in indra.sources.reach.
  • Refactor ISI reader API and processor for containerization in indra.sources.isi.

Core assembly modules

  • Full integration of Gilda disambiguation with grounding mapper both as
    a package and a web service in indra.preassembler.grounding_mapper.
  • Refactor grounding mapper module to separate out standardization functions
    in indra.preassembler.grounding_mapper.standardize.

Output assemblers

  • Many improvements to the HTML assembler including refactoring,
    improved grouping and heading generation, and support Influences in
    indra.assemblers.html.
  • Improvements to grounding and introduction of part_of relations in
    PyBEL assembler in indra.assemblers.pybel.

Resources

  • Integrate a set of known MeSH to GO mappings.

Explanation

  • Improvements to reporting paths in the explanation module in
    indra.explanation.

Tools

  • Many new features in the Live curation, including actively loading
    and saving corpora on S3 in indra.tools.live_curation.
  • Add new high-throughput reader management for ISI and TRIPS readers
    in indra.tools.reading
  • Significant refactoring of indra.tools.reading to separate reader
    classes and improve containerization.
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INDRA v1.15.2

04 Feb 16:14
@bgyori bgyori
1.15.2
59499e8
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INDRA v1.15.2

Package structure

  • Remove the top-level data folder from version control (not part of package)
  • Make INDRA compatible with networkx 2.4 (which removed several deprecated
    features).

Input processors

  • Refactoring of the BEL input API in indra.sources.bel.
    Access to Selventa corpora is now via https://github.com/cthoyt/selventa-knowledge.
  • Multitude of improvements to the CWMS processor in indra.sources.cwms,
    including extracting migration events.
  • Refactoring of INDRA DB REST API in indra.sources.indra_db_rest to use
    a class-based processor structure for all endpoints.
  • Add Gilda grounding option to the ISI reader in indra.sources.isi.

Core assembly modules

  • Normalization across equivalent and opposite concepts in indra.preassembler
    based on an ontology.
  • Improved custom preassembly functions for location and time matching in
    indra.preassembler.custom_preassembly.
  • Preliminary integration of a Gilda client with Grounding mapper in
    indra.preassembler.grounding_mapper.gilda.

Output assemblers

  • Improved headings and grounding display in the HTML assembler in
    indra.assemblers.html.
  • Generalize INDRA Net assembler to causal influences and associations in
    indra.assemblers.indranet.
  • Make PySB assembler compatible with PySB 1.9 in indra.assemblers.pysb.

Resources

  • Integrate new WorldModelers ontologies with INDRA in
    indra.preassembler.make_wm_ontologies.
  • Updates to FamPlex and other grounding resources.
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INDRA v1.14.1

23 Sep 18:35
@bgyori bgyori
1.14.1
cbce65d
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INDRA v1.14.1

Representation

  • New MovementContext class to represent movement time/places for Events
  • New QuantitativeState class to represent specific quantities associated with Events

Input sources

  • Support for extracting Migration statements from CWMS in indra.sources.cwms
  • Adaptation to changes in Eidos API and output format in indra.sources.eidos
  • Adaptation to changes in Hume API and output format in indra.sources.hume
  • Custom processor for migration tables in indra.sources.eidos.migration_table_processor
  • Support for representing source counts in INDRA DB REST in indra.sources.indra_db_res

Internal assembly

  • Significantly improved and generalized DB refs name standardization, and preassembly matching/refinement for all entities including chemicals and biological processes
  • New custom matches/refinement function feature in Preassembler in indra.preassembler and BeliefEngine in indra.belief
  • Support for new World Modelers ontology
  • Grounding mapper refactored with new misgrounding map functionality in indra.preassembler.grounding_mapper

Model assemblers

  • New IndraNet assembler to assemble custom networks for path finding in indra.assemblers.indranet
  • New NiceCxAssembler for streamlined CX network assembly in indra.assemblers.cx
  • Significantly improved HTML assembler with source count badges and support for templates indra.assemblers.html
  • Refactored index card assembler with extended metadata support in indra.assemblers.index_card

Database/literature clients

  • New PubChem client in indra.databases.pubchem_client
  • New miRBase client in indra.databases.mirbase_client
  • New Experimental Factor Ontology (EFO) client in indra.databases.efo_client
  • New Phenotype Ontology (HP) client in indra.databases.hp_client
  • New Disease Ontology (DOID) client in indra.databases.doid_client
  • New mapping functionalities in HGNC, MeSH and ChEBI clients
  • ScienceDirect search feature added in Elsevier client in indra.literature.elsevier_client
  • Additional article info extraction and support for getting MeSH annotations in PubMed client in indra.literature.pubmed_client.

Model analysis

  • Refactored ModelChecker with four new subclasses for analysis of specific model/network types in indra.explanation

Tools

  • S3 corpus upload feature in LiveCuration tool in indra.tools.live_curation
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