Ontology meeting 2014-07-17

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Alpha-glucosidase definition is more specific than its name


isa vs partof in GO and Uberon

we have cases where we need to resolve if isa or partof is the correct relation to use:

uberon has been modified to follow GO's classification except for a few cases where GO needs to change:

phases and cycles

I've added 'biological phase ; GO:0044848' as discussed last week.

I think we should use happpens_during between phases and cycles, and between phases and processes that occur during them e.g.:

  • cell cycle phase happens_during cell cycle
  • uterine wall breakdown happens_during menstruation

I also think for consistency phases shouldn't have regulation terms - i.e. you can regulate the processes that happen during a phase, but not the phase itself. The cell cycle phase regulation terms were already obsoleting but we have some regulation of hair cycle phase terms remaining.

Everyone happy?

Protege 5 testing


New search tool problems: Submit bug & feature requests or roll our own?

Annotating protein complexes - blurring the line between the ontology and annotation

Rachael asks

   "for annotation of a protein complex entity to a GO:protein complex term, the default annotation 
   part_of doesn't seem correct as you would be saying the complex is part_of GO:<x> complex. 
   Should we be using is_a in these cases?"

I replied:

   "There could be an is_a 'relationship' between an annotated protein complex and one in GO, 
    but this is not guaranteed, so would need to be recorded by the annotator (probably as a qualifier)."

I had a meeting yesterday with Sylvie Ricard and Birgit Meldal on terms for ECM components & things that bind them. There was much confusion about what counted as annotation and what goes into the ontology. Not surprising when we have complex term for homotrimers of collagens, and these have part relations to other, larger complexes and have their function recorded via capable_of / capable_of_part_of relations to MF / BP. i.e., in these cases we already have something like CC, MF & BP annotation for collagen gene products (at least when they are part of homotrimers - which is much of the time.

Both of these examples are symptoms of a blurring of the lines between annotation and ontology building. I think we need a longer term plan to manage the division of labour here. Should we be aiming for protein complexes to become the responsibility of Intact + annotators rather than being in GO?