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

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(Agenda)
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Slides: https://drive.google.com/folderview?id=0B0BzQEtrvNZlfjJmbk5wRG5PYlZPU1N3R0tmZ2M2aUxTTTNIWHVJYnNiTUlTdWpoN0hieWc&usp=sharing
 
Slides: https://drive.google.com/folderview?id=0B0BzQEtrvNZlfjJmbk5wRG5PYlZPU1N3R0tmZ2M2aUxTTTNIWHVJYnNiTUlTdWpoN0hieWc&usp=sharing
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===Questions for consideration===
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* 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.
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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.
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* 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.
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* MF/BP of complex (case 4 in the slides, Full MF/BP evidence available)
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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.

Revision as of 14:45, 18 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.