Annotation Conf. Call 2018-12-18

Meeting URL

• https://stanford.zoom.us/j/976175422

GO 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

Agenda

Progress Reports

• Thank you to everyone who submitted or worked on a progress report.
• Any questions or outstanding issues?

Annotation Review Stats

• We will discuss the overall progress on annotation review for 2018.
• Annotation Review Summary

HTP Publication

• Congratulations and thanks to Helen and the HTP working group on the acceptance (with minor revisions) of the Database manuscript on annotating GO from HTP experiments.

Ontology Editor's Geneva Meeting

• The ontology editor's met in Geneva last week to discuss plans to align reactions amongst GO - Rhea - Reactome.
• The plan is that, going forward, Rhea reactions will be the authoritative source for GO catalytic activity terms.
• We also reviewed and discussed conversion of Reactome pathways to GO-CAM models (Ben Good's work).
  • Proposal for new RO relations to describe participants in reactions and metabolic processes.
    • This proposal will address the incorrect inferences that are currently generated from GO-CAM due to insufficient equivalence axioms in the ontology.
  • Touched on representation of protein complexes in GO-CAM.
  • Working on a report of genes annotated to a process and regulation of that process (broadly speaking) for future curation review.

Pipeline - PAINT annotations

• Retrieving PAINT annotations for MODs
• PAINT annotations that have gone through QA/QC pipeline can be retrieved from MOD-specific production annotation files on snapshot or current

Annotation Guidelines

• We would like to discuss new guidelines written for annotating from mutant phenotypes:
  • Annotating from phenotypes

2019

• Next consortium-wide call: Tuesday, January 8th, 2019

Minutes

• On call: Chris G., Chris, M., Suzi L., David, Giulia, Kevin, Kimberly, Laurent-Philippe, Li, Michele, Midori, Pascale, Patrick, Paul T., Sabrina, Seth, Shur-Jen, Stan, Tanya

Progress Reports

• If possible, add information about number of unique publications in annotation sets, as this is an increasingly important metric for the GO to report
• Also, if there have been significant changes in the extent of curation resources in your group, please note that so this can be correlated with any changes in annotation progress.

Annotation Review

• Suggestion from Suzi: it would be interesting to look at the distribution of number of annotations across a genome to see what an "average" number of associations is and how many genes deviate from that.
• Each aspect of the ontology would need to be looked at separately, as there may be many more annotation for BP than CC, for example.

GO-Rhea-Reactome Alignment

• Ontology editors are working with Rhea and Reactome to align classification and definitions of reactions.
• UniProt curators are now assigning Rhea reactions to UniProt records.
• Michele M. will inquire about if/how those assignments trickle down to GO annotations.

PAINT

• MODS should retrieve PAINT annotations from the production GAFs on either snapshot or current.

Phenotype Annotation Guidelines

• Reviewed new guidelines
• Will add 'Date last reviewed' section to the page and links from evidence code pages.
• Brainstormed about how we could make annotation guidelines easier to find on wiki.
• If people have suggestions, please let us know.
• Also, if there are wiki pages people routinely look for or consult, let us know as these should be made easy to find from the Annotation home page.