Annotation Conf. Call 2018-01-09

Meeting URL

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

Agenda

Review of Cambridge meeting action items and milestones for 2018-05 GOC meeting in NYC

In geneontology/go-annotation on github, there is a Milestone '2018-05 GOC meeting'

Requests for Proposals

Protein Complexes Working Group

• Inferring MF annotations for complex members
• Proposal for guidelines for using contributes_to
• should we really use "colocalizes_with" with cc complex terms
• Protein complex representation in Noctua
• Do we have to hard-code CC complex terms to MF and BP relationships in the ontology?
  • Working group established, one meeting in late November
  • Next meeting?
• Updates from Birgit:
  • Latest: I have to design a user survey to answer some of the open questions from our call. It's on my to-do list for this month.
  • Other discussion points rely on us finishing the complex IDs. Our developers were rather stretched this autumn so it's taking a little longer than expected but they are back on it and it's really close!

Annotation Relations - Cellular Component

• should we really use "colocalizes_with" with cc complex terms
• Relations to describe gene product - component annotation
• Draft proposal (Kimberly) - need input from Chris on RO
  • Relations between gene products and organelles/locations
  • Relations between gene products and macromolecular complexes

Annotation Relations - Biological Process

• New qualifiers for biological processes - including how to deal with legacy annotations

Cellular Component Annotations for Transmembrane Proteins

https://github.com/geneontology/go-annotation/issues/1621

InterPro2GO Pipeline

• InterPro2GO pipeline
  • Need to establish a working group here

Engaging External Experts

• Recommendations and guidelines for next time we engage an external group of experts
  • Need to have a working group or responsible persons here, too

Annotation Review

HTP Annotations

• Review HTP annotations
  • HTP_Guidelines_condensed_version
    • Forward genetic screens - may need further clarification and examples of what is/is not high throughput
• HTP-types will not be allowed as evidence for ISS+ISO
  • Set date for meeting to discuss ISS/ISO transfer from HTP to be discussed in Feb.

Signaling Workshop

In geneontology/go-annotation on github, there is a label 'GO workshop signaling 2017'

General Signaling Issues

• Review annotation to 'receptor ligand activity' (GO:0048018)
• MP cell surface receptor signaling pathway

Ca2+ Signaling - Fertilization

• Revision of relationship of GO:0060468 (prevention of polyspermy) and GO:0060471 ( cortical granule exocytosis)

GPCR-mediated cAMP Signaling

• Review annotations to 'cAMP biosynthetic process'
• Review annotation for GPCR
• NTR: regulation terms for adenylate cyclase-activating adrenergic receptor signaling pathway
• cAMP biosynthetic process - merges & obsoletion
• GO:0007189 adenylate cyclase-activating G-protein coupled receptor signaling pathway... missing parent

MAPK Cascade

• How to name specific MAPK pathways

Canonical Wnt Signaling Pathway

• PAINT:PTN000226268 Wnt signaling pathway to positive regulation of...
• Review annotations to beta catenin
• PANTHER:PTN000139394: remove wnt binding annotation to smoothened receptors
• https://github.com/geneontology/go-ontology/issues/14275 NTR: “receptor ligand agonist activity” and “receptor ligand antagonist activity”]

GO-CAM and Noctua

• No call tomorrow
• Software team has been working on the priority issues for Noctua 1.0 release
• QC for Noctua models

Protein2GO Reports

• Protein2GO users please remember to check the monthly reports and work on updating/fixing flagged annotations

Two Working Meetings

• January 22nd - 26th: Docathon at Berkeley
• February 12 - 16th: Ontology GitHub jamboree in Denver

Minutes

• On call: David H, George, Harold, Helen, Kimberly, Liz, Rachael, Rob, Sabrina, Sage, Stan, Suzi, Val