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) as well as the relationship between the signaling pathway and other processes such as developmental processes, behaviors, etc.

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
• Insulin
• 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: