EnvO CSHL workshop
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Main Page->CVs and Ontologies ->EnvO Project -> Inaugural EnvO Workshop -> Second EnvO CSHL Workshop Also See the forthcoming: EnvO Manchester workshop
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[edit] Second Environment Ontology Workshop at CSHL, November 14-16, 2007
[edit] EnvO project
EnvO Project
Developing an ontology for describing the environment of organisms / biological samples
[edit] Workshop Notes
[edit] Workshop Logistics
[edit] Dates
Thursday 14th to Friday 16th, November, 2007
[edit] Meeting Location
The workshop will take place in the Banbury Center, at Cold Spring Harbor Laboratory in Long Island NY.
The full address of the venue is :
Banbury Center
PO Box 534
Cold Spring Harbor NY 11724-0534
USA
[edit] Meeting contacts
For questions on the travel, local transportation and lodging please contact Banbury by e-mail or phone.
Phone: (516) 367-8398
Fax: (516) 367-5106
e-mail: e-mail Banbury
[edit] Directions
Please see the instructions provided by the Banbury Center's travel website.
[edit] Travel
PLEASE READ IT CAREFULLY
- Everyone must buy their your own tickets and arrange to arrive on November 14.
- Everyone is expected to stay up to the end of the meeting on Day-2, therefore, reserve your return flights accordingly.
- It takes about 1 - 1.30hr to reach the airports. So schedule sufficient time (3hrs) for transit to the airport and checkin.
- BUY COACH/ECONOMY CLASS TICKETS ONLY and BUY IT ASAP
- Please keep in mind that we will be able to reimburse the trip for everyone. However make sure YOU BUY TICKETS ON AN AMERICAN FLAGSHIP CARRIER! No non-US carrier is allowed for reimbursements. Here is a suggested list of US-Flag carriers
- In case of the participants flying on international carriers having "code-sharing" arrangement for that particular flight with a U.S.-flag carrier, the reimbursements are ALLOWED ONLY if you purchase the ticket through the U.S.-flag carrier. DO NOT purchase the ticket for the code-shared leg from the foreign-flag carrier, or we are not allowed to reimburse the cost!
- All Domestic (US) participants must fly on a U.S.-flag carrier.
- YOU MUST SAVE YOUR other half of the ORIGINAL BOARDING PASSES. CSHL requires them at the time of reimbursements.
[edit] Accommodation
Accommodation for delegates will be arranged at the Banbury Center (yes, its the same place we will have the workshop) for the nights of November 14, 15 and 16. You must arrange to arrive on November 14. Please schedule the departures for either late evening on November 16 or Early forenoon November 17. For more information on accommodation please visit Banbury's facilities site.
[edit] Evening Meal
Tentative arrangements
November 14 at Banbury
November 15 at a local restaurant
November 16 at Banbury
[edit] Program
[edit] Workshop program
| SECOND ENVIRONMENT ONTOLOGY WORKSHOP The Banbury Center, Cold Spring Harbor Laboratory, 14-16 November 2007 |
|
| Wednesday, 14 November |
|
| Morning & afternoon | Arrival at Robertson House, Banbury Center, for registration and room assignment |
| 6.00 pm | Reception at Robertson House |
| 7.30 pm | Dinner at Robertson House |
| Thursday, 15 November | |
| 7.00-8.15 am | Breakfast at Robertson House |
| 8.55-9.00 am | Jan A. Witkowski, Banbury Center, Cold Spring Harbor Laboratory Introductory remarks |
| 9.00-12.00 pm | SESSION-1 Chair: Pankaj Jaiswal, Cornell University, Ithaca, New York |
| 9.00-9.05 am |
Pankaj Jaiswal, Cornell University, Ithaca, New York Welcome and Introductory remarks |
| 9.05-9.15 am |
Participants introduction - All |
| 9.15-9.45 am | Barry Smith, University at Buffalo, New York EnvO introduction |
| 9.45-10.00 am | Michael Ashburner, University of Cambridge, United Kingdom: Progress on EnvO+GAZ ontology development. |
| 10:00-10:15 am | Norman Morrison, University of Manchester, United Kingdom: Ontology maintenance and website + database logistics. |
| 10:15-10:45 am | Chris Mungall, Lawrence Berkeley National Laboratory, California Phenote annotation tool |
| 10:45-11:00 am | Break |
| 11.00-12.00 pm | Case Studies with EnvO annotations (15 minutes each presentation)
Locating microbial life through the StrainInfo.net bioportal
