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geneontology / noctua

Graph-based modeling environment for biology, including prototype editor and services
http://noctua.geneontology.org/
BSD 3-Clause "New" or "Revised" License
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Add support for use of Reactome Entity Ontology to NEO - (noctua - minerva) #624

Closed goodb closed 4 years ago

goodb commented 4 years ago

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 https://github.com/geneontology/go-shapes/issues/142

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

goodb commented 4 years ago

Assuming this is accepted https://github.com/geneontology/go-ontology/pull/19288 that closes this issue.

goodb commented 4 years ago

fixed by https://github.com/geneontology/go-ontology/pull/19288