Extend golr pattern to include subj/obj equivalents and xrefs

SciGraph / golr-loader

Convert SciGraph queries into json that can be loaded by Golr

Apache License 2.0

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Extend golr pattern to include subj/obj equivalents and xrefs #26

Open cmungall opened 7 years ago

cmungall commented 7 years ago

In addition sub/obj_closure, it would be useful to have

sub/obj_equivalents - all members of equivalence clique (reflexive: includes self)
sub/obj_xrefs- all xrefs annotations for all members of clique (reflexive: includes self.curie)

These would be useful for query purposes. Currently in biolink we take the input ID and use subject_closure, which includes equivalence, but also allows parents which we don't want.

xrefs are useful for near-equivalence. E.g. when querying for gene-disease, we want to allow input of uniprot protein xref

cmungall commented 7 years ago

cc @kltm, this would be useful for GO too. Currently we don't really have a good way of keeping the schemas in sync. I think we may want a master yaml, from which to derive individual views

kltm commented 7 years ago

@cmungall not sure I'm following here. Are you talking about keeping the uber schema in sync (to maximize widget reuse, etc.) or about individual views (e.g. the very specific yaml used to autogenerate settings on a particular page, e.g. http://amigo.geneontology.org/amigo/dd_browse and https://github.com/geneontology/amigo/blob/master/metadata/ann-config.browse.yaml)? And if there was an uber schema, how would I keep my dozen or so app-level views in sync?