Annotation Conf. Call 2016-01-26

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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


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
  • 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 -
    • 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