Ontology meeting 2022-02-28

From GO Wiki
Jump to navigation Jump to search
  • Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
  • Present:
  • Regrets:


Announcements

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InterPro file out of date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

https://github.com/geneontology/go-ontology/issues/22721

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

https://github.com/geneontology/go-ontology/projects/1


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.

Retrieved from "https://wiki.geneontology.org/index.php?title=Ontology_meeting_2022-02-28&oldid=82051"