2011 UCL Meeting Agenda: Difference between revisions

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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]


=Agenda=
= Photos =


[http://www.facebook.com/pages/Gene-Ontology/305908656519 on the GOC Facebook page]
= Venue =
'''Main meeting Monday to Wednesday'''
Wilkins Haldane Room ([http://crf.casa.ucl.ac.uk/screenRoute.aspx?s=1019&d=187&w=False])
'''GO managers and PIs'''
Tuesday 1pm to 2:30pm Wilkins JBR Meeting Room ([http://crf.casa.ucl.ac.uk/screenRoute.aspx?s=1019&d=189&w=False])
'''GO curators and ChEBI'''
Wednesday 10:30am to 1:30pm Cruciform Foyer Seminar Room 3 ([http://crf.casa.ucl.ac.uk/screenRoute.aspx?s=1019&d=62&w=False])
=Monday=
'''Morning'''
Coffee from 9.00am
Coffee from 9.00am


Morning session to start at 9:30am
Morning session to start at 9:30am


End of sessions: 6pm Monday and Tuesday, 2pm on Wednesday
Philippa Talmud to welcome the GO Consortium to UCL.
 
PIs to kick off meeting...?


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?). Ruth is looking into booking additional rooms. [Jane]
Minutes on Google doc [[https://docs.google.com/document/d/1P4jzTTJrGTDBkjRaIiu1VVWf7cwHZET9s7k9GBby93Y/edit edit as required]]


GOC dinner Monday 6:30pm: Sardo 47 Grafton Way http://www.sardo-restaurant.com/index.html
== Project Management==
- Overall project management under new grant goals<br>
- Manage documentation<br>
- Manage staff <br>
- 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===
==Software (requested time: 3 hours)==


* Presentation on GOMine (Stanford group)
# Overview of software group activities and [https://sourceforge.net/apps/trac/geneontology/roadmap Roadmap] [Chris]
* [[Migration of GO to SVN (Proposal)]] Chris
# Personnel Updates [Chris]


==== Milestones Report ====
* [[Migration of GO to SVN (Proposal)]] Chris (15 mins)


* Overview of software group activities and [https://sourceforge.net/apps/trac/geneontology/roadmap Roadmap] ~~ Chris
** New architecture (30 mins)
** New architecture
* [https://sourceforge.net/apps/trac/geneontology/milestone/AmiGO2%20alpha AmiGO 2 alpha] ~~ Seth
* [https://sourceforge.net/apps/trac/geneontology/milestone/AmiGO2%20alpha AmiGO 2 alpha] ~~ Seth
** [http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo amigo2 walkthrough demo]
** [http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo amigo2 walkthrough demo]
Line 30: Line 59:
** overview of architecture, use of Solr. Demo of Solr API
** overview of architecture, use of Solr. Demo of Solr API
** opportunities for integration with QuickGO ~~ Tony, Chris
** opportunities for integration with QuickGO ~~ Tony, Chris
* [https://sourceforge.net/apps/trac/geneontology/milestone/GOLD%20beta GOLD beta] ~~ Chris - on behalf of Shahid
 
** GAF services
* OBO-Edit ~~ Heiko/Chris (20 mins)
*** 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
** 2.1 Release
** 2.2 Plans : mostly maintenance, a few key features, integration of obo2owl code
** 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?
** Beyond 2.2. - should there be a 3.0? Proteg4 plugin? Web-based tool? Lego?
* [https://sourceforge.net/apps/trac/geneontology/milestone/TG1%20beta TermGenie 1 beta] ~~ Heiko
 
* [https://sourceforge.net/apps/trac/geneontology/milestone/obo%20to%20owl%20roundtripping obo2owl roundtripping] ~~ Heiko/Chris (20 mins)
** Using [[Ontology Release Files Proposal|OORT]] to produce releases  ~~ Chris (!keep this item here - Jane)
 
* [https://sourceforge.net/apps/trac/geneontology/milestone/TG1%20beta TermGenie 1 beta] ~~ Heiko (25 mins)
** Retiring TG0
** Retiring TG0
** Extensions - additional templates
** Extensions - additional templates
** Integration with ontology roadmap
** Integration with ontology roadmap
** Use of TG as SF replacement ("freeform" term creation)
** Use of TG as SF replacement ("freeform" term creation)
* [https://sourceforge.net/apps/trac/geneontology/milestone/obo%20to%20owl%20roundtripping obo2owl roundtripping] ~~ Heiko
 
