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Meeting URL
Agenda
2019 Plans
Annotation Group Priorities
Annotation Review
- Reports from pipeline
- Manual annotations
- Mapping files, e.g. InterPro2GO
- Still some 'gocheck_do_not_annotate' mappings in InterPro2GO
- Molecular Function refactor
- Transcription
- Annotation to regulation terms - what does GO mean by 'regulation'?
- Other methods to identify annotations to review
Metrics
- Tracking, reporting number of publications as a measure of information content
- Tracking changes to annotations over time
Topic-Specific Projects
- Tie-up an loose ends for existing signaling projects
- GPCR, JAK/STAT, Wnt (ideally a GO-CAM model for each pathway - as a template)
- Continue with additional signaling pathways
- Transcription
- Protein-containing complexes
GO-CAM/Noctua
- Continued discussion of modeling questions
- Generation and use of templates
- Import of Reactome pathways
- Import of whole genomes
Documentation
- Relations and their use in annotation and ontology development
- gp2term relations
- GO-CAM relations
- new relations in ontology development, e.g. describing participants in metabolic processes
PAINT
- Continue curation of families with at least one human gene
- Review families with new or revised experimental annotation
Pipeline
- Any questions or issues that groups are having?
- Finalize specs for new gpad/gpi file formats and transition to using these two files for internal consortium data exchange
- Literature tracking system - gather requirements
- Track curation status of papers
- Add comments to papers
Meetings
Conference Calls
- Tuesdays at 8am PDT
- 1st Tuesday: Alliance Biological Function
- 2nd Tuesday: GO Consortium
- 3rd Tuesday: GO-CAM Working Group
- 4th Tuesday: GO-CAM Working Group
- 5th Tuesday: Alliance Biological Function
- One Zoom URL for all - https://stanford.zoom.us/j/976175422
Consortium Meetings
- GOC meeting - Cambridge, UK April 11th - 12th (right after ISB meeting)
- GOC meeting - Berkeley, CA October 7th - 10th ???
Working Meetings
- Whole genome import - CA last week of January
Minutes
- On call: Barbara, Birgit (late), Chris M., David, Dustin, Giulia, Harold, Helen, Kevin M, Kimberly, Laurent-Philippe, Li, Liz, Midori, Patrick, Petra, Rob, Ruth, Sabrina, Seth, Shur-Jen, Stacia, Stan, Suzi, Tanya
2019 Plans
Annotation Group Priorities
Annotation Review
- We discussed the various topics and methods for and of annotation review
- InterPro2GO mappings - need to follow-up with InterPro on the gocheck_do_not_annotate subset
- Transcription
- Some work still to be done here
- Issues surrounding SO terms used; plan is to collaborate with SO on refining the ontology wrt definitions and placement of promoter and related terms
- Process and regulation of process
- This will likely be a big project, but we want to get the ball rolling.
- Jim B.'s work may help here, as well as the matrix tool
- QC/QA working group will follow-up with this
Metrics
- Lists of papers used for annotation can be retrieved from GAFs, QuickGO
- Tracking annotation changes over time will need to be part of our metrics going forward
- ISB - there will be a workshop on evaluating curation database resources; metrics is part of this discussion
Topic-Specific Projects
- Signaling
- AI: Add documentation on annotating specific signaling pathways to the existing, more general documentation
- Include in this documentation, GO-CAM models and templates that delineate what activities are considered part of the pathway vs regulatory or causally upstream
- Additional pathways to consider reviewing in 2019
- Notch, insulin
- FlyBase has found that one difficulty in delineating pathway members is how to consider transcription factors and branched pathways
- Protein-containing complexes
- Protein complexes WG will re-form in 2019 and try to address the remaining outstanding issues
- Would also be helpful to review criteria for what constitutes membership in a protein-containing complex
Pipeline
- Literature tracking system will likely be developed in collaboration with the Alliance