Annotation Conf. Call 2019-01-08: Difference between revisions

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= Meeting URL =
= Meeting URL =
*https://stanford.zoom.us/j/976175422
*check shared GO Google calendar


= Agenda =
= Agenda =
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=== Annotation Group Priorities ===
=== Annotation Group Priorities ===
==== Annotation Review ====
==== Annotation Review ====
*Reports from pipeline
*[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
*Molecular Function refactor
*Transcription
*Transcription
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==== Topic-Specific Projects ====
==== Topic-Specific Projects ====
*Tie-up an loose ends for existing signaling projects
*Tie-up an loose ends for existing signaling projects
**GPCR, JAK/STAT, Wnt
**GPCR, JAK/STAT, Wnt (ideally a GO-CAM model for each pathway - as a template)
*Continue with additional signaling pathways
*Continue with additional signaling pathways
*Transcription
*Transcription
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*Generation and use of templates
*Generation and use of templates
*Import of Reactome pathways
*Import of Reactome pathways
*Import of whole genomes


==== Documentation ====
==== Documentation ====
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==== Consortium Meetings ====
==== Consortium Meetings ====
*GOC meeting - Cambridge, UK April 11th - 13th (right after ISB meeting)
*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
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= 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

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
  • 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