2012 Annotation Meeting Stanford

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Agenda

Preparation/Goals for the meeting

Over all goals for the meeting are available here

Group Photo

GOC-Stanford-2012.jpg

Remote Attendees

We will use the GO phone conference line and webex. An email will be sent to the GO consortium mailing list about how to join the Webex.
Toll-free USA number 1-866-953-9688 (US Toll number 1-212-548-2460 in case of problems with 866 number)
Toll-free UK 0808 238 6001 (toll number: 646 834-9311)
Toll-free Switzerland 0800 562 830 (toll number: 646 834-9311)

Participant Pin: (801-561)

Feb 26, 2012, Day 1 (half day) - Overview

Arrive at: 11:00AM
Meeting: 12:00PM

Current GO annotation status

Minutes: Emily, Yasmin File:GOConsortiummeetingminutesFeb26 am.pdf

  • Overview of current pipeline experimental information submitted by annotation groups (Paul T & Mike) File:GOC SurveyQ2.pdf, File:GOCquestionnaire3.pdf, File:GOCquestionnaire4.pdf
  • Overview of rates of GO annotation production (break out metrics separately by group and by ontology aspect; for BP also report metrics separately for cellular process, multicellular organismal process; for CC also report metrics separately for macromolecular complex)
  • Current annotation status and the trend over time will be presented here along with the proposed report page. E.g. What is our current rate of new annotation production, annotation information content assessment, current rate of annotation loss (due to sunset clause, average % of annotations that can't be loaded, etc.), annotation “completeness” (how many genes with annotations in all three aspects considering: EXP only; EXP+ISS; EXP+ISS+IEA; ND only) (Amelia, Chris and Suzi)
  • Completeness and adherence to standards of "gp2protein" files (Paul T).

GPI format: (http://wiki.geneontology.org/index.php/Gene_Product_Association_Data_%28GPAD%29_Format#Proposed_Gene_Product_Information_.28GPI.29_file_format)

Vision for GO annotation process

Minutes: Rama, Karen

Minutes: File:GOC2012MinutesSession2.pdf

Feb 27, 2012, Day 2 (full day)

Breakfast: 8:00AM
Meeting: 9:00AM

Case studies of state-of-the-art annotation approaches

Minutes: Jane, Paola

Each of these presentations will consider the experiences they have had and what the bottlenecks and issues that have been encountered. We will use these lessons to determine the best path forward to streamline and enrich the process.

  • Community approaches for recording annotations
    • Wiki-based annotation in CACAO: proposed improvements and potential generalizations (Jim Hu and Brenley McIntosh)
    • CANTO experiences (Val Wood). CANTO is a PomBase tool that is being developed by Kim Rutherford to include GOC requirements to make it become available to community experts, who would like to submit small sets of GO annotations to the GO Consortium, which would then need to be reviewed by GOC groups. (Kim and PomBase will be keeping Kimberly and the CAF working group in the loop as to developments)
  • What additional gene function information is used to supplement GO annotation?
    • at UniProt (Claire)
    • at MGI, e.g. cell types; temporal -spatial (David & Harold)File:MGI GO EI 2.pdf
  • GOC Domain-specific curation and ontology development

Proposal for GOC use of common annotation framework to support literature annotation and subsequent phylogenetic annotation process

Minutes: Chris, Seth

  • Overview of the common annotation framework (Chris and Paul T.)
  • Details of the common annotation framework (Paul S, Paul T, Judy, Mike, Suzi)
  • Common annotation Software prototype demos (Kimberly et al.).
    • Kimberly is currently talking to all curation groups about individual GO annotation tools, what features they have and what features curators would like. By the GO Consortium meeting, Kimberly will present the features that GOC curators feel are most important.
      • Any other aspects curators would require in an annotation tool.
      • What additional data should be supplied by annotation groups.
      • How best to use text-mining in the CAF for prioritizing curation work (e.g. Textpresso).
      • CAT Project development goals for next 3-6 months. (Kimberly & Chris Mungall)
      • PAINT as used for Quality Assurance: Dual perspectives (biological topic focus); cross-checking annotations; Phylogenetic inference: Synthesis, QA and inference across organisms using PAINT.
      • Integration and prioritization of phylogenetic annotations within the framework of experimental annotations.

