Difference between revisions of "2011 USC Meeting Agenda"

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(Discussion of the Vision defined in the GOC NIH grant application)
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# Literature-based annotations (Rama)
 
# Literature-based annotations (Rama)
 
#* vision (i.e. efficiency, quality and consistency goals)
 
#* vision (i.e. efficiency, quality and consistency goals)
 +
#* implementation: what will be necessary to accomplish this goal?
 
#** mention QC checks? How groups should be kept up-to-date? See Managers discussion [http://wiki.geneontology.org/index.php/Manager_23March11 here]
 
#** mention QC checks? How groups should be kept up-to-date? See Managers discussion [http://wiki.geneontology.org/index.php/Manager_23March11 here]
 
#* current status/accomplishments
 
#* current status/accomplishments
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# Biological focus-group annotations (Emily)
 
# Biological focus-group annotations (Emily)
 
#* vision (and entire text-book TOC?)
 
#* vision (and entire text-book TOC?)
 +
#* implementation: what will be necessary to accomplish this goal?
 
#* current status/accomplishments
 
#* current status/accomplishments
 
#** New ontologies terms added at recent meetings?
 
#** New ontologies terms added at recent meetings?
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# Phylogenetically-based annotations (Paul T)
 
# Phylogenetically-based annotations (Paul T)
 
#* vision (e.g. dynamically adding a new protein to the right family, versioning with stable IDs for ancestral nodes)
 
#* vision (e.g. dynamically adding a new protein to the right family, versioning with stable IDs for ancestral nodes)
 +
#* implementation: what will be necessary to accomplish this goal?
 
#* current status/accomplishments
 
#* current status/accomplishments
 
#* possible metrics
 
#* possible metrics
 
# Common Annotation Framework (Suzi and Paul S)
 
# Common Annotation Framework (Suzi and Paul S)
 
#* vision
 
#* vision
 +
#* implementation: what will be necessary to accomplish this goal?
 
#* ''Current Efforts''
 
#* ''Current Efforts''
 
#** PomBase community annotation tool (Val?)
 
#** PomBase community annotation tool (Val?)
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# Ontology development (David)
 
# Ontology development (David)
 
#* Overall goals (e.g. cross-products completion)
 
#* Overall goals (e.g. cross-products completion)
 +
#* implementation: what will be necessary to accomplish this goal?
 
#* recent projects - notes/accomplishments
 
#* recent projects - notes/accomplishments
 
#** Transcription factors (Karen C; available Thursday or Friday morning)
 
#** Transcription factors (Karen C; available Thursday or Friday morning)
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# Community resources and Dissemination (Emily & Rama)
 
# Community resources and Dissemination (Emily & Rama)
 
#* recent projects - notes/accomplishments
 
#* recent projects - notes/accomplishments
 +
#* implementation: what will be necessary to accomplish this goal?
 
#** '''Current Efforts in Community GO Annotation''' (Emily)
 
#** '''Current Efforts in Community GO Annotation''' (Emily)
 
#*** BHF-UCL team training programs for MSc students and staff training at UCL. How productive are UCL students and staff at annotating? (Ruth)  
 
#*** BHF-UCL team training programs for MSc students and staff training at UCL. How productive are UCL students and staff at annotating? (Ruth)  

Revision as of 08:04, 4 May 2011

Minutes: (By hosts of previous meeting: MGI)

