Annotation Conf. Call 2016-01-26

Agenda

Bluejeans

• Recurring meeting URL: https://bluejeans.com/993661940

Status Reports

• Gene Ontology meeting in Geneva, April 15-16 after Biocuration 2016
  • 2016 Geneva GOC Meeting Logistics
  • Agenda still TBD
  • Please add your name to the list of attendees if going
• 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

• • 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

• Review of the TAIR paper
  • Conventional Annotation from previous call/review of the paper
    • Annotation Conf. Call 2015-11-24
  • Discuss LEGO Model
    • LEGO Model for MYB36 paper http://noctua.berkeleybop.org/editor/graph/gomodel:5662325600000049
  • Discuss the GAF generated from the LEGO model

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
    • New protein family binding terms will not be added to the MF ontology
    • See github ticket: https://github.com/geneontology/go-ontology/issues/11693
    • For MF annotations that concern protein family binding, proposal is to use annotation extension and a protein family classification

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