Annotation Conf. Call 2019-01-08: Difference between revisions
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= Meeting URL = | = Meeting URL = | ||
* | *check shared GO Google calendar | ||
= Agenda = | = Agenda = | ||
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=== Annotation Group Priorities === | === Annotation Group Priorities === | ||
==== Annotation Review ==== | ==== Annotation Review ==== | ||
*[http://snapshot.geneontology.org/reports/index.html 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'? | *Annotation to regulation terms - what does GO mean by 'regulation'? | ||
*Other methods to identify annotations to review | |||
**Matrix | |||
==== Metrics ==== | |||
*Tracking, reporting number of publications as a measure of information content | |||
*Tracking changes to annotations over time | |||
==== Topic-Specific Projects ==== | ==== 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 | |||
**Revive the working group | |||
**[https://docs.google.com/document/d/1vRbTsaPJQEToMPQW4CRogGUS82Zo-xzGQhI60nR4N8s/edit?usp=sharing Summary of open protein complexes issues] | |||
==== GO-CAM/Noctua ==== | ==== GO-CAM/Noctua ==== | ||
*Continued discussion of modeling questions | |||
*Generation and use of templates | |||
*Import of Reactome pathways | |||
*Import of whole genomes | |||
==== Documentation ==== | ==== Documentation ==== | ||
*Relations and their use in annotation | *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 ==== | ==== Pipeline ==== | ||
*Any questions or issues that groups are having? | *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 === | === Meetings === | ||
Line 26: | Line 63: | ||
==== Consortium Meetings ==== | ==== Consortium Meetings ==== | ||
*GOC meeting - Cambridge, UK April 11th - | *GOC meeting - Cambridge, UK April 11th - 12th (right after ISB meeting) | ||
*GOC meeting - Berkeley, CA October 7th - 10th ??? | *GOC meeting - Berkeley, CA October 7th - 10th ??? | ||
**SAB | **SAB | ||
Line 32: | Line 69: | ||
==== Working Meetings ==== | ==== Working Meetings ==== | ||
*Whole genome import - CA January | *Whole genome import - CA last week of January | ||
= Minutes = | = Minutes = | ||
*On call: | *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 | |||
[[Category:Annotation Working Group]] | [[Category:Annotation Working Group]] |
Latest revision as of 12:49, 19 February 2019
Meeting URL
- check shared GO Google calendar
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
- Matrix
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
- Revive the working group
- Summary of open protein complexes issues
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 ???
- SAB
- GO user's meeting
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
- Notch, insulin
- AI: Add documentation on annotating specific signaling pathways to the existing, more general documentation
- 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