2010 Stanford Meeting Logistics
- 1 Dates
- 2 Venue
- 3 Maps
- 4 Registration
- 5 Lodging Information
- 6 Agenda for GOC meeting March 30 and March 31
- 6.1 Tuesday, March 30 – Morning [Start - Break]
- 6.2 Tuesday, March 30 – Morning [Break – Lunch]
- 6.3 Tuesday, March 30 Afternoon [After lunch - Break]
- 6.4 Tuesday, March 30 Afternoon [Break – Dinner]
- 6.5 Wednesday, March 31 Morning – Break
- 6.6 Wednesday, March 31 Morning [Break – Lunch]
- 6.7 Wednesday, March 31 Afternoon [Lunch - Break]
- 6.8 Wednesday, March 31 Afternoon [Break - end of day]
- 7 Agenda GO SAB Meeting April 1 2010
- 8 Attendees
- 9 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 $$
- Sheraton Palo Alto Hotel $$$$
- Westin Palo Alto $$$$
Agenda for GOC meeting March 30 and March 31
Tuesday, March 30 – Morning [Start - Break]
- Review Agenda; intro new people, grant info [Judy]
- who is taking minutes?
- who is tracking the teleconferencers?
Communication and Process for the GOC [Suzi]
- GO vision
- Changes in Managers structure
Tuesday, March 30 – Morning [Break – Lunch]
Ref Genome Project and PAINT [Pascale and Kara]
- Current focus on process sets
- Update on Annotation
- Curation: About eleven protein families have been done with beta version of PAINT, primarily by Mike Livstone in Kara's group at Princeton.
- References for PAINT annotations: One reference is available for each family's annotation.
- PAINT update (need slides from Paul)
- Where annotations not consistent, can be because links missing from ontology. Can be used to ensure term has most specific parent possible.
- Propagating NOT annotations - experimental evidence required for all NOT annotations. Propagate on a case-by-case basis? Need to determine at which point in evolutionary history the function has been lost. Also an issue with isoforms where the second isoform does NOT have the same function/process as the first.
- Bottleneck - all MODs getting through manual annotation for each gene.
- Any way of publicizing results from PAINT? Publications, stuff on website, captured in AmiGO?
- Project-based approach increases efficiency. Allows synergy with other groups, tighter integration and co-ordination.
- Can some of this be automated? e.g. looking at active site residue for enzymes to determine loss of function. Can also use the taxonomic restrictions for the ontologies. Also use gene-structure/model calculations - already in use.
- PAINT demo (link?)
- Uses a grid display to show where annotations missing, and need to change ontology/go back to MOD. Displays multiple information simultaneously, like OBO-Edit. Grid filled in as annotations completed.
- Should be straightforward for PAINT to pull in taxon rules
- In tabular display, more GO terms grouped, more specific to less specific within groups.
- In display, NOT annotations propagated up tree as long as no contradictory positive annotations (visual clue only)
- Are there cases where you can't automatically triangulate annotation up tree? Yes, there are examples of this - but this can be prevented using taxonomic restricdtions
- We should figure out a mechanism by which taxonomic restrictions derived from PAINT could be fed back into the ontology taxon restrictions file.
- Multiple sequence alignment view - for double-checking with tree
- Future Developments for PAINT
- Semantic zooming - a cartoon view to visualize how domains have been shuffled/duplicated. Talking to InterPro about developing cartoons.
Tuesday, March 30 Afternoon [After lunch - Break]
AmiGO and GO database updates/report (Seth and Chris)
- New search features 
- PAINT-style displays in AmiGO and family-based annotation reports 
- Improved tree view 
- loading the database with full gene product sets for reference genome groups
- plans for displaying col 16
- using reasoner as part of loading
- to what purpose evidence codes?
- needs of computational biologists to distinguish predicted vs. experimental annotations
- why to curators want to track NOT, ISS and RCA variants?
- why would we compute on evidence codes? why would others?
- What is role of ECO vs OBI?
- new evidence codes, particularly to support NOT annotations in tree
- "ISR" -> "Inferred from specific residues“ presence/absence of domains, active site etc
- "ISD" -> "Inferred from sequence divergence“ presence/absence of sequences have rapidly diverged (e.g., paralogs)
- "IDS" -> "Inferred from descendant sequence(s)“ (i.e. annotation of ancestors based on extant sequences) presence/absence function is annotated due to existing descendant protein that have been previously annotated
- "IAS" -> "Inferred from ancestral sequence“ (i.e. annotation of descendants based on ancestral annotation) presence/absence function is annotated due to ancestral protein that have been previously annotated
- Disentangling evidence codes (Kara/Chris). Annotation_method (Kara) Extending_evidence_codes (Chris)
- Position of ISM
- RCA usage and documentation
- Notice of ISMB workshop on Assays, ECO and OBI [Judy]
Tuesday, March 30 Afternoon [Break – Dinner]
Impact of recent ontology changes from an annotator/ontology developer perspective [David]
- MF-BP links, what they are and how they impact annotation
- Scope of regulation relationship
- Scope of has_part relationship
Annotation 1: Binding (Rama, Emily)
- Guidelines for 'binding' terms'
- proposed guidelines
- What, if any, binding term annotations can be transferred via ISS/ISO?
