Annotation Conf. Call July 9, 2013

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Agenda

QC check for Enzyme binding

  • We would like to propose that there shouldn't be any direct annotations to 'enzyme binding' term. We will add a 'not for direct manual annotation' tag to this term.

Protein oligomerization

Continuing our discussion on Protein oligomerization, we want to bring up some options to curtors.

  • Protein di/tri/oligomerization terms: In many cases where the functional unit is a hetero or homo dimer or oligmer, the best option would be to use col-16 to indicate the functional unit using a PRO ID (or other type of complex ID).
  • In cases where geneproduct A is involved in the oligomerization of another gene product B, then the appropriate term would protein complex assembly and indicate the complex in col-16.

Protein binding annotations

  • Moving protein binding to its own file. Chris came up with the idea of keeping the protein binding terms in the GO, but pulling all protein binding annotations from various curation streams into one GAF file. This seems like a good solution that will make both parties happy.

Discussion

  • Enzyme Binding check:
    • Ruth- How specific should the enzyme binding term be? i.e. is it okay to annotate to ligase as opposed to a specific ligase.
    • Rama- general guideline should be to annotate to specific term. If the authors show what type of ligase the gp bound to, then the term should be specific to what was reported.
    • While requesting new enzyme binding terms, make sure the specific enzyme activity term exists to begin with, and consider only annotating to the granularity available for the MF enzyme activity term. May be a TermGenie template can be made.
    • Li - would it be possible to add some of the high level enzyme binding terms, eg ligase binding, based on the MF enzyme activity ontology that exists?
    • We don't want to add enzyme binding terms for all enzyme activity terms proactively. We will add them on a need to have basis.
  • Protein oligomerization terms
    • Some people find these annotations useful, some don't. GOC should come up with a policy to make sure everybody is doing it consistently.
    • One option would be to make complex terms for these dimers/oligomers and then start annotating complexes since the complex is the functional unit
    • Since there are several curation and publishing policies may be the best solution would be to be all inclusive which lead to the next agenda item.
    • Protein oligomerization status may also be an important piece of information for LEGO curation, i.e. what is the functional unit?
  • Consolidating Protein binding curation
    • There are several curation pipelines to curate interactions. It doens't make sense to duplicate efforts and come up with rules for when to annotate protein binding although it seems like people are more strict when they annotate binding for GO compared to an interaction database.
    • IntAct captures self-binding (dimerization etc)
    • Consolidate all interaction data (BioGRID, IntACT, ?) into a single GAF file.
    • What are groups' criteria for capturing protein binding annotations? Are we consistent about what is annotated for GO?
    • Midori will share pombe's guidelines for protein binding curation (see here:

http://sourceforge.net/apps/trac/pombase/wiki/GOAnnotationGuidelines) and Rachael will look into sharing IntAct's guidelines for exporting binary interactions to UniProt-GOA (see here: http://www.ebi.ac.uk/intact/pages/faq/faq.xhtml;jsessionid=12973C8DDB1BEE6F56CE4CEF2ED8B4CE#4)

    • Some issues to think about - methods used for assaying physical interaction, biological relevance of physical interaction - can this always be determined?
    • Look into mapping some of the protein binding annotations to more specific binding terms (rules need to be worked out)
    • We will circulate a proposal for all of these.
  • SF digest emails
    • We are not getting daily digest emails from SF since they upgraded. The script that sent these emails need to be fixed to point to the new/correct URLs.
    • MikeC probably has this script. Rama will talk to MikeC.
  • New Curators
    • Aleksandra is a new curator with the GOA/EBI group
    • Moni is a new curator with Suzi/Berkeley group