2011 UCL Meeting Agenda: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
No edit summary
 
(140 intermediate revisions by 10 users not shown)
Line 1: Line 1:
[[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
GOC dinner Monday 6:30pm


===Software===
Philippa Talmud to welcome the GO Consortium to UCL.


* Presentation on GOMine (Stanford group)
PIs to kick off meeting...?


==== Milestones Report ====
Minutes on Google doc [[https://docs.google.com/document/d/1P4jzTTJrGTDBkjRaIiu1VVWf7cwHZET9s7k9GBby93Y/edit edit as required]]


* [https://sourceforge.net/apps/trac/geneontology/roadmap Roadmap] Chris
== Project Management==
* [https://sourceforge.net/apps/trac/geneontology/milestone/AmiGO2%20alpha AmiGO 2 alpha] Seth
- Overall project management under new grant goals<br>
* [https://sourceforge.net/apps/trac/geneontology/milestone/GOLD%20beta GOLD beta]
- Manage documentation<br>
* [https://sourceforge.net/apps/trac/geneontology/milestone/TG1%20beta TermGenie 1 beta] Heiko
- Manage staff <br>
* [https://sourceforge.net/apps/trac/geneontology/milestone/obo%20to%20owl%20roundtripping obo2owl roundtripping] Heiko/Shahid
- Discussion on appropriate software tools to help manage and report progress on individual project milestones
** OORT
*Jira demo [Tony]
* [https://sourceforge.net/apps/trac/geneontology/milestone/GPAD%20Specification%20and%20tools GPAD specification and tools] Amelia
- Discussion on a replacement for the Webex screen sharing tool.
* GO Galaxy
- Communication between managers projects.
 
==Software (requested time: 3 hours)==
 
# Overview of software group activities and [https://sourceforge.net/apps/trac/geneontology/roadmap Roadmap] [Chris]
# Personnel Updates [Chris]
 
* [[Migration of GO to SVN (Proposal)]] Chris (15 mins)
 
** New architecture (30 mins)
* [https://sourceforge.net/apps/trac/geneontology/milestone/AmiGO2%20alpha AmiGO 2 alpha] ~~ Seth
** [http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo 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?
 
* [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
** Extensions - additional templates
** Integration with ontology roadmap
** Use of TG as SF replacement ("freeform" term creation)
 
* GO Galaxy ~~ Chris (for Amelia) (5 mins)
** 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


=== 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]


* [[Ontology_Release_Files_Proposal]] Chris
* 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)===
==Wednesday==
* 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
===Meeting Wrap-Up===
** Action Items
** Dates for next meeting


* Annotation Proposals and Discussions
====Annotation Discussion====
** IMEX Consortium's work on representing protein-protein interaction data: presentation by Sandra Orchard, IntAct, EBI, Cambridge UK (25 mins)
** Progress and Direction of the Reference Genome Project (Pascale)
*** The annotation of the stoichiometry of binding by GO groups.  Under the spotlight: protein homodimerization, protein tetramerization etc.
** 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


*** 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].


*** Use of the new relationship Ontology to describe relationships between entities in an annotation, and for the generation of detailed, composite GO terms
====Ontology editors discussion with ChEBI group (separate room booked)====
**** 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?===
[[GOCHE_meeting_2011-11-09]]
- presentation on the new GAF uploader tool? Supply of hard, soft and inferred annotations to submitters?
- presentation on AmiGO2 and column 16 display intentions?

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