20th GO Consortium Meeting

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Logistics

Instructions_for_Registration


Agenda

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

http://wiki.geneontology.org/index.php/SLC_GO_Consortium_Meeting_Minutes_April_2008#ACTION_ITEMS

Ontology Content Development

Work in progress

  • MF-BP links
    • Progress on using Reactome (Chris)
    • Manually curated links [is that a good wording?] - pilot projects (Jen, Harold)
  • Plans to add regulates relationships within the molecular function (MF) ontology, and between MF and BP (David, Tanya, Chris)
  • Ontology content QC
    • Ongoing regulation-term QC (David, Tanya, Chris)
    • Other QC reports (Chris? editors?)
  • "Trigger" files for annotation QC - first set based on taxon correlation (Jen, Chris)
  • Signal transduction - overhaul well under way (Jen, David)
  • Processes affecting cellular components, e.g. CC organization and biogenesis (Midori, Jane, David?)
  • Examples of ontology changes stemming from Reference Genome annotation (David?)

not sure we need presentations on these; may be enough just to include in summary:

  • PAMGO collaboration - new term additions in progress (Jane)
  • Collaboration with IMG to map to IMG terms to GO terms (Jane)
  • Peptidase activity terms - reorganization completed

Ontology development discussion topics

  • New relationship types, e.g. has_part, spatial relations in CC
  • Relationship composition, including implications for annotation, searching, etc. draft presentation
  • 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?

Organization/Management

  • 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

Reference Genome

  • Can we have half a day??

Progress on curation tool (POGO)

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

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.

Taxa

  • 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

Infrastructure

OBO-Edit

  • Update on latest version
  • Michael Schroeder et al. plug-in

GO Database

  • GHOUL GO Hibernate Object Utility Layer. An API to the GO database for Java programmers
  • Regular reporting of statistics, sanity checks, and such on the GO database.

Web presence, Outreach and User Advocacy

Outreach

There have been a number of good annotation outreach meetings since the last Consortium meeting. If 15-20 minutes are available then some of the meeting organisers could present a summary of these meetings. The principle people involved are Fiona McCarthy, Trudy Torto-Alalibo, and the TAIR curators.

AmiGO 1.7 for Reference Genome (Seth & Amelia)

  1. Present progress on AmiGO graphical views

Resource Usage statistics (Mike)

GO Papers, Publications and Presentations

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

Other items

Consortium meetings

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