2010 Stanford Meeting Logistics
- 1 Dates
- 2 Venue
- 3 Maps
- 4 Registration
- 5 Lodging Information
- 6 Agenda
- 6.1 March 30 – Morning - Break
- 6.2 March 30 – Morning Break – Lunch
- 6.3 March 30 Afternoon - Break
- 6.4 Ontology Updates
- 6.5 Ontology files and GAFS
- 6.6 Annotation Issues
- 6.7 Software
- 7 Attendees
- 8 Remote Attendees
GO consortium & SAB meetings March 30-31, April 1, 2010
- We wish all attendees to attend from the morning of March 30 through the morning of April 1st. The afternoon of April 1st will be for all GO subcontract PIs, GOC PIs and our SAB. We suggest you arrive the evening of March 29th and leave after noon on the 1st, unless you are a PI or SAB member.
Meetings will be at the Stanford University, Stanford, CA, USA.
The GOC and SAB meeting will take place at the Arrillaga Alumni Center.
Lunches will be at the Arrillaga Center.
There will be a group dinner on March 31st for the GOC and SAB.
We will also facilitate dinners on March 29th and 30th. There are a large variety of restaurants in the area.
Meeting will be held at the Arrillaga Alumni Center, 341 Galvez Street, Stanford, CA 
Registration will open in early 2010.
- Registration Fee. We anticipate a minimal registration fee to cover lunch and a light breakfast. The meeting will be sponsored by the Cherry Lab.
Four hotels are within a 15-20 minute walk to the Alumni Center. Ordered below by price per night, lowest to highest.
- Hotel California $
- Cardinal Hotel $
- Stanford Terrace Inn $$
- Sheraton Palo Alto Hotel $$$$
- Westin Palo Alto $$$$
March 30 – Morning - Break
- Review Agenda
Communication and Process for the GOC
- Changes in Mangers structure; description of roles [Suzi]
- Communication about project goals, timetables, shepherds and reporters
- Need better definition of process for projects
- Need statement of key goals and timeline for each project
- Need Shepherd and Reporter for each project; Shepherd to oversee progress and resolve bottlenecks, Reporter to keep all GOC informed as to progress and implications
- Use and utility of various mailing lists
- MF-BP links, what they are and how they impact annotation (David Hill)
- what worked, what can work better, in project management; using MF-BP example
March 30 – Morning Break – Lunch
Ref Genome Project and PAINT [Pascale and Kara
- current focus on process sets
- need for MOD incorporation
- Update on PAINT
- Evidence codes from PAINT and Inferences from MF-BP links
- Notice of ISMB workshop on Assays, ECO and OBI.
March 30 Afternoon - Break
- File Management Issues
a. Taxon IDs b. Making ext GO ‘main’ c. new column in GAF-Annotation Method d. Mechanics of file dissemination. e. streamlining addition of compositional terms f. GAF2 update g. improved support for OBO/OWL/Protégé intersections
March 30 Afternoon break – Dinner
Update on Cross-Products: the Chebi example (David) OBO-Foundry Report (Jane)
4. Update on Cell Type Ontology (Terry)
￼ March 31 Morning – Break
Action Items Review (Judy)
a. from last GOC b. from yesterday, March 30 2. AMIGO updates/report (Seth – 15 min) 3. OBO_EDIT updates/report (Amina – 15 min)
March 31 Morning Break – Lunch
1. Annotation [Rama, Emily ] a. Guidelines for ‘binding’ terms b. Other Annotation Issues c. Geneva GO Annotation Workshop 2. Requirements and QC for contributed annotations [Rama] a. M. tuberculosis example 3. . Incorporating IMEX data into GOC? [Emily]
March 31 Afternoon
1. Ontology Content Projects a. bringing the NIF ontologies into GO (Chris) b. GO-Pathway database integration (Chris) c. PRO, MouseCyc, Reactome and GO: Complexes in PRO and GO (Harold)
2. Open for further discussion or catch-up reports 3. Open forum on thoughts regarding upcoming competitive renewal applications
Cross products (18 slides, David)
- Internal cross products
- Cross-products already in place
- Cross-products "in production"
- External cross-products
- Internal cross products
Aligning chemicals (11 slides, David)
Ontology Content Additions
- Term additions from the ASCB and SDB meeting (6 slides, Tanya)
- Additions from the kidney and heart development meeting (14 slides, David)
- PAMGO (Jane)
OBO-Foundry report (Jane)
Ontology files and GAFS
I'd like a discussion of taxon IDs and subspecies. --JimHu 17:28, 4 February 2010 (UTC)
Making ext GO 'main'
A suggestion from the OBO Foundry meeting: we make GO ext the main GO file, the one that new users see. The other files continue to exist in the same place, but make it clear they are legacy files. That way anyone new coming to GO will build tools using GO ext. [Jane]
New column in GAF- Annotation Method
Proposal to add a new column to the GAF to indicate if an annotation was reviewed by a curator or no.
Alternative proposal from CJM to extend Evidence codes to support chains of evidence
- Also need to discuss references for PAINT annotations. Will one generic reference work?
Mechanics of file dissemination
I'd like to discuss the use of ftp rather than CVS for disseminating GAFs, gp2protein and other files (Tony S)
Guidelines for 'binding' terms
Discuss guideline documentation, progess and unresolved issues (Emily and Ruth; 12 slides).
