Ontology meeting 2022-02-28

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  • Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
  • Present:
  • Regrets:


Convert GitHub issue references to IRI values

Following up on previous discussion points

Ontology Curator Pathway book

Added a link in the GO doc: Ontology_Development#Documentation

InterPro file out of date

See ticket https://github.com/geneontology/go-site/issues/1786 and https://github.com/geneontology/goontology/blob/7e1c1691c31dfc25b4ce6149c016c1c188d98683/src/ontology/Makefile

The file generated by InterPro is more recent: https://ftp.ebi.ac.uk/pub/databases/interpro/interpro2go

Actions from last week (but these were possibly incorrect)

  1. Change the Makefile (in go-ontology/src/ontology/Makefile )
  2. Check with InterPro for mappings of the databases they represent - are these maintained ? See also: https://github.com/geneontology/go-ontology/issues/16989

Transport or maintains localization relation


Discussion points

Updating KEGG links

Steven's email

Here’s a link to a spreadsheet showing current associations between KEGG metabolic pathways and GO BP terms (as shown on the KEGG webpages). https://docs.google.com/spreadsheets/d/1K7Pzmo5wpFmbCA9NdxLlBC2NNA7VNviSSG-1pr2t9T8/edit#gid=0

I recently reviewed all the associations relevant to flies and suggested some corrections/additions to KEGG (which they mostly implemented) but there may be some other cases where a GO term could be added or changed etc.

As mentioned, might be useful to add all these KEGG pathway IDs as xrefs to BP terms within the GO. Looking at go-basic.obo, I only see 3 current xrefs of type “KEGG_PATHWAY:” (and one of them (map00440) looks slightly wrong)

FYI: I contacted them using support@genome.ad.jp and my contact was Atsuko Yano.

Taxon constraints changed at each PR??

Recently there is always a big difference in changed files (specifically reasoned-pr.owl/reasoned.owl), that seem to related to taxon constraints: See for eg https://github.com/geneontology/go-ontology/pull/22879

I have been ignoring because I dont modify this file; but it would be interesting to know why this happens.

Hormone metabolic process

https://github.com/geneontology/go-ontology/issues/22899 https://github.com/geneontology/go-ontology/issues/19624 Obsolete, to only keep the chemical hierarchy for metabolic process?

Next calls

Focus on specific topics?

  • taxon constraints
  • boomer tickets
  • any other suggestion
    • relations - review work that needs to be done for 'transports or maintains localization of' as outlined in ticket

Other Business


Points from previous meetings not yet addressed

Next Priorities for Ontology group

  • Ongoing:
    • Multi-org
    • transcription
    • roles
    • aging
  • Content meetings?

Following up on previous items

  • ChEBI: Chris, Paul: Make a list of requests for ChEBI - including requesting 'developer' versions of ChEBI so we can test it ahead of releases
  • Design patterns

Changing the relation for transport and transporter activity from 'transports or maintains localization of' to 'has input'

New taxon constraints

Property range violations

  • Looks like an issue in GO, where 'cavity development' may be redundant with the equivalent 'tube' terms, or the 'tube terms are missing'?

ACTIONS: Review 'cavity terms

Sinus terms: Not sure why only 'pronephric sinus development' is causing problems others do have LDs: Chris: only 'pronephric sinus development' describes a sinus; other describe valves, venosus

Protein-complex organization/assembly/disassembly

Problem with relations used in logical definition https://github.com/geneontology/go-ontology/issues/22488

RO has been changed, so that the logical issue is fixed; however do we want to use 'results in assembly of' or 'has output' for protein-containing complex assembly? This decision impacts the relations used in GO-CAM and extensions, since we aim to align them.