OntologyRelations

Workshop on the Relationship Ontology

The National Center for Biomedical Ontology will host a two-day workshop focused on the relationship between terms (classes) in ontologies.

Guidelines and Goals

• Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:
  • simple
  • example-driven
  • expressed in a clear, consistent symbol-free syntax

• The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:
  • All outstanding items on the request tracking system are solved
  • All relations in ro_proposed are "blessed" and move into RO proper
  • A release of the cross-product (xp) files is generated
  • We will produce a new release of the RO

Preparation

• The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon
• Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd
• Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO

TOPICS

General (Barry/Chris)

• review of principles
  • all-some(time) (Barry)
• review of website, tracker (Chris)
  • process for adding terms
• review of current primary representation in .obo, .owl conversion (Chris)
• ID policy (BFO), ontology lifecycle issues etc
• cross-products

Development and anatomy (DavidOS)

• stages and temporal relations
  • DavidOS/Fabian
  • Interval calculus
  • ZFA stages use case: start, end
• develops_from (Melissa)
• relations from CARO paper (Fabian)
• review biological_process_xp_cell (Chris/MikeB)
• replaced_by - endochondral bone replaces cartilege (Wasila)
• agent_in - is it valid? "heart process" example - DavidH/Chris

Biological qualities and phenotypes (Chris)

• lacks_part (Werner)
• inheres_in
  • relational qualities
    • towards relation
    • relational qualities and relations - what's the difference. lacks_part example
• relations between qualities, comparisons and abnormality

Spatial relations (Melissa/Suzi)

• surrounded_by
• overlaps - bone + joint use case (Melissa)
• connected_to - axon tracts and neuropil (fiat binary)
• attached_to - bone + bone use case (Melissa)
• RCC8 - can we just import directly?
• bona fide vs fiat - when does it matter
• spatial.obo

Regulation (David/Tanya/Chris)

• regulates, +, -
• composition of regulation relations
• [1] TAIR relations

Biochemical (Mike B)

• pathways (BioPAX-OBO, AlanR)
• review bp_xp_chebi (Bada)

Evolutionary

• homologous_to & evo_derives_from

Epistemic (Larry)

• supported_by et al

Logical/representation issues (breakout session?)

• FOL representations of RO (Thom, Fabian)
• RO and BFO
• OBO and OWL issues (Alan, Chris, Nigam)
• instance vs type level; punning vs separate IDs
• the time issue. OWL representation (Alan)
• ternary relations in RO: DavidS's use case (DavidOS/Chris)
• Erick's list of meta-relations
• idiosyncratic relations in the FMA (Suzi/Nigam)

Draft Agenda

Monday, May 19th 2008

8:30 Suzi Lewis: Logistics and protocols

8:45 Introductions: why you attended, background and expertise

9:00 Barry Smith (moderator): Discussion of methodology for creating new relations (e.g. some-part question)

10:00 break

10:30 (continued) Discussion of methodology for creating new relations (e.g. all-some question)

11:30 Set priorities and ordering of the listed discussion topics.

12:00 Lunch

13:00 Discussion of topics

15:00 break

15:30 Discussion of topics

17:30 Done for the day

19:30 dinner

Tuesday, May 20th 2008

8:30 Discussion of topics

10:30 break

11:00 Discussion of topics

12:00 lunch

1:30 Discussion of topics

2:30 Suzi Lewis: Summary of the meeting, action items, resolutions, and future plans.

3:30 Departures

Dates

Monday and Tuesday, May 19-20, 2008

Logistics

University of Colorado Medical School

This meeting will take place on the Anschutz medical Campus of the University of Colorado at Denver, probably in room 204 of the Nighthorse Campbell building.

Fly in to the Denver International Airport.

A good nearby hotel is the East Denver Drury Inn. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need visitor parking information.

If you need advice or want to talk to someone regarding logistics, email Kathy Thomas and mention the Relation Ontology expert meeting in May.

Invited Participants

Confirmed

1. Mike Bada (host / Denver, CO)
2. Tanya Berardini (TAIR / Stanford, CA)
3. Bill Bug (BIRN / San Diego, CA)
4. Werner Ceusters (ORG / Buffalo, NY)
5. Wasila Dahdul (NESCENT)
6. Melissa Haendel (ZFIN / Eugene, OR)
7. David Hill (MGD / Bar Harbor, ME)
8. Larry Hunter (host / Denver, CO)
9. Suzi Lewis (NCBO / Berkeley, CA)
10. Chris Mungall (Flybase / Berkeley, CA)
11. Fabian Neuhaus (NIST / Washington, DC)
12. David Osumi-Sutherland (FlyBase / Cambridge, UK)
13. Cornelius Rosse (FMA / Seattle, WA)
14. Alan Ruttenberg (Science Commons / Cambridge, MA)
15. Nigam Shah (NCBO / Stanford, CA)
16. Barry Smith (NCBO / Buffalo, NY)

Invited

1. Thomas Bittner (ORG / Buffalo, NY)
2. Waclaw Kusnierczyk (Bergen, Norway)

Background Material

Relation Ontology Home

Current Proposals for new relations