Difference between revisions of "OntologyRelations"

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* review of principles
* review of principles
** all-some(time) (Barry)
** all-some(time) (Barry)
** desired level of granularity (Barry)
* review of website, tracker (Chris)
* review of website, tracker (Chris)
** process for adding terms
** process for adding terms

Revision as of 12:29, 11 April 2008

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


  • 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

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)
  • 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)

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

Evolutionary (Melissa & Wasila)

  • homologous_to & evo_derives_from

Biochemical (Mike B)

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

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)


  • 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


  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 (MGI / Bar Harbor, ME)
  8. Larry Hunter (host / Denver, CO)
  9. Suzi Lewis (NCBO / Berkeley, CA)
  10. Peter Midford (NESCent)
  11. Chris Mungall (Flybase / Berkeley, CA)
  12. Fabian Neuhaus (NIST / Washington, DC)
  13. David Osumi-Sutherland (FlyBase / Cambridge, UK)
  14. Cornelius Rosse (FMA / Seattle, WA)
  15. Alan Ruttenberg (Science Commons / Cambridge, MA)
  16. Nigam Shah (NCBO / Stanford, CA)
  17. Barry Smith (NCBO / Buffalo, NY)
  18. Mary Dolan (MGI / Bar Harbor, ME)


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

Background Material

Relation Ontology Home

Current Proposals for new relations

Personal tools