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]
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= Venue =
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'''Main meeting Monday to Wednesday'''
 +
 +
Wilkins Haldane Room ([http://crf.casa.ucl.ac.uk/screenRoute.aspx?s=1019&d=187&w=False])
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'''GO managers and PIs'''
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Tuesday 1pm to 2:30pm Wilkins JBR Meeting Room ([http://crf.casa.ucl.ac.uk/screenRoute.aspx?s=1019&d=189&w=False])
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'''GO curators and ChEBI'''
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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=
 
=Monday=
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PIs to kick off meeting...?
 
PIs to kick off meeting...?
  
==Software==
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Minutes on Google doc [[https://docs.google.com/document/d/1P4jzTTJrGTDBkjRaIiu1VVWf7cwHZET9s7k9GBby93Y/edit edit as required]]
 +
 
 +
== 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 (requested time: 3 hours)==
  
 
# Overview of software group activities and [https://sourceforge.net/apps/trac/geneontology/roadmap Roadmap] [Chris]
 
# Overview of software group activities and [https://sourceforge.net/apps/trac/geneontology/roadmap Roadmap] [Chris]
 
# Personnel Updates [Chris]
 
# Personnel Updates [Chris]
  
 +
* [[Migration of GO to SVN (Proposal)]] Chris (15 mins)
  
* Presentation on GOMine (Stanford group)
+
** New architecture (30 mins)
* [[Migration of GO to SVN (Proposal)]] Chris
 
 
 
* GO Common Authentication interface ~~ Seth
 
** 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]
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** opportunities for integration with QuickGO ~~ Tony, Chris
 
** opportunities for integration with QuickGO ~~ Tony, Chris
  
** Loading of phylogenetic data ~~ Sven
+
* OBO-Edit ~~ Heiko/Chris (20 mins)
* 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
 
 
** Using [[Ontology Release Files Proposal|OORT]] to produce releases  ~~ Chris (!keep this item here - Jane)
 
  
* GO Galaxy  ~~ Amelia
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* 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
+
 
 +
* 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 Software'''
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'''GOC dinner Monday 6:30pm: Sardo 47 Grafton Way http://www.sardo-restaurant.com/index.html'''
 
'''GOC dinner Monday 6:30pm: Sardo 47 Grafton Way http://www.sardo-restaurant.com/index.html'''
  
==Tuesday==
+
== Annotation (requested time: 5 hours) ==
  
Separate lunchtime meeting for GO managers and PIs. 
+
==== Annotation Projects====
  
=== Software and Annotation Group: Annotation Display and Support activities?===
+
* Annotation [http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2011 Roadmap] overview (Rama)
  
* [https://sourceforge.net/apps/trac/geneontology/milestone/GPAD%20Specification%20and%20tools GPAD specification and tools] ~~ Amelia
+
* Annotation Progress Report [Rama and Emily] [[file: Annotation_update_UCL11.pdf]]
 
 
* [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]]
 
 
 
* [[LEGO_Model_Draft_Specification]] ~~ Amelia, Chris, PaulT
 
[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
 
 
 
== Annotation Group ==
 
 
 
* Annotation Progress Report [Rama and Emily] 10 mins
 
 
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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* Progress of CACAO biocurator training on GONUTS [http://gowiki.tamu.edu/wiki/index.php/Category:CACAO_Fall_2011]
 
* Progress of CACAO biocurator training on GONUTS [http://gowiki.tamu.edu/wiki/index.php/Category:CACAO_Fall_2011]
 
[Jim 10 mins]
 
[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)
 
* Annotation Extension Field (column 16)
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*** Rules for transferring column 16 via ISS and via F->P inferences.
 
*** Rules for transferring column 16 via ISS and via F->P inferences.
  
 +
===Annotation Proposals===
  
* Protein Binding (covering both ontology and annotation issues)
+
*GO evidence codes to ECO identifiers
** Protein binding data now being captured fully by IMeX Consortium collaborators (Sandra Orchard)
 
** Level of detail required under GO:0005515 protein binding (Jane)
 
  
* Annotation to Protein Complex objects: a suggested annotation format??
+
* 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]
  
* 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
  
* Progress and Direction of the Reference Genome Project (Pascale)
+
* [https://sourceforge.net/apps/trac/geneontology/milestone/GOLD%20beta GOLD beta] ~~ Chris - on behalf of Shahid
* 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)
+
** GAF services
* suitable projects to engage all groups
+
*** Annotation file QC
 +
*** Inference of new annotations
 +
**** Use of logical definitions to suggest deeper annotations
 +
**** Cross-ontology inference using [[part_of]] and [[occurs_in]]
  
==Ontology==
 
  
* [[2011_Timeline|Roadmap]]/project overview [Jane/David]
+
====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
 
* 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
 +
** 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  ~~ Jane
+
** 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
 +
 +
*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
 
* Aligning with external ontologies
Line 135: Line 171:
 
*** Neuro-cell work
 
*** Neuro-cell work
 
** Update on GOCHE ~~ David
 
** Update on GOCHE ~~ David
** Behaviour alignment and NBO - a proposal [Jane]
+
** [[Neuro_Behaviour_Ontology_(NBO)-GO_alignment|Behaviour alignment and NBO]] - a proposal [Jane]
 
 
*Content Projects
 
** Update on signaling ~~ Rebecca
 
** Update on [[Virus_terms|viruses]] ~~ Jane
 
** Update on [[Transcription|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 [[GO_slim_overhaul|generic GO slim]] (was this done at LA?) [Val]
 
*** Processes and components
 
*** Functions
 
  
 
* Relations
 
* Relations
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** 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
  
=Wednesday=
+
==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]
+
===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]]
 
 
 
 
=== 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.
 

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