OBO Foundry Workshop 2008

From OBOFoundry

Contents 1 Introduction 2 Goals 3 Outcomes 4 Proposed Agenda 4.1 Monday, July 7th, 2008 4.2 Tuesday, July 8th, 2008 5 Directions / Lodging / Transportation / 6 Confirmed Participants 7 Links 8 Further Reading

Introduction

The 1st OBO Foundry workshop is hosted by the European Bioinformatics Institute (EBI) and set to bring together the representatives of the ontologies working under the Foundry umbrella.

This workshop is held back-to-back with the OBI workshop, attended by the OBI Coord group only.

OBO Foundry coordinators:

• Michael Ashburner
• Suzanna Lewis
• Chris Mungall
• Alan Ruttenberg
• Barry Smith
• Richard Scheuermann

Local organizers:

• Philippe Rocca-Serra (OBI)
• Susanna-Assunta Sansone (OBI)
• Dominic Clark (EBI Industry Programme Manager)
• Andrew Lyall (ELIXIR - Scientific Manager)
• Holly Edwards (ELIXIR - Logistics Manager)

Date:

Monday July 7th and Tuesday 8th, 2008

Venue:

EBI IT Training room (A2-111), Hinxton, Cambridge, UK. More details below.

Attendees:

This workshop is designed specifically to bring together the editors who manage the content of OBO Foundry ontologies. Because of space constraints attendance is limited. The list of those invited is provided below.

Related projects sponsoring this workshop:

BBSRC funds for Workshop on Data Standards (BBSRC WODS) and the EU ELIXIR (Working Package 7) project will provide accommodations, local transportations and meals for the attendees. More information are available in the ELIXIR Overview document.

Goals

1. Get broad buy-in to the new OBO Foundry formalization of best practices / procedures;
2. Address issues of orthogonality between existing and potential candidate Foundry ontologies;
3. Share experiences on linking together different ontologies (cross-products);
4. Have tutorials (how-to) from experienced groups on best practices such as: deprecation policy, import strategies for OBO foundry ontologies, naming conventions and metadata capture;
5. Define a plan to start work collaboratively to develop common practices;
6. Set actions, identify lead persons/groups, and communication strategy to ensure these best practices are applied.

Outcomes

An initial set of actions, notes and links to presentations are now available.

A summary report and roadmap for OBO Foundry will be authored by the attendees and published in open journal, e.g. BMC Proceedings, peer-reviewed and indexed by PubMed.

Proposed Agenda

Monday, July 7th, 2008

8.15 Transport from Homerton College to EBI

8.45 - 9.00 Registration and coffee

9.00 - 9.05 Welcome and housekeeping

Susanna Sansone

9.05 - 9.35 ELIXIR introduction and focus on WP7

Dominic Clark /or/ Andrew Lyall and Susanna Sansone

9.35 - 11.00 Foundry session 1a: OBO Foundry: Practices and procedures

Moderator: Suzanne Lewis

Ratification of existing practices

Areas where we still need clear guidelines

Examples:

What does it mean to work collaboratively?

Orthogonality

Use of external terms

11.00 - 11.15 Coffee break

11.15 - 12.00 Foundry session 1b: OBO Foundry: Practices and procedures

12.00 - 12.45 Foundry session 2: Example of practices within OBI: proposing to be adopted by foundry

Moderator: Susanna Sansone

Short 5 slides/min presentations on:

import and release process (Melanie Courtot),

metadata and (Daniel Schober),

intra/inter term composition aka quick terms (Philippe Rocca-Serra)

12.45 - 13.45 sponsored lunch (just outside the meeting room)

13.45 - 15.30 Foundry session 3a: Common top level structure and Relation Ontology

Moderator: Barry Smith

Introduction to BFO

Overview of RO developments and next steps

15.30 - 15.45 coffee break

15.45 - 16.30 Foundry session 3b: Relation Ontology (cont.)

