biolink / biolink-model

Schema and generated objects for biolink data model and upper ontology
https://biolink.github.io/biolink-model/
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Two discrepencies in `OMIM` prefix #1485

Open gaurav opened 6 months ago

gaurav commented 6 months ago

(This is a minor issue, so please feel free to close it as won't-fix if these issues aren't important to Biolink.)

Here is the definition of OMIM in Biolink:

https://github.com/biolink/biolink-model/blob/1698cf997785490304a617123d5e3a242c6b2bc0/project/prefixmap/biolink_model_prefix_map.json#L131

When comparing their definitions to the OMIM linking documentation I noticed two discrepencies:

  1. http://purl.obolibrary.org/obo/OMIM_ does not actually work as an IRI stem, e.g. OMIM:608450 ("BLACE") cannot be resolved as http://purl.obolibrary.org/obo/OMIM_608450. The OMIM documentation says that either https://omim.org/entry/608450 or https://omim.org/MIM:608450 should be used instead. I suggest we change the IRI stem for OMIM unless it would be too disruptive.
  2. OMIM says that the prefix that should be used is MIM:, not OMIM:. This would be a pretty major change, but would bring us in line with e.g. the Disease Ontology, which is changing xrefs from OMIM: to MIM:.