2011 UCL Meeting Agenda: Difference between revisions

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** Use in FANTOM5
** Use in FANTOM5
** Neuro-cell work
** Neuro-cell work
* [[Cellular_component_disjoint_classes#Spatial_disjointness:_Disconnected_from|Proposal to introduce new disjointness axioms into GO CC]] ~~ Chris
* Update on GOCHE
* Update on GOCHE
* [[Ontology Release Files Proposal]] ~~ Chris
* [[Ontology Release Files Proposal]] ~~ Chris
* Roadmap for new logical definitions and relationships - [[:Category:Cross_Products]]
* Roadmap for new logical definitions and relationships - [[:Category:Cross_Products]]
* Update on RO and BFO ~~ Chris
* Relations
** Update on RO and BFO ~~ Chris
** GO subset of RO
** GO subset of RO
** Coordinating between annotation group and ontology group on GO subset of new RO
** Coordinating between annotation group and ontology group on GO subset of new RO

Revision as of 13:36, 6 October 2011

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Agenda

Coffee from 9.00am Morning session to start at 9:30am End of sessions: 6pm Monday and Tuesday, 2pm on Wednesday GOC dinner Monday 6:30pm

Software

Milestones Report

  • Overview of software group activities and Roadmap ~~ Chris
    • 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
    • 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
  • GPAD specification and tools ~~ Amelia
  • GO Galaxy ~~ Amelia
  • LEGO_Model_Draft_Specification ~~ Amelia, Chris, PaulT
  • PAINT report ~~ Suzi, PaulT

Ontology

  • Ontology editing workflow ~~ Chris
    • Dual mode Obo-Edit and Protege editing
    • Introduction to fast OWL reasoners, what they can do for the ontology group
    • MIREOTing subsets of external ontologies into editors version
    • Using OORT to produce releases
    • Greater use of ontology constraints (disjointness, taxonomic constraints)
  • Update on cell ontology ~~ Chris
    • Integration with Uberon
    • Use in FANTOM5
    • Neuro-cell work
  • Proposal to introduce new disjointness axioms into GO CC ~~ Chris
  • Update on GOCHE
  • Ontology Release Files Proposal ~~ Chris
  • Roadmap for new logical definitions and relationships - Category:Cross_Products
  • Relations
    • Update on RO and BFO ~~ Chris
    • GO subset of RO
    • Coordinating between annotation group and ontology group on GO subset of new RO

Annotation Working Group (Emily, Rama)

  • Progress Report
    • 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.
    • Column 16 usage and development by groups
  • 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

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?

General Discussions

- Discussion on appropriate software tools to help manage and report progress on individual project milestones