Ontology meeting 2016-02-04

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Attendees: Paola, Tanya, Harold, Chris, David OS, Melanie, Heiko, Paul

Minutes: Melanie

Peptide vs. protein

Stemming from https://github.com/geneontology/go-ontology/issues/12259

Last I remember, we discussed a related issue about a year ago, in an email thread on the editors list ("polypeptide vs. protein"). Following that, we moved from referring to CHEBI:15841 polypeptide and/or CHEBI:36080 protein, to using PR:000000001 ! protein. E.g.

protein complex has_part PR:000000001 ! protein

protein-DNA complex has_part PR:000000001 ! protein

Do we have a (different) SOP for peptides (less than 50 aa) vs proteins, or do we consider any polypeptide a protein? (It seems that PRO doesn't distinguish between <50aa or >50aa long, is that correct?)

We probably discussed this before, is it recorded anywhere?

Minutes Harold: protein implies it is coded. Peptides could be pieces of protein coming from anywhere. What is difference between peptidase and protease activity? If only talking about peptide bonds none. Unless we want to consider substrate specificity. Decision: have peptidase activity, and make protease a narrower synonym. Synonyms are used to help find the right term. Peptidase reflects the general peptide bond hydrolase activity, and in some cases they are also proteins.

Review Trello board

Action item from yesterday's managers call:

  • GO managers will need to update the sections for which they are responsible by next week
    • Add questions if needed
    • Remove old issues
  • PIs will review at next week's GO top call

https://trello.com/b/IdtTLGEt/go-priorities

Minutes

  • LEGO examples: some on GO wiki (hand copied and out of date). AEs under github, e,g, has_regulation_target - https://github.com/geneontology/annotation_extensions/tree/master/doc - has LEGO model. (needs to be retrieved - Chris to do). No plans to have sub relations of has_input in Noctua. How does that fit with automated classification as they are widely used? Wider discussions to be had at LEGO meeting. Card renamed to “ensure relations are consistent between LEGO, extensions and ontology”
  • MF masterplan: key thing was to add axiomatization to the branch, e.g. substrates, products etc for reaction. Can Chris script something? Multiple inheritance -> rich axiomatisation would help automate classification. David OS will add link to new MF document to Trello and create individual tracker items under MF refactoring github. Somewhat related (though not “MF refactoring" stricto sensu): David has already done a round of TF renaming, will do 2nd round. Need patterns for compound functions.
  • Deepening annotations. Idea was to use col 16 and target of protein binding to push down to more specific term in ontology. Chris presented in Barcelona. Paul: should we talk to PRO to take it on? E.g., something that binds actin class of protein (structure/class rather than function related) AI: Paul to follow up to get a protein family ontology in place. Need to be able to refer to a class of protein (Harold mentions PRO doesn’t have insulin as a general class for example). Harold will also bring this up at next PRO call on Monday.
  • David adding card for ETINEs and another for design patterns

AI for all: clean up Trello board

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