Welcome; Review of schedule and agenda

  • Introductions.
  • GO PI announcements

Action Items from Bar Harbor GOC meeting

Working plans for deliverables over the next 4 & 12 months

  1. Annotation (Rama and Emily)
    • Timeline: discuss progress and priorities
    • New annotation sanity checks being proposed
    • ECO presentation.
      • Would be nice to establish how the ECO project should be used by GOC, now that the first draft has been published. Edimmer 17:14, 28 February 2011 (UTC) (Marcus will present ECO update)
    • Pre- vs post-composition of GO terms, and use of column 16. Should we be adding in terms for E.g. apoptosis of individual cell types (if they have no other parent in a different node), or should we be capturing this at the annotation stage using column 16? What is the time-scale of using column 16 and what data types can be included? (Becky)
    • Biological focus-group annotations (Emily)
      • Transcription factor workshop?
      • Working in a research environment and the impact on annotation targets? (Ruth)
        • BHF-UCL team involved in annotating specific genes identified through GWAS or microarray (Ruth)
  2. Reference Genome (Pascale)
  3. Software (Chris)
  4. Ontology development (David)
    • Timeline: discuss progress and priorities
    • OBO/OWL migration (Chris)
    • Notifying a wider audience about large-scale changes to the ontology: when a project is starting up, and when key changes have been done (Becky)
    • Notifying a wider audience about proposed term obsoletions.
    • Protein complexes(Harold)
      • What is within the scope of GO, and what is in the scope of PRO?
      • Should GO capture gene product specific protein complexes, or species-specific protein complexes?
      • Should protein complexes be defined based on function or component information? (Becky and Peter D'E)
  5. Community resources and Dissemination (Emily & Rama)
    • InterPro2GO presentation
      • Sarah Burge, InterPro. Time requested: 40 min presentation, 20 mins discussion.
      • Contents: Brief summary of the revised guidelines for the GO mapping of InterPro entries. To include: InterPro evidence requirements, new policy of mapping Domain, Site and Repeat entries, changes in coverage between the old and new approaches, occasions where InterPro is unable to GO map an entry and finally, the automatic checks to prevent taxonomy violations and assignment of redundant terms.

Discussion of the Vision defined in the GOC NIH grant application

(This includes presentations of our current efforts and how these will map into the vision. Also what goals are needed to reach the aims stated in the application.)

  1. Literature-based annotations (Rama)
    • vision (i.e. efficiency, quality and consistency goals)
    • implementation: what will be necessary to accomplish this goal?
      • mention QC checks? How groups should be kept up-to-date? See Managers discussion here
    • current status/accomplishments
    • possible metrics
    • timeline
  2. Biological focus-group annotations (Emily)
    • vision (and entire text-book TOC?)
    • implementation: what will be necessary to accomplish this goal?
    • current status/accomplishments
      • New ontologies terms added at recent meetings?
    • possible metrics/milestones
  3. Phylogenetically-based annotations (Paul T)
    • vision (e.g. dynamically adding a new protein to the right family, versioning with stable IDs for ancestral nodes)
    • implementation: what will be necessary to accomplish this goal?
    • current status/accomplishments
    • possible metrics
  4. Common Annotation Framework (Suzi and Paul S)
    • vision
    • implementation: what will be necessary to accomplish this goal?
    • Current Efforts
      • PomBase community annotation tool (Val?)
      • Textpresso, Phenote, PAINT-web, and all the rest...
    • timeline and milestones
  5. Ontology development (David)
    • Overall goals (e.g. cross-products completion)
    • implementation: what will be necessary to accomplish this goal?
    • recent projects - notes/accomplishments
      • Transcription factors (Karen C; available Thursday or Friday morning)
      • Signaling (Becky)
      • Chemicals (David or Tanya)
      • software utilities (Reasoners, QC - Chris)
    • timeline
  6. Community resources and Dissemination (Emily & Rama)
    • recent projects - notes/accomplishments
    • implementation: what will be necessary to accomplish this goal?
      • Current Efforts in Community GO Annotation (Emily)
        • BHF-UCL team training programs for MSc students and staff training at UCL. How productive are UCL students and staff at annotating? (Ruth)
        • Texas A&M annotation competition? (CACAO)
        • TAIR GO annotations from submitted publications?
      • software status update (AmiGO, GOOSE, GOLD, etc. - Seth)
    • Monitoring customer satisfaction
    • GO Help Rotation/designated person to deal with GO help (Rama)

Satellite meetings

  1. Cardiac Conduction ontology development workshop (Ruth&David) [1]
    • pre-workshop discussion (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
    • probably straight after main meeting closes on 19th May
    • workshop date not yet set, aiming for Sept-Nov 2011
    • Please let Ruth know if interested in attending workshop/pre-meeting