towards a richer set of information to describe our complete genome collection

EnvO Manchester workshop

From Genomic Standards Consortium

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[edit] Third Environment Ontology Workshop at The University of Manchester, March 13-15, 2008

[edit] EnvO project

Developing an ontology for describing the environment of organisms / biological samples

[edit] Workshop Logistics

[edit] Useful Stuff to Print Out Before You Leave!

  • Print out this page!
  • Map for locating the Days Hotel / Manchester Conference Centre, including directions from Manchester Piccadilly Train Station (10 mins walk) (link to map)
  • The University of Manchester campus map.
    • Building Keys:
      • Days Inn Hotel, Manchester conference Centre (Number 11).
      • Kilburn Building, School of Computer Science (Number 39).

[edit] Dates

Thursday 13th to Saturday 15th, March, 2008

[edit] Meeting Location

The workshop will take place in the Atlas Suite in the School of Computer Science, at The University of Manchester UK.

The full address of the venue is :
School of Computer Science,
University of Manchester,
Kilburn Building,
Oxford Road,
Manchester, M13 9PL.

NB: The entrance to the Kilburn Building is on the first floor level (something that confuses many visitors!). Climb the wide brick steps, located next to the precinct centre bridge that passes over Oxford road, then follow the signs to the Kilburn Building. I will post signs on the doors directing you towards the Atlas Suite.

[edit] Travel

  • Please buy your own tickets and arrange to arrive by March 13th 2008.
  • Everyone is expected to stay up to the end of the meeting on Day-3, therefore, please make your arrangements accordingly.

[edit] Travel by Air

Manchester Airport is one of the largest and busiest in the country. It is located about 10 miles (16km) south of the city centre, about 30 minutes from the university.

The airport has a number of transport links to the city:

  • Train - The airport's two terminals are linked directly to the city centre by a fast, frequent 24 hour train link to both Piccadilly and Oxford Road stations.
  • Taxi - A taxi from the airport to the University will cost approximately £15.
  • Bus - Local buses also run to the Oxford Road and Sackville Street areas of the campus.

Most major airlines fly to and from Manchester. For more information please visit the Manchester Airport Website

[edit] Further Travel Info

The Manchester University Maps & Travel pages have lots of useful information about getting to/from the University.

[edit] Accommodation

Accommodation for delegates has been arranged at the Manchester Conference Centre. Information about getting to the centre can be found here.

Days Hotel Manchester, Weston Building, Sackville Street, Manchester, M1 3BB, UK Tel: +44 161 955 8400

[edit] Eating Out

Initial reservations have been made at three different restaurants in Manchester over the course of the workshop.

  • Please indicate your availability for each of the evenings here.
  • Wed 12th - 7.30pm. East-Z-East. Punjabi Restaurant, very close to the hotel.
    • http://www.eastzeast.com/homepage.html
    • Note: For those of you arriving on Wednesday evening, there has been a suggestion to meet up before going to the restaurant at the Lass O'Gowrie pub at 6pm. It's very close to the hotel and I'm sure the receptionist will be able to point you in the right direction.
  • Thurs 13th - 7.30pm. Sam's Chop House. Classic British food in victorian surroundings.

[edit] Meeting contacts

For questions on the travel, local transportation and accommodation please contact Norman Morrison by email or telephone:

Email: norman.morrison AT manchester.ac.uk Phone: +44 161 275 0646

[edit] Expenses

IMPORTANT: Please include all original receipts/invoices/tickets and make a copy for your records (just in case anything gets lost). Credit card receipts will not be accepted. Please submit all forms within one month to the following address:
EnvO III Workshop
FAO: Caroline Wills-Wright
CEH Oxford
Mansfield Rd
Oxford, UK. OX1 3SR

An electronic copy of the expenses claim form can be found here: Expenses Claim Form

[edit] Participants

Michael Ashburner Department of Genetics, University of Cambridge
Brandon Bennett University of Leeds
Andy Brass School of Computer Science, The University of Manchester, UK / Wellcome Trust Host/Pathogen Project.
Maureen Donnelly Center of Excellence in Bioinformatics and Life Sciences / University at Buffalo
Dawn Field NERC Environmental Bioinformatics Centre (NEBC) / NERC Centre for Ecology and Hydrology, Oxford.
Mark Hill NERC Centre for Ecology and Hydrology, Wallingford.
Lynette Hirschman MITRE
Peter Kille School of Biosciences, Cardiff University
Suzanna Lewis Lawrence Berkeley National Laboratory
Roy Lowry NERC - British Oceanographic Data Centre
Norman Morrison NERC Environmental Bioinformatics Centre (NEBC) / School of Computer Science, The University of Manchester, UK
Neil Sarkar Marine Biological Laboratory / Encyclopedia of Life
Lynn Schriml University of Maryland School of Medicine
Barry Smith National Center for Biomedical Ontology / University at Buffalo
Matthew Stiff
Bart VanBrabant StrainInfo Bioportal / Ghent University
Mike Worboys Department of Spatial Information Science and Engineering / National Center for Geographic Information and Analysis, University of Maine.