** OORT
* GO Galaxy  ~~ Chris (for Amelia) (5 mins)
* [https://sourceforge.net/apps/trac/geneontology/milestone/GPAD%20Specification%20and%20tools GPAD specification and tools] ~~ Amelia
* GO Galaxy  ~~ Amelia
** http://galaxy.berkeleybop.org:8080/
** http://galaxy.berkeleybop.org:8080/
** Use by Phenoscape for obo-diffs
** Use by Phenoscape for obo-diffs
** Wrapping multiple term enrichment tools
** Wrapping multiple term enrichment tools
** Use case - miRNA pipeline
* [[LEGO_Model_Draft_Specification]] ~~ Amelia, Chris, PaulT
* PAINT report ~~ Suzi, PaulT


=== Ontology ===
* Presentation on GOMine (Stanford group) (Rama)
** New tool from Stanford group, accessing GO data like GOOSE (http://goad.stanford.edu:8080/gomine/begin.do)
 
'''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 [http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2011 Roadmap] overview (Rama)
 
* Annotation Progress Report [Rama and Emily] [[file: Annotation_update_UCL11.pdf]]
to include:
** GO Consortium outreach activities and integration of external data sources into primary species GAFs.
** Development of GO annotation guidelines,
**[http://wiki.geneontology.org/index.php/Ideas_for_GOC_community_curation_tool Community Annotation Tool]
**[http://wiki.geneontology.org/index.php?title=Evidence_Code_Ontology_(ECO) ECO codes]
**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]
 
==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. [http://wiki.geneontology.org/index.php/Relationships_between_annotation_objects_and_ontology_terms see wiki]
 
* [https://sourceforge.net/apps/trac/geneontology/milestone/GPAD%20Specification%20and%20tools GPAD specification and tools] ~~ Amelia
 
* [https://sourceforge.net/apps/trac/geneontology/milestone/GOLD%20beta 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====
* [[LEGO_Model_Draft_Specification Re-development of the Annotation Model]] ~~ Amelia, Chris, Pau lT [15mins talk + 20min discussion]
 
==Ontology (requested: 3 hours)==
 
* [[2011_Timeline|Roadmap]]/project overview [Jane]
 
* 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 [http://wiki.geneontology.org/index.php/File:SourceForge_UCL_Nov2011.pdf]
 
* 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
 
*Content Projects
** 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 [[Transcription|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 [[GO_slim_overhaul|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
** [[Neuro_Behaviour_Ontology_(NBO)-GO_alignment|Behaviour alignment and NBO]] - a proposal [Jane]


* Roadmap reporting ?
** Roadmap for new logical definitions and relationships - [[:Category:Cross_Products]]
* 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
** Report on how the GO editors are using SourceForge: triage, jamborees etc  ~~ Jane
** Greater use of ontology constraints (disjointness, taxonomic constraints)
* 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
* Behaviour ontology and integration with GO proposal ~~ Jane
* 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 GOCHE: ~~ David
* Update on GO apoptosis project (Paola and Pablo)
* [[Cellular_component_disjoint_classes#Spatial_disjointness:_Disconnected_from|Proposal to introduce new disjointness axioms into GO CC]] ~~ Chris
* [[Ontology Release Files Proposal]] ~~ Chris
* Relations
* Relations
** Update on RO and BFO ~~ Chris
** 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
* Cross-products
** Short update on where the GO cross-products are up to: involved in, biosynthesis etc. ~~ Jane
===Annotation Working Group (Emily, Rama)===
* 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.


** Column 16 usage and development by groups
==Wednesday==
*** 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
===Meeting Wrap-Up===
** IMEX Consortium's work on representing protein-protein interaction data: presentation by Sandra Orchard, IntAct, EBI, Cambridge UK (25 mins)
** Action Items
*** The annotation of the stoichiometry of binding by GO groups.  Under the spotlight: protein homodimerization, protein tetramerization etc.
** Dates for next meeting


*** Annotation to Protein Complex objects: a suggested annotation format. [http://wiki.geneontology.org/index.php/Protein_Complex_ids_as_GO_annotation_objects see wiki page].
====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


*** 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. [http://wiki.geneontology.org/index.php/Relationships_between_annotation_objects_and_ontology_terms see wiki]


=== Software Group: Annotation Display and Support activities?===
====Ontology editors discussion with ChEBI group (separate room booked)====
*presentation on the new GAF uploader tool? Supply of hard, soft and inferred annotations to submitters?
*presentation on AmiGO2 and column 16 display intentions?


=== Project Management===
[[GOCHE_meeting_2011-11-09]]
- Overall project management under new grant goals<br>
- Manage documentation<br>
- Manage staff <br>
- Discussion on appropriate software tools to help manage and report progress on individual project milestones

Latest revision as of 12:33, 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

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