Protein Complex Conference Call July15, 2015

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Agenda

Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015

Matters arising from last meeting

  • Export of annotations from CP to GO:
  • Annotating in CP vs GO - philosophical contemplations by Birgit...
    • The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)
    • So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!
  • Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.
  • Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.

Bumped from last meeting

Annotating to non-protein molecule binding

Example: Maltose transport complex http://www.ebi.ac.uk/intact/complex/details/EBI-6477643 where I did annotate with the maltose binding term although maltose is an integral part of the complex. On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.

Telomerase catalytic core complex http://www.ebi.ac.uk/intact/complex/details/EBI-10045577 where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!

  • We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?
  • Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).


Mixed species evidence

  • Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!
  • Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.


Inferring annotations between species

  • In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.
  • We use ISO between species and ISS when the proteins are homologues from the same species, usually within the same protein family.


Process annotations

  • Ruth: Does it make sense to have process annotations with IPI?