Difference between revisions of "Manager 20Oct10"

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(Evidence Proposal)
 
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[[Category:GO_Managers_Meetings]]
 
==Present:==
 
==Present:==
Kara Dolinski, Pascale Gaudet, Rachel, Jane, David Hill, Rama, Chris
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Kara Dolinski, Pascale Gaudet, Rachel, Jane, David Hill, Rama, Chris, Mike C, Judy, Suzi, Paul Sternberg, Paul Thomas
  
 
==Discussion topics==
 
==Discussion topics==
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*Protein binding:
 
*Protein binding:
**At the GOC meeting we agreed to explore the possibility of incorporating interaction data from bioGRID/Intact/IMAX. In terms of priority, where does this fit? Should we form a working group?
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**At the GOC meeting we discussed taking the data from these interaction databases to incorporate these data into GO, and vice-versa.  Since the GOC, BioGRID has been working with WormBase and ZFin on leveraging their GO protein binding annotations to add these as interactions into BioGRID/IMEX.  Kara and Harold will discuss what to do for MGI.  Chris will explore the data flow in the other direction (BioGRID/IMEX -> GO). [[Binding Workflow Proposal]]  In general, we need to think about whether/how we want to remain in the protein binding/interaction annotation business.
  
 
*Evidence summation:  
 
*Evidence summation:  
**I started a wiki page with some notes. Again, not sure where it fits in terms of priority. Seems like ECO needs to be in place first. Can we form a WG and start discussing this regularly?
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**Rama started a wiki page with some notes
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http://gocwiki.geneontology.org/index.php/Chain_of_Evidence
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Again, not sure where it fits in terms of priority. Seems like ECO needs to be in place first. We have a WG assembled from Bar Harbor and start discussing this regularly. (Rama will add a link to Alex's page).  For the WG task list:  pilot study on richer annotation, three different use cases.
  
 
==Ref Genome==
 
==Ref Genome==
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Discussed pilot study for tree annotation.  To do this correctly, we should add at least a couple more tree annotators and do a wider range, ~20 hrs for two weeks, plan to do this for the first two weeks in December.
  
 
==Ontology Development==
 
==Ontology Development==
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==Software==
 
==Software==
 
*AmiGO 1.8 out soon
 
*AmiGO 1.8 out soon
*OBO-Edit 2.1 - addresses outstanding bugs. There will be another maintenance release - 2.2 - before freeze.
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*OBO-Edit 2.1 - addresses outstanding bugs. There will be another maintenance release - 2.2 - before freeze.  See Time Line page for details.
*Have money for 3 one-year positions - Berkeley position filled, two still available at Stanford.==Agenda==
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*Have money for 3 one-year positions - Berkeley position filled, two still available at Stanford.

Latest revision as of 11:21, 27 June 2014

Present:

Kara Dolinski, Pascale Gaudet, Rachel, Jane, David Hill, Rama, Chris, Mike C, Judy, Suzi, Paul Sternberg, Paul Thomas

Discussion topics

Annotation

  • Updating annotation documentation: Rama. Talking to Amelia about final touches (tabs on pages); text is good to go.

Evidence Proposal

http://gocwiki.geneontology.org/index.php/Chain_of_Evidence

  • ECO proposal:
    • Pascale mentioned that other curators were interested in knowing about the new ECO proposal.
    • Put the proposal (and all the comments so far) together, get some specific use cases.
    • Have a conf.call with Michele to come consensus and to further flesh out/finalize
    • After it is more polished, suggest to Michele that she perhaps send proposal to GO Friends, biocurator mailing list.
  • Protein binding:
    • At the GOC meeting we discussed taking the data from these interaction databases to incorporate these data into GO, and vice-versa. Since the GOC, BioGRID has been working with WormBase and ZFin on leveraging their GO protein binding annotations to add these as interactions into BioGRID/IMEX. Kara and Harold will discuss what to do for MGI. Chris will explore the data flow in the other direction (BioGRID/IMEX -> GO). Binding Workflow Proposal In general, we need to think about whether/how we want to remain in the protein binding/interaction annotation business.
  • Evidence summation:
    • Rama started a wiki page with some notes

http://gocwiki.geneontology.org/index.php/Chain_of_Evidence

Again, not sure where it fits in terms of priority. Seems like ECO needs to be in place first. We have a WG assembled from Bar Harbor and start discussing this regularly. (Rama will add a link to Alex's page). For the WG task list: pilot study on richer annotation, three different use cases.

Ref Genome

Discussed pilot study for tree annotation. To do this correctly, we should add at least a couple more tree annotators and do a wider range, ~20 hrs for two weeks, plan to do this for the first two weeks in December.

Ontology Development

  • Ruth emailed to request some ontology development meetings - Judy will forward email
  • GOCHE completion - in time for grant? Paper probably be finished in time for renewal in Jan 2011, implementation some time later.
  • BP x BP cross-products implemented

Software

  • AmiGO 1.8 out soon
  • OBO-Edit 2.1 - addresses outstanding bugs. There will be another maintenance release - 2.2 - before freeze. See Time Line page for details.
  • Have money for 3 one-year positions - Berkeley position filled, two still available at Stanford.