Difference between revisions of "2011 UCL Meeting Agenda"

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[[Category:GO Consortium Meetings]]
 
back to [http://wiki.geneontology.org/index.php/2011_UCL_Meeting_Logistics meeting logistics page]
 
back to [http://wiki.geneontology.org/index.php/2011_UCL_Meeting_Logistics meeting logistics page]
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= Photos =
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[http://www.facebook.com/pages/Gene-Ontology/305908656519 on the GOC Facebook page]
  
 
= Venue =
 
= Venue =
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PIs to kick off meeting...?
 
PIs to kick off meeting...?
  
[[https://docs.google.com/document/d/1P4jzTTJrGTDBkjRaIiu1VVWf7cwHZET9s7k9GBby93Y/edit]]
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Minutes on Google doc [[https://docs.google.com/document/d/1P4jzTTJrGTDBkjRaIiu1VVWf7cwHZET9s7k9GBby93Y/edit edit as required]]
  
 
== Project Management==
 
== Project Management==
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* Annotation [http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2011 Roadmap] overview (Rama)
 
* Annotation [http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2011 Roadmap] overview (Rama)
  
* Annotation Progress Report [Rama and Emily]  
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* Annotation Progress Report [Rama and Emily] [[file: Annotation_update_UCL11.pdf]]
 
to include:  
 
to include:  
 
** GO Consortium outreach activities and integration of external data sources into primary species GAFs.
 
** GO Consortium outreach activities and integration of external data sources into primary species GAFs.
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====Longer-term Annotation Projects====
 
====Longer-term Annotation Projects====
 
* [[LEGO_Model_Draft_Specification Re-development of the Annotation Model]] ~~ Amelia, Chris, Pau lT [15mins talk + 20min discussion]
 
* [[LEGO_Model_Draft_Specification Re-development of the Annotation Model]] ~~ Amelia, Chris, Pau lT [15mins talk + 20min discussion]
 
*Common Annotation Framework ((Aim 4 of the Grant) - a centralized curation system to help curators efficiently capture annotations from the literature
 
**Brainstorming session on GO curation tool features - what features are essential, what features would be great to have, what do curators ''not'' want
 
  
 
==Ontology (requested: 3 hours)==
 
==Ontology (requested: 3 hours)==
  
* [[2011_Timeline|Roadmap]]/project overview [Jane/David]
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* [[2011_Timeline|Roadmap]]/project overview [Jane]
  
 
* Ontology editing workflow
 
* Ontology editing workflow
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** Dual mode Obo-Edit and Protege editing ~~ Chris
 
** Dual mode Obo-Edit and Protege editing ~~ Chris
 
** Introduction to fast OWL reasoners, what they can do for the ontology group ~~ Chris
 
** Introduction to fast OWL reasoners, what they can do for the ontology group ~~ Chris
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** OOrt and file releases - [[Ontology_Release_Files_Proposal]]
 
** MIREOTing subsets of external ontologies into editors version ~~ Chris
 
** MIREOTing subsets of external ontologies into editors version ~~ Chris
** Report on how the GO editors are using SourceForge: triage, jamborees etc  ~~ Becky
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** Report on how the GO editors are using SourceForge: triage, jamborees etc  ~~ Becky [http://wiki.geneontology.org/index.php/File:SourceForge_UCL_Nov2011.pdf]
 
 
* Cross-products
 
** Roadmap for new logical definitions and relationships - [[:Category:Cross_Products]]
 
  
 
* Greater use of ontology constraints (disjointness, taxonomic constraints) ~~ Chris
 
* Greater use of ontology constraints (disjointness, taxonomic constraints) ~~ Chris
 
**[[Cellular_component_disjoint_classes#Spatial_disjointness:_Disconnected_from|Proposal to introduce new disjointness axioms into GO CC]] ~~ Chris
 
**[[Cellular_component_disjoint_classes#Spatial_disjointness:_Disconnected_from|Proposal to introduce new disjointness axioms into GO CC]] ~~ Chris
 
* Aligning with external ontologies
 
** Update on cell ontology ~~ Chris (NB: would be good to do this by email before the meeting, to get an update on CL funding and workflow).
 
*** Integration with Uberon
 
*** Use in FANTOM5
 
*** Neuro-cell work
 
** Update on GOCHE ~~ David
 
** [[Neuro_Behaviour_Ontology_(NBO)-GO_alignment|Behaviour alignment and NBO]] - a proposal [Jane]
 
  
 
*Content Projects
 
*Content Projects
** Update on signaling ~~ Rebecca
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** Update on [http://gocwiki.geneontology.org/index.php/Signaling signaling] ~~ Rebecca [http://wiki.geneontology.org/index.php/File:Signaling_UCL_Nov2011.pdf]
 
** Update on [[Virus_terms|viruses]] ~~ Jane
 
** Update on [[Virus_terms|viruses]] ~~ Jane
 
** Update on [[Transcription|transcription]] ~~ Karen (please make this a late time slot so Karen can call in: 3pm UK time at the earliest)
 
** Update on [[Transcription|transcription]] ~~ Karen (please make this a late time slot so Karen can call in: 3pm UK time at the earliest)
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** Protein binding data now being captured fully by IMeX Consortium collaborators (Sandra Orchard)
 
** Protein binding data now being captured fully by IMeX Consortium collaborators (Sandra Orchard)
 
** Level of detail required under GO:0005515 protein binding (Jane)
 
** Level of detail required under GO:0005515 protein binding (Jane)
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 +
* Aligning with external ontologies
 +
** Update on cell ontology ~~ Chris (NB: would be good to do this by email before the meeting, to get an update on CL funding and workflow).
 +
*** Integration with Uberon
 +
*** Use in FANTOM5
 +
*** Neuro-cell work
 +
** Update on GOCHE ~~ David
 +
** [[Neuro_Behaviour_Ontology_(NBO)-GO_alignment|Behaviour alignment and NBO]] - a proposal [Jane]
  
