Protein Complex Conference Call June19, 2015

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Agenda

Background

IntAct Portal is curating complexes and associating these complexes with GO terms. This meeting is to come up with guidelines on annotating complexes to GO terms.

  • There are two levels of annotation:
    • Annotation that are shown on the Complex Portal Website
    • Annotations that are exported from IntAct to GO or directly annotated in P2GO

Here, we are discussing which annotations should be exported from IntAct and which Complex identifiers should be available as annotation objects in P2GO.

Slides: https://drive.google.com/folderview?id=0B0BzQEtrvNZlfjJmbk5wRG5PYlZPU1N3R0tmZ2M2aUxTTTNIWHVJYnNiTUlTdWpoN0hieWc&usp=sharing


Questions for consideration

  • Does it make sense to annotate an IntAct complex to a GO complex? Is this meaningful? is this a mapping or an annotation? Should we instead annotate it to the location in the cell? e.g. ATPase complex (IntAct ID) is part_of mitochondrion (GO:5635). This will be similar to gene_product A is part of mitochondrion.

The other issue with associating an IntAct complex with a GO complex is the evidence code. If you use IPI you need to say the subunits in the With column, but this requires that you know which subunit interacts with which.

  • The other issue is the current default relation between the entity in Column 2 and the GO term for CC is part_of, which is not true in this case. So annotating complexes to complexes should be revisited.
  • MF/BP of complex (case 4 in the slides, Full MF/BP evidence available)

How does IMP work here? If authors are deleting one subunit and inferring the MF/BP of the complex, can that be used for the entire complex? Would you put the allele information in With column ?

  • Case 6, BP inferred from MF (where MF has evidence)4- BP can be inferred from MF. Since there is Exp. evidence for MF annotation, use the same PMID for the BP annotation.

Discussion

Present: Rama, Birgit, Sandra, JudyB, Harold, Kimberly, Chris, Ruth, Pascale

  • Birgit showed their IntAct interface where they associate IntAct complexes with GO terms.
  • Rama: Considering that you guys and protein2GO are neighbors, why aren't you using protein2go to curate? protein2go can handle complex IDs now and it is easier to maintain the annotations in one place. In the GOC we are encouraging curators to curate into one tool to help with consistency/data checks etc.
    • Sandra: There is a significant time lag in getting the IntAct complex IDs in protein2GO and we wanted to make the GO annotations while we were curating the complex and not wait for the complex ID to be available/integrated into protein2GO.
    • Judy: If this step can be sped up would you consider moving to protein2GO?
    • Sandra: Yes.

AI: Sandra/Judy will talk to Tony.

  • Case 3: Handling complexes that are inferred based on Chemogenomics etc (as opposed to verified)? We should have a rule to not export those annotations and IDs. The ECO code can be used to flag such complexes in IntAct as 'do not export'.

AI: discuss at GOC meeting.

  • Case 1: Should we associate IntAct complexes to GO complexes? Is this merely a mapping?
    • Harold: In PRO (which is an ontology) the logical definition takes care of the relationship between a GO and PRO complex. So this association wouldn't be necessary. PRO also annotates to MF and BP.
    • Rama: IntAct is not an Ontology though (it is just a hierarchy). So we can't treat it the same way.
    • Ruth: What if we want to capture that the complex is found in a certain cell type using col-16?
    • Pascale: The complex terms in GO are generic, while the IntAct ones are specific. So it might be okay to make this association.
    • Birgit: We will have this mapping on the Complex Portal website but can flag it as 'do not export' if we decide to go that way. Although that doesn't help Ruth's case.

AI: GOC meeting

  • Case 1: Using IPI to associate IntAct complex with GO complex. Although we said we could use IPI for this annotation, it is not very satisfactory because we can't put anything in the With column. Switch it to IDA?

AI: GOC meeting. If we decide to go with IDA we need to re-annotate in IntAct. Also depends on decision for point above.

  • Cases 2/5/7: If there is Exp evidence for a protein complex in Mouse, and if IntAct inferred the complex in Human using ISO, should we make GO MF/BP annotations for the inferred complexes?
    • Rama: I would say no.
    • Birgit: So should be tagged as 'do not export' in IntAct.

AI: discuss at GOC meeting

  • Case 4: Can we use IMP to annotate MF or BP to complexes?
    • Sandra: Maybe not, as whole chain is usually knocked out/omitted.
    • Rama: If we capture this, we should put the missing chain in the With/From column.

AI: discuss at GOC meeting

  • Case 6: For the IC annotation, Reference should be the PMID and not the GO_REF and the IntAct ID of the complex should be put in the With/From column. Should we allow IntAct IDs or the GO complex ID in the With/From column? The GO complex ID helps with book keeping though. Not sure!

AI: discuss at GOC meeting

  • Case 2 (7 for MF/BP): If we export complexes inferred by orthology/homology, put complex AC into With/From column.
  • Annotating to X binding? e.g. heme binding in hemaglobin complex.
    • Rama: Hemaglobin's function is not heme binding. So don't make that heme binding.

AI: Birgit to correct annotations in IntAct.

  • 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. But we need to decide on a similarity cut-off.

AI: discuss at next call.

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

AI: discuss at next call.