2011 UCL Meeting Agenda: Difference between revisions

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==Tuesday==
==Tuesday==


9:30am  
9:30am Annotation


** [[LEGO_Model_Draft_Specification]] ~~ Amelia, Chris, PaulT
=== Software Group: Annotation Display and Support activities?===
[15mins talk + 20min discussion]
*presentation on the new GAF uploader tool? Supply of hard, soft and inferred annotations to submitters?
*presentation on AmiGO2 and column 16 display intentions?
*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


** Common Annotation Framework tool discussion
* Annotation Progress Report [Rama and Emily] 10 mins
Presenter?
**Development of GO annotation guidelines. (Geneva and Transcription factors).
**Progress on the Community Annotation Tool (PomBase) [http://wiki.geneontology.org/index.php/Ideas_for_GOC_community_curation_tool See wiki]
**ECO codes for GO annotation. [http://wiki.geneontology.org/index.php?title=Evidence_Code_Ontology_(ECO) See wiki]
**Annotation QCs, including taxon constraints.


* Progress of CACAO biocurator training on GONUTS [http://gowiki.tamu.edu/wiki/index.php/Category:CACAO_Fall_2011]
[Jim 10 mins]


'''11am mid morning coffee/tea/juice'''
Discussion topics:


End of sessions: 6pm Monday and Tuesday, 2pm on Wednesday
* [[LEGO_Model_Draft_Specification]] ~~ Amelia, Chris, PaulT
[15mins talk + 20min discussion]


11am mid morning coffee/tea/juice
* Common Annotation Framework tool discussion
Presenter?


1pm lunch
* Annotation Extension Field (column 16)


3:30pm afternoon coffee/tea
* Protein Binding (ontology and annotation issues)
** Protein binding data being captured elsewhere (Sandra Orchard and IMEX)
** Level of detail required under GO:0005515 protein binding (Jane)


On Wed morning, several of us intend to meet with the CHEBI group who are going to come over to UCL. We were thinking perhaps we do the meeting wrap-up first thing on the Wed morning - action items, next meeting date etc. and then we can meet with CHEBI immediately afterwards. We thought perhaps another smaller group meeting might run in parallel (annotation-based? possibly focusing on the Reference Genome effort, group participation issues, next Reference Genome projects, do people want to volunteer to run different projects? and how to work together to meet targets?). Ruth is looking into booking additional rooms. [Jane]
* Annotation to Protein Complex objects: a suggested annotation format??


The GO managers would like to have a lunchtime meeting with the GO PIs on Mon or Tues, so if we could have a separate table/room or something?
==Ontology==
 
GOC dinner Monday 6:30pm: Sardo 47 Grafton Way http://www.sardo-restaurant.com/index.html
 
=== Ontology ===


* [[2011_Timeline|Roadmap]]/project overview [Jane/David]
* [[2011_Timeline|Roadmap]]/project overview [Jane/David]
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** 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
** MIREOTing subsets of external ontologies into editors version ~~ Chris
** MIREOTing subsets of external ontologies into editors version ~~ Chris
** Using [[Ontology Release Files Proposal|OORT]] to produce releases  ~~ Chris
** Report on how the GO editors are using SourceForge: triage, jamborees etc  ~~ Jane
** Report on how the GO editors are using SourceForge: triage, jamborees etc  ~~ Jane
** Greater use of ontology constraints (disjointness, taxonomic constraints) ~~ Chris
** Greater use of ontology constraints (disjointness, taxonomic constraints) ~~ Chris
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* Cross-products
* Cross-products
** Short update on where the GO cross-products are up to: involved in, biosynthesis etc. ~~ Jane
** Short update on where the GO cross-products are up to: involved in, biosynthesis etc. ~~ Jane
=Wednesday=
On Wed morning, several of us intend to meet with the CHEBI group who are going to come over to UCL. We were thinking perhaps we do the meeting wrap-up first thing on the Wed morning - action items, next meeting date etc. and then we can meet with CHEBI immediately afterwards. We thought perhaps another smaller group meeting might run in parallel (annotation-based? possibly focusing on the Reference Genome effort, group participation issues, next Reference Genome projects, do people want to volunteer to run different projects? and how to work together to meet targets?). Ruth is looking into booking additional rooms. [Jane]
The GO managers would like to have a lunchtime meeting with the GO PIs on Mon or Tues, so if we could have a separate table/room or something?
GOC dinner Monday 6:30pm: Sardo 47 Grafton Way http://www.sardo-restaurant.com/index.html


===Annotation Working Group (Emily, Rama)===
===Annotation Working Group (Emily, Rama)===
* Progress Report
* Progress Report
** Development of GO annotation guidelines. (Geneva and Transcription factors).
 
