Annotation Conf. Call, January 14, 2014: Difference between revisions

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Should 'enzyme regulator activity ; GO:0030234' be limited to gene
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?
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?
*Do we require experimental evidence for a physical interaction to use the 'enzyme regulator activity' terms?


==Histone kinase terms (mentioning specific residues in term names)==
==Histone kinase terms (mentioning specific residues in term names)==

Revision as of 10:40, 14 January 2014

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?

  • Do we require experimental evidence for a physical interaction to use the 'enzyme regulator activity' terms?

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;

  • 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.