Wednesday, March 31 Morning – Break
Action Items Review (Judy)
- from last GOC meeting
- from yesterday, Tuesday, March 30
Annotation 2 (Rama, Emily)
- Discuss guideline documentation, progress 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'?
- Discussion of taxon IDs and subspecies [Jim Hu]
- Requirements and QC for contributed annotations [Rama]
- M. tuberculosis example
- Ideas for incorporating IMEX data into GOC? [Emily]
- Plans for Geneva GO Annotation Workshop [Pascale]
Wednesday, March 31 Morning [Break – Lunch]
- Term additions from the ASCB and SDB meeting (6 slides, Tanya)
- Additions from the kidney and heart development meeting (14 slides, David)
- PAMGO/multi-organism process update (Jane)
- Generic GO slim (2 slides, Jane)
- Cross products (18 slides, David)
- Internal cross products
- Cross-products already in place
- Cross-products "in production"
- External cross-products
- Aligning chemicals (11 slides, David)
Cell Ontology (Terry)
- Content update (Terry)
- Improved support for OBO/OWL/Protégé intersections (Chris)
- OBO_EDIT updates/report (Amina)
- streamlining addition of compositional terms [Chris]
Ontology Content Projects
- Bringing the NIF ontologies into GO. Allowing other groups write access to parts of GO (Jane)
- GO-Pathway database integration (Chris)
- PRO, MouseCyc, Reactome and GO: Complexes in PRO and GO (Harold)
Wednesday, March 31 Afternoon [Lunch - Break]
GOC website redesign (Rama)
- 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.
- Ease of file dissemination
- GAF2 update
- Proposal for new gene product data file format for submitting gene/protein data independently of annotations
- Proposal for new annotation file format containing only annotation data (complementary to the GP data file format above)
- Proposal to add a new column to the GAF to indicate if an annotation was reviewed by a curator or not.
Wednesday, March 31 Afternoon [Break - end of day]
Renewal, SAB and AOB
- OBO-Foundry Report (Jane)
- Parking lot item discussions or catch-up reports
- Strawman proposal for upcoming competitive renewal (Suzi, Chris, & Paul)
- Preparation for SAB next day
Agenda GO SAB Meeting April 1 2010
- 8:30: Welcome, Agenda Review
- 9:00am - 9:20 Grant news: 5 year Aims, Structure with Subcontracts, Metrics of Ontology and Annotation Success [Judy]
- 9:20 – 10:00 Management structure (Suzi)
- 10:00- 10:20 AmiGO and GO usage stats (Mike)
- 10:20 – 10:45 Break
- 10:45 – 11:00 Vision and Questions for Competitive Renewal/Future of GO (Michael)
- 11:00 – 12:00 Discussion of Aims and Objectives for Competitive Renewal (Suzi: Judy and others note-taking)
- 12:00 – 1:00 pm working lunch, open discussion
- 1:00 – 2:00 SAB executive session
- 2:00 – 3:00 SAB and PIs
- 3:00 – 3:30 Break
- 3:30 – 4:30 Summary [open to all GOC still round]
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||Public|
|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 miss wed 10am-4pm|
|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||MGIfirstname.lastname@example.org||Yes||Yes||alone from work/home|
|Li Ni||MGIemail@example.com||Yes||Yes||alone from home|
|Dmitry Sitnikov||MGIfirstname.lastname@example.org||Yes||No||alone from work/home|
|Michael Livstone||Princetonemail@example.com||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. Available 9AM-5PM EDT, 6AM-2PM PDT.|
|Lakshmi Pillai||AgBasefirstname.lastname@example.org||Yes||No||group call from work|
|Fiona McCarthy||AgBaseemail@example.com||Yes||No||group call from work|
|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||No||alone from home|
|Varsha Khodiyar||BHF-UCL annotator||v.khodiyar at ucl.ac.uk||Yes||No||alone from home|
|Valerie Wood||PomBase!||val at sanger.ac.uk||Yes||Yes||Probably alone from home.|
|Rebecca Foulger||EBI UniProt/GO office||rfoulger at ebi.ac.uk||Yes||No||Probably alone from home.|
|Daniel Renfro||EcoliWiki / EcoliHubfirstname.lastname@example.org||yes||yes||From the Hu lab, probably alone.|
|Peter Good||NHGRI Program Staff||goodp at mail.nih.gov||maybe||as much as possible||Alone where ever I can|
|Mary Dolan||MGIemail@example.com||Yes||Yes||alone from home|
|Amelia Ireland||BBOP / GO EBI||see above||Tues only; in person Weds||No||alone from the office|
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