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) | ||
Line 24: | Line 23: | ||
*Model searching (production) | *Model searching (production) | ||
*Model titles - need guidelines | *Model titles - need guidelines | ||
== Model Seeding == | == Model Seeding == | ||
*From GAFs | *From GAFs | ||
Line 46: | Line 44: | ||
= Minutes = | = Minutes = | ||
*On call: Ben, Dustin, Edith, Harold, Jim, Karen, Kimberly, Laurent-Philippe, Li, Liz, Pascale, Peter, Rob, Sabrina, Sandy, Stacia, Suzi A., Tremayne | *On call: Ben, Dustin, Edith, Harold, Jim, Karen, Kimberly, Laurent-Philippe, Li, Liz, Pascale, Peter, Rob, Sabrina, Sandy, Seth, Stacia, Suzi A., Tremayne | ||
== Internals == | == Internals == | ||
*Need to work on the middleware to make things more robust and scalable | *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 = | = GO-CAM Modeling Working Group = | ||
*[https://doodle.com/poll/zwxmfztwxzifyfxv Link to Doodle Poll] | *[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