2013 Cambridge GOC Meeting Agenda: Difference between revisions
Jump to navigation
Jump to search
m (Added Doug to annotation extension breakout group) |
Paul Thomas (talk | contribs) No edit summary |
||
Line 1: | Line 1: | ||
The 2013 GO Consortium meeting will be held 11-13 April, in Cambridge, UK, immediately following [http://www.ebi.ac.uk/biocuration2013/home Biocuration 2013]. | The 2013 GO Consortium meeting will be held 11-13 April, in Cambridge, UK, immediately following [http://www.ebi.ac.uk/biocuration2013/home Biocuration 2013]. | ||
=Thursday (starts at 8: | =Thursday (starts at 8:45)= | ||
==Usability== | ==Usability== | ||
GOAL:Provide community with ability to obtain and use GO resources | GOAL:Provide community with ability to obtain and use GO resources | ||
* Update on [http://galaxy.berkeleybop.org/ Galaxy] (Chris) (8: | * Update on [http://galaxy.berkeleybop.org/ Galaxy] (Chris) (8:45-9:15) | ||
* New Web Site http://beta.geneontology.org - drupal (Seth) (9-9: | * New Web Site http://beta.geneontology.org - drupal (Seth) (9:15-9:45) | ||
* [http://amigo2.berkeleybop.org/ AmiGO 2.0] (Seth & Chris) | * [http://amigo2.berkeleybop.org/ AmiGO 2.0] (Seth & Chris) | ||
* Platinum standard data sets for enrichment analyses (Paul S, Rama) (9: | * Platinum standard data sets for enrichment analyses (Paul S, Rama) (9:45-10:30) | ||
==Coffee break (10: | ==Coffee break (10:30-11)== | ||
Line 15: | Line 15: | ||
== Comparative and Phylogenetic Annotations == | == Comparative and Phylogenetic Annotations == | ||
* PAINT progress, including overview of SOPs | * PAINT progress, including overview of SOPs | ||
** PAINT progress overview (Paul T.) ( | ** PAINT progress overview (Paul T.) (11-11:15) | ||
** SOP overview plus example (Donghui) (11-11: | ** SOP overview plus example (Donghui) (11:15-11:45) | ||
** Examples of annotation issues in PAINT, plus discussion (11: | ** Examples of annotation issues in PAINT, plus discussion (11:45-12:30) (Paul T, Pascale) | ||
== Lunch (12-1) == | == Lunch (12:30-1:30) == | ||
** Update on JsPAINT (Chris/Suzi) (1-1: | ** Update on JsPAINT (Chris/Suzi) (1:30-1:45) | ||
* Jenkins for QC - http://build.berkeleybop.org/view/GAF/ (Heiko) (1: | * Jenkins for QC - http://build.berkeleybop.org/view/GAF/ (Heiko) (1:45-2) | ||
* ECO update (Chris) ( | * ECO update (Chris) (2-2:15) | ||
* New rules for ISO mouse/human/rat when M:N gene sets (Judy) ( | * New rules for ISO mouse/human/rat when M:N gene sets (Judy) (2:15-2:35) | ||
== Literature Annotation == | == Literature Annotation == | ||
* apoptosis (re)annotation effort (Paola) [[File: GOC_2013_Cambridge.pdf]] (2- | * apoptosis (re)annotation effort (Paola) [[File: GOC_2013_Cambridge.pdf]] (2:35-3:10) | ||
* production statistic reports (Paul S) ( | * production statistic reports (Paul S) (3:10-3:30) | ||
== Coffee break ( | == Coffee break (3:30-4) | ||
* Curation tools: transition to Protein-GO, prospects for text-mining integratrion ( | * Curation tools: transition to Protein-GO, prospects for text-mining integratrion (4-5) | ||
== Biological Knowledge == | == Biological Knowledge == | ||
*[[Transition to OWL]] progress and status (Chris) ( | *[[Transition to OWL]] progress and status (Chris) (5-5:30) | ||
*Interaction between ontology development and annotation ( | *Interaction between ontology development and annotation (5:30-6) | ||
**Current mechanisms: tracker, TG, Jira (Jane) | **Current mechanisms: tracker, TG, Jira (Jane) | ||
**Update on existing TG templates, tree browser esp CHEBI, numbers of terms added (Jane) [[Media:TGreview_Cambridge_April13.pdf]] | **Update on existing TG templates, tree browser esp CHEBI, numbers of terms added (Jane) [[Media:TGreview_Cambridge_April13.pdf]] | ||
Line 72: | Line 72: | ||
**LEGO | **LEGO | ||
***Test example: Wnt signaling (David) (9:30-10) | ***Test example: Wnt signaling (David) (9:30-10) | ||
***Implementation plan (Chris) (10-10: | ***Implementation plan (Chris) (10-10:30) | ||
== Coffee break (10: | == Coffee break (10:30-11) == | ||
***Mapping to community representations, e.g. [http://www.biopax.org/ BioPAX], [http://www.sbgn.org/Main_Page SBGN] (Huaiyu) ( | ***Mapping to community representations, e.g. [http://www.biopax.org/ BioPAX], [http://www.sbgn.org/Main_Page SBGN] (Huaiyu) (11-11:15) | ||
**Annotation extensions (Rachael) (11: | **Annotation extensions (Rachael) (11:15-11:45) | ||
***Annotation relations | ***Annotation relations | ||
**GPAD status (Chris) (11: | **GPAD status (Chris) (11:45-11:55) | ||
==Meeting wrap up and action item review (11: | ==Meeting wrap up and action item review (11:55-12:30) == | ||
= Action Item Review and Reports = | = Action Item Review and Reports = |
Revision as of 03:40, 11 April 2013
The 2013 GO Consortium meeting will be held 11-13 April, in Cambridge, UK, immediately following Biocuration 2013.
