Difference between revisions of "2014 College Station GOC Meeting Agenda"

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[[Category: Reports]]
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==Agenda==
 
==Agenda==
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=====Community and Outreach=====
 
=====Community and Outreach=====
  
* Website [http://berkeleybop.org/document/go-community-update-college-station-meeting]
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* Website [http://berkeleybop.org/document/go-community-update-college-station-meeting | Slides available here.]
** http://beta.geneontology.org
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** Test drive the new GOC website at http://beta.geneontology.org
**Content status (Moni)
+
** Content status (Moni)
 
** Report on Outreach & Multimedia breakout group: video tutorials, adding content. (Moni)
 
** Report on Outreach & Multimedia breakout group: video tutorials, adding content. (Moni)
 
** New documentation pages in Drupal (Chris, Seth)
 
** New documentation pages in Drupal (Chris, Seth)
** Exports of GO, retiring GO full - Mike, Chris, Seth
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** Exports of GO, retiring GO full (Chris, Seth)
 
** Tools Registry (Chris)
 
** Tools Registry (Chris)
 
*** How to find tools
 
*** How to find tools
 
*** How to register tools
 
*** How to register tools
* AmiGO 2 [http://berkeleybop.org/document/amigo-2-update-college-station-goc]
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* AmiGO 2 [http://berkeleybop.org/document/amigo-2-update-college-station-goc | Slides available here.]
 
** <strike>Beta status</strike> (Seth)
 
** <strike>Beta status</strike> (Seth)
 
** Production status (Mike)
 
** Production status (Mike)
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====10:30 - 11:00 Break====
 
====10:30 - 11:00 Break====
  
* GO term enrichment analysis (Paola, Chris, Paul T.)
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* GO term enrichment analysis (Chris)
* jsPAINT status (Seth, Suzi) <br /> http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/phylo_graph
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* jsPAINT status (Suzi) <br /> Explore the jsPAINT beta version at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/phylo_graph
 
* 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.
 
* 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====
 
====12:30 - 2:00 pm Lunch====
[[Category:Meetings]]
 
 
====Annotation issues and infrastructure====
 
====Annotation issues and infrastructure====
* PAINT annotation progress
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* PAINT annotation progress (Huaiyu) [[File:PAINTupdateMar2014.pptx]]
 +
* Apoptosis assessment (Pascale) [[File:PAINT-Apoptosis-summary-Pascale.pptx]]
 
* Quality control and consistency (Pascale, Paul T.)
 
* Quality control and consistency (Pascale, Paul T.)
  
 +
====3:30 - 3:45 pm Break====
 
* Adoption of Protein2GO
 
* Adoption of Protein2GO
 
** Summary of plans for upgrading Protein2GO for non-protein identifiers (Tony)
 
** Summary of plans for upgrading Protein2GO for non-protein identifiers (Tony)
 
** non-protein identifiers (Kimberly)
 
** non-protein identifiers (Kimberly)
** MiRNA annotation
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** MiRNA annotation (Ruth)
  
* Extended annotation tool (AKA LEGO, CAF, and most newly minted name - Orion)
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* Ontology development - Completed work
** Behavior terms (Summary and stats [[File:Behavior2.docx]])
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** Overview of ontology changes (Jane) [[File:GOC-Texas-2014-stats.pdf|slides]]
  
====3:30 - 3:45 pm Break====
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====5:30 Group Photo====
  
====5:30 Group Photo====
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====<i>7PM Conference Dinner</i>====
 +
Veritas. Shuttle is available but it's also walking distance
  
====<i>Conference Dinner</i>====
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<hr/>
  
 
===Monday 17 March - Annotation Infrastructure, Ontology Development, and Planning===
 
===Monday 17 March - Annotation Infrastructure, Ontology Development, and Planning===
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====8:30 Start====
 
====8:30 Start====
 
Room 129: AgriLife Building. See [[2014_College_Station_Logistics |Logistics page]]
 
