monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
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mode of inhertance in OMIA #996

Open cmungall opened 3 years ago

cmungall commented 3 years ago
<https://monarchinitiative.org/MONARCH_b01942868932e748feaa> <http://purl.org/oban/association_has_object> <http://purl.obolibrary.org/obo/GENO_0000150> .
<https://monarchinitiative.org/MONARCH_b01942868932e748feaa> <http://purl.org/oban/association_has_predicate> <http://purl.obolibrary.org/obo/RO_0000091> .
<https://monarchinitiative.org/MONARCH_b01942868932e748feaa> <http://purl.org/oban/association_has_subject> <https://omia.org/OMIA000218-9615> .
<https://monarchinitiative.org/MONARCH_b01942868932e748feaa> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/oban/association> .

Which translates to:

'Collie eye anomaly in dog' has-disposition obsolete autosomal recessive inheritance

http://purl.obolibrary.org/obo/GENO_0000150 replaced by http://purl.obolibrary.org/obo/GENO_0000148

  1. we should have a general check for references to obsolete classes across the KG
  2. we shouldn't use abstract non-user friendly predicates like has-disposition
  3. let's align with how we do this in mondo (we use http://purl.obolibrary.org/obo/RO_0002573 but we may want to change this)

question for @mbrush do we really need two classes for AR inheritance, one in GENO, one in HPO? I don't think HPO will give us theirs but can we not treat the HPO one as generic?

We may also want to fold the omia dipper into mondo (cc @matentzn )