OntologyRelations

Workshop on the Relationship Ontology

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

Minutes, Notes and Presentation

• Media:May 2008 RO meeting minutes v2.doc
• OntologyRelationsMay19MeetingNotes
• Media:ROMeetingNotesPhenoscape.doc
• Media:relations_for_representing_developmental_anatomy.ppt
• Media:regulates.ppt
• Media:overlaps.ppt
• Media:RO-denver-cjm.ppt
• Media:dahdul-ROmeeting.ppt
• Media:Fabian developmental relations.pdf
• Media:Fabian develops_from.pdf
• Media:melissa development examples.ppt
• Media:Homology.ppt
• Media:Hunter Epistemic relations.ppt
• Media:Ruttenberg-ro.pdf

• OntologyRelationsMeetingNotesCompiled

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

Note: At least Alan Ruttenberg has expressed that these goals are too much to achieve in the time we have

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

8:30-10:30am General (Barry/Chris/Mike)

• review of principles
  • all-some / time (Barry) Slides
  • desired level of granularity (Barry/Mike)
• 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

10:45am - 12:00 noon: Development and anatomy (DavidOS)

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

12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner)

• 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

2:45 - 4pm: Spatial relations (Melissa/Suzi)

• RCC8-can we reuse? (Chris)
• surrounded_by (Chris)
• overlaps - bone + joint use case (Peter)
• connected_to and attached_to (Wasila)
  • bona fide vs fiat - when does it matter?
  • Example: axon tracts and neuropil (fiat)
  • Example: tooth attachment use case (bona fide)
• spatial.obo (Wasila)

4:15 - 5:30pm: Regulation (David/Tanya/Chris)

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

Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008

9:00-10:15am Evolutionary (Melissa, Wasila, Peter)

• homologous_to & evo_derives_from
• ternary relations in RO: DavidS's use case (DavidOS/Chris)

10:30am - noon Biochemical (Larry / Mike B)

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

12:30pm - 2pm Epistemic (Larry)

• supported_by et al

2:15pm - 4pm Other issues, and follow ups

• the time issue. OWL representation (Alan)
• 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.

Attended (alphabetically)

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

Invited

1. Thomas Bittner (ORG / Buffalo, NY)
2. Waclaw Kusnierczyk (Bergen, Norway)
3. Cornelius Rosse (FMA / Seattle, WA)
4. Bill Bug (BIRN / San Diego, CA)

Background Material

Relation Ontology Wiki

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