https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&user=Suzi&feedformat=atomNCBO Wiki - User contributions [en]2024-03-29T08:32:03ZUser contributionsMediaWiki 1.35.9https://www.bioontology.org//mediawiki/index.php?title=Tutorials_and_Classes&diff=8050Tutorials and Classes2008-10-26T20:50:03Z<p>Suzi: </p>
<hr />
<div>Tutorials and classes co-located with the [http://icbo.buffalo.edu International Conference on Biomedical Ontology], July 24-26, 2009<br />
<br />
----<br />
<br />
'''Half-Day Tutorials ''' <br />
<br />
'''July 20'''<br />
<br />
Mathias Brochhausen (IFOMIS): [[The Ontology of Paleobiology]] <br />
<br />
'''July 21''' <br />
<br />
* Colin Batchelor (Royal Society of Chemistry): [[An Introduction to Chemistry Ontology]]<br />
<br />
* Ontology development tools<br />
** The Protégé Ontology Editor and Knowledge Acquisition System<br />
** The OBO-Edit Ontology Developer's Environment<br />
<br />
'''July 22'''<br />
<br />
Fabian Neuhaus (NIST): Reasoning with First Order Logic <br />
<br />
----<br />
<br />
'''Two-Day Classes''' <br />
<br />
'''July 20-21''' <br />
<br />
Randall Dipert and Neil Williams (Buffalo): The Ontology of Powers and Dispositions <br />
<br />
David Hershenov (Buffalo): [[Metaphysical Foundations of Biomedical Ethics]]<br />
<br />
Thomas Bittner and Maureen Donnelly (Buffalo): [[Bittner and Donnelly | Spatial Ontology and Qualitative Reasoning]]<br />
<br />
'''July 22-23'''<br />
<br />
Olivier Bodenreider (National Library of Medicine): An Introduction to Biomedical Ontology <br />
<br />
Werner Ceusters (Buffalo), Barry Smith (Buffalo) and Alan Ruttenberg (Science Commons): [[From BFO to IAO | From Basic Formal Ontology to the Information Artifact Ontology]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=File:May_2008_RO_meeting_minutes_v2.doc&diff=7339File:May 2008 RO meeting minutes v2.doc2008-07-03T15:39:25Z<p>Suzi: </p>
<hr />
<div></div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7338OntologyRelations2008-07-03T15:39:10Z<p>Suzi: /* Minutes, Notes and Presentation */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] hosted a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Minutes, Notes and Presentation ==<br />
* [[Media:May 2008 RO meeting minutes v2.doc]]<br />
* [[OntologyRelationsMay19MeetingNotes]]<br />
* [[Media:ROMeetingNotesPhenoscape.doc]]<br />
* [[Media:relations_for_representing_developmental_anatomy.ppt]]<br />
* [[Media:regulates.ppt]]<br />
* [[Media:overlaps.ppt]]<br />
* [[Media:RO-denver-cjm.ppt]]<br />
* [[Media:dahdul-ROmeeting.ppt]]<br />
* [[Media:Fabian developmental relations.pdf]]<br />
* [[Media:Fabian develops_from.pdf]]<br />
* [[Media:melissa development examples.ppt]]<br />
* [[Media:Homology.ppt]]<br />
* [[Media:Hunter Epistemic relations.ppt]]<br />
* [[Media:Ruttenberg-ro.pdf]]<br />
<br />
* [[OntologyRelationsMeetingNotesCompiled]]<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are too much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
=== Attended (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=File:May_2008_RO_meeting_minutes_v2.pdf&diff=7337File:May 2008 RO meeting minutes v2.pdf2008-07-03T15:38:20Z<p>Suzi: </p>
<hr />
<div></div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7336OntologyRelations2008-07-03T15:37:18Z<p>Suzi: /* Minutes, Notes and Presentation */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] hosted a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Minutes, Notes and Presentation ==<br />
* [[Media:May 2008 RO meeting minutes v2.pdf]]<br />
* [[Media:May 2008 RO meeting minutes v2.doc]]<br />
* [[OntologyRelationsMay19MeetingNotes]]<br />
* [[Media:ROMeetingNotesPhenoscape.doc]]<br />
* [[Media:relations_for_representing_developmental_anatomy.ppt]]<br />
* [[Media:regulates.ppt]]<br />
* [[Media:overlaps.ppt]]<br />
* [[Media:RO-denver-cjm.ppt]]<br />
* [[Media:dahdul-ROmeeting.ppt]]<br />
* [[Media:Fabian developmental relations.pdf]]<br />
* [[Media:Fabian develops_from.pdf]]<br />
* [[Media:melissa development examples.ppt]]<br />
* [[Media:Homology.ppt]]<br />
* [[Media:Hunter Epistemic relations.ppt]]<br />
* [[Media:Ruttenberg-ro.pdf]]<br />
<br />
* [[OntologyRelationsMeetingNotesCompiled]]<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are too much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
=== Attended (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7335OntologyRelations2008-07-03T15:34:29Z<p>Suzi: /* Minutes, Notes and Presentation */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] hosted a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Minutes, Notes and Presentation ==<br />
* [[Media:May 2008 RO meeting minutes v2.doc]]<br />
* [[OntologyRelationsMay19MeetingNotes]]<br />
* [[Media:ROMeetingNotesPhenoscape.doc]]<br />
* [[Media:relations_for_representing_developmental_anatomy.ppt]]<br />
* [[Media:regulates.ppt]]<br />
* [[Media:overlaps.ppt]]<br />
