OntologyClass metadata additions: alternative_names, alternative_identifiers, relations #2239
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…the OntologyClass class
…erm as a first step
…xact mappings and examples
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Adds metadata to
OntologyClassso that its collection in Mongo and its table in Postgres can hold cross-references (curie form), synonyms, and term descriptions available from external ontologies. It also adds a new class,OntologyRelation,to capture NMDC-search/display-relevant axioms/relationships (in particular,subclassOfandpart_ofrelations).In particular,r in the example data, @turbomam @cmungall - I'd like some feedback on the difference between "is_a" and "BFO:0000050" as the value for "predicate" in an OntologyRelation (using "is_a" follows the obographs convention, but I picked
rdfs:subclassOfas the predicate for "is_a" because it sort of enables consistent processing of this field by downstream software?).These changes support generic ontology metadata loading into NMDC.
Some related tickets:
microbiomedata/nmdc-server#1388 - support more facets for GO in search
microbiomedata/pilot#17 - support metadata search from ontologies
microbiomedata/pilot#12 - support ENVO search facets
microbiomedata/nmdc-field-notes#187 - field notes ENV triad term selection
We also want to provide users with more details about our existing terms. For example, we could extend the widget on the data portal search to include ontology metadata like cross-references, definitions, etc, to enable more informed selections.
Storing these metadata in Mongo and, subsequently, in Postgres might make this data more accessible for downstream tools.