OntologyRelations

2008-05-08T18:38:05Z

Paula Mabee: /* Confirmed (alphabetically) */

'''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.

== 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: 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 (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)

=== Regulation (David/Tanya/Chris) ===

* 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]

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

=== Evolutionary (Melissa, Wasila, Peter) ===

* homologous_to & evo_derives_from

=== Biochemical (Larry / Mike B) ===

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

=== 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)

== Logistics ==

* 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].

* 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 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.

== Invited Participants ==
=== Confirmed (alphabetically) ===
# 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 (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)
# Cornelius Rosse (FMA / Seattle, WA)
# 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)

== Background Material ==

[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]]

NCBO Wiki - User contributions [en]

OntologyRelations