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monarch-initiative / mondo-ingest

Coordinating the mondo-ingest with external sources
https://monarch-initiative.github.io/mondo-ingest/
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Create ORDO subset ROBOT template: Delete `ordo-construct-subsets.ru`? #514

Open joeflack4 opened 1 month ago

joeflack4 commented 1 month ago

Overview

Regarding $(COMPONENTSDIR)/ordo.owl. I noticed it has --update ../sparql/ordo-construct-subsets.ru \.

ordo-construct-subsets.ru

```sparql INSERT { ?cls oio:inSubset ?subset } WHERE { ?category rdfs:subClassOf phenome: . ?cls rdfs:subClassOf+ ?category . ?category rdfs:label ?categoryLabel . BIND( URI(CONCAT("http://purl.obolibrary.org/obo/mondo#ordo_", REPLACE(?categoryLabel, " ", "_"))) AS ?subset) } ```

But this now seems out of date. With #510, it seems like we don't care about what this query is doing; we don't care what the new/changed ORDO subset labels are. We're mapping these subset classes to the MONDO subset properties we've been using in the past:

SUBSET_MAP = {
    'Orphanet:557493': 'http://purl.obolibrary.org/obo/mondo#ordo_disease',  # disorder
    'Orphanet:557492': 'http://purl.obolibrary.org/obo/mondo#ordo_group_of_disorders',  # group of disorders
    'Orphanet:557494': 'http://purl.obolibrary.org/obo/mondo#ordo_clinical_subtype' }  # subtype of a disorder

I can think of additional ways we might want to tweak here. But it seems like we can get rid of ordo-construct-subsets.ru?

Additional info

Context:

matentzn commented 1 month ago

Low priority.