Thursday (starts at 8:45)
Usability
GOAL:Provide community with ability to obtain and use GO resources
- Update on Galaxy (Chris) (8:45-9:15)
- New Web Site http://beta.geneontology.org - drupal (Seth) (9:15-9:45)
- AmiGO 2.0 (Seth & Chris)
- Platinum standard data sets for enrichment analyses (Paul S, Rama) (9:45-10:30)
Coffee break (10:30-11)
Comparative and Phylogenetic Annotations
- PAINT progress, including overview of SOPs
- PAINT progress overview (Paul T.) (11-11:15)
- SOP overview plus example (Donghui) (11:15-11:45)
- Examples of annotation issues in PAINT, plus discussion (11:45-12:30) (Paul T, Pascale)
Lunch (12:30-1:30)
- Update on JsPAINT (Chris/Suzi) (1:30-1:45)
- Jenkins for QC - http://build.berkeleybop.org/view/GAF/ (Heiko) (1:45-2)
- ECO update (Chris) (2-2:15)
- New rules for ISO mouse/human/rat when M:N gene sets (Judy) (2:15-2:35)
Literature Annotation
- apoptosis (re)annotation effort (Paola) File:GOC 2013 Cambridge.pdf (2:35-3:10)
- production statistic reports (Paul S) (3:10-3:30)
== Coffee break (3:30-4)
- Curation tools: transition to Protein-GO, prospects for text-mining integratrion (4-5)
Biological Knowledge
- Transition to OWL progress and status (Chris) (5-5:30)
- Interaction between ontology development and annotation (5:30-6)
- Current mechanisms: tracker, TG, Jira (Jane)
- Update on existing TG templates, tree browser esp CHEBI, numbers of terms added (Jane) Media:TGreview_Cambridge_April13.pdf
- TermGenie freeform demo (Jane)
Dinner at Moller Centre (7pm)
Friday afternoon breakout sessions
1. Annotation Extension
- New property_values replacing domain/range (Chris and Tony)
- Subsets of relations to enable easy use by curators (http://wiki.geneontology.org/index.php/Ontology_meeting_2013-03-21#Annotation_relations) (Jane and Rachael)
- Transferring annotation extensions by sequence similarity (Rachael)
- Annotation extension unfolding and conversion to LEGO (Chris)
Interested in attending: Jane, Rachael, Susan, Petra, Mary, David, Midori, Chris, Kimberly, Ruth, Donghui, Tanya, Val, Harold, Rama, SGD curators, Rebecca, Li, Prudence, Doug
2. PAINT Meeting - Huaiyu
- including ontology developers
- Look at annotation consistency
Interested in attending: Jane, Susan, Ruth, Donghui,Val, Rama, Li
3. Cell cycle
- WG to work through outstanding issues
Interested in attending: Jane, Rachael, Susan, David, Tanya, Val, Paola, Rebecca, Prudence
Saturday
Biological Knowledge (continued)
- Cross-product status, inc cell type (David) (8:30-9)
- Cell cycle report (Val) (9-9:30)
- Annotation expressivity
- LEGO
- Test example: Wnt signaling (David) (9:30-10)
- Implementation plan (Chris) (10-10:30)
- LEGO
Coffee break (10:30-11)
Meeting wrap up and action item review (11:55-12:30)
Action Item Review and Reports
Caltech meeting minutes meeting minutes as a Google Doc
See also