2014 College Station GOC Meeting Agenda: Difference between revisions
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==Minutes== | ==Minutes== | ||
[https://docs.google.com/document/d/1fGu11dlchhUMn4_jBWEhuWfPZRaMOGmUSXSwm3AF2jo/edit MINUTES] | |||
==Progress Reports== | ==Progress Reports== | ||
* Progress reports by Aim (add links here) | * Progress reports by Aim (add links here) | ||
*# Literature Annotation | *# Literature Annotation [[Annotation Advocacy]] | ||
*# PAINT Annotation | *# PAINT Annotation | ||
*# Common Annotation Framework | *# Common Annotation Framework | ||
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* Questions for SAB | * Questions for SAB | ||
==Agenda== | ==Agenda== | ||
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|- | |- | ||
|10:30-12:00 CDT | |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 | |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 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. | ||
|colspan="2" | Paul T, Suzi, Kimberly, Jane, Chris, Heiko, Seth, Rachael, Huaiyu, Tony, David H, David O-S, Tanya, Paola, Mary, Val | |colspan="2" | 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 | |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>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" | <b>miRNA Annotations</b> - Guidelines for annotation of miRNAs, with specific annotation examples to be provided by attending groups. [[File:GOCmiRNA2014.pdf]] 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, Val | |colspan="1" | Paul T, Chris, Heiko, Seth, Tony, Huaiyu, Mary, Val | ||
|colspan="1" | Ruth, Rachael, Donghui, Doug, Jennifer, Rama, Kimberly, Huaiyu, Dmitry, Judy | |colspan="1" | Ruth, Rachael, Donghui, Doug, Jennifer, Rama, Kimberly, Huaiyu, Dmitry, Judy | ||
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|2:00-3:00 CDT | |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>Ontology</b> - Sort out how to do multi-species annotation and the overall OWL modeling | ||
|colspan="1" | <b> | |colspan="1" | <b>Outreach: website & multimedia bootcamp</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]. Also, bring your questions about editing content on the GO (Drupal) website. | ||
|colspan="1" | Paul T, Suzi, Jane, Chris, Heiko, Seth, David H, David O-S, Tanya, Paola, Mary | |colspan="1" | Paul T, Suzi, Jane, Chris, Heiko, Seth, David H, David O-S, Tanya, Paola, Mary | ||
|colspan="1" | Rachael, Rama, Suzi, Moni, Val anyone else who would like to become involved | |colspan="1" | Rachael, Rama, Suzi, Moni, Val anyone else who would like to become involved | ||
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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]] | ||
* Welcome and introductions | * Welcome and introductions [[File:WelcomeMar2014.pptx]] | ||
** A gentle reminder if each MOD/DB could please email round when they have new curators. | ** A gentle reminder if each MOD/DB could please email round when they have new curators. | ||
* Goals for meeting, and Consortium priorities (PI's) | * Goals for meeting, and Consortium priorities (PI's) | ||
=====Community Outreach===== | =====Community and Outreach===== | ||
* Website | * Website [http://berkeleybop.org/document/go-community-update-college-station-meeting | Slides available here.] | ||
**content | ** 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) | ** New documentation pages in Drupal (Chris, Seth) | ||
** Exports of GO, retiring GO full | ** Exports of GO, retiring GO full (Chris, Seth) | ||
** | ** Tools Registry (Chris) | ||
* AmiGO 2 | *** How to find tools | ||
** Beta status (Seth) | *** How to register tools | ||
* AmiGO 2 [http://berkeleybop.org/document/amigo-2-update-college-station-goc | Slides available here.] | |||
** <strike>Beta status</strike> (Seth) | |||
** Production status (Mike) | ** Production status (Mike) | ||
* | * Preview of new QuickGO interface [[File:New_QuickGO.pptx]] | ||
====10:30 - 11:00 Break==== | ====10:30 - 11:00 Break==== | ||
* GO term enrichment analysis ( | * GO term enrichment analysis (Chris) | ||
* | * 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==== | ||
====Annotation issues and infrastructure==== | ====Annotation issues and infrastructure==== | ||
* PAINT annotation progress | * 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 | ** MiRNA annotation (Ruth) | ||
* | * Ontology development - Completed work | ||
** | ** Overview of ontology changes (Jane) [[File:GOC-Texas-2014-stats.pdf|slides]] | ||
====5:30 Group Photo==== | |||
==== | |||
==== | ====<i>7PM Conference Dinner</i>==== | ||
Veritas. Shuttle is available but it's also walking distance | |||
<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) | ** 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) | ** Overview of cilial and Giardia work (Paola) [[File:GOC_Texas_2014_Paola.pdf]] | ||
** Update on apoptosis (Paola) | ** 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) | ||
** DNA replication (Tanya) | ** DNA replication (Tanya) | ||
** Multi-organism BP/CC annotation model (David OS) | ** Multi-organism BP/CC annotation model (David OS) | ||
====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>==== | ====<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>==== | ||
[[File:GOC Texas 2014.JPG|400px|thumb|left|Group Photo]] | |||
[[Category:GO Consortium Meetings]] |
Latest revision as of 10:05, 15 April 2019
Logistics
Minutes
Progress Reports
- Progress reports by Aim (add links here)
- Literature Annotation Annotation Advocacy
- PAINT Annotation
- Common Annotation Framework
- Ontologies
- Delivery of Annotation and Ontologies to the Community
- Response to SAB
- SAB report from Cambridge April 2013 ( [1])
- 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.
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
- PAINT annotation progress (Huaiyu) File:PAINTupdateMar2014.pptx
- Apoptosis assessment (Pascale) File:PAINT-Apoptosis-summary-Pascale.pptx
- Quality control and consistency (Pascale, Paul T.)
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)
- Ontology development - Completed work
- Overview of ontology changes (Jane) File:GOC-Texas-2014-stats.pdf
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
- 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
- New viral terms with mapping to ViralZone/UniProtKW (Jane)File:GOC-Texas-2014-stats.pdf
- Progress report on transition to OWL (Chris)
- Overview of cilial and Giardia work (Paola) File:GOC Texas 2014 Paola.pdf
- Update on apoptosis (Paola) File:GOC Texas 2014 Paola.pdf
- Wikipedia links to GO (David OS)
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