2012 Annotation Meeting Stanford: Difference between revisions

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=Agenda=
=Agenda=
==Preparation needed in advance of GO Consortium meeting==
==Preparation/Goals for the meeting ==
#Preparation for each GO annotation group
[[Over all goals for the meeting are available here ]]
#*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?
#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)


==Goals==
==Group Photo==
GO annotations are the primary product of the GO and curator time is our most valuable resource: we need a defined process for how they will be produced efficiently and at high quality.
[[Image: GOC-Stanford-2012.jpg|800px]]
* Overall objective: to briefly review the existing GO annotation streams, and delve into how we can make GO annotations better, faster.
* We will define new processes to identify and set annotation goals by production numbers and by domain coverage.
** rate of production by annotation:  # of annotations/quarter (ACTION ITEM: pick a realistic GOAL for increasing this # over the next 5 years)
** rate of production by domain:  # of domain evaluations / quarter (ACTION ITEM: pick a goal for first quarter and evaluate for future goals)
** rate of refinement:  increase in information content/year (ACTION ITEM: pick a realistic GOAL for increasing this # over the next 5 years)
** quality standards and metrics:  minimal requirements for community contributions (ACTION ITEM: publishing these requirements)
** what additional information shall we aim to collect to enrich the annotations coming from GO funded efforts (ACTION ITEM: List of new data types in relation to existing annotation)
* We will review and evaluate the current components of a process
** what are the current bottlenecks (ACTION ITEM: list of areas we need to address)
** what changes will we make in our process to eliminate bottlenecks and improve quality (ACTION ITEM: a prioritized list of these steps to work on over the next 3 months)
** what changes will we make to our data flow (ACTION ITEM: data flow diagram)


==Proposed Agenda==
==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. <br>
Toll-free USA number 1-866-953-9688 (US Toll number 1-212-548-2460 in case of problems with 866 number)<br>
Toll-free UK 0808 238 6001 (toll number: 646 834-9311)<br>
Toll-free Switzerland 0800 562 830 (toll number: 646 834-9311)<br>


=== One idea for structuring meeting===
Participant Pin: (801-561)<br>
*Sunday Afternoon – The Vision: from experimental data to structured knowledge
**1.Collective vision of idealized work flow (30 minutes open discussion: David Hill, discussion leader)  20 min
**2.Overview of Annotations Now (Mike Cherry, discussion leader) 20 min
**3.Overview of Experimental Literature Curation now (Judy Blake discussion leader) 20 min
**4.Overview of synergies of curation and ontology development Now (Suzi Lewis discussion leader) 20 min
**5.Overview of Phylogenetic Annotations (Paul Thomas discussion leader) 20 min
**6 Overview of current curation tools and procedures (Paul Sternberg, discussion leader) 20 min
**7.Collective vision revisited (30 minutes open discussion: Rama Balakrishnan, discussion leader


*Monday Morning - What can we collectively do to make curation of experimental data more efficient?
==Feb 26, 2012, Day 1 (half day) - Overview==
*Monday Afternoon – What can we collectively do to make phylogenetically based curation more efficient?
<font size = "+1">Arrive at: 11:00AM<br>
*Tuesday Morning A – What are our goals, how do we measure completeness, what is a minimal GO annotation?
Meeting: 12:00PM</font>
*Tuesday Morning B-workshops on 1) Common Annotation Tools – Kimberley and Val and 2) PAINT curation - Pascale
===Current GO annotation status===
*Tuesday Afternoon-  Action Items for Curation Pipeline – building the data flow matrix together.
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]]
** Paul's summary slides [[File: survey_summary_3E_thru_4.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 [http://wiki.geneontology.org/index.php/Gp2protein_file "gp2protein" files] (Paul T). <br>
GPI format: (http://wiki.geneontology.org/index.php/Gene_Product_Association_Data_%28GPAD%29_Format#Proposed_Gene_Product_Information_.28GPI.29_file_format)


