Ontology meeting 2018-07-09

From GO Wiki
Jump to navigation Jump to search

Conference Line

Agenda

Editors Discussion

Project Update

Reactome-Rhea-GO Alignment----https://github.com/geneontology/go-ontology/projects/10

ECM Project--- https://github.com/geneontology/go-ontology/projects/9

Regenerate Imports File

Docker has worked successfully for regenerating the CL import and appears to have worked for the ChEBI import.

We will continue to test this for a little while longer and then train all editors in the procedure.

Obsoletion plugin for Protege

Pascale need to update their plugins. If there are issues, can you contact Jim for help?

Ontology Documentation

Nothing last week, too busy. We will resume again tomorrow.

Ontology Developers' workshop possibility

  • Now completely up in the air. November in Denver, December in Geneva?? We need to have a concrete agenda.

GH project link

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

Minutes

  • On call: Barbara, Ben, Chris, David, Eric, Harold, Jim, Karen, Kimberly, Laurent-Philippe, Paul T., Tanya

Project Update

ECM Project--- https://github.com/geneontology/go-ontology/projects/9

  • Some terms being resurrected
  • Other terms will be merged later this week

Reactome-Rhea-GO Alignment----https://github.com/geneontology/go-ontology/projects/10

  • Reactome xrefs have been updated
  • Rhea reaction xrefs will be made to the master reaction
  • Some GO functions are specifically pointing to the bidirectional reaction and these xrefs will need to be fixed
  • In order to reason, we need to incorporate all of the reactants in the ChEBI import
  • David used Docker to regenerate the ChEBI import with the new reactants
  • Size of ChEBI import is now 33MB - getting to the limit of what we can currently manage in github
  • David, Harold, and Peter will examine the new defs, do a sanity check
  • The new ChEBI file does not seem to slow down Protege, though
  • Part of the issue with the size of the ChEBI import is that the conjugate bases need to be handled in OWL
  • There are also some issues with generic chemicals as represented in Rhea that resulted in two enzymes getting the same logical definitions
  • Could these be handled manually? There might be several thousand of these (5-10%)
  • Jim - maybe the ChEBI import doesn't need to be RDF-XML; other file format options might be better here
    • Release could be RDF-XML, but the editors version doesn't need to be
    • Release files are not served off of Github, they're served off of Amazon S3

Regenerate Imports File

  • Docker has worked successfully for regenerating the CL import and appears to have worked for the ChEBI import.
  • We will continue to test this for a little while longer and then train all editors in the procedure.

Obsoletion plugin for Protege

  • Does Pascale still need to update her plugin, or is her up-to-date plugin not working?

Ontology Documentation

Nothing last week, too busy. David and Pascale will resume again tomorrow.

Ontology Developers' workshop possibility

  • Now completely up in the air. November in Denver, December in Geneva?? We need to have a concrete agenda.

Slim yaml Files

  • Pascale created yaml files for each of the slims in ontology/subsets
  • Most of these are now complete
    • Have contact information, e.g. helpdesk, and contributors
  • Travis is not actually set up to check these yet
  • Note that we have both slims and anti-slims
    • How are the anti-slims maintained?
    • What should the plan be for this subset?
    • Tools would need to implement this subset?
    • For PANTHER, they'd like to make a slim for the direct annotations propagated in PAINT, although this is still a positive slim.
      • Would you still want to subtract out the ancestors?
  • We also have subsets for annotation, e.g. 'do not manually annotate'
  • goslim_goa
    • No terms in this, will be removed
  • goslim_metagenomics
    • Terms in this one, but not clear how they were selected
    • Reach out to the metagenomics group (Rob Finn) at the EBI to see if they actually use this
  • goslim_virus
    • Developed by Jane - Pascale will ask her
  • gosubset_prok
    • Terms that don't apply to prokaryotes are in this set
    • Already labeled obsolete
    • Lots of terms (thousands) so it's not really a slim
  • termgenie_unvetted
    • Came from TermGenie free form
  • goslim_generic
    • Val maintains this one
    • There is also a comment attached to these terms, so if we remove this slim, we won't lose any information
  • mf_needs_review
    • 23 terms; David, Peter, Harold to review

Editors Discussion Tickets

  • Please review your tickets with this label and prepare a discussion or remove the label
  • Synapse disassembly
    • One TAS annotation
    • Any other annotations to synapse disassembly that haven't been released yet by the SynGO group? Barbara will check.
    • We try not to change the meaning of terms that much without obsoleting them.