Feb 28, 2012, Day 3 (full day)

Breakfast: 8:00AM
Meeting: 9:00AM

Concurrent sessions (4 hr)

How MODs can achieve full breadth of genome coverage: Focused annotation session for ~5-7 GO annotators per group: Led by Pascale, Paul, & Huaiyu handling groups individually: small groups to make each session manageable and productive. Annotations to transfer would be selected on the basis of recent annotation work by GO Consortium groups that are now in the GO database, to terms from the ontology which have been reviewed and likely to remain stable (e.g. from the recent transcription annotation effort)


  • Mixed groups
    • those with previous training in PAINT annotation
    • no training, however strong possibility in using PAINT later on to create GO annotations (e.g. GO NIH funded curators)
    • Group 1: Pascale, Rama, Kimberly, - Prudence, Petra, Stacia, Dianna, Doug, Susan, Varsha, Aurore, Steven, Martha,
    • Group 2: Paul, Li, David, Tanya, - Julie, Karen, Cindy, Peter, Brenley, Paola, Ruth, Rex N, Lucas, Rajni
    • Group 3: Huaiyu, Donghui, Harold, Emily - Yasmin, Rob, Selina, Kalpana, Jim, Val, Jane, Carson, Diane

Decisions made, reorganization of manager groups and their coordinators.

Minutes: David, Kimberly, Harold

Minutes:File:Tuesday 02 28 Minutes.pdf

  • Defined tasks that will occur over the next six months.
  • The PIs will affirm that the Managers are responsible for communicating the tasks required to reach the projects agreed to goals.
    • The Directors empower the Managers to activity monitor the working groups progress and report any problems that inhibit reaching our goals.
    • There are commitments that need to be met by all members for the GOC to be a success.
  • To conclude the meeting we will finalize goals and what we’ve agreed to do going forward. (GO Directors)
    • Annotation and Ontology productivity working group
      • Pick a realistic goal for increasing the # of annotations/quarter over the next 5 years
      • Pick a realistic goal for increasing the information content (specificity) of the annotations over the next 5 years
      • Define and publish what is minimally required for community contributions and mechanisms to ensure quality standards are met. That is, minimal requirements for submitting GO annotations (for projects and MODs *not* funded via the GOC)
      • Efficient ways of leveraging the community
      • What tools and other infrastructure would assist.
      • Respond in a timely manner to community & sourceforge term requests
    • Annotation Integration & ontology review working group
      • Quality Control: Independent secondary checks of annotations
        • Automated checks
        • Semi-manual checks
        • Manual checking through random sampling
        • What criteria should be used: comprehensively annotated gene products via final paint approval, other QC checks
      • How to select targeted gene sets
      • Define what additional information we ideally would aim to collect to enrich the annotations coming from GO funded efforts. That is, What would an ideal annotation consist of and what are the responsibilities for GO curators (for projects and MODs *funded* via the GOC)
      • Ontology modeling, consistency and review
    • Framework working groups
      • Database infrastructure:
        • Define concrete steps for implementation of required infrastructure for meeting these annotation goals.
        • LEGO annotation framework
        • Sign off on the new annotation flow proposal.
        • Mechanism for sending GO annotations to the MODs. GO annotations will be generated by dedicated GO curators using the central CAT tool, and resultant
      • GO annotation tools working group
      • User and community interactions
    • Ad hoc groups
      • Fixed timeframe
      • Fixed deliverable(s)
    • GO Directors (Paul T, Paul S, Suzi, Mike, & Judy
      • Decision making
      • Set priorities for each working groups
      • Attend working group calls