Annotation Conf. Call 2016-02-23

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Bluejeans

Agenda

  • GOC Meeting - Geneva, April 2016
  • Review new IGI documentation
    • Based on comments from the last call, there's a draft of the revised documentation here:
      • http://wiki.geneontology.org/index.php/IGI_Documentation
      • Specific changes were made wrt: 1) the section on experiments where expression of one gene alters the phenotype of a mutation in a second gene, 2) additional IGI examples, 3) additional example of when NOT to use IGI - rescue of mutant phenotype by expression of the same gene
  • Call for information
    • We would like to develop documentation on GO annotation from experiments using cell lines
    • What types of cell lines are acceptable? What cell lines can reasonably be used as models for in vivo cell types? Should we document cell lines that are traditionally used to model in vivo cells, C2C12---myoblast? When do the experiments reflect normal biology vs pathology, e.g. cancer biology?
    • If your group has documentation or policies on this, please forward to DavidH and Kimberly
  • New miRNA guidelines
    • Reminder to please look at updates to miRNA annotation guidelines sent by Rachael on 12th February 2016 in an email entitled "Updates to miRNA annotation guidelines". If no comments are received by Friday 26th February we will assume everyone is happy with these changes and they will be added to the existing guidelines.
  • Annotation Consistency Exercise

Minutes

  • On call:
    • Berkeley: Chris, Moni, Suzi
    • EBI: Aleks, Alex, Melanie, Paola
    • Flybase: Giulia, Helen
    • MGI: David H, Li
    • RGD: Stan
    • SGD: Edith, Stacia,
    • SIB: Pascale
    • TAIR: Tanya
    • UCL: Barbara, Paul, Rachael, Rebecca
    • USC: Paul T.
    • WB: Kimberly

IGI Documentation

  • Revised documentation written; please any additional comments
    • Note: New IGI curation guidelines now on GO website

Use of Cell Lines for GO Annotation

  • Please send David H any guidelines your group may currently use for annotating experiments that use cell lines
  • If you have examples, please also send the PMID
  • We could like to develop documentation on how GO annotation uses cell line information, e.g. a test tube vs an experimental model for a specific cell type in an organism

miRNA Annotation Guidelines

  • Please review latest revisions from Barbara and Rachael by Friday, 2/26

Annotation Consistency Exercise

  • Bulk of discussion surrounded the issue of how to annotate to the process (part_of), regulation of the process, and causally upstream of the process
  • We discussed the corresponding LEGO model and the GAF representation and how close the LEGO model and resulting GAF come to manual annotation
  • We re-visited some of the discussion we had in Barcelona about a qualifier that allows curators to essentially say that the gene annotated has some effect on a process, but we don't know the mechanism
    • The Action Item from the Barcelona meeting:
 Action Items:  Implement a ‘OR’ situation for when you don’t know whether the protein is involved in the process or regulation of 
 process.  This will affect protein2GO, paint, GAF checks (software pipeline for loading annotations and conversion to OWL), 
 retrofitting, display/search annotations (AmiGO, QuickGO).