==='''''Sunday afternoon: 1pm until 4:30pm'''''===
===Vision for GO annotation process===
====GOC Vision - From experimental data to structured knowledge for biologists ====
Minutes: Rama, Karen
* The hourglass model: gathering in of data, munging data, broad spectrum of output for consumption by biologists
* Annotation submission (Suzi, Paul T., Chris and Emily) [[File:min_ideal_GO_annotation_requirements.pdf]]
* Overview - Experimental Data In - Where does it come from? How can we as a community be more efficient?
** minimum annotation
** Most experimental data currently comes from biomedical literature
** enhanced expressivity for GO annotations (Paul T.) [[File:enhanced_expressivity.pdf]]
** Priorities can be either gene set or domain based
** Data could also come from data centers - pros and cons
** Define a minimal GO annotation (see notes from Emily)
** GO curators should be able to annotate for genes from all organisms (different than MOD curators)and need support to do this.
*PRIMARY MEETING ACTION ITEM: What can we collectively do to make curation of experimental data more efficient?
** not expected to answer now, but at the end of the meeting....needs to be held in mind throughout this meeting.
** Tracking experimental annotations, QC. metrics (further discussions later)
* Building on Experimental Annotations
** Defining data flow after deposit of experimental annotations
** How often can/should we update phylogenetic analysis? 
** How can we stream PAINT annotations effectively to consumers
** How can we measure completeness of annotation stream both by gene and by domain??
* Focus of Meeting
** Finding efficiencies in generating experimental annotations
** Exploring GO SWAT option where GOC staff oversee domain effort with distributed curation supported
** how can curators focused on experimental literature contribute to PAINT-like annotation stream
*PRIMARY MEETING ACTION ITEM: What is the measure of completeness by gene or by domain that we want to employ?
** in contrast to others, vertebrates have tens of members of the thousands of small gene families.
** in contract to others, vertebrates have hundreds of publications for primarily-studied set of ~10,000 genes.
**
*PRMIARY MEETING ACTION ITEM: What do different sets of GO users want?  How do we provide this?
**'What does this gene do?'
** How do sets of genes coordinate actions?  in what spatial / temporal context?
** What do we know that is shared between experimental organisms vs. what is unique for a given organism or class of organisms?


====General Discussion of Integrated Annotation Pipeline (Mike Cherry 20-23 minutes)====
Minutes: [[File:GOC2012MinutesSession2.pdf]]
* Can we define data flow from publication to PAINT annotation?
* Will, in general, each curator work from gene or from domain perspective?
* Will in general, each curator complete chain from experimental data through phlyo-inference; or how will these processes flow from one to the other.
* GO SWAT teams (PaulT and Judy)


====Current Status of Annotation Production (20-30 minutes) i.e. Where are we now with basic EXP annotation? ====
==Feb 27, 2012, Day 2 (full day)==
* What is our current rate of new annotation production
<font size = "+1">Breakfast: 8:00AM<br>
* What is our current rate of annotation loss (due to sunset clause, average % of annotations that can't be loaded, etc.)
Meeting: 9:00AM</font>
* Annotation Information Content assessment (how detailed are the existing annotations and what has been the trend over time)
===Case studies of state-of-the-art annotation approaches===
* Completeness and adherence to standards of "gp2protein" files
[[minutes_annotation_approaches_stanford_2012 | Minutes]]: Jane, Paola<br>
=====Goal for this Session=====


====Outline of the current EXP-based annotation process. (20-30 minutes)====
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.
# Knowledge extraction (both into the ontology and new annotations)(David, Val)
#* Curators working directly from the literature
#* Curators working with experts in the field (who summarize and provide links to the primary literature)
# Knowledge capture
#* Ontology requests for change
#* MODs
#* others
# Quality Assurance
# Data flow
#* Current
#* Straw-man proposal
=====Goal for this Session=====


