Annotation Conf. Call 2017-07-11

Meeting URL - NOTE CHANGE TO ZOOM

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

Agenda

Annotation of Signaling Pathways in GO

Logistics

• October Cambridge Meeting Agenda
• Github Projects Page for GO-Annotation

Literature Reviews

• Cell Signaling Biology - Cell Signaling Pathways
  • Cell Signaling Biology - Contents

Annotation Guidelines

• Existing Guidelines:
  • Annotation Conventions - General Ligand-Receptor Pathway
  • Ontology signaling project started 2009
• New Guidelines:
  • A primary goal of this workshop will be to add to, and improve upon, existing annotation guidelines.

Proposed Workflow

Pathway Overview

• Initially focus on what is in the pathway
  • Identify a pathway
  • Determine what gene products and molecular functions are in the pathway
• Eventually we will also look at other gene products annotated to the pathway to determine what their true relationship is, e.g. causally upstream of, regulates

Review Existing Annotations

• What gene products have been annotated for different organisms?
  • Start with your own organism, if desired, but it is instructive to look at other organisms
• What are the existing annotations?
• What experiments support those annotations?

Review the Ontology

• Do term definitions clearly state the meaning/use of the term?
• Is there redundancy or deficiency in the ontology?

Construct a GO-CAM Model

• Can the existing annotations be used directly in a GO-CAM model?
  • If not, why?
    • Are annotations missing?
    • Are annotations incorrect?
• Are the expected annotations produced in the GPAD output?
  • If not, why?

Suggested Pathways from Curators

• Apoptosis
• GPCR
  • Gastrin
• Hippo
• Jak/STAT
• MAPK
  • Erk
  • Jnk
  • p38
  • HOG
• Nodal
• Notch
• Receptor Tyrosine Kinase
  • VEGF
• Sonic Hedgehog
• TOR
• Wnt

Steps Forward

• Curators claim pathways (work together, if desired)
• David and Kimberly will create tickets in github for the initial pathways chosen and link to project page in go-annotation
• Curators will articulate and submit specific tickets to the appropriate github repository for issues that need to be addressed

Minutes

• On call: