Difference between revisions of "OntologyRelations"

Latest revision as of 07:27, 16 November 2008

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

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

10:30am-10:45am: Coffee

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

12:00 noon - 12:30: Lunch

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

5:30pm: Transportation to dinner

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)

Mike Bada (host / Denver, CO)
Tanya Berardini (TAIR / Stanford, CA)
Vinay Chaudhri (SRI / Menlo Park, CA)
Werner Ceusters (ORG / Buffalo, NY)
Wasila Dahdul (Phenoscape/NESCENT)
Mary Dolan (MGI / Bar Harbor, ME)
Melissa Haendel (ZFIN / Eugene, OR)
David Hill (MGI / Bar Harbor, ME)
Larry Hunter (host / Denver, CO)
Suzi Lewis (NCBO / Berkeley, CA)
Peter Midford (Phenoscape/ NESCent)
Chris Mungall (Flybase / Berkeley, CA)
Darren Natale (PRO / Georgetown, Washington, DC)
Fabian Neuhaus (NIST / Washington, DC)
David Osumi-Sutherland (FlyBase / Cambridge, UK)
Alan Ruttenberg (Science Commons / Cambridge, MA)
Nigam Shah (NCBO / Stanford, CA)
Barry Smith (NCBO / Buffalo, NY)
Karin Verspoor (host / Denver, CO)

Invited

Thomas Bittner (ORG / Buffalo, NY)
Waclaw Kusnierczyk (Bergen, Norway)
Cornelius Rosse (FMA / Seattle, WA)
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

@@ Line 1: / Line 1: @@
 '''Workshop on the Relationship Ontology'''
-The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.
+The [http://ncbo.us 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 meeting biologist driven. This means that any logical theories discussed must be kept:
+* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:
-** simple
+** simple, with well-thought out definitions
-** example-driven
+** example-driven, that is an instance-level definition must exist (see RO paper)
 ** expressed in a clear, consistent symbol-free syntax
@@ Line 15: / Line 33: @@
 ** 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 ==
@@ Line 22: / Line 42: @@
 * 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 ==
+== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==
-=== General (Barry/Chris) ===
+=== 8:30-10:30am General (Barry/Chris/Mike) ===
 * review of principles
-** all-some(time) (Barry)
+** all-some / time (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]
-** desired level of granularity (Barry)
+** desired level of granularity (Barry/Mike)
 * review of website, tracker (Chris)
 ** process for adding terms
@@ Line 35: / Line 55: @@
 * cross-products
-=== Development and anatomy (DavidOS) ===
+=== 10:30am-10:45am: Coffee ===
+=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===
 * stages and temporal relations
@@ Line 41: / Line 63: @@
 ** Interval calculus
 ** ZFA stages use case: start, end
-* develops_from (Melissa)
+* develops_from
 * 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) ===
+=== 12:00 noon - 12:30: Lunch ===
+=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===
 * lacks_part (Werner)
@@ Line 56: / Line 79: @@
 * relations between qualities, comparisons and abnormality
-=== Spatial relations (Melissa/Suzi) ===
+=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===
-* surrounded_by
+*  RCC8-can we reuse? (Chris)
-* overlaps - bone + joint use case (Melissa)
+* surrounded_by (Chris)
-* connected_to - axon tracts and neuropil (fiat binary)
+* overlaps - bone + joint use case (Peter)
-* attached_to - bone + bone use case (Melissa)
+* connected_to and attached_to (Wasila)
-* RCC8 - can we just import directly?
+** bona fide vs fiat - when does it matter?
-* bona fide vs fiat - when does it matter
+** Example: axon tracts and neuropil (fiat)
-* spatial.obo
+** Example: tooth attachment use case (bona fide)
+* spatial.obo (Wasila)
-=== Regulation (David/Tanya/Chris) ===
+=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===
 * regulates, +, -
@@ Line 72: / Line 96: @@
 * [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]
-== Agenda: 8:00AM-3:30PM Tuesday, May 20th 2008 ==
+=== 5:30pm: Transportation to dinner ===
+== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==
-=== Evolutionary (Melissa & Wasila) ===
+=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) ===
 * homologous_to & evo_derives_from
+* ternary relations in RO: DavidS's use case (DavidOS/Chris)
-=== Biochemical (Mike B) ===
+=== 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. (Bada)
+* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)
-=== Epistemic (Larry) ===
+=== 12:30pm - 2pm Epistemic (Larry) ===
 * 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)
-* ternary relations in RO: DavidS's use case (DavidOS/Chris)
-* Erick's list of meta-relations
 * idiosyncratic relations in the FMA (Suzi/Nigam)
@@ Line 109: / Line 130: @@
 * If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.
-== Invited Participants ==
+=== Attended (alphabetically) ===
-=== Confirmed ===
 # Mike Bada (host / Denver, CO)
 # Tanya Berardini (TAIR / Stanford, CA)
-# Bill Bug (BIRN / San Diego, CA)
+# Vinay Chaudhri (SRI / Menlo Park, CA)
 # Werner Ceusters (ORG / Buffalo, NY)
-# Wasila Dahdul (NESCENT)
+# Wasila Dahdul (Phenoscape/NESCENT)
+# Mary Dolan (MGI / Bar Harbor, ME)
 # Melissa Haendel (ZFIN / Eugene, OR)
 # David Hill (MGI / Bar Harbor, ME)
 # Larry Hunter (host / Denver, CO)
 # Suzi Lewis (NCBO / Berkeley, CA)
-# Peter Midford (NESCent)
+# Peter Midford (Phenoscape/ NESCent)
 # Chris Mungall (Flybase / Berkeley, CA)
+# Darren Natale (PRO / Georgetown, Washington, DC)
 # Fabian Neuhaus (NIST / Washington, DC)
 # David Osumi-Sutherland (FlyBase / Cambridge, UK)
-# Cornelius Rosse (FMA / Seattle, WA)
 # Alan Ruttenberg (Science Commons / Cambridge, MA)
 # Nigam Shah (NCBO / Stanford, CA)
 # Barry Smith (NCBO / Buffalo, NY)
-# Mary Dolan (MGI  / Bar Harbor, ME)
+# Karin Verspoor (host / Denver, CO)
 === Invited ===
 # Thomas Bittner (ORG / Buffalo, NY)
 # Waclaw Kusnierczyk (Bergen, Norway)
+# Cornelius Rosse (FMA / Seattle, WA)
+# Bill Bug (BIRN / San Diego, CA)
 == Background Material ==
+[http://www.bioontology.org/wiki/index.php/RO:Main_Page Relation Ontology Wiki]
 [http://obofoundry.org/ro/ Relation Ontology Home ]
 [[RO:Main_Page | Current Proposals for new relations ]]
+[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]
+White paper  on the relations used in the AURA biology system [[media:AURA_relations.pdf]]