====Lessons learned from recent EXP-based curation efforts ( >2 hours)====
* Community approaches for recording annotations
Focus is on how the processes might be generalized, with specific details only as supporting examples.
** [[Media:GO_201202_CACAO.pdf|Wiki-based annotation in CACAO: proposed improvements and potential generalizations]] (Jim Hu and Brenley McIntosh)
* '''Domain-specific curation and ontology development (Knowledge extraction)'''
** 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)
** apoptosis annotation (Paola Roncaglia and Emily Dimmer)
* What additional gene function information is used to supplement GO annotation?
** transcription overhaul (Karen Christie & Varsha Khodiyar)
** at UniProt (Claire)
* '''Approaches for recording annotations (Knowledge capture)'''
** at MGI, e.g. cell types; temporal -spatial (David & Harold)[[File:MGI_GO_EI_2.pdf‎]]
** Wiki-based annotation in CACAO: proposed improvements and potential generalizations (Jim Hu and Brenley)
* GOC Domain-specific curation and ontology development
** Integrating annotations coming from multiple sources for a single organism (Experiences at Swiss-Prot and GOA)
** apoptosis annotation (Paola and Emily )
** CANTO experiences (Val Wood)
** transcription overhaul (Rama & Karen) [[Media:TxnOH-OntDev-Report.pdf]], [[Media:TxnOH-AnnotReport.pdf]]
This 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)
** summary of recommendations (Mike)
* '''Discussion of annotation strategy'''
** What are the bottlenecks
=====Goal for this Session=====


==='''''Monday: 9am to 5pm'''''===
===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 <b>Paul T.</b>)
** Data flow proposal. [[File: current_and_proposed_annotation_flow.pdf]]
* Details of the common annotation framework  (<b>Paul S</b>, 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.


====Towards a common annotation framework (Kimberly and Chris)====
==Feb 28, 2012, Day 3 (full day)==
* '''Kimberly to report on user requirements for CAF.'''
<font size = "+1">Breakfast: 8:00AM<br>
Kimberly is currently talking to all curation groups about individual GO annotation tools, what features they have and what features curators would like. Therefore, by the GO Consortium meeting, Kimberly will be able to present the features that GOC curators feel are most important.
Meeting: 9:00AM</font>
* '''Discussion'''
** 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)
* '''Project plan, development goals for next 3-6 months (Chris Mungall)'''


====Phylogenetic inference process (Paul Thomas and Pascale/Suzi)====
===Concurrent sessions (4 hr)===
* '''PAINT as used for Quality Assurance'''
* Software group will go off for a concurrent meeting (Chris, Seth, Ben, Mary, Heiko, Hans-Michael)
**Dual perspectives (biological topic focus)
* '''Instructions to download and launch PAINT, and general user guide:''' http://wiki.geneontology.org/index.php/PAINT_User_Guide
**cross-checking annotations
* PAINT training (Suzi and/or Huaiyu)
**Phylogenetic inference: Synthesis, QA and inference across organisms using PAINT
** PAINT background and intro to function evolution in gene families (Paul T.) [[File:basic_PAINT_annotation_background.pdf]]
* '''PAINT: How MODs can achieve full breadth of genome coverage'''
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)
** Focused annotation session for ~10 GO annotators per group
** Led by Pascale and/or PaulT with Mike L., Rama, Li Ni, Donghui, Huaiyu handling groups individually
** small groups to make each session manageable and productive
** 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)
** 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)
** Time required: minimum: 5 hours.
=====Goal for this Session=====


==='''''Tuesday: 8:30am to 4pm'''''===


====Minimal requirement for GO annotations (Emily Dimmer, Harold Drabkin, Rama) i.e. What does an annotation consist of, both minimally and ideally ====
:* Mixed groups
* Minimal requirements for submitting GO annotations (for projects and MODs *not* funded via the GOC)
:** those with previous training in PAINT annotation
* What would an ideal annotation consist of and what are the responsibilities for GO curators (for projects and MODs *funded* via the GOC)
:** no training, however strong possibility in using PAINT later on to create GO annotations (e.g. GO NIH funded curators)
* LEGO annotation framework
:** 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


====Towards a biological topic-focused approach====
===Decisions made, reorganization of manager groups and their coordinators.===
* '''How and who should select targeted gene sets'''
** Is 9 genes a reasonable # to tackle per annotation milestone
** What criteria should be used to declare a milestone has been reached. (comprehensively annotated gene products, final paint approval, other QC checks)
* '''What skills are needed among the members of the annotation focus group and what tools do they need'''
** Ontology expert, biological expertise, GO curator
** Efficient ways of leveraging the community
** What tools and other infrastructure would assist.
* '''Next steps towards integral quality control'''
** Define our specific tactical approach to new annotation strategy


====Responsibilities and review of milestones for next meeting====
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
[[Category:Workshops]]

Latest revision as of 10:08, 15 April 2019

Agenda

Preparation/Goals for the meeting

Over all goals for the meeting are available here

Group Photo

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?
  • 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