Annotation Conf. Call 2020-01-21

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Agenda and Minutes

  • Present: Chris, David, Dmitry, Edith, Harold, Karen, Kimberly, Laurent-Philippe, Li, Michele, Patrick, Pascale, Penelope, Petra, Rob, Sabrina, Stan, Suzi, Tremayne, Val

Pipeline

  • gp2protein, gp2rna, gp_unlocalized files
    • plan is to retire these from GOC, but want to double-check if there is any use for these files that would require GOC to keep them
  • Announcement sent to go-friends, 2020-01-16
  • Summary of ticket:
    • the GOC pipeline is not using gp2protein files for any data processing
    • gpi files
      • produced as complementary file for gpad
      • produced to populate annotatable entity ontology for Noctua
  • Possible future work
    • a gene/gene product identifier mapping file, with clear semantics, would be of use to the broader scientific community
    • exact file format, who should produce this file, how should it be distributed might all be topics for discussion
      • GO's gpi file format
      • Alliance bgi.json
      • UniProtKB also produces an idmapping file as part of the Quest for Orthologs work
      • MODs may also have id mapping files (e.g. WB ftp)
    • form a working group of representatives from the Alliance and other databases/projects to develop a common standard here?
    • breakout session at ISB in Bar Harbor?
      • GO's gpi file format might be a good place to start
      • UniProtKB also produces an idmapping file as part of the Quest for Orthologs work

*ACTION: Chris, Kimberly, Stacia to follow-up offline to see what concrete steps could be taken to move discussion forward on a more broadly used id mapping file

Noctua Form 2.0

  • Software updates made to ensure correct environment of all components
  • Additional updates:
    • Entity identifiers now displayed along with labels (particularly helpful when annotating gene product isoforms)
    • Causal relations decision tree (available via Connect on the Noctua form table)
  • Available (SOON!) from Noctua landing page and workbenches menu on graph editor (NOW)
  • Noctua Manual
  • User Guide - Google doc from Berkeley meeting, will be retired
  • ACTION: curators should try out the new form, give us feedback; we will continue to update and organize the documentation to try to help with workflow

*ACTION: New software updates on Noctua development site will be rolled out to production; Kimberly will email when new Noctua form is on production.

Annotation Relations

  • Goal is to review use of relations across annotations (standard and GO-CAM) and the ontology to ensure consistency wherever possible
  • Review retired relations:
    • 'has direct input' -> 'has input' for MF
    • 'occurs at' -> 'occurs in' for MF
    • annotation tools need to updated

*ACTION: Groups that have these relations in their annotation tools, should remove them.

*ACTION: Commented on existing ticket in RO tracker to obsolete 'has direct input'.