Difference between revisions of "OntologyRelations"

Latest revision as of 08:27, 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 ==
+'''Workshop on the Relationship Ontology'''
-== Goals ==
+The [http://ncbo.us National Center for Biomedical Ontology] hosted a two-day workshop focused on the relationship between terms (classes) in ontologies.
-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 goals of this workshop are to develop the content of the relationship ontology. In particular we will discuss these areas:
+== 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]]
-# To add new relationships to RO: [[RO:Main_Page | Current Proposals for new relations ]]
+* [[OntologyRelationsMeetingNotesCompiled]]
-#* The "regulates" relationship
-#* The relations that are required for anatomies and development
-#* The relations that are required for describing phenotypic data
-#* The relations that are required for cross-products between anatomy and biological process
-# To consolidate the methodology for doing so
-== Draft Agenda ==
+== Guidelines and Goals ==
-=== Monday, May 19th 2008 ===
+* 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
-:30 Suzi Lewis: Logistics and protocols
+* 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
-:45 Introductions: why you attended, background and expertise
+''Note: At least Alan Ruttenberg has expressed that these goals are too much to achieve in the time we have''
-:00 Barry Smith (moderator): Discussion of methodology for creating new relations (e.g. some-part question)
+== Preparation ==
-:00 break
+* 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 ==
-:30 (continued) Discussion of methodology for creating new relations (e.g. some-part question)
+=== 8:30-10:30am General (Barry/Chris/Mike) ===
-:30 Set priorities and ordering of the listed discussion topics.
+* review of principles
+** all-some / time (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt 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
-:00 Lunch
+=== 10:30am-10:45am: Coffee ===
-:00 Discussion of topics
+=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===
-:00 break
+* 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
-:30 Discussion of topics
+=== 12:00 noon - 12:30: Lunch ===
-:30 Done for the day
+=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===
-:30 dinner
+* 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
-=== Tuesday, May 20th 2008 ===
+=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===
-:30 Discussion of topics
+*  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)
-:30 break
+=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===
-:00 Discussion of topics
+* regulates, +, -
+* composition of regulation relations
+* [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]
-:00 lunch
+=== 5:30pm: Transportation to dinner ===
-:30 Discussion of topics
+== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==
-:30 Suzi Lewis: Summary of the meeting, action items, resolutions, and future plans.
+=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) ===
-:30 Departures
+* homologous_to & evo_derives_from
+* ternary relations in RO: DavidS's use case (DavidOS/Chris)
-== Dates ==
+=== 10:30am - noon Biochemical (Larry / Mike B) ===
-'''Monday and Tuesday, May 19-20, 2008'''
+* 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 ==
-'''University of Colorado Medical School'''
+* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the  [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building].
-This meeting will take place on the [[http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver]], probably in room 204 of the Ben Nighthorse Campbell building.
-Fly in to the [[http://www.flydenver.com/ Denver International Airport]].
+* Fly in to the [http://www.flydenver.com/ Denver International Airport].
-A good nearby hotel is the [[http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]].  It's not quite walking distance, but we will carpool.
+* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm 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 [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].
-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.
+* 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)
-# Judith Blake (JAX / Bar Harbor, ME)
+# 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 (Center for Ontology / Buffalo, NY)
+# Thomas Bittner (ORG / Buffalo, NY)
-# Melissa Haendel (ZFIN / Eugene, OR)
-# David Hill (MGI / Bar Harbor, ME)
 # Waclaw Kusnierczyk (Bergen, Norway)
-# Chris Mungall (Flybase / Berkeley, CA)
-# Fabian Neuhaus (NIST / Wash, DC)
 # Cornelius Rosse (FMA / Seattle, WA)
-# Nigam Shah (NCBO / Stanford, CA)
+# 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]]