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] | ||
= | = 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 | ||
Philippa Talmud to welcome the GO Consortium to UCL. | |||
PIs to kick off meeting...? | |||
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] | |||
** New architecture | # 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 | * [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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** 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 | ||
* 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) | ||
* GO Galaxy ~~ Chris (for Amelia) (5 mins) | |||
* 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 | ||
=== 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] | |||
* Relations | * Relations | ||
** Update on RO and BFO ~~ Chris | ** Update on RO and BFO ~~ Chris | ||
Line 76: | Line 178: | ||
** 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== | ||
===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]] | |||
- |
Latest revision as of 12:33, 8 April 2014
back to meeting logistics page
Photos
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)
- Overview of software group activities and Roadmap [Chris]
- Personnel Updates [Chris]
- Migration of GO to SVN (Proposal) Chris (15 mins)
- 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?
- obo2owl roundtripping ~~ Heiko/Chris (20 mins)
- Using OORT to produce releases ~~ Chris (!keep this item here - Jane)
- 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/
- Use by Phenoscape for obo-diffs
- Wrapping multiple term enrichment tools
- 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 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,
- 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
- GPAD specification and tools ~~ Amelia
- GOLD beta ~~ Chris - on behalf of Shahid
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)
- 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 [5]
- Greater use of ontology constraints (disjointness, taxonomic constraints) ~~ Chris
- 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]
- 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).
- 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