Difference between revisions of "Protein Complex Conference Call June19, 2015"

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(Discussion)
Line 26: Line 26:
 
** Judy: If this step can be sped up would you consider moving to protein2GO?
 
** Judy: If this step can be sped up would you consider moving to protein2GO?
 
** Sandar: yes. She/Judy will talk to Tony.
 
** Sandar: yes. She/Judy will talk to Tony.
 +
 +
* Handling complexes that are inferred based on Chemogenomics etc (as opposed to verified)? We should have a rule to not associate those complexes with GO terms. The ECO code can be used to flag such complexes.
  
 
* Should we associate IntAct complexes to GO complexes? Is this merely a mapping?
 
* 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.  
 
** 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.  
** Rama: IntAct is not an Ontology though (it is just a hierarchy)
+
** 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
 +
 
 +
* 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?
 +
 
 +
* 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 annotations for the inferred complexes (Case 5)?
 +
** Rama: I would say no.
 +
 
 +
* 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!
 +
 
 +
* Annotating to heme binding? Hemaglobin's function is not heme binding. So don't make that heme binding.
 +
 
 +
* How do you handle human proteins expressed in mouse, mixed species? something to think about!
 +
 
 +
* Add to agenda for the GOC meeting.

Revision as of 10:49, 22 June 2015

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.

Discussion

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

  • 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?
    • Sandar: yes. She/Judy will talk to Tony.
  • Handling complexes that are inferred based on Chemogenomics etc (as opposed to verified)? We should have a rule to not associate those complexes with GO terms. The ECO code can be used to flag such complexes.
  • 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.
    • 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
  • 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?
  • 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 annotations for the inferred complexes (Case 5)?
    • Rama: I would say no.
  • 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!
  • Annotating to heme binding? Hemaglobin's function is not heme binding. So don't make that heme binding.
  • How do you handle human proteins expressed in mouse, mixed species? something to think about!
  • Add to agenda for the GOC meeting.