Annotation Conf. Call, January 14, 2014

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Agenda

Jenkins Report

Are groups checking the Jenkins report for their GAF? Any questions?

Guidelines for Enzyme regulator activity

Should 'enzyme regulator activity ; GO:0030234' be limited to gene products that directly regulate (e.g. bind to) an enzyme. Should the definition be modified and the term also be a child of enzyme binding?

  • How much do curators need to know about the mechanism of regulation to use the MF term?
  • Do we require experimental evidence for a physical interaction to use the 'enzyme regulator activity' terms?
  • If binding is demonstrated for an ortholog, but inhibition for the protein of interest, is that enough to make the 'enzyme regulator activity' annotation?
    • Example: C. elegans MAI-2 shows inhibitory activity for the mitochondrial F0F1-ATPase, but direct binding between the inhibitor and catalytic subunit of the enzyme has been demonstrated in yeast.
  • Are there other enzyme regulator activities that don't involve direct binding to the enzyme?
  • If mechanism is not known, should curators only use the BP term?

Histone kinase terms (mentioning specific residues in term names)

Continued from last call: There are some histone kinase terms that include the name of the residue that is being phosphorylated in the term name itself (http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0035174#lineage). Although histones are very well conserved, there are still some differences in the sequence and the serine is always not in the same position in all organisms, but often the context is the same (i.e it is +/- one or two residues).

  • It is not clear if curators should request granular term with specific residues in the term name.
  • how do we capture functional equivalence in GO term name?

UniProt-GOA species-specific files

We plan to stop submitting the GOA species-specific GAFs if the species is one owned by another group, that is the following files; http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/gene-associations/

  • gene_association.goa_arabidopsis
  • gene_association.goa_mouse
  • gene_association.goa_rat
  • gene_association.goa_zebrafish

Users will still be able to get these files from the UniProt-GOA ftp site, or from the UniProt multispecies file.

We will announce this in our next release (10th December) and probably stop providing them early next year (end of January).

However, if you are one of the groups above, could you ensure that you are picking up annotations from other groups for your species so that you have a full set of annotations (remembering to consider the annotation extension column, your database may have the same annotation but without an annotation extension that another group has provided).

If your group is using Protein2GO then you will be getting the full set of annotations back from us anyway.