Moderator: Barry Smith

Cross-products (Chris Mungall)

16.30 - 17.15 Foundry session 4: OBO and OBO Foundry Namespaces

Moderator: Alan Ruttenberg

17.15 - 17.45 Free time for networking or catching up with your emails

17.45 Transport back to Homerton College

19.30 - 22.00 Dinner on your own: list of restaurants in Cambridge will be provided

Tuesday, July 8th, 2008

8.15 Transport from Homerton College to EBI

9.00 - 10.00 Foundry session 5: PATO and CARO

Moderator: Chris Mungall

10.00 - 11.00 Foundry session 6: ChEBI and SO

Moderator: Colin Batchelor

11.00 - 11.15 coffee break

11.15 - 12.45 Foundry session 7: Reference Ontologies and Application Ontologies with special reference to the Disease Ontology

Moderator: Michael Ashburner

including presentation on the Infectious Disease Ontology (Lindsay Cowell) and Disease Ontology (Lynn Schriml)

12.45 - 14.00 sponsored lunch (just outside the meeting room)

Lunch session (Business meeting for OBO Foundary Coordinators, including discussion of the future of the OBO repository and Elixir strategy on ontology)

14.00 - 15.45 Foundry session 8.a: Peer Review of OBO Foundry Ontologies

Moderator: Richard Scheuermann

presentation by Matthew Day (NPG)

15.45 - 16.00 coffee break

16.00 - 17.00 Foundry session 8.b: Peer Review of OBO Foundry Ontologies

17.00 - 18.15 Foundry session 10: Wrap-Up

Moderator: Suzanne Lewis

18.15 Transport to restaurant

18.30 - 22.00 Sponsored drinks and dinner at The Tickell Arms in Whittlesford

22.00 Transport back to Homerton College

Directions / Lodging / Transportation /

Final details will be included in the workshop(s) information package.

Travel directions:

Directions to EBI, Wellcome Trust Genome Campus, Cambridge, UK

The closest airports to Cambridge are London Stansted Airport (approx. 30 minutes), London City Airport and Luton Airport (both approx. 50 minutes). Heathrow and Gatwick are both more than 2 hours from Cambridge/Hinxton by car (3 to 4 hours by public transport). Consequently, we advise you to book a flight that lands in London Stansted, London Luton or London City Airport. British Airways' low cost airline EasyJet, Ryanair, Virgin Express, and Lufthansa all land in Stansted and fly from most larger European cities.

Buses operate from every airport (except London City airport) to Cambridge or even Stansted airport. For bus times and to book your ticket on-line see: http://www.nationalexpress.com/home/hp.cfm.

If travelling by train please see train times on: http://www.networkrail.co.uk.

If you wish to pre-book a taxi for the journey(s) we can recommend the following companies:

Melbury, http://www.melburycars.co.uk, Tel: +44 (0) 1763 261 949, Fax: +44 (0) 1763 261 026, Email: melburycars@btopenworld.com

Kenway Cars, Tel: +44(0)1223-832515; Fax: +44(0)1223-833538

Mid-Anglia, Tel: +44(0)1223-836000; Fax: +44(0)1223-833399

Mastercab, Tel: +44(0)1223-566654; Fax: +44(0)1223-579257

Abbots Car Service, Tel: +44(0)7855-341060

Partly sponsored accommodation and parking:

Single room accommodation (incl. bed and breakfast) has been organized for you at Homerton College, located in the center of Cambridge. On arrival please collect your keys from Porter’s Lodge.

If you are planning to drive to Homerton College, the car parking code is 5719. Please note that the car parking code will change on Friday 11th July at 15:00 to 5864.

Two nights only will be sponsored and upon request, additional nights have been booked. However the college does not have 'check in/out' facilities on site, so the EBI has pre-paid these extra nights for you (in addition to the nights sponsored by Elixir/BBSRC). Those participants will receive an invoice at the workshop to reimburse EBI of these extra expenses.

Sponsored transportation:

The EBI is approximately 20 minutes from central Cambridge by car. Public transport is infrequent and unreliable which is why we shall be providing transportation from/to the accommodation (right outside the College entrance, in parking area) and EBI, on Monday 7th and Tuesday 8th. Please, refer to the workshop agenda for the organized transportation times.

Sponsored meals:

Coffee breaks and lunches, will be sponsored on Monday 7th and Tuesday 8th. Sponsored dinner will be on Tuesday 8th at The Tickell Arms in Whittlesford; for those staying at the Homerton College transportation will be provided.