* [[Media:RO-denver-cjm.ppt]]<br />
* [[Media:dahdul-ROmeeting.ppt]]<br />
* [[Media:Fabian developmental relations.pdf]]<br />
* [[Media:Fabian develops_from.pdf]]<br />
* [[Media:melissa development examples.ppt]]<br />
* [[Media:Homology.ppt]]<br />
* [[Media:Hunter Epistemic relations.ppt]]<br />
* [[Media:Ruttenberg-ro.pdf]]<br />
<br />
* [[OntologyRelationsMeetingNotesCompiled]]<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are too much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
=== Attended (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=File:May_2008_RO_meeting_minutes.doc&diff=7196File:May 2008 RO meeting minutes.doc2008-06-02T01:43:06Z<p>Suzi: </p>
<hr />
<div></div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7195OntologyRelations2008-06-02T01:42:35Z<p>Suzi: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] hosted a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Minutes, Notes and Presentation ==<br />
* [[Media:May 2008 RO meeting minutes.doc]]<br />
* [[OntologyRelationsMay19MeetingNotes]]<br />
* [[Media:relations_for_representing_developmental_anatomy.ppt]]<br />
* [[Media:regulates.ppt]]<br />
* [[Media:overlaps.ppt]]<br />
* [[Media:RO-denver-cjm.ppt]]<br />
* [[Media:dahdul-ROmeeting.ppt]]<br />
* [[Media:Fabian developmental relations.pdf]]<br />
* [[Media:Fabian develops_from.pdf]]<br />
* [[Media:melissa development examples.ppt]]<br />
* [[Media:Homology.ppt]]<br />
* [[Media:Hunter Epistemic relations.ppt]]<br />
* [[Media:Ruttenberg-ro.pdf]]<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
=== Attended (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=7194OntologyRelations2008-06-02T01:42:15Z<p>Suzi: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] hosted a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Notes and Presentation ==<br />
* [[Media:May 2008 RO meeting minutes.doc]]<br />
* [[OntologyRelationsMay19MeetingNotes]]<br />
* [[Media:relations_for_representing_developmental_anatomy.ppt]]<br />
* [[Media:regulates.ppt]]<br />
* [[Media:overlaps.ppt]]<br />
* [[Media:RO-denver-cjm.ppt]]<br />
* [[Media:dahdul-ROmeeting.ppt]]<br />
* [[Media:Fabian developmental relations.pdf]]<br />
* [[Media:Fabian develops_from.pdf]]<br />
* [[Media:melissa development examples.ppt]]<br />
* [[Media:Homology.ppt]]<br />
* [[Media:Hunter Epistemic relations.ppt]]<br />
* [[Media:Ruttenberg-ro.pdf]]<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== 8:30-10:30am General (Barry/Chris/Mike) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]<br />
** desired level of granularity (Barry/Mike)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== 10:30am-10:45am: Coffee ===<br />
<br />
=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from <br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== 12:00 noon - 12:30: Lunch ===<br />
<br />
=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===<br />
<br />
* RCC8-can we reuse? (Chris)<br />
* surrounded_by (Chris)<br />
* overlaps - bone + joint use case (Peter)<br />
* connected_to and attached_to (Wasila)<br />
** bona fide vs fiat - when does it matter?<br />
** Example: axon tracts and neuropil (fiat)<br />
** Example: tooth attachment use case (bona fide)<br />
* spatial.obo (Wasila)<br />
<br />
=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
=== 5:30pm: Transportation to dinner ===<br />
<br />
== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==<br />
<br />
=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) === <br />
<br />
* homologous_to & evo_derives_from<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
<br />
=== 10:30am - noon Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== 12:30pm - 2pm Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== 2:15pm - 4pm Other issues, and follow ups === <br />
<br />
* the time issue. OWL representation (Alan)<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
=== Attended (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Vinay Chaudhri (SRI / Menlo Park, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (Phenoscape/NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (Phenoscape/ NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Karin Verspoor (host / Denver, CO)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]<br />
<br />
[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]<br />
<br />
White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6795OntologyRelations2008-04-17T00:31:19Z<p>Suzi: /* Biochemical (Mike B) */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:00AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== General (Barry/Chris) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
** desired level of granularity (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
== Agenda: 8:00AM-3:30PM Tuesday, May 20th 2008 ==<br />
<br />
