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Add support for use of Reactome Entity Ontology to NEO - (noctua - minerva) #624

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goodb opened this issue Aug 23, 2019 · 2 comments
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goodb commented Aug 23, 2019

In order for the GO-CAMs generated from Reactome pathways to work properly, software that works with the models needs access to an ontology that defines the physical entities within them. This ontology currently resides here: https://github.com/geneontology/pathways2GO/blob/master/exchange/generated/Reactome_physical_entities.owl

One solution would be to add this ontology into the go_lego import collection. This would make Minerva work with these models. A potential issue here is that these entities could then invade the type-ahead tools.

Note also that, as currently implemented, shex validation depends on accessing the subclass hierarchy from a sparql endpoint (rdf.geneontology.org) for each class used to type an instance. Hence the RE ontology needs to be loaded there as well - or another pattern for shex validation needs to be developed. See geneontology/go-shapes#142

Attaching a sample from the ontology.
bmp_Reactome_physical_entities.owl.txt

@goodb goodb changed the title Add support for use of Reactome Entity Ontology Add support for use of Reactome Entity Ontology to NEO - (noctua - minerva) Oct 14, 2019
@goodb goodb added the software the issue is for developers to solve label Oct 15, 2019
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goodb commented Apr 18, 2020

Assuming this is accepted geneontology/go-ontology#19288 that closes this issue.

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goodb commented May 9, 2020

fixed by geneontology/go-ontology#19288

@goodb goodb closed this as completed May 9, 2020
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