Confirmed Participants

Name	Ontology represented
1. Michael Ashburner	(OBO ontologies and ELIXIR WP7)
2. Erick Antezana	(cell cycle ontology: CCO)
3. Colin Batchelor	(sequence: SO)
4. Dominic Clark	(Industry Programme and ELIXIR)
5. Melanie Courtot	(experiment: OBI Coord)
6. Lindsay Cowell	(Immunology and Infectious Disease: IDO)
7. Bernard de Bono	(pathways: Reactome)
8. Paula de Matos	(chemical: ChEBI)
9. Kirill Degtyarenko	(chemical: ChEBI)
10. Dawn Field	(environment: EnvOand OBI Coord)
11. Frank Gibson	(experiment: OBI Coord)
12. George Gkoutos	(qualities: PATO)
13. Janna Hastings	(chemical: ChEBI)
14. David Hill	(gene: GO)
15. Oliver Hofmann	(cell type: CL)
16. Duncan Hull	(chemical: ChEBI)
17. Nick Juty	(system biology: SBO)
18. Nicolas Le Novere	(system biology: SBO)
19. Suzanna Lewis	(OBO ontologies)
20. Allyson Lister	(experiment: OBI Coord)
21. Jane Lomax	(gene: GO)
22. James Malone	(experiment: OBI Coord)
23. Jose Leonardo Mejino	(adult human anatomy: FMA)
24. Luisa Montecchi	(proteomics: PSI-MI, MS, MOD and OBI Coord)
25. Norman Morrison	(environment: EnvO and OBI Coord)
26. Chris Mungall	(OBO ontologies)
27. Darren Natale	(protein: PRO)
28. David Osumi-Sutherland	(common anatomy: CARO)
29. Helen Parkinson	(experiment: OBI Coord)
30. Bjoern Peters	(experiment: OBI Coord)
31. Philippe Rocca-Serra	(experiment: OBI Coord)
32. Alan Ruttenberg	(relation: RO, OBO ontologies and OBI Coord)
33. Susanna-Assunta Sansone	(experiment: OBI Coord)
34. Richard H. Scheuermann	(clinical: OCI, OBO ontologies and OBI Coord)
35. Daniel Schober	(experiment: OBI Coord)
36. Lynn Schriml	(disease: DO, EnvO, Gaz and transmission prcess)
37. Barry Smith	(OBO ontologies)
38. Christian Stoeckert	(experiment: OBI Coord)
39. Chris Taylor	(experiment: OBI)

Links

Top ten types of errors to avoid when building an ontology

• 1. mixing of singulars and plurals ("National Socialism is_a political systems" - MeSH)
• 2. mixing of concepts with entities in reality ("concepts (such as protons) may be precisely defined" -- Jim Cimino)
• 3. mixing of words with entities in reality (distinguishing 26 kinds of chemicals ("chemicals whose names begin with A", ...) -- Read Codes)
• 4. mixing of ontology and epistemology
• 5. use of 'other' ("Other problems with special functions"; " Other motor vehicle non-traffic accident of other and unspecified nature injuring passenger in motor vehicle other than motorcycle" -- early versions of Disease ontology)
• 6. classification of entities on the basis of incidental features (classification of humans by bra cup size -- CYC)
• 7. is_a overloading ("virus is_a environment ontology" - Gramene Environment Ontology)
• 8. definitions of general terms as if they had specific meanings ("Water is a type of Nursing Phenomenon of Physical Environment with the specific characteristics: Clear liquid compound of hydrogen and oxygen that is essential for most plant and animal life influencing life and development of human beings." - International Classification of Nursing Procedures
• 9. general terms used as leaf nodes ("Blood disease" has no children in Disease Ontology)
• 10. term suggests lack of thinking ("menopause part_of death" -- early versions of GO; "vomitus contains carrot" -- GALEN; "repair and maintenance of wheelchair is_a disease" -- early versions of DO)

More details and more examples of types of errors can be found in:

• [1]
• [2]
• [3]

Streaming video lecture course on ontology methodology:

• [4]

Further Reading

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration, Nature Biotechnology 25 (2007), 1251-1255.