GO-CAM Noctua Call 2018-05-23: Difference between revisions

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** live updates
** live updates
** login and groups across clients and workbenches
** login and groups across clients and workbenches
== Annotation ==
== Annotation ==
*Editing ('conventional' and GO-CAM)
*Editing ('conventional' and GO-CAM)
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*Annotation extension relations white list
*Annotation extension relations white list
== Landing Page ==
== Landing Page ==
*Model searching
*Model searching (production)
*Model titles - need guidelines
== Model Seeding ==
== Model Seeding ==
*From GAFs
*From GAFs
Line 44: Line 44:


= Minutes =
= Minutes =
*On call: Dustin, Harold, Karen, Kimberly, Laurent-Philippe, Li, Liz, Pascale, Peter, Rob, Sabrina, Sandy, Tremayne
*On call: Ben, Dustin, Edith, Harold, Jim, Karen, Kimberly, Laurent-Philippe, Li, Liz, Pascale, Peter, Rob, Sabrina, Sandy, Seth, Stacia, Suzi A., Tremayne
[[Category: Annotation Working Group]]
 
 
== Internals ==
*Need to work on the middleware to make things more robust and scalable
*Align internals, decide what can be reused
*Overall goal is to facilitate long-term maintenance
== Annotation ==
*Tremayne and Laurent-Philippe working on queries and UI for editing conventional and GO-CAM annotations
== Error checks ==
*Software group will work on incorporating annotation rules
== GPAD Outputs ==
*Protein complexes - protein complex working group needs to provide different models for helping to determine how MF annotations should be propagated to individual complex members
*Annotation extension relations white list - Jim, David, and Kimberly will continue to look at annotation extensions, shore up any remaining issues with what to include
== Landing Page ==
*Model searching (production)
**Model searching is equally important for searching models in 'Development'
**We may start with a basic set of searches, e.g. GO terms, references, genes, curator, and then provide a more detailed search interface to enable searching over any annotation field or piece of metadata
*Model titles - need guidelines
**Currently no rules or guidelines for model titles, but if we are going to keep giving titles, some standardization is needed.
**Some more brainstorming needed here.
== Model Seeding ==
*From GAFs
**Dustin working on this for PomBase GAF; may also work with David H
*From Reactome
**Ben has seeded GO-CAMs for human pathways based on Reactome annotation
**Feedback from curuators (see working group below) would be helpful
**Waiting on some technical developments, but in the meantime working on imports from other sources
== Relations ==
*We need to review:
**CC annotation relation alignment with CC ontology relations
**Use of has_input vs has_participant for binding annotations
**Differences between 'directly positively regulates' and 'directly activates' (also for negatively regulates and inhibits)
== Templates ==
*Create and use templates for curation
*This should also be part of the working group's task
== Text Mining ==
*TPC integration into form
*Graph editor allows for searching TPC corpus for MF annotations
*Need to integrate with form editor and expand to BP and CC
 
= GO-CAM Modeling Working Group =
*[https://doodle.com/poll/zwxmfztwxzifyfxv Link to Doodle Poll]
*GO-CAM working group will convene to discuss specific modeling issues, add to documentation
*Group may also help to guide specifications for tool enhancements, further development
 
= Onboarding Additional Curation Groups =
*Need to start with basic use of the Noctua form and entering simple annotations
*Uncertainty about which relations to use and how to correctly apply evidence has been a hurdle for some groups
 
 
[[Category:GO-CAM]]

Latest revision as of 05:46, 16 April 2019

Meeting URL

https://stanford.zoom.us/j/679970729

Discuss Development Priorities

Internals

  • refactoring
  • stack alignment
    • common widgets/UI
  • paying down debt
  • functional parity
    • live updates
    • login and groups across clients and workbenches

Annotation

  • Editing ('conventional' and GO-CAM)
  • Model cloning

Error checks

  • Incorporating annotation rules into Noctua

Evidence codes

  • Working with ECO to create manual/automatic assertion children

GPAD Outputs

  • Protein complexes
  • Annotation extension relations white list

Landing Page

  • Model searching (production)
  • Model titles - need guidelines

Model Seeding

  • From GAFs
  • From Reactome

Relations

  • Reconcile CC annotation relations with CC ontology relations
  • Use of has_input vs has_participant for binding annotations

Templates

  • Create and use templates for curation

Text Mining

  • TPC integration into form

GO-CAM Modeling Working Group

  • Engage at least one curator from each annotation group in GOC
  • Discuss specific modeling issues
  • Add to GO-CAM curation documentation
  • When to meet?

Onboarding Additional Curation Groups

  • Next groups to bring onboard

Minutes

  • On call: Ben, Dustin, Edith, Harold, Jim, Karen, Kimberly, Laurent-Philippe, Li, Liz, Pascale, Peter, Rob, Sabrina, Sandy, Seth, Stacia, Suzi A., Tremayne


Internals

  • Need to work on the middleware to make things more robust and scalable
  • Align internals, decide what can be reused
  • Overall goal is to facilitate long-term maintenance

Annotation

  • Tremayne and Laurent-Philippe working on queries and UI for editing conventional and GO-CAM annotations

Error checks

  • Software group will work on incorporating annotation rules

GPAD Outputs

  • Protein complexes - protein complex working group needs to provide different models for helping to determine how MF annotations should be propagated to individual complex members
  • Annotation extension relations white list - Jim, David, and Kimberly will continue to look at annotation extensions, shore up any remaining issues with what to include

Landing Page

  • Model searching (production)
    • Model searching is equally important for searching models in 'Development'
    • We may start with a basic set of searches, e.g. GO terms, references, genes, curator, and then provide a more detailed search interface to enable searching over any annotation field or piece of metadata
  • Model titles - need guidelines
    • Currently no rules or guidelines for model titles, but if we are going to keep giving titles, some standardization is needed.
    • Some more brainstorming needed here.

Model Seeding

  • From GAFs
    • Dustin working on this for PomBase GAF; may also work with David H
  • From Reactome
    • Ben has seeded GO-CAMs for human pathways based on Reactome annotation
    • Feedback from curuators (see working group below) would be helpful
    • Waiting on some technical developments, but in the meantime working on imports from other sources

Relations

  • We need to review:
    • CC annotation relation alignment with CC ontology relations
    • Use of has_input vs has_participant for binding annotations
    • Differences between 'directly positively regulates' and 'directly activates' (also for negatively regulates and inhibits)

Templates

  • Create and use templates for curation
  • This should also be part of the working group's task

Text Mining

  • TPC integration into form
  • Graph editor allows for searching TPC corpus for MF annotations
  • Need to integrate with form editor and expand to BP and CC

GO-CAM Modeling Working Group

  • Link to Doodle Poll
  • GO-CAM working group will convene to discuss specific modeling issues, add to documentation
  • Group may also help to guide specifications for tool enhancements, further development

Onboarding Additional Curation Groups

  • Need to start with basic use of the Noctua form and entering simple annotations
  • Uncertainty about which relations to use and how to correctly apply evidence has been a hurdle for some groups