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 Relations Ontology biology driven. This means that any relations proposed must be kept:
  • simple, with well-thought out definitions
  • example-driven, that is an instance-level definition must exist (see RO paper)
  • 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

Agenda: 8:00AM-5:30PM Monday, May 19th 2008

9-10:30am General (Barry/Chris)

• review of principles
  • all-some(time) (Barry)
  • desired level of granularity (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)
• 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 (Peter)
• connected_to - axon tracts and neuropil (fiat binary)
• attached_to - bone + bone use case (Wasila)
• RCC8 - can we just import directly?
• bona fide vs fiat - when does it matter
• spatial.obo (Wasila)

Regulation (David/Tanya/Chris)

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

Agenda: 8:00AM-3:30PM Tuesday, May 20th 2008

Evolutionary (Melissa, Wasila, Peter)

• homologous_to & evo_derives_from

Biochemical (Larry / Mike B)

• pathways (BioPAX-OBO, AlanR)
• review bp_xp_chebi (Bada)
• Molecular interactions and the PSI-MI relation(esque) terms. (Larry)

Epistemic (Larry)

• supported_by et al

Logical/representation issues

• 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)

Logistics

• 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 (alphabetically)

1. Mike Bada (host / Denver, CO)
2. Tanya Berardini (TAIR / Stanford, CA)
3. Bill Bug (BIRN / San Diego, CA)
4. Vinay Chaudhri (SRI / Menlo Park, CA)
5. Werner Ceusters (ORG / Buffalo, NY)
6. Wasila Dahdul (Phenoscape/NESCENT)
7. Mary Dolan (MGI / Bar Harbor, ME)
8. Melissa Haendel (ZFIN / Eugene, OR)
9. David Hill (MGI / Bar Harbor, ME)
10. Larry Hunter (host / Denver, CO)
11. Suzi Lewis (NCBO / Berkeley, CA)
12. Peter Midford (Phenoscape/ NESCent)
13. Chris Mungall (Flybase / Berkeley, CA)
14. Darren Natale (PRO / Georgetown, Washington, DC)
15. Fabian Neuhaus (NIST / Washington, DC)
16. David Osumi-Sutherland (FlyBase / Cambridge, UK)
17. Cornelius Rosse (FMA / Seattle, WA)
18. Alan Ruttenberg (Science Commons / Cambridge, MA)
19. Nigam Shah (NCBO / Stanford, CA)
20. Barry Smith (NCBO / Buffalo, NY)
21. Karin Verspoor (host / Denver, CO)

Invited

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

Background Material

Relation Ontology Home

Current Proposals for new relations

SMBM paper discussing the relations in the PASBio predicates

White paper on the relations used in the AURA biology system media:AURA_relations.pdf