Room 129: AgriLife Building. See [[2014_College_Station_Logistics |Logistics page]]
 +
 +
* Extended annotation tool (AKA LEGO, CAF, and most newly minted name - Orion)
 +
** Example from [[File:Paul's_LEGO_presentation_from_Bar_Harbor_Sept_2010.pdf]]: http://go-genkisugi.rhcloud.com/seed/model/gomodel:goa_human-5323da180000002
 +
** Behavior terms (Summary and stats [[File:Behavior2.docx]])
  
 
* Ontology development - Completed work
 
* Ontology development - Completed work
** New viral terms with mapping to ViralZone/UniProtKW (Jane)
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** New viral terms with mapping to ViralZone/UniProtKW (Jane)[[File:GOC-Texas-2014-stats.pdf]]
 
** Progress report on transition to OWL (Chris)
 
** Progress report on transition to OWL (Chris)
** Overview of cilial and Giardia work (Paola)
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** Overview of cilial and Giardia work (Paola) [[File:GOC_Texas_2014_Paola.pdf]]
** Update on apoptosis (Paola)
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** Update on apoptosis (Paola) [[File:GOC_Texas_2014_Paola.pdf]]
 
** Wikipedia links to GO (David OS)
 
** Wikipedia links to GO (David OS)
 +
  
 
====10:30 - 11:00 Break====
 
====10:30 - 11:00 Break====
 +
 
* Ontology development - Modeling
 
* Ontology development - Modeling
 
** Biochemical Pathways using has_part.(David H)
 
** Biochemical Pathways using has_part.(David H)
*** Glycolysis expanded (are we ready to implement?)
 
**** Coordinate annotation
 
*** Molybdopterin cofactor biosynthesis
 
**** Coordinate annotation
 
 
** DNA replication (Tanya)
 
** DNA replication (Tanya)
 
** Multi-organism BP/CC annotation model (David OS)
 
** 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====
 
====12:30 - 2:00 pm Lunch====
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** Common Annotation Framework (Paul T., Chris, Kimberly, Seth)
 
** Common Annotation Framework (Paul T., Chris, Kimberly, Seth)
  
====<i>SAB Dinner</i>====
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====<i>7 PM SAB / GOC Council Dinner</i>====
 +
The SAB Dinner will be at the Republic, which is 0.5 miles from the Hyatt Place.  Note that Google maps puts the pin slightly off the correct location (but in the correct complex).
  
 
===Tuesday 18 March - SAB meeting ===
 
===Tuesday 18 March - SAB meeting ===
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====<b>3:30 pm End of meeting</b>====
 
====<b>3:30 pm End of meeting</b>====
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[[File:GOC Texas 2014.JPG|400px|thumb|left|Group Photo]]
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 +
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[[Category:GO Consortium Meetings‏‎‏‎]]

Latest revision as of 07:05, 15 April 2019

Logistics

Minutes

MINUTES

Progress Reports

  • Progress reports by Aim (add links here)
    1. Literature Annotation Annotation Advocacy
    2. PAINT Annotation
    3. Common Annotation Framework
    4. Ontologies
    5. Delivery of Annotation and Ontologies to the Community
  • Response to SAB
    1. SAB report from Cambridge April 2013 ( [1])
    2. 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. We will start in N127 in the NMR wing.

