Release

- New omim.ttl
- Also now generating omim.sssom.tsv for release

makefile
- Added SSSOM command

Requirements
- Added sssom to Pipfile

data/
- Updated HGNC mapping file to a better one.
- Removed some TSV variations on canonical OMIM files

Ingest updates
- Now creates TSVs in data/ cache
- Now downloads genemap2.txt
- oboInOwl:hasDbXref --> skosExactMatch
  - Did for UMLS
  - Did for Orphanet
  - Did in one other location
- Updated curie_map

.gitignore
- Added some new files

.gitignore

@@ -13,8 +13,18 @@ __pycache__/
 
 # OMIM data sources
 mim2gene.txt
+mim2gene.tsv
 mimTitles.txt
+mimTitles.tsv
 genemap2.txt
+genemap2.tsv
 morbidmap.txt
+morbidmap.tsv
 phenotypicSeries.txt
+phenotypicSeries.tsv
 allelicVariants.txt
+allelicVariants.tsv
+
+# SSSOM command outputs
+omim.sssom.log.txt
+omim.sssom.log_unique-messages.txt

Pipfile

@@ -13,6 +13,7 @@ pandas = "*"
 pyyaml = "*"
 requests = "*"
 python-dotenv = "*"
+sssom = "*"
 
 [requires]
 python_version = "3.8"

data/dipper/curie_map.yaml

@@ -76,7 +76,7 @@
 'OMIA': 'https://omia.org/OMIA'                                     # Online Mendelian Inheritance in Animals (disease/species)
 # LIDIA seems retired. so these are not resovable                   # Also: http://www.vetsci.usyd.edu.au/lida/
 'LIDA': 'http://sydney.edu.au/vetscience/lida/dogs/search/disorder/'  # Listing of Inherited Disorders in Animals (defunct?)
-'OMIM': 'http://omim.org/entry/'                                    # Online Mendelian Inheritance in Man (human disease and variants)
+'OMIM': 'https://omim.org/entry/'                                    # Online Mendelian Inheritance in Man (human disease and variants)
 'OMIMPS': 'http://www.omim.org/phenotypicSeries/PS'                   # Online Mendelian Inheritance in Man (phenotypes)
 'ORPHA': 'http://www.orpha.net/ORDO/Orphanet_'                      # Rare diseases and Orphan drugs
 'PATO': 'http://purl.obolibrary.org/obo/PATO_'                      # Phenotypic Quality Ontology

data/metadata.sssom.yml

@@ -0,0 +1,9 @@
+mapping_set_id: http://example.org
+license: http://w3id.org/sssom/license/unspecified
+creator_id: https://orcid.org/0000-0002-2906-7319
+curie_map:
+  HGNC: "https://identifiers.org/hgnc:"
+  HGNC_symbol: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/
+  OMIM: https://omim.org/entry/
+  UMLS: http://linkedlifedata.com/resource/umls/id/
+  ORPHA: http://www.orpha.net/ORDO/Orphanet_