** Progress on the Community Annotation Tool (PomBase) [http://wiki.geneontology.org/index.php/Ideas_for_GOC_community_curation_tool See wiki]
** ECO codes for GO annotation. [http://wiki.geneontology.org/index.php?title=Evidence_Code_Ontology_(ECO) See wiki]
** Annotation QCs, including taxon constraints.
** Progress of CACAO biocurator training on GONUTS [http://gowiki.tamu.edu/wiki/index.php/Category:CACAO_Fall_2011]


** Column 16 usage and development by groups
** Column 16 usage and development by groups
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*** suitable projects to engage all groups
*** suitable projects to engage all groups


=== Software Group: Annotation Display and Support activities?===
*presentation on the new GAF uploader tool? Supply of hard, soft and inferred annotations to submitters?
*presentation on AmiGO2 and column 16 display intentions?
*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


=== Project Management===
=== Project Management===

Revision as of 09:42, 1 November 2011

back to meeting logistics page

Agenda

Monday

Morning Coffee from 9.00am

Morning session to start at 9:30am

9:30-9:40 Philippa Talmud to welcome the GO Consortium to UCL.

9:40 PIs to kick off meeting...

10:00 - 16:00 Software

  1. Overview of software group activities and Roadmap [Chris]
  2. Personnel Updates [Chris]

...order and timings needed for remaining Software items:

  • GO Common Authentication interface ~~ Seth
    • New architecture
  • 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
  • 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
    • Loading of phylogenetic data ~~ Sven
  • OBO-Edit ~~ Heiko/Chris
    • 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
    • Retiring TG0
    • Extensions - additional templates
    • Integration with ontology roadmap
    • Use of TG as SF replacement ("freeform" term creation)
  • obo2owl roundtripping ~~ Heiko
    • OORT (makes more sense to report on this in Ontology session?)
  • GPAD specification and tools ~~ Amelia

16:00-17:00 Annotation Software

  • Annotation Tools
    • PAINT report ~~ Suzi, PaulT


Tuesday

9:30am Annotation

Software Group: Annotation Display and Support activities?

  • presentation on the new GAF uploader tool? Supply of hard, soft and inferred annotations to submitters?
  • presentation on AmiGO2 and column 16 display intentions?
  • 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
  • Annotation Progress Report [Rama and Emily] 10 mins
    • Development of GO annotation guidelines. (Geneva and Transcription factors).
    • Progress on the Community Annotation Tool (PomBase) See wiki
    • ECO codes for GO annotation. See wiki
    • Annotation QCs, including taxon constraints.
  • Progress of CACAO biocurator training on GONUTS [1]

[Jim 10 mins]

Discussion topics:

[15mins talk + 20min discussion]

  • Common Annotation Framework tool discussion

Presenter?

  • Annotation Extension Field (column 16)
  • Protein Binding (ontology and annotation issues)
    • Protein binding data being captured elsewhere (Sandra Orchard and IMEX)
    • Level of detail required under GO:0005515 protein binding (Jane)
  • Annotation to Protein Complex objects: a suggested annotation format??

Ontology

  • Ontology editing workflow
    • Ontology_Release_Files_Proposal -- Chris
    • Dual mode Obo-Edit and Protege editing ~~ Chris
    • Introduction to fast OWL reasoners, what they can do for the ontology group ~~ Chris
    • MIREOTing subsets of external ontologies into editors version ~~ Chris
    • Report on how the GO editors are using SourceForge: triage, jamborees etc ~~ Jane
    • Greater use of ontology constraints (disjointness, taxonomic constraints) ~~ 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
    • Behaviour alignment and NBO - a proposal [Jane]
  • Content Projects
    • Update on signaling ~~ Rebecca
    • Update on viruses ~~ Jane
    • Update on transcription ~~ David (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
  • Relations
    • Update on RO and BFO ~~ Chris
    • GO subset of RO
    • Coordinating between annotation group and ontology group on GO subset of new RO
  • Cross-products
    • Short update on where the GO cross-products are up to: involved in, biosynthesis etc. ~~ Jane

Wednesday

On Wed morning, several of us intend to meet with the CHEBI group who are going to come over to UCL. We were thinking perhaps we do the meeting wrap-up first thing on the Wed morning - action items, next meeting date etc. and then we can meet with CHEBI immediately afterwards. We thought perhaps another smaller group meeting might run in parallel (annotation-based? possibly focusing on the Reference Genome effort, group participation issues, next Reference Genome projects, do people want to volunteer to run different projects? and how to work together to meet targets?). Ruth is looking into booking additional rooms. [Jane]

The GO managers would like to have a lunchtime meeting with the GO PIs on Mon or Tues, so if we could have a separate table/room or something?

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



Annotation Working Group (Emily, Rama)

  • Progress Report


    • Column 16 usage and development by groups
      • Examples of how existing ontology terms will be replaced by annotation extension using column 16 (E.g. structural molecule activity, response element binding). ~~Jane
      • Protein binding - limiting child terms?
  • Annotation Proposals and Discussions
    • IMEX Consortium's work on representing protein-protein interaction data: presentation by Sandra Orchard, IntAct, EBI, Cambridge UK (25 mins)
      • The annotation of the stoichiometry of binding by GO groups. Under the spotlight: protein homodimerization, protein tetramerization etc.
      • Annotation to Protein Complex objects: a suggested annotation format. see wiki page.
      • Use of the new relationship Ontology to describe relationships between entities in an annotation, and for the generation of detailed, composite GO terms
        • specific use for column 16 (annotation extension field
        • specific use proposed for explicitly defining a gp to GO term relationship. see wiki
    • Progress and Direction of the Reference Genome Project
      • 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


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.