Annotation Conf. Call 2018-04-24

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GOC Meeting, NYU, New York, NY, May 12-14th

  • Reminder to register, and reserve your hotel room before April 6th if staying at the Shelburne NYC
  • Logistics
  • Agenda

20th Anniversary GO Meeting, Montreal, Canada

  • Dates set for Oct 17-19

Annotation Survey

  • We are conducting a survey on annotation practices across the GOC
  • This will allow us to have a better overall view of different group's workflows, pipelines
  • Only need one response per annotation group
  • Would like results before the GOC meeting in NY
  • Please could each group respond by May 1st

Ontology Development and Annotation Review

Transcription factor refactoring

Annotation Review requests

  • There will be more annotations reviews to come in the upcoming days/weeks. For most the work load is expected to be small, a few proteins per group at the most.
  • Please let Pascale know if you are trying to annotate a function and cannot find the term - this will help decide whether some terms are missing or if we need to improve some term labels/definitions.

Updates on Projects

MAPK Cascade

Extracellular Matrix

Canonical Wnt Signaling Pathway

  • Working on compiling annotations to review
  • Main issues:
    • Distinguishing gene products that are involved in canonical Wnt signaling vs +/- regulation of canonical Wnt signaling
    • Annotating to more granular child of Wnt signaling pathway when appropriate
    • Annotation of downstream targets to the canonical Wnt signaling pathway



    • Proposal to change the cardinality of the reference field to be 1.
    • MOD paper IDs would only be used if there is no PMID, doi, GO_REF, etc.


  • Next call tomorrow, Wednesday, April 25th at 11:00am EDT (see Google calendar)


  • As part of cleaning up the users.yaml file and setting Noctua editing permissions, we have added a new tag, previous_groups, to the users.yaml schema
    • This tag will allow us to keep track of affiliations accurately

Protein Complexes Working Group

  • Birgit will send around a Doodle poll for the next call.


  • On call: Chris, Dustin, Edith, George, Giulia, Harold, Karen, Kevin, Kimberly, Liz, Midori, Mila, Patrick, Pascale, Paul T. (?), Penelope, Petra, Rachael, Ruth, Sage, Sandra, Shur-Jen, Stacia, Stan, Suzi L., Tanya, Val

GOC Meeting

  • Please check the agenda and contact the consortium if you have any questions/concerns

Annotation Survey

  • Five groups have responded:
    • dictyBase
    • FlyBase
    • MGI
    • TAIR
    • Zfin
  • Please respond by May 1st so we can collate the results in time for the consortium meeting

Transcription - Ontology Updates

  • Discussion:
    • Meaning of gene-specific transcription factor activity (possible new name for DNA-binding transcription factor activity)
      • Does this indicate a different mechanism of action than other (i.e. more general) transcription factors?
      • Strong objection from Karen, Stacia to the gene-specific vs general terms - how would these terms actually be defined?
      • What level of specificity is helpful/needed wrt the ontology terms?
    • Users often want to retrieve lists of transcription factors; what classification is most helpful for this? This can actually be much more difficult to do than might be expected.
      • Biological process?
        • Can we define in GO the beginning and end of the transcription process?
        • Yes, but we'd need to be aware that there might be substantial re-annotation as many genes are annotated to regulation of transcription-type terms.
      • Complex membership?
      • Is doing this via MF too hard, i.e. hard to uniquely distinguish functions for all the gene products involved in transcription?
    • What type of query would be most helpful to users?
  • ACTION ITEM:Curators please address the high priority annotation review tickets as soon as possible.