2012 Annotation Meeting Stanford

Agenda

Preparation needed in advance of GO Consortium meeting

1. Preparation for each GO annotation group
   • How does GO annotation fit into your overall curation process? Ideally as a high-level flowchart
   • What is your process for GO annotation? Ideally as a detailed flowchart
     • What software tools do you use for GO annotation?
     • Do you regularly make both literature and inferred (e.g. ISS) annotations?
     • How do you prioritize which papers, genes, etc. are targeted for GO annotation?
     • How do you create a GAF file for submission to the GOC?
   • What information do you want to capture in a controlled vocabulary that you currently CANNOT capture with GO terms?
2. Develop proposal for annotation process (Suzi, Harold, Rama, Emily, Kimberly, Paul)
   • Literature-based annotation process using examples from transcription overhaul (Karen & Varsha) and apoptosis (Paola & Emily)
     • Ontology development support of annotation (David, Chris, Paola)
     • Prioritization, e.g. biological domain focus (Suzi, Emily, Rama)
   • Phylogenetic annotation (Pascale and/or PaulT)

Overview of goals of meeting

At this meeting we will be discussing specific proposals with the prime objective being to reach agreement on an implementation path going forward to efficiently and accurately create functional annotations capturing molecular information about gene products that are of high quality. Ideally we will achieve the following:

1. We will agree on specific annotation goals relative to the experimental literature. These #s will be reassessed at subsequent GOC meetings and used as a means of tracking progress.
   1. Each annotation group will track completeness
      1. Globally: Out of the potential GO annotations that could be made, what fraction are completed? What fraction of all relevant papers (or genes, or however the group prioritizes GO annotation) have been curated?
      2. By gene: Which genes are currently “comprehensive” wrt the available experimental literature?
   2. The dedicated annotation staff will track adherence to annotation guidelines
   3. The dedicated annotation staff will track the number of non-redundant, accepted annotations each period
   4. The dedicated annotation staff will track the information content (specificity) of the accepted annotations
2. We will extend our quality control methods and strategies by creating a working group dedicated to this role.
   1. Agreement that all contributed annotations will undergo secondary QA steps before being accepted
   2. Agreement that dedicated QA curators have the authority to reject contributed annotations
   3. Contributing curators agree to follow annotation guidelines and remove or revise annotations that do not meet these guidelines
   4. The dedicated QA curators will agree to use and maintain the documented methodologies for inferred annotation
   5. The dedicated QA curators will agree to use the prioritization scheme that is available on GO site.
3. We will define concrete steps for implementation of required infrastructure for meeting these annotation goals.
   1. Contributing groups will sign off on the new annotation flow proposal and their ability and plans for implementation.
   2. Sign off on the initial proposed requirements for the common annotation tool.

Day 1 (half day) - Overview

Current GO annotation status

• Overview of current pipeline experimental information submitted by annotation groups (Paul T & Mike C)
• 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 (Tony or Eleanor? or Paul T?)

Vision for GO annotation process

• Overall management group reorganization and roles (Paul x 2, Judy, Mike, Suzi)
• Annotation submission (Suzi, Paul T., Chris and Emily)
  • minimum annotation
  • ideal, “complete” annotation
  • current diff between ‘minimum’ and ‘complete’ and why
• Overview of the common annotation framework (Chris and Paul T. - 20 minutes)
  • Data flow proposal.

Day 2 (full day)

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

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 Swiss-Prot and GOA, e.g. UniPath (Claire & Rolf)
    • at MGI, e.g. cell types; temporal -spatial (David & Harold)
  • GOC Domain-specific curation and ontology development
    • apoptosis annotation (Paola Roncaglia and Emily Dimmer)
    • transcription overhaul (Karen Christie & Varsha Khodiyar)
    • summary of recommendations (Paul and Suzi)

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

• Details of the common annotation framework (Paul x 2, 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.

Day 3 (full day)

Concurrent sessions (4 hr)

• Software group will go off for a concurrent meeting (Chris, Seth, Ben, Mary, Heiko, Hans-Michael)
• PAINT training (Suzi and/or Huaiyu)

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, - Yasmin, Rob, Selina, Kalpana, Jim, Val, Jane, Emily, Carson, Diane

Decisions made, reorganization of manager groups and their coordinators.

• 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 PIs empower the Managers to activity monitor the working groups progress and report to the directors any problems that inhibit reaching our goals. ** This is not a volunteer consortium and 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.
  • Annotation productivity working group (Rama & Emily)
    • 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)
    • 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)
    • How to select targeted gene sets
    • Efficient ways of leveraging the community
    • What tools and other infrastructure would assist.

• • Annotation & ontology review working group (David & Huaiyu)
    • 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
    • Ontology modeling, consistency and review

• • Framework working groups (Chris & Jane)
    • Database infrastructure (Chris):
      • 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 (Kimberly)
    • User and community interactions (Jane)