2013 Cambridge GOC Meeting Agenda: Difference between revisions
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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 8:30)= | ||
==Usability == | ==Usability== | ||
GOAL:Provide community with ability to obtain and use GO resources | GOAL:Provide community with ability to obtain and use GO resources | ||
* New Web Site http://beta.geneontology.org - drupal (Seth) | * Update on [http://galaxy.berkeleybop.org/ Galaxy] (Chris) (8:30-9) | ||
* New Web Site http://beta.geneontology.org - drupal (Seth) (9-9:30) | |||
* [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) | * Platinum standard data sets for enrichment analyses (Paul S, Rama) (9:30-10:15) | ||
==Coffee break (10:15-10:45)== | |||
= Biological Knowledge = | |||
*[[Transition to OWL]] progress and status (Chris) | |||
*Interaction between ontology development and annotation | == Comparative and Phylogenetic Annotations == | ||
* PAINT progress, including overview of SOPs | |||
** PAINT progress overview (Paul T.) (10:45-11) | |||
** SOP overview plus example (Donghui) (11-11:20) | |||
** Examples of annotation issues in PAINT, plus discussion (11:20-12) (Paul T, Pascale) | |||
== Lunch (12-1) == | |||
** Update on JsPAINT (Chris/Suzi) (1-1:15) | |||
* Jenkins for QC - http://build.berkeleybop.org/view/GAF/ (Heiko) (1:15-1:30) | |||
* ECO update (Chris) (1:30-1:40) | |||
* New rules for ISO mouse/human/rat when M:N gene sets (Judy) (1:40-2) | |||
== Literature Annotation == | |||
* apoptosis (re)annotation effort (Paola) [[File: GOC_2013_Cambridge.pdf]] (2-2:30) | |||
* production statistic reports (Paul S) (2:30-2:45) | |||
== Coffee break (2:45-3:15) | |||
* Curation tools: transition to Protein-GO, prospects for text-mining integratrion (3:15-4:15) | |||
== Biological Knowledge == | |||
*[[Transition to OWL]] progress and status (Chris) (4:15-4:45) | |||
*Interaction between ontology development and annotation (4:45-5:15) | |||
**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]] | ||
**TermGenie freeform demo (Jane) | **TermGenie freeform demo (Jane) | ||
= | == Dinner at Moller Centre (7pm) == | ||
= Friday afternoon breakout sessions = | = Friday afternoon breakout sessions = | ||
Line 70: | Line 63: | ||
'''Interested in attending:''' Jane, Rachael, Susan, David, Tanya, Val, Paola, Rebecca, Prudence | '''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) (10-10:20) | |||
== Coffee break (10:20-10:45) == | |||
***Mapping to community representations, e.g. [http://www.biopax.org/ BioPAX], [http://www.sbgn.org/Main_Page SBGN] (Huaiyu) (10:45-11:05) | |||
**Annotation extensions (Rachael) (11:05-11:30) | |||
***Annotation relations | |||
**GPAD status (Chris) (11:30-11:40) | |||
==Meeting wrap up and action item review (11:40-12:15) == | |||
= Action Item Review and Reports = | = Action Item Review and Reports = |
Revision as of 11:58, 10 April 2013
The 2013 GO Consortium meeting will be held 11-13 April, in Cambridge, UK, immediately following Biocuration 2013.
Thursday (starts at 8:30)
Usability
GOAL:Provide community with ability to obtain and use GO resources
- Update on Galaxy (Chris) (8:30-9)
- New Web Site http://beta.geneontology.org - drupal (Seth) (9-9:30)
- AmiGO 2.0 (Seth & Chris)
- Platinum standard data sets for enrichment analyses (Paul S, Rama) (9:30-10:15)
Coffee break (10:15-10:45)
Comparative and Phylogenetic Annotations
- PAINT progress, including overview of SOPs
- PAINT progress overview (Paul T.) (10:45-11)
- SOP overview plus example (Donghui) (11-11:20)
- Examples of annotation issues in PAINT, plus discussion (11:20-12) (Paul T, Pascale)
Lunch (12-1)
- Update on JsPAINT (Chris/Suzi) (1-1:15)
- Jenkins for QC - http://build.berkeleybop.org/view/GAF/ (Heiko) (1:15-1:30)
- ECO update (Chris) (1:30-1:40)
- New rules for ISO mouse/human/rat when M:N gene sets (Judy) (1:40-2)
Literature Annotation
- apoptosis (re)annotation effort (Paola) File:GOC 2013 Cambridge.pdf (2-2:30)
- production statistic reports (Paul S) (2:30-2:45)
== Coffee break (2:45-3:15)
- Curation tools: transition to Protein-GO, prospects for text-mining integratrion (3:15-4:15)
Biological Knowledge
- Transition to OWL progress and status (Chris) (4:15-4:45)
- Interaction between ontology development and annotation (4:45-5:15)
- 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
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) (10-10:20)
- LEGO
Coffee break (10:20-10:45)
Meeting wrap up and action item review (11:40-12:15)
Action Item Review and Reports
Caltech meeting minutes meeting minutes as a Google Doc
See also