=== Evolutionary (Melissa & Wasila) === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Larry / Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues === <br />
<br />
* FOL representations of RO (Thom & Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6794OntologyRelations2008-04-16T20:42:01Z<p>Suzi: /* Guidelines and Goals */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:<br />
** simple, with well-thought out definitions<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:00AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== General (Barry/Chris) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
** desired level of granularity (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
== Agenda: 8:00AM-3:30PM Tuesday, May 20th 2008 ==<br />
<br />
=== Evolutionary (Melissa & Wasila) === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues === <br />
<br />
* FOL representations of RO (Thom & Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6793OntologyRelations2008-04-16T20:36:08Z<p>Suzi: /* Guidelines and Goals */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* At the same time, we want to keep the RO small in size, using well-thought out definitions for each relation.<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:00AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== General (Barry/Chris) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
** desired level of granularity (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
== Agenda: 8:00AM-3:30PM Tuesday, May 20th 2008 ==<br />
<br />
=== Evolutionary (Melissa & Wasila) === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues === <br />
<br />
* FOL representations of RO (Thom & Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6792OntologyRelations2008-04-16T20:35:30Z<p>Suzi: /* Guidelines and Goals */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* At the same time, we want to keep the RO small in size, with well-thought out relations<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:00AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== General (Barry/Chris) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
** desired level of granularity (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
== Agenda: 8:00AM-3:30PM Tuesday, May 20th 2008 ==<br />
<br />
=== Evolutionary (Melissa & Wasila) === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues === <br />
<br />
* FOL representations of RO (Thom & Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Darren Natale (PRO / Georgetown, Washington, DC)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6787OntologyRelations2008-04-11T22:37:42Z<p>Suzi: /* Confirmed */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:00AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== General (Barry/Chris) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
** desired level of granularity (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
== Agenda: 8:00AM-3:30PM Tuesday, May 20th 2008 ==<br />
<br />
=== Evolutionary (Melissa & Wasila) === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues === <br />
<br />
* FOL representations of RO (Thom & Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed (alphabetically) ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6786OntologyRelations2008-04-11T22:37:12Z<p>Suzi: /* Confirmed */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:00AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== General (Barry/Chris) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
** desired level of granularity (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
== Agenda: 8:00AM-3:30PM Tuesday, May 20th 2008 ==<br />
<br />
=== Evolutionary (Melissa & Wasila) === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues === <br />
<br />
* FOL representations of RO (Thom & Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6785OntologyRelations2008-04-11T22:27:04Z<p>Suzi: /* Guidelines and Goals */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven, that is an instance-level definition must exist (see RO paper)<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:00AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== General (Barry/Chris) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
** desired level of granularity (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
== Agenda: 8:00AM-3:30PM Tuesday, May 20th 2008 ==<br />
<br />
=== Evolutionary (Melissa & Wasila) === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
* Molecular interactions and the PSI-MI relation(esque) terms. (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues === <br />
<br />
* FOL representations of RO (Thom & Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
# Mary Dolan (MGI / Bar Harbor, ME)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6777OntologyRelations2008-04-11T18:16:55Z<p>Suzi: /* Invited Participants */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:00AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== General (Barry/Chris) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
== Agenda: 8:00AM-3:30PM Tuesday, May 20th 2008 ==<br />
