Comments (7)
@RichardBruskiewich has already done a lot of this, e.g. 9951bee
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The UMLS semantic "Groups" (e.g. GENE, CHEM, DISO, etc.) are posted to the Biolink Model, but I've not yet put in the finer grained codes (e.g. 'aapp' etc. see https://metamap.nlm.nih.gov/Docs/SemanticTypes_2013AA.txt). I guess I could tackle these soon when I'm bored with straight computer software development :-)
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the goal isn't to include all of these. We're calling this done when existing entity types in BLM have a mapping
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Is this completed?
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Ancient issue, long neglected... I note that the "semantic types" were note added. They are more fine grained than the UMLS semantic groups. I vaguely seem to recall that MediKanren may have been using them, but don't know if that is still the case.
I can strive to add them into Biolink today.
I'll use the CURIE xmlns prefix UMLSST (ST == Semantic Type). I'll obviously be selective on which ones to include since the scope of types is a superset of what Biolink covers.
For good measure(?), I can add the "codes" as UMLSSC:
e.g.
T083 geoa Geographic Area GEOG Geographic Areas
will have mappings:
UMLSSG:GEOG
UMLSST:geoa
UMLSSC:T083
Also, I assume that Biolink categories can be "one-to-many" UMLS semantic types, where the Biolink model does not make fine grained distinction between the UMLS semantic types of a given UMLS Semantic Group,
For example, the UMLS Semantic Group "DEVI" doesn't seem to have any is_a: device categories in the model, so I'll aggregate all the DEVI semantic types as mappings to the one 'device' category in Biolink.
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@cmungall are biolink category mappings supposed to be one-to-one? The reason I ask is that we have two UMLSSG:GENE mappings: one to the Biolink category "genomic entity" and the other (obviously) to "gene".
I wonder if this presents any practical difficulties with software using the Biolink model? I suspect perhaps...
The UMLS semantic types under the Semantic Group "GENE" are:
T028 gngm Gene or Genome GENE Genes & Molecular Sequences
T085 mosq Molecular Sequence GENE Genes & Molecular Sequences
T086 nusq Nucleotide Sequence GENE Genes & Molecular Sequences
T087 amas Amino Acid Sequence GENE Genes & Molecular Sequences
T088 crbs Carbohydrate Sequence GENE Genes & Molecular Sequences
Which are (carelessly) broad in Biolink scope.
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Completed the above task (I think...) and issued a pull request: #209
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Related Issues (20)
- Missing enum for approval status HOT 3
- biolink prefix in biolink-model.yaml returns 404
- Hazardous or Poisonous Substance (T131) mapped incorrectly to SmallMolecule
- Add a biolink:CommonDataElementBundle to provide an ordered list of biolink:CommonDataElement
- Incorrect mapping? skos:relatedMatch HOT 1
- SEMMED mappings to related to
- FMA identifiers don't resolve HOT 1
- Importing biolink raises ModuleNotFoundError HOT 1
- Inverses of mixin predicates don't establish an is_a path to a "root" mixin
- Obsolete Bacterium, or place it correctly
- Make the hierarchy is-a complete
- `biolink` base namespace does not redirect correctly? HOT 1
- Two discrepencies in `OMIM` prefix
- A URL from Reactome database HOT 11
- Move prefix map to src
- Prediction Qualifiers HOT 2
- Generated Python/Pydantic Models as Package? HOT 1
- Pathway `preceded_by`/`followed_by` HOT 2
- Sequence Motif PWMs
- What is the Prefix for microRNA?
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