20th GO Consortium Meeting

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ALERT: GO Top needs to sign off on agenda prior to these meetings. If there is no action item, or discussion point proposed in advance, the meeting is not the forum for first initiating a discussion.

Action Items


Ontology Content Development

Work in progress

The electron transport working group have been discussing this issue in depth. We present our conclusions. In brief, our proposal is that links between function and process should only be made when we can use part_of (rather than has_part) or when there is a single step process term. (Jennifer presenting 29 Slides)
  • Plans to add regulates relationships within the molecular function (MF) ontology, and between MF and BP (David, Tanya, Chris) -- this is now covered
Jennifer and David have been working on a proposal for a new set of high level signaling terms. The new terms are ready to go live and we present them for comment. (~5 min talk) Slides

Ontology development discussion topics

  • Setting priorities across different types of content development task
    • How to allocate effort among (a) overall logical enhancements (e.g. improving genus-differentia aspects of definitions or adding new relationship types); (b) keeping up with SF submissions; (c) content meeting changes; anything else
    • More generally, what's the right balance between retrofitting the existing ontology (definition style, relationship types just two examples) versus new additions?



  • SourceForge clearout done
  • Possible forthcoming changes to day-to-day editing practices (David, Midori, Chris?)
    • Creating and using cross-products
    • Using new relationship types
    • Integrating QC into editing pipeline

General Annotation

Evidence Codes

  • Using the ECO as the primary source (and definition) for evidence codes. The documentation should reflect (not define) the evidence codes found in the ontology. Also, need to make sure that there is a tracker for this.

Plan to get some people together to work on it for 2-3 days and fix it (somewhat)

Annotation and ontologies

  • A (re-)introduction to the new column 16, Annotation_Cross_Products
  • Ontological relationships between gene products and functions, processes and components

GO Database

  • APIs
    • GHOUL GO Hibernate Object Utility Layer. An API to the GO database for Java programmers
    • Lucene indexing
  • Regular reporting of statistics, sanity checks, and such on the GO database.
  • New way of calculating the Transitive_closure


  • How to address the problem that comes up in trying to do dual taxon annotations when one of the partners has no taxon ID number at NCBI [e.g. when a microbe is interacting with a plant which has no taxon ID number (and this also is a problem because different cultivars of a plant also do not have different ID numbers)]. Can we discuss how to handle the requirement for a taxon ID (especially the second one in the Dual Taxon situation) when one has not yet been assigned by NCBI? -Candace Collmer
  • Update on loading dual taxon into database/AmiGO

22 OCT AM: Reference Genome 1/2 day

8:30 Progress Report

Improvements in annotation depth and breadth

(Chris and Mike's data)

Improvement in ontology structure

  • Examples of ontology changes stemming from Reference Genome annotation (David?)

8:45 PANTHER update

Paul and Kara

  1. generating homology sets, including protein set generation
  2. process for making ISS inferences
  3. implementation and merging with PPOD data

Discussion about protein set generation


  • Issues:
    • augmentation
    • isoforms vs canonical protein
    • complete proteome; partial gene predictions
    • possible solution: try to work with Swiss Prot?
  • Paul will present a table of problems for each genome
  • We will add documentation as to how to generate files and protein sequences
  • Regarding gp2protein files: The original aim was to support BLAST server.
    • Do we need another file? g2protein? predicted_non_redundant_protein? this file would have just protein??

Annotation Consistency and Quality Issues


  1. HTP evidence code?
  2. Discuss use of binding/regulation terms (GOC meeting)
  3. Establish guidelines for annotation to a process versus regulation of that process
  4. Process IC or IDA? (from Jamboree 18 July 2008-minutes; example : GCH1)
  5. There will likely be several other topics to discuss from the two electronic jamborees; so far: Reference_Genome_Annotation_Project#Annotation_Consistency_Issues

Web presence, Outreach and User Advocacy


  • Short update on Outreach going on throughout the Consortium. Highlights presented by Tanya Berardini (Author submission of annotations - 3 Slides) and Michelle Gwinn-Giglio (PAMGO outreach and University of Maryland Annotation courses - 6 Slides).
  • Swiss-Prot to do GO annotations (Michael)

AmiGO 1.6 for Reference Genome (Seth & Amelia)

  1. Present progress on AmiGO graphical views

Resource Usage statistics (Mike)

User Support

  1. Evaluation of helpdesk performance

GO Papers, Publications and Presentations

  1. Ref Genome paper status report
  2. AmiGO app. note
  3. News letter impact

Other items

Consortium meetings

Breakout sessions to fit in somehow

  • Final preparations for SAB meeting
  • Amina, Chris and OBO-Edit users (including cross-products)
  • Pascale, Suzi and reference genome curators

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