View source for 2014 College Station GOC Meeting Agenda

==Logistics==
* [[2014 College Station Logistics]]

==Minutes==
*(Add link to google doc here)

==Progress Reports==
* Progress reports by Aim (add links here)
*# Literature Annotation
*# PAINT Annotation
*# Common Annotation Framework
*# Ontologies
*# Delivery of Annotation and Ontologies to the Community

* Response to SAB
*# SAB report from Cambridge April 2013 ( [https://docs.google.com/document/d/1njii8D0XLCS-c1hdjs8hH1IbPwj0Qcc-Z7JgfxTseFo/edit])
*# Our reponse...

* Questions for SAB

==Agenda==
* Assign 'official' note takers, set up Google doc for notes and so everyone can augment, introductions of new people
===Saturday 15 March - Pre-Meeting Working Group(s)===
Jim will direct pre-meeting working group(s?) to empty classrooms to meet.

{| border=1
|+ Working group schedule
|- align='center' bgcolor='#CCffcc'
! scope="col" |Time
! colspan="2" scope="col" |Topic
! colspan="2" scope="col" |Attending
|- 
|width="8%" | 9:30-10:30 CDT
|colspan="2" width="47%" | <b>Framework</b> - We'll draw up some pictures of the different pieces and how they fit together to get everyone on the same page. We'll discuss where questions still remain.
|colspan="2" width="45%" | Everyone - Paul T, Paul S, Suzi, Kimberly, Jane, Chris, Heiko, Seth, Rachael, Huaiyu, Tony, David H, David O-S, Tanya, Ruth, Paola, Mary
|- 
|10:30-12:00 CDT
|colspan="2" | <b>Molecular Modeling Environment</b> - We are now at the stage where we have a working annotation UI available for initial feedback. It connects to the existing LEGO data (stored at present in files under SVN) and thus provides a realistic tool for evaluation. We can also extends these by seeding them with existing GO annotations if a curator wants to work on a particular module. After such seeding a curator can review what's already been annotated and incorporate it into the module.
|colspan="2" | Paul T, Suzi, Kimberly, Jane, Chris, Heiko, Seth, Rachael, Huaiyu, Tony, David H, David O-S, Tanya, Paola, Mary
|-
|1:00-2:00 CDT
|colspan="1" | <b>Integration</b> - We currently have several useful annotation tools for different pieces, but would like to make this more seamless for curators. What code can we share? What signals can we pass?
|colspan="1" | <b>miRNA Annotations</b> - Guidelines for annotation of miRNAs, with specific annotation examples to be provided by attending groups. Please add information to the wiki [http://gocwiki.geneontology.org/index.php/miRNA_guidelines miRNA guidelines]
|colspan="1" | Paul T, Chris, Heiko, Seth, Tony, Huaiyu, Mary
|colspan="1" | Ruth, Rachael, Donghui, Doug, Jennifer, Rama, Kimberly, Huaiyu, Dmitry, Judy
|-
|2:00-3:00 CDT
|colspan="1" | <b>Ontology</b> - Sort out how to do multi-species annotation and the overall OWL modeling
|colspan="1" | <b>2-minute video GO tutorials</b> - Put your brilliant minds together, and break down the material that we would like to teach into content for short videos. [http://gocwiki.geneontology.org/index.php/video_tutorial_ideas Video tutorial ideas]
|colspan="1" | Paul T, Suzi, Jane, Chris, Heiko, Seth, David H, David O-S, Tanya, Paola, Mary
|colspan="1" | Rachael, Rama, Suzi, Moni, anyone else who would like to become involved
|-
|3:00-4:00 CDT
|colspan="2" | <b>Catalytic activity/Metabolic Process</b> - likely modeling of biochemical pathways in GO, some specifics of EC/GO mapping/interaction, some lingering SF items relating to catalytic activity children and the underlying general problems they revealed
|colspan="2" | Jim, Tanya, David, Chris, Heiko, Peter, Harold, Jane, TAMU experts, Paola, Huaiyu, Mary
|-
|4:00-5:00 CDT
|colspan="2" | <b>Roadmap</b> - Milestones and 6-month to year plan for bringing this into eventual production. We can revisit the framework from the morning and revise it based on the day's discussion (for showing at the big meeting the next day)
|colspan="2" | Everyone - Paul T, Paul S, Suzi, Kimberly, Jane, Chris, Heiko, Seth, Rachael, Huaiyu, Tony, David H, David O-S, Tanya, Ruth, Paola, Mary
|- class="tableEdit_footer" 
|}

===Sunday 16 March - Community relations and Annotation Production ===

Breakfast on your own

====8:30 Start====

* Welcome and introductions (8:30-8:45)
* Goals for meeting, and Consortium priorities (PI's, 8:45-9:15)

=====Community facing=====

* Website
**content status (Moni, 8:30-9:30)
** New documentation pages in Drupal (Chris, Seth)
** Exports of GO, retiring GO full - Mike, Chris, Seth
* Amigo2 (9:30-10)
** Beta status (Seth)
** Production status (Mike)

====10:30 - 11:00 Break====

* GO term enrichment analysis (Paola, Chris, Paul T., 10-10:15)
* JS-PAINT status (Seth, Suzi, 10:15-10:30)
* It would be good if the GOC could take a proactive stance on GO-related papers, by letting journal editors know that GOC members would be happy to review papers that discuss GO.

====12:30 - 2:00 pm Lunch====
====Annotation issues====
* PAINT annotation progress
* Quality control and consistency (Pascale, Paul T.)

* Adoption of Protein2GO
** non-protein identifiers (Kimberly)
** MiRNA annotation

* Extended annotation tool (AKA LEGO, ORION)
** Behavior terms

====3:30 - 3:45 pm Break====

====5:30 Group Photo====

====<i>Conference Dinner</i>====

===Monday 17 March - Annotation Infrastructure, Ontology Development, and Planning===

Breakfast on your own

====8:30 Start====

* Ontology development - Completed work
** New viral terms with mapping to ViralZone/UniProtKW (Jane)
** Progress report on transition to OWL (Chris)
** Overview of cilial and Giardia work (Paola)
** Update on apoptosis (Paola)
** Wikipedia links to GO (David OS)

====10:30 - 11:00 Break====
* Ontology development - Modeling
** Biochemical Pathways using has_part.(David H)
*** Glycolysis expanded (are we ready to implement?)
**** Coordinate annotation
*** Molybdopterin cofactor biosynthesis
**** Coordinate annotation
** DNA replication (Tanya)
** Multi-organism BP/CC annotation model (David OS)
** Proposed new structure for extracellular/extraorganismal cc (David OS)
** Uberon/CL update (Chris)
* Interaction with other groups (on ubiquitin, Giardia, cilia, Sejal's project on Alzheimer's disease) (David H or Jane)

====12:30 - 2:00 pm Lunch====
* A gentle reminder if each MOD/DB could please email round when they have new curators.

====Review SAB presentations====
* Community (Paul S., Moni, Seth, Rama)
* Annotation (Mike, Rama, Pascale)

====3:30 - 3:45 pm Break====
* Ontologies (Suzi, Chris, David H, Tanya, Jane, David OS)
* Common Annotation Framework (Paul T., Chris, Kimberly, Seth)

====<i>SAB Dinner</i>====

===Tuesday 18 March - SAB meeting ===
====8:30 - Presentations of progress====

* Presentations to SAB (~3 hours. Mike, Suzi, Paul S, Paul T)

====11:30 - 1:30 pm Lunch====

* SAB discussions privately

====1:30 - 3:30 Feedback====

* SAB reports to PIs

====<b>3:30 pm End of meeting</b>====