<br />
=== Evolutionary (Melissa & Wasila) === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues === <br />
<br />
* FOL representations of RO (Thom & Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Peter Midford (NESCent)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6776OntologyRelations2008-04-11T18:08:33Z<p>Suzi: /* Agenda: 8:00AM-3:30PM Tuesday, May 20th 2008 */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:00AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== General (Barry/Chris) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
== Agenda: 8:00AM-3:30PM Tuesday, May 20th 2008 ==<br />
<br />
=== Evolutionary (Melissa & Wasila) === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues === <br />
<br />
* FOL representations of RO (Thom & Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6775OntologyRelations2008-04-11T18:07:09Z<p>Suzi: /* Dates, Hours, and Logistics */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:00AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== General (Barry/Chris) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
== Agenda: 8:00AM-3:30PM Tuesday, May 20th 2008 ==<br />
<br />
=== Evolutionary === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues === <br />
<br />
* FOL representations of RO (Thom, Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Logistics ==<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6774OntologyRelations2008-04-11T18:06:36Z<p>Suzi: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:00AM-5:30PM Monday, May 19th 2008 ==<br />
<br />
=== General (Barry/Chris) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
== Agenda: 8:00AM-3:30PM Tuesday, May 20th 2008 ==<br />
<br />
=== Evolutionary === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues === <br />
<br />
* FOL representations of RO (Thom, Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Dates, Hours, and Logistics ==<br />
<br />
*'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6773OntologyRelations2008-04-11T18:05:35Z<p>Suzi: /* Agenda: Monday, May 19th 2008 */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: 8:00AM-5:30PM, Monday, May 19th 2008 ==<br />
<br />
=== General (Barry/Chris) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
== Agenda: Tuesday, May 20th 2008 ==<br />
<br />
=== Evolutionary === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues === <br />
<br />
* FOL representations of RO (Thom, Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Dates, Hours, and Logistics ==<br />
<br />
*'''Monday and Tuesday, May 19-20, 2008''' <br />
*'''Beginning at 8:00AM on Monday'''<br />
*'''Ending at 3:30PM on Tuesday'''<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6772OntologyRelations2008-04-11T18:04:37Z<p>Suzi: /* Logical/representation issues (breakout session?) */</p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: Monday, May 19th 2008 ==<br />
<br />
=== General (Barry/Chris) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
== Agenda: Tuesday, May 20th 2008 ==<br />
<br />
=== Evolutionary === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues === <br />
<br />
* FOL representations of RO (Thom, Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Dates, Hours, and Logistics ==<br />
<br />
*'''Monday and Tuesday, May 19-20, 2008''' <br />
*'''Beginning at 8:00AM on Monday'''<br />
*'''Ending at 3:30PM on Tuesday'''<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6771OntologyRelations2008-04-11T18:03:57Z<p>Suzi: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda: Monday, May 19th 2008 ==<br />
<br />
=== General (Barry/Chris) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== Development and anatomy (DavidOS) ===<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
== Agenda: Tuesday, May 20th 2008 ==<br />
<br />
=== Evolutionary === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues (breakout session?) === <br />
<br />
* FOL representations of RO (Thom, Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Dates, Hours, and Logistics ==<br />
<br />
*'''Monday and Tuesday, May 19-20, 2008''' <br />
*'''Beginning at 8:00AM on Monday'''<br />
*'''Ending at 3:30PM on Tuesday'''<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6770OntologyRelations2008-04-11T18:02:36Z<p>Suzi: </p>
<hr />
<div>'''Workshop on the Relationship Ontology'''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda == <br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
==== General (Barry/Chris) ==== <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
==== Development and anatomy (DavidOS) ====<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
=== Evolutionary === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues (breakout session?) === <br />
