Annotation Conf. Call 2017-07-11

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Annotation of Signaling Pathways in GO


Literature Reviews

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 cellular structure organization, developmental processes, behaviors, etc.

Review Existing Annotations Specifically for that Pathway

  • 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
    • Sample Wnt Spreadsheet
  • What are the existing annotations?
    • Annotations to signaling pathway?
    • Annotations to regulation of the signaling pathway?
    • Annotations to sub-processes of the signaling pathway?
  • 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 (GO-Causal Activity 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

Below is a list of pathways that curators expressed interest in reviewing. We do not anticipate that we'll be able to cover all of these pathways right away, and we strongly encourage people to work together, if possible, to divide up the labor.

  • Apoptosis
    • Upstream signaling pathways?
  • Ca2+ signaling
    • Fertilization - Penelope
  • GPCR
    • Gastrin
  • Hippo
  • Insulin
  • Jak/STAT
  • MAPK (DavidH ; sabrina-zfin)
    • Erk
    • Jnk
    • p38
    • HOG
  • NFAT
  • Nodal
  • Notch
  • Receptor Tyrosine Kinase
    • VEGF
  • Sonic Hedgehog
  • TGFbeta
  • TOR
  • Wnt - Kimberly, Giulia, Helen
    • Canonical Wnt
    • Planar cell polarity
    • Wnt/Ca2+

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
  • Although we are selecting some pathways to focus on, at least some of the issues we encounter will likely be more generally applicable to annotating signaling pathways in general
    • To get the most out of this work, we want to generalize the issues as much as possible - keep the big picture in mind!


  • On call: Chris, David H., Edith, George, Giulia, Helen, Jim, Karen, Kevin, Kimberly, Li, Liz, Midori, Pascale, Penelope, Petra, Ruth, Sabrina, Sandra, Shur-Jen, Stacia, Stan, Tanya, Terry, Val

Signaling Workshop


  • Check agenda and logistics page for Cambridge meeting in October

Pre-Workshop Preparations

  • Want to look at signaling pathways both generally and specifically
  • Read the review Judy shared (linked above) - it's very comprehensive and a helpful starting point
  • Review previous work by the signaling group
    • Guidelines on the GO website
    • Wiki page for previous signaling work

Proposed Workflow

  • Select a pathway
  • Identify the gene products in the pathway
  • Determine what MFs are in that pathway
  • Suspect annotations can then be qualified with the new BP qualifiers, if possible
  • Review existing annotations
    • Can start with your organism, include others if possible
    • Look at supporting experiments
  • Review the ontology
    • Can use comments to clarify term usage
  • Create a GO-CAM model
    • Will be used as gold standards for how to annotate a given signaling pathway
  • Create github tickets
    • Annotation
    • Ontology
    • GO-CAM/Noctua
  • Demonstration of MAPK Spreadsheet - David
    • Survey of gene products and annotations for MFs associated with the MAPK cascade BP term(s)
    • This example illustrates the importance of defining the beginning and end of the pathway