Annotation Conf. Call 2018-03-27

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Agenda

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, CA

  • Dates set for Oct 17-20

Updates on Projects

Evidence Codes

RCA

  • Review RCA evidence code
    • Thank you to everyone who has reviewed their existing RCA annotations.
    • Many RCA annotations were removed, but some groups are keeping annotations from papers that use methodology consistent with the definition of RCA.
    • Since these annotations come from papers, the originally proposed one-year restriction does not make sense and will not be an annotation rule.
      • Please send Kimberly PMIDs for papers that were kept for use as examples in our evidence code documentation.
    • That said, periodic annotation review is always a good idea.
    • Remaining groups will be contacted individually.

Annotating High Throughput Experiments

Annotation Survey

  • We are putting together a survey on annotation practices across the GOC
  • Should be ready very soon
  • Would like results before the GOC meeting in NY

GO-CAM/Noctua

  • Next call tomorrow, Wednesday, March 28th at 11:00am EDT (see Google calendar)

Protein Complexes Working Group

  • Next call on Monday, April 23rd at 1:10pm EDT (see Google calendar)

Minutes

  • On call: Chris, David H., Dustin, Edith, Giulia, Harold, Helen, Jim, Judy, Karen, Kevin M, Kimberly, Li, Midori, Pascale, Paul T, Penelope, Petra, Rachael, Rob, Sabrina, Sage, Stacia, Stan, Suzi A., Suzi L.

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

  • Register and reserve your hotel room before April 6th if staying at the Shelburne NYC
  • If you have any issues with reserving a room, please contact Peter D'Eustachio right away

Updates on Projects

MAPK Signaling

  • Some ontology updates to how MAPK signaling pathways are named in GO
  • Upcoming: annotation review for potentially re-housing annotations according to the new MAPK pathway terms
  • Some existing annotations to upstream genes may need to be re-housed
  • The MAPK cascade is a signaling cassette or module that begins with MAP4K or MAP3K and ends with MAPK
  • How a MAPK cascade relates to a larger signaling pathway or another downstream process, e.g. neurite extension, remains to be determined in both the ontology and GO-CAM models

Extracellular Matrix Revisions

  • All extracellular matrices have at least some protein component
  • David and Rachael working on revisions to the ontology
  • Some annotation review will likely be coming
  • Will be calling on people for help with top level taxonomic groupings

Evidence Codes

RCA

  • Most groups have reviewed their RCA annotations and removed many, but some have stayed
  • Propose to remove the one-year restriction on RCA annotations that does not seem to have been enacted formally anyway
  • We will work with other annotation groups to review their RCA annotations

Annotating High Throughput Experiments

  • We need an evidence code for combinatorial curation using HTP results further validated by other methods
  • Can work with ECO to find or create a suitable code
  • Reference field will need to clearly indicate the combined curation methodology
    • As a first step towards doing this, we need to determine how to indicate the combined references, e.g. a PMID plus a GO_REF that describes the subsequent analysis
    • Currently, some groups include redundant, pipe-separated references in the Reference field of the GAF
    • Do we need to continue doing this? Proposal is to include only one, unique ID for each reference and then, if needed, combine a paper reference with a GO_REF

Annotation Survey

  • We will be sending out an annotation practices survey for groups to fill in
  • Survey will go out later this week or early next
  • We'd like the results in time for the May GOC meeting in NYC