<br />
* FOL representations of RO (Thom, Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Dates, Hours, and Logistics ==<br />
<br />
*'''Monday and Tuesday, May 19-20, 2008''' <br />
*'''Beginning at 8:00AM on Monday'''<br />
*'''Ending at 3:30PM on Tuesday'''<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6769OntologyRelations2008-04-11T18:02:06Z<p>Suzi: </p>
<hr />
<div>''''Workshop on the Relationship Ontology''''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda == <br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
==== General (Barry/Chris) ==== <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
==== Development and anatomy (DavidOS) ====<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
=== Evolutionary === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues (breakout session?) === <br />
<br />
* FOL representations of RO (Thom, Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Dates, Hours, and Logistics ==<br />
<br />
*'''Monday and Tuesday, May 19-20, 2008''' <br />
*'''Beginning at 8:00AM on Monday'''<br />
*'''Ending at 3:30PM on Tuesday'''<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6768OntologyRelations2008-04-11T18:01:40Z<p>Suzi: </p>
<hr />
<div><h1>Workshop on the Relationship Ontology</h1><br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda == <br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
==== General (Barry/Chris) ==== <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
==== Development and anatomy (DavidOS) ====<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
=== Evolutionary === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues (breakout session?) === <br />
<br />
* FOL representations of RO (Thom, Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Dates, Hours, and Logistics ==<br />
<br />
*'''Monday and Tuesday, May 19-20, 2008''' <br />
*'''Beginning at 8:00AM on Monday'''<br />
*'''Ending at 3:30PM on Tuesday'''<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6767OntologyRelations2008-04-11T18:00:58Z<p>Suzi: </p>
<hr />
<div>''Workshop on the Relationship Ontology''<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda == <br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
==== General (Barry/Chris) ==== <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
==== Development and anatomy (DavidOS) ====<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
=== Evolutionary === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues (breakout session?) === <br />
<br />
* FOL representations of RO (Thom, Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Dates, Hours, and Logistics ==<br />
<br />
*'''Monday and Tuesday, May 19-20, 2008''' <br />
*'''Beginning at 8:00AM on Monday'''<br />
*'''Ending at 3:30PM on Tuesday'''<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6766OntologyRelations2008-04-11T18:00:39Z<p>Suzi: </p>
<hr />
<div>'Workshop on the Relationship Ontology'<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda == <br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
==== General (Barry/Chris) ==== <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
==== Development and anatomy (DavidOS) ====<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
=== Evolutionary === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues (breakout session?) === <br />
<br />
* FOL representations of RO (Thom, Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Dates, Hours, and Logistics ==<br />
<br />
*'''Monday and Tuesday, May 19-20, 2008''' <br />
*'''Beginning at 8:00AM on Monday'''<br />
*'''Ending at 3:30PM on Tuesday'''<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6765OntologyRelations2008-04-11T17:58:49Z<p>Suzi: /* Dates, Hours, and Logistics */</p>
<hr />
<div>= Workshop on the Relationship Ontology =<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda == <br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
==== General (Barry/Chris) ==== <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
==== Development and anatomy (DavidOS) ====<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
=== Evolutionary === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues (breakout session?) === <br />
<br />
* FOL representations of RO (Thom, Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Dates, Hours, and Logistics ==<br />
<br />
*'''Monday and Tuesday, May 19-20, 2008''' <br />
*'''Beginning at 8:00AM on Monday'''<br />
*'''Ending at 3:30PM on Tuesday'''<br />
<br />
* 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]. <br />
<br />
* Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
* 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].<br />
<br />
* 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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6764OntologyRelations2008-04-11T17:57:37Z<p>Suzi: </p>
<hr />
