Difference between revisions of "OntologyRelations"

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(Agenda: 8:00AM-5:30PM Monday, May 19th 2008)
(Agenda: 8:00AM-3:30PM Tuesday, May 20th 2008)
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=== 5:30pm transportation to dinner
 
=== 5:30pm transportation to dinner
  
== Agenda: 8:00AM-3:30PM Tuesday, May 20th 2008 ==
+
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==
  
=== Evolutionary (Melissa, Wasila, Peter) ===  
+
=== 9-10:15am Evolutionary (Melissa, Wasila, Peter) ===  
  
 
* homologous_to & evo_derives_from
 
* homologous_to & evo_derives_from
 +
* ternary relations in RO: DavidS's use case (DavidOS/Chris)
  
=== Biochemical (Larry / Mike B) ===  
+
=== 10:30am - noon Biochemical (Larry / Mike B) ===  
  
 
* pathways (BioPAX-OBO, AlanR)
 
* pathways (BioPAX-OBO, AlanR)
Line 85: Line 86:
 
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)
 
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)
  
=== Epistemic (Larry) ===  
+
=== 12:30pm - 2pm Epistemic (Larry) ===  
  
 
* supported_by et al
 
* supported_by et al
  
=== Logical/representation issues ===  
+
=== 2:15pm - 4pm Other issues, and follow ups ===  
  
* 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)
 
* 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)
 
* idiosyncratic relations in the FMA (Suzi/Nigam)
  

Revision as of 11:31, 12 May 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.

Contents

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: 9:00AM-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

10:45am - Noon 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

12:30 -2:30pm 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

2:45 - 4pm 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)

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

=== 5:30pm transportation to dinner

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

9-10:15am 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

  • 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

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