Skip to content
This repository has been archived by the owner on Apr 12, 2023. It is now read-only.

Class info page should show axiom annotations, synonym types etc #1548

Open
cmungall opened this issue Feb 28, 2018 · 0 comments
Open

Class info page should show axiom annotations, synonym types etc #1548

cmungall opened this issue Feb 28, 2018 · 0 comments

Comments

@cmungall
Copy link
Member

Currently the monarch class page misses a lot of information

  • definition xrefs (modeled as axiom annotations in OWL, which currently are not available in scigraph) important to have this, ontologies like MONDO use a lot of defs from other ontologies
  • synonym xrefs
  • other axiom types

In fact this corresponds exactly to problems in amigo: geneontology/amigo#473

amigo and monarch developers will coordinate on the development of this, cc @kltm @kshefchek @deepakunni3

The amigo and monarch widgets will both consume the same JSON format for representing the class info, documented here https://github.com/geneontology/obographs/ and also described here https://douroucouli.wordpress.com/2016/10/04/a-developer-friendly-json-exchange-format-for-ontologies/ (all monarch devs should read this to understand the ontology model we are using).

I see no reason not to use the same javascript widget for rendering. amigo and mi may want to plug in slightly different href renderers but this should be straightforward, cc @putmantime @DoctorBud

The json may be delivered in slightly different ways. Currently amigo gets its entire knowledge of the world from solr, so we are caching the class info blob in the solr document.

mi gets it's info on ontologies from SG but unfortunately SG is lacking here, the neo4j property graph model only allows edge properties if the value is a node, not a literal. However, this should be straightforward. We either

  • come up with a SG fix to cleanly support all axiom annotations
  • cache the blob in SG as a string
  • cache the blob in solr, as for amigo
  • use biolink

Either way, the json format remains the same

Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant