Difference between revisions of "Protein Complex Conference Call July15, 2015"

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(Created page with "Category:Protein Complex ==Agenda== Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015 ==annotating to non-prot...")
 
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Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015
 
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015
  
==annotating to non-protein molecule binding==
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==Matter arising from last meeting==
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# Integration of curation via P2GO: any communication between Sandra, Judy and Tony?
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# Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.
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==Bumped from last meeting==
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# annotating to non-protein molecule binding
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Example:
 
Example:
 
Maltose transport complex
 
Maltose transport complex
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http://www.ebi.ac.uk/intact/complex/details/EBI-10045577
 
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!
 
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?
 +
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- 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 everyones 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).
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# Mixed species evidence
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- Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!
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- 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.
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# Ruth: Does it make sense to have process annotations with IPI?

Revision as of 01:28, 13 July 2015


Agenda

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

Matter arising from last meeting

  1. Integration of curation via P2GO: any communication between Sandra, Judy and Tony?
  2. Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.

Bumped from last meeting

  1. 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 everyones 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).

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

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