Working group schedule
Time Topic Attending
9:30-10:30 CDT Framework - 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. Everyone - Paul T, Paul S, Suzi, Kimberly, Jane, Chris, Heiko, Seth, Rachael, Huaiyu, Tony, David H, David O-S, Tanya, Ruth, Paola, Mary, Val
10:30-12:00 CDT Molecular Modeling Environment - 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 extend 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. We should also go over proposed refactoring of MF. Paul T, Suzi, Kimberly, Jane, Chris, Heiko, Seth, Rachael, Huaiyu, Tony, David H, David O-S, Tanya, Paola, Mary, Val
1:00-2:00 CDT Integration - 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? miRNA Annotations - Guidelines for annotation of miRNAs, with specific annotation examples to be provided by attending groups. File:GOCmiRNA2014.pdf Please add information to the wiki miRNA guidelines Paul T, Chris, Heiko, Seth, Tony, Huaiyu, Mary, Val Ruth, Rachael, Donghui, Doug, Jennifer, Rama, Kimberly, Huaiyu, Dmitry, Judy
2:00-3:00 CDT Ontology - Sort out how to do multi-species annotation and the overall OWL modeling Outreach: website & multimedia bootcamp - Put your brilliant minds together, and break down the material that we would like to teach into content for short videos. Video tutorial ideas. Also, bring your questions about editing content on the GO (Drupal) website. Paul T, Suzi, Jane, Chris, Heiko, Seth, David H, David O-S, Tanya, Paola, Mary Rachael, Rama, Suzi, Moni, Val anyone else who would like to become involved
3:00-4:00 CDT Catalytic activity/Metabolic Process - 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 Jim, Tanya, David, Chris, Heiko, Peter, Harold, Jane, TAMU experts, Paola, Huaiyu, Mary, Val
4:00-5:00 CDT Roadmap - 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) Everyone - Paul T, Paul S, Suzi, Kimberly, Jane, Chris, Heiko, Seth, Rachael, Huaiyu, Tony, David H, David O-S, Tanya, Ruth, Paola, Mary, Val

Sunday 16 March - Community relations and Annotation Production

Breakfast on your own

8:30 Start

Room 129: AgriLife Building. See Logistics page

  • Welcome and introductions File:WelcomeMar2014.pptx
    • A gentle reminder if each MOD/DB could please email round when they have new curators.
  • Goals for meeting, and Consortium priorities (PI's)
Community and Outreach
  • Website | Slides available here.
    • Test drive the new GOC website at http://beta.geneontology.org
    • Content status (Moni)
    • Report on Outreach & Multimedia breakout group: video tutorials, adding content. (Moni)
    • New documentation pages in Drupal (Chris, Seth)
    • Exports of GO, retiring GO full (Chris, Seth)
    • Tools Registry (Chris)
      • How to find tools
      • How to register tools
  • AmiGO 2 | Slides available here.
    • Beta status (Seth)
    • Production status (Mike)
  • Preview of new QuickGO interface File:New QuickGO.pptx

10:30 - 11:00 Break

  • GO term enrichment analysis (Chris)
  • jsPAINT status (Suzi)
    Explore the jsPAINT beta version at http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/phylo_graph
  • 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 and infrastructure

3:30 - 3:45 pm Break

  • Adoption of Protein2GO
    • Summary of plans for upgrading Protein2GO for non-protein identifiers (Tony)
    • non-protein identifiers (Kimberly)
    • MiRNA annotation (Ruth)

5:30 Group Photo

7PM Conference Dinner

Veritas. Shuttle is available but it's also walking distance


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

Breakfast on your own

8:30 Start

Room 129: AgriLife Building. See Logistics page


10:30 - 11:00 Break

  • Ontology development - Modeling
    • Biochemical Pathways using has_part.(David H)
    • DNA replication (Tanya)
    • Multi-organism BP/CC annotation model (David OS)


12:30 - 2:00 pm Lunch

  • Review SAB presentations - part I
    • Community (Paul S., Moni, Seth, Rama)
    • Annotation (Mike, Rama, Pascale)

3:30 - 3:45 pm Break

  • Review SAB presentations - part II
    • Ontologies (Suzi, Chris, David H, Tanya, Jane, David OS)
    • Common Annotation Framework (Paul T., Chris, Kimberly, Seth)

7 PM SAB / GOC Council Dinner

The SAB Dinner will be at the Republic, which is 0.5 miles from the Hyatt Place. Note that Google maps puts the pin slightly off the correct location (but in the correct complex).

Tuesday 18 March - SAB meeting

ILSB 3147 See Logistics page

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

3:30 pm End of meeting

Group Photo