[edit] Participants unable to attend

Peter Dawyndt StrainInfo Bioportal / Ghent University
Aaron Gussman Institute for Genome Sciences, Baltimore School of Medicine
Pankaj Jaiswal Gramene Database / Dept. of Plant Breeding and Genetics, Cornell University, Ithaca, NY
Nikos Kyrpides DOE JGI / Lawrence Berkeley National Laboratory
Joanne Luciano MITRE
Chris Mungall Lawrence Berkeley National Laboratory
Sujeevan Ratnasingham University of Guelph / Barcode of Life Data Systems
Phillippe Rocca-Serra European Bioinformatics Institute
Alan Ruttenberg
Robert Stevens School of Computer Science, The University of Manchester, UK
Tatiana Tatusova National Center for Biotechnology Information
Jeff White USDA-ARS

[edit] Program

[edit] Workshop program

Day 1 - Thursday 13th March 2008.

Workshop Opens

10:00

Registration & Coffee

Session I: Updates & Activities
Session Chair: Barry Smith

10:30 - 10:40

Welcome, background and scope of the workshop.
Norman Morrison & EnvO/Gaz coordination committee

10:40 - 10:50 Review of actions from previous meeting.
Suzanna Lewis - Lawrence Berkeley National Laboratory.
Ontology updates & activities
10:50 - 11:00

Gaz
Michael Ashburner - University of Cambridge.

11:00 - 11:10 EnvO
Norman Morrison - NEBC & University of Manchester.

User updates & Activities

11:10 - 11:20

Gemina Project
Lynn Schriml - University of Maryland.

11:20 - 11:30

Genomic Standards Consortium (GSC)
Dawn Field - NERC Centre for Ecology & Hydrology.

11:30 - 11:45

Coffee Break

11:45 - 11:55

Habitat-Lite
Lynette Hirschman - MITRE.

11:55 - 12:05 Encyclopedia of Life Project
Neil Sarkar - Marine Biological Laboratory, Woods Hole.

12:05 - 12:15

StrainInfo Portal
Bart VanBrabant, University of Ghent.

12:15 - 12:30 Discussion (Any other updates & activities)

12:30 - 13:30

Lunch

Session II: Introductory presentations & background from new members
Session Chair: Dawn Field

13:30 - 13:45

NERC DataGrid Vocabulary Server: an embryonic ontology server.
Roy Lowry - British Oceanographic Data Centre.

13:45 - 14:00

EUNIS: European nature information system database.
Mark Hill - NERC Centre for Ecology & Hydrology.

14:00 - 14:15

Geospatial Change.
Mike Worboys - University of Maine.

14:15 - 14:30

Landscape Genomics: Making the link between environmental factors, trypanosomiasis and cattle.
Andy Brass - University of Manchester.

14:30 - 15:00

Discussion

15:00 - 15:15

Coffee

Session III: Workshop Planning
Session Chair: Michael Ashburner

15:15 - 18:00

An agenda driven by adopters / users of EnvO and Gaz:

- For what purpose / function have you been using EnvO/Gaz?
- What does EnvO/Gaz do well?
- What does EnvO/Gaz NOT do so well?
- What's missing? Are there problem areas in the ontology and/or
software tools that you would like to see addressed?
- What 'real world' areas present challenges to you, in terms of
accurate representation?
- Are there any specific items you would like to see addressed on the
agenda that have not been discussed previously?
- Are there any other groups / communities that you think would use
EnvO/Gaz?

18:00

Close


Day 2 - Friday 14th March 2008.

09:00

Coffee

Session IV: Technical Issues
Session Chair: Suzanna Lewis

09:15 -12:30

Write access to the ontology. Who? How? Including, guidance on normal operating procedures.

What sort of searches do we need to support?

What mechanisms are available for requesting changes (and logging them)? Are they working? Can they be improved?

12:30 - 13:30

Lunch

Session V: TBA (User driven, action for end of day 1)
Session Chair: Norman Morrison

13:30 - 15:00

TBA (see above)

15:00 - 15:15

Coffee

Session VI: Where do we go from here?
Session Chair: Lynn Schriml

15:15 - 18:00

Mechanisms for collaboration

     Exposure: ISMB poster abstract.
Timeline for publication(?)
Future funding

18:00

Close


Day 3 - Saturday 15th March 2008.

Session VII: Development of Environmental & Gaz Ontologies

09:00

Coffee

9:15

Break out group 1                         

Break out group 2

10:40

Coffee

11:00

Break out group 1                         

Break out group 2 *Dedicated session: Future Funding*

13:00

Lunch

14:00

Wrap up: Review of Actions
Workshop Co-organizers

15:00

Formal close of workshop and Coffee

15:30

Departures

[edit] Meeting Documentation

Meeting White Board Notes

[edit] Post-Meeting Curation Priorities

[Prioritized Curation Tasks for EnvO and Gaz]

[edit] Links of interest

[edit] EnvO ontology

[edit] GAZ ontology

[edit] Phenote annotation tool

[edit] EnvO mailing list

[edit] Previous meetings

[edit] EnvO I

[edit] EnvO II

[edit] Photos from the meetings

[edit] Sponsors

This meeting has been sponsored by:
NEBC Logo

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