 
* Relations
 
* Relations
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====Ontology editors discussion with ChEBI group (separate room booked)====
 
====Ontology editors discussion with ChEBI group (separate room booked)====
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[[GOCHE_meeting_2011-11-09]]

Latest revision as of 09:33, 8 April 2014

back to meeting logistics page

Photos

on the GOC Facebook page

Venue

Main meeting Monday to Wednesday

Wilkins Haldane Room ([1])


GO managers and PIs

Tuesday 1pm to 2:30pm Wilkins JBR Meeting Room ([2])


GO curators and ChEBI

Wednesday 10:30am to 1:30pm Cruciform Foyer Seminar Room 3 ([3])

Monday

Morning Coffee from 9.00am

Morning session to start at 9:30am

Philippa Talmud to welcome the GO Consortium to UCL.

PIs to kick off meeting...?

Minutes on Google doc [edit as required]

Project Management

- Overall project management under new grant goals
- Manage documentation
- Manage staff
- Discussion on appropriate software tools to help manage and report progress on individual project milestones

  • Jira demo [Tony]

- Discussion on a replacement for the Webex screen sharing tool. - Communication between managers projects.

Software (requested time: 3 hours)

  1. Overview of software group activities and Roadmap [Chris]
  2. Personnel Updates [Chris]
    • New architecture (30 mins)
  • AmiGO 2 alpha ~~ Seth
    • amigo2 walkthrough demo
    • Example queries using c16
      • CL examples (mouse annotations)
      • POMBE examples
      • Treatment of evidence types
    • overview of architecture, use of Solr. Demo of Solr API
    • opportunities for integration with QuickGO ~~ Tony, Chris
  • OBO-Edit ~~ Heiko/Chris (20 mins)
    • 2.1 Release
    • 2.2 Plans : mostly maintenance, a few key features, integration of obo2owl code
    • Beyond 2.2. - should there be a 3.0? Proteg4 plugin? Web-based tool? Lego?
  • TermGenie 1 beta ~~ Heiko (25 mins)
    • Retiring TG0
    • Extensions - additional templates
    • Integration with ontology roadmap
    • Use of TG as SF replacement ("freeform" term creation)

Annotation Software

  • Annotation Tools
    • PAINT report ~~ Suzi, PaulT

GOC dinner Monday 6:30pm: Sardo 47 Grafton Way http://www.sardo-restaurant.com/index.html

Annotation (requested time: 5 hours)

Annotation Projects

  • Annotation Roadmap overview (Rama)

to include:

    • GO Consortium outreach activities and integration of external data sources into primary species GAFs.
    • Development of GO annotation guidelines,
    • Community Annotation Tool
    • ECO codes
    • Annotation QCs, including taxon constraints.
  • Progress of CACAO biocurator training on GONUTS [4]

[Jim 10 mins]

Tuesday

Separate lunchtime meeting for GO managers and PIs. Wilkins JBR Meeting Room 1pm to 2:30pm

Annotation discussions (cont.)

  • Annotation Extension Field (column 16)
    • Development of the column 16 format (Val)
    • Discussion:
      • Rules for transferring column 16 via ISS and via F->P inferences.

Annotation Proposals

  • GO evidence codes to ECO identifiers
  • Specific use proposed for explicitly defining a gp to GO term relationship. see wiki
  • GOLD beta ~~ Chris - on behalf of Shahid
    • GAF services
      • Annotation file QC
      • Inference of new annotations
        • Use of logical definitions to suggest deeper annotations
        • Cross-ontology inference using part_of and occurs_in


Longer-term Annotation Projects

Ontology (requested: 3 hours)

  • Ontology editing workflow
    • Dual mode Obo-Edit and Protege editing ~~ Chris
    • Introduction to fast OWL reasoners, what they can do for the ontology group ~~ Chris
    • OOrt and file releases - Ontology_Release_Files_Proposal
    • MIREOTing subsets of external ontologies into editors version ~~ Chris
    • Report on how the GO editors are using SourceForge: triage, jamborees etc ~~ Becky [5]
  • Content Projects
    • Update on signaling ~~ Rebecca [6]
    • Update on viruses ~~ Jane
    • Update on transcription ~~ Karen (please make this a late time slot so Karen can call in: 3pm UK time at the earliest)
    • Update on GO apoptosis project (Paola and Pablo)
    • Update on generic GO slim (was this done at LA?) [Val]
      • Processes and components
      • Functions
  • Protein Binding (covering both ontology and annotation issues)
    • Protein binding data now being captured fully by IMeX Consortium collaborators (Sandra Orchard)
    • Level of detail required under GO:0005515 protein binding (Jane)
  • Aligning with external ontologies
    • Update on cell ontology ~~ Chris (NB: would be good to do this by email before the meeting, to get an update on CL funding and workflow).
      • Integration with Uberon
      • Use in FANTOM5
      • Neuro-cell work
    • Update on GOCHE ~~ David
    • Behaviour alignment and NBO - a proposal [Jane]
  • Relations
    • Update on RO and BFO ~~ Chris
    • GO subset of RO
    • Coordinating between annotation group and ontology group on GO subset of new RO

Wednesday

Meeting Wrap-Up

    • Action Items
    • Dates for next meeting

Annotation Discussion

    • Progress and Direction of the Reference Genome Project (Pascale)
    • Ways in which PAINT annotation can be carried out to quickly generate annotations as a first draft annotation set (raised on the annotation call 25/10/2011)
    • suitable projects to engage all groups


Ontology editors discussion with ChEBI group (separate room booked)

GOCHE_meeting_2011-11-09