Annotation Conf. Call 2016-01-26

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Agenda

Bluejeans

Status Reports

  • Gene Ontology meeting in Geneva, April 15-16 after Biocuration 2016
  • IGI documentation
    • Working on draft of new IGI documentation to include guidelines for co-transfection as discussed on 2016-01-12 call, and to clarify some other points
    • Kimberly will send around a draft for comments before adding to the GO web site

Ontology Updates

  • Proposal for protein binding annotations
    • Original discussion on Editor's call Ontology_meeting_2015-03-19#Protein_family_binding_terms
    • Notes from Washington DC Meeting
      • David H on eliminating direct annotations to ‘protein binding’
        • Decision: protein family binding terms will be removed from GO. Annotations will be to ‘protein binding’ and the ‘with’ column (or, preferably, col. 16 using the has_input relation) will be required. If desired, an external protein classification can be used to create virtual protein family binding terms for grouping gene products for, e.g. enrichment analysis.
      • Images from Aleks' presentation

IPI 1.png IPI 2.png

    • At this point, we cannot go the route of annotating the binding target in annotation extensions because not all groups have the ability to do this.

Annotation Consistency Exercises

Minutes

On call

  • Berkeley - Chris, Heiko, Suzi
  • CCG - Lan, Yang
  • dictyBase - Bob, Petra
  • EBI - Aleks, Alex, Elena, Melanie, Paola, Paul
  • FlyBase - Giulia
  • MGI - David, Li
  • PomBase - Antonia, Midori
  • RGD - Shur-Jen, Stan
  • SGD - Stacia
  • SIB - Pascale
  • TAIR - Tanya
  • UCL - Becky, Rachael, Ruth
  • WB - Kimberly
  • ZFIN - Sabrina

Protein Binding Annotations

  • Several issues where raised wrt annotating protein binding
    • Cross-species experiments
      • Can annotate using IPI and the With/From column but the information captured here does not reflect the in vivo biology
      • Proposal is to use annotation extension has_input to capture the orthologous interacting gene from the species annotated in Col. 2
      • Some groups do no use annotation extensions, but this should not make any annotations incorrect, just some annotations will not be as information-rich as others
    • Ontology terms to indicate binding to protein families

LEGO Model of TAIR Annotation Consistency Paper

  • David reviewed the LEGO model created for the TAIR consistency exercise paper at the Geneva annotation camp
  • http://noctua.berkeleybop.org/editor/graph/gomodel:5662325600000049
  • This model represents a general approach to modeling transcription with LEGO
  • Note that each transcriptional instance (target) is represented separately
  • Use of has_output annotation extensions when GO term did not exist for cellular component organization of the Casparian strip
  • Evidence codes - IMP and IDA, and chromatin immunoprecipitation evidence
  • Created ticket to see GO IDs in the Noctua display - https://github.com/geneontology/noctua/issues/274
    • Issues addressed and closed.
  • Users can download both GAF and OWL representations from the Select menu on Noctua
  • Will review GAF output on next call