- Should we include transporters in these guidelines?
- Should we capture drug information?
- Should the guidelines include a statement suggesting that the specific substrate for an enzyme with 'GO:0032451 demethylase activity' can be included in column 16?
- Should we create terms like ‘ATP binding involved in kinase activity'?
- What, if any, binding term annotations can be transferred via ISS/ISO?
30th/31st: end of afternoon.
Participants in newly-formed annotation working groups (formed for the June GO Camp) to gather together to begin to discuss issues 
Discussion on how ontology development relates to annotations
- scope of regulation relationship
- clarifying what 'regulation' terms mean from an annotator/ontology developer perspective (David, 18 slides)
- scope of has_part relationship
Airport codes: SFO = San Francisco International; SJC = San Jose International Airport
|Name||Organization||Arrival Date/Time to Airport (see codes above)||Departure Date/Time from Airport|
|Mike Cherry||GO / SGD||walking|
|Judy Blake||GO / MGI||March 29 SFO||April 2 SFO|
|Suzi Lewis||GO / BBOP||Driving|
|Mary Shimoyama||RGD||March 29 SFO||April 2 SFO|
|Chris Mungall||GO / BBOP||CalTrain|
|Seth Carbon||GO / BBOP||Driving|
|Amina Abdulla||GO / BBOP||Driving|
|Amelia Ireland||GO / BBOP||Hitching a ride|
|Kara Dolinski||GO / PPOD||TBA||TBA|
|Eva Huala||TAIR||March 29||April 2|
|Karen Eilbeck||SO (U of Utah)||San Jose 29th March||San Jose April 1 - evening|
|Barry Smith||SAB (U at Buffalo)||March 31 SFO||April 1 SFO|
|Richard Scheuermann||SAB (UT Southwestern)||March 31 SJC 9:30 am||April 1 SJC 6:15 pm|
|Tanya Berardini||TAIR||on site||on site|
|Donghui li||TAIR||on site||on site|
|Larry Hunter||SAB (U Colorado)||March 31 SFO||April 2 SFO|
|Paul Sternberg||WormBase and Caltech||San Jose||San Jose|
|Doug Howe||ZFIN||SFO March 29|
|Dianna Fisk||SGD||on site||on site|
|Ben Hitz||SGD||on site||on site|
|Jane Lomax||GO-EBI||March 29 SFO||April 2 SFO|
|Harold Drabkin||MGI||March 29th SFO||April TBA|
|Terry Meehan||MGI||March 28th SFO||April 2|
|Jim Hu||EcoliWiki||March 29 SFO 8PM||April 2 SFO 1:40PM|
|Stan Laulederkind||RGD||March 28 SFO 7:47PM||April 1 SJC 2:20PM|
|Monte Westerfield||ZFIN||April 1 SFO|
|Selina Dwight||SGD||on site||on site|
|Kate Dreher||TAIR||on site||on site|
|Rama Balakrishnan||SGD||on site||on site|
|Ranjana Kishore||WormBase||SJC 3/29 5.50 PM||SJC 4/01 3.00 PM|
|Kimberly Van Auken||WormBase||TBD||TBD|
|Petra Fey||dictyBase||N/A||SFO 4/01 1:55 PM|
|Peter D'Eustachio||Reactome / NYUMC||SJC 3/29 7:02 PM||SJC 4/1 10:25 PM|
|Serenella Ferro Rojas||UniProtKB/Swiss-Prot||March 29 SFO||April 4 SFO|
|Eurie Hong||SGD||on site||on site|
|Emily Dimmer||GOA||March 29 SFO||April 2 SFO|
|Tony Sawford||GOA||March 29 SFO||April 2 SFO|
|Karen Christie||SGD||on site||on site|
|Julie Park||SGD||on site||on site|
Webex and Telephone Conferencing will be provided
|Name||Organization||email (needed to set up your remote access)||Attending GOC (March 30-31)||Attending SAB (April 1)||Calling in alone or in a group (with whom and from where, if known)|
|Midori Harris||EBI GO||midori at ebi dot ac dot uk||yes||yes||TBD|
|Jennifer Deegan||GO Editorial Office||jdeegan at ebi.ac.uk||Yes||Yes||Probably alone from home.|
|Ruth Lovering||BHF-UCL annotator||r.lovering at ucl.ac.uk||Yes||Yes||From home, but will have to miss some parts|
|Rachael Huntley||GOA Curator||huntley at ebi.ac.uk||Yes||Yes||From home.|
|Michelle Giglio||IGS, UMD||mgiglio at som.umaryland.edu||Yes||No||alone from work/home|
|Marcus Chibucos||IGS, UMD||mchibucos at som dot umaryland dot edu||Yes||No||alone from work/home|
|Alexander Diehl||MGIemail@example.com||Yes||Yes||alone from work/home|
|Michael Livstone||Princetonfirstname.lastname@example.org||No||Yes||alone from work/home, can present PAINT families that have been curated via webex if that is on the agenda for the SAB|
|Susan Tweedie||FlyBase||sart2 at gen dot cam dot ac dot uk||Yes||Yes||alone from home|
|Yasmin Alam-Faruque||EBI GOA||yalam at ebi.ac.uk||Yes||Yes||alone from home|
|Varsha Khodiyar||BHF-UCL annotator||v.khodiyar at ucl.ac.uk||Yes||No||alone from home|
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