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.

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.