The GEMINA database: The bumpy road of ontology development
Using EnvO and Gaz to annotate real data: GSC and EnvBase case studies
|
| 12.15 pm | Luncheon at Robertson House |
| 1:45-6:00 pm | SESSION-2: Chair: Norman Morrison, University of Manchester, United Kingdom |
| 1:45-2:45 pm | New Case Studies for Potential EnvO Annotations (10 minutes each presentation)
Characterization of agricultural environments
Environmental Description in the USDA Germplasm Resources Information Network (GRIN) Database
|
| 2:45-4:00 pm | Michael Ashburner, University of Cambridge, United Kingdom: Hands on work on ontology. |
| 4:00-4:15 pm | Break |
| 4:15-6:00 pm | Michael Ashburner, University of Cambridge, United Kingdom: Hands on work on ontology. |
| 6:15 pm | Reception at Robertson House |
| 7:00 pm |
Dinner at Robertson House |
| Friday, 16 November |
|
| 7:15-8:15 am | Breakfast at Robertson House |
| 8:30-12:30 pm | SESSION-3: Chair: Barry Smith, University of Buffalo, New York |
| 8:30-8:50 am | Suzanna Lewis, University of California, Berkeley: Summary from Day-1. |
| 8:50-10:30 am | Michael Ashburner, University of Cambridge, United Kingdom: Hands on work on ontology. |
| 10:30-10:45 am | Break |
| 10:45-12:30 pm | Michael Ashburner, University of Cambridge, United Kingdom: Hands on work on ontology. |
| 12:45-1:30 pm | Buffet Luncheon at Conference Center [may be a working lunch to accommodate the short afternoon session. There are some important agenda items listed for this session] |
| 1:30-4:00 pm | SESSION-4: Chair: Suzanna Lewis, University of California, Berkeley |
| 1:30-2:30 pm | Michael Ashburner, University of Cambridge, United Kingdom: Hands on work on ontology. |
| 2:30-3:00 pm | Barry Smith, University of Buffalo, New York: Discuss funding possibilities. |
| 3:00-3:15 pm | Break |
| 3:15-3:30 pm | Norman Morrison, University of Manchester, United Kingdom: Identify potential projects, databases and collaborators. |
| 3:30-4:00 pm | Suzanna Lewis, University of California, Berkeley: Summarize the meeting, action items and wrap up. |
| Evening | Departures (Banbury Center will arrange the transport) |
| TBA pm | Dinner at Robertson House for those departing late and staying overnight. |
[edit] Organizers
| Pankaj Jaiswal | Gramene Database / Dept. of Plant Breeding and Genetics, Cornell University, Ithaca, NY |
| Norman Morrison | NERC Environmental Bioinformatics Centre (NEBC) / School of Computer Science, The University of Manchester, UK |
| Dawn Field | NERC Centre for Ecology and Hydrology |
| Suzanna Lewis | Lawrence Berkeley National Laboratory |
| Barry Smith | National Center for Biomedical Ontology / University at Buffalo |
| Michael Ashburner | Department of Genetics, University of Cambridge |
[edit] Other Attendees
| Chris Mungall | Lawrence Berkeley National Laboratory |
| Aaron Gussman | Institute for Genome Sciences, Baltimore School of Medicine |
| Neil Hall | School of Biological Sciences, University of Liverpool |
| Neil Sarkar | Marine Biological Laboratory |
| Lynn Schriml | University of Maryland School of Medicine |
| Peter Dawyndt | StrainInfo Bioportal / Ghent University |
| Bart van Brabant | StrainInfo Bioportal / Ghent University |
| Victor Markowitz | Lawrence Berkeley National Laboratory |
| Nikos Kyrpides | DOE JGI / Lawrence Berkeley National Laboratory |
| Maureen Donnelly | Center of Excellence in Bioinformatics and Life Sciences / University at Buffalo |
| Peter Kille | School of Biosciences, Cardiff University |
| Lynette Hirschman | MITRE |
| Lincoln Stein | CSHL |
| Stephanie Greene | USDA, ARS National Temperate Forage Legume Genetic Resources Unit |
| Sujeevan Ratnasingham | University of Guelph |
| Jeff White | USDA-ARS |
[edit] Sponsors
This meeting is supported by the US National Science Foundation [1] Research Coordination Network grant (DBI 0234147 [2]) to the Gramene Database [3].
[edit] Links of interest
[edit] EnvO ontology
[edit] GAZ ontology
[edit] Phenote annotation tool
[edit] EnvO mailing list
[edit] Photos from the workshop
[edit] Previous meetings
[edit] Oxford 2007
- EnvO Workshop held at Oxford, UK (August 29-31, 2007)
- Workshop Report: .doc format (Image:EnvO Meeting Report Final.doc) and .pdf format (Image:1st EnvO Workshop report final.pdf)