<div>= Workshop on the Relationship Ontology =<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== Agenda == <br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
==== General (Barry/Chris) ==== <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
==== Development and anatomy (DavidOS) ====<br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
=== Evolutionary === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues (breakout session?) === <br />
<br />
* FOL representations of RO (Thom, Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Dates, Hours, and Logistics ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
'''Beginning at 8:00AM on Monday'''<br />
'''Ending at 3:30PM on Tuesday'''<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
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]. <br />
<br />
Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
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].<br />
<br />
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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6763OntologyRelations2008-04-11T17:50:17Z<p>Suzi: </p>
<hr />
<div>= Workshop on the Relationship Ontology =<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
== Guidelines and Goals == <br />
<br />
* Our over-arching guiding principle is to keep the meeting biologist driven. This means that any logical theories discussed must be kept:<br />
** simple<br />
** example-driven<br />
** expressed in a clear, consistent symbol-free syntax<br />
<br />
* 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:<br />
** All outstanding items on the request tracking system are solved<br />
** All relations in ro_proposed are "blessed" and move into RO proper<br />
** A release of the cross-product (xp) files is generated<br />
** We will produce a new release of the RO<br />
<br />
== Preparation == <br />
<br />
* 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<br />
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd<br />
* 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<br />
<br />
== TOPICS == <br />
<br />
=== General (Barry/Chris) === <br />
<br />
* review of principles<br />
** all-some(time) (Barry)<br />
* review of website, tracker (Chris)<br />
** process for adding terms<br />
* review of current primary representation in .obo, .owl conversion (Chris)<br />
* ID policy (BFO), ontology lifecycle issues etc<br />
* cross-products<br />
<br />
=== Development and anatomy (DavidOS) === <br />
<br />
* stages and temporal relations<br />
** DavidOS/Fabian<br />
** Interval calculus<br />
** ZFA stages use case: start, end<br />
* develops_from (Melissa)<br />
* relations from CARO paper (Fabian)<br />
* review biological_process_xp_cell (Chris/MikeB)<br />
* replaced_by - endochondral bone replaces cartilege (Wasila)<br />
* agent_in - is it valid? "heart process" example - DavidH/Chris<br />
<br />
=== Biological qualities and phenotypes (Chris) ===<br />
<br />
* lacks_part (Werner)<br />
* inheres_in<br />
** relational qualities<br />
*** towards relation<br />
*** relational qualities and relations - what's the difference. lacks_part example<br />
* relations between qualities, comparisons and abnormality<br />
<br />
<br />
=== Spatial relations (Melissa/Suzi) ===<br />
<br />
* surrounded_by<br />
* overlaps - bone + joint use case (Melissa)<br />
* connected_to - axon tracts and neuropil (fiat binary)<br />
* attached_to - bone + bone use case (Melissa)<br />
* RCC8 - can we just import directly?<br />
* bona fide vs fiat - when does it matter<br />
* spatial.obo<br />
<br />
=== Regulation (David/Tanya/Chris) ===<br />
<br />
* regulates, +, -<br />
* composition of regulation relations<br />
* [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]<br />
<br />
=== Biochemical (Mike B) === <br />
<br />
* pathways (BioPAX-OBO, AlanR)<br />
* review bp_xp_chebi (Bada)<br />
<br />
=== Evolutionary === <br />
<br />
* homologous_to & evo_derives_from<br />
<br />
=== Epistemic (Larry) === <br />
<br />
* supported_by et al<br />
<br />
=== Logical/representation issues (breakout session?) === <br />
<br />
* FOL representations of RO (Thom, Fabian)<br />
* RO and BFO<br />
* OBO and OWL issues (Alan, Chris, Nigam)<br />
* instance vs type level; punning vs separate IDs<br />
* the time issue. OWL representation (Alan)<br />
* ternary relations in RO: DavidS's use case (DavidOS/Chris)<br />
* Erick's list of meta-relations<br />
* idiosyncratic relations in the FMA (Suzi/Nigam)<br />
<br />
== Draft Agenda ==<br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
8:30 Suzi Lewis: Logistics and protocols<br />
<br />
8:45 Introductions: why you attended, background and expertise<br />
<br />
9:00 Barry Smith (moderator): Discussion of methodology for creating new relations (e.g. some-part question)<br />
<br />
10:00 break<br />
<br />
10:30 (continued) Discussion of methodology for creating new relations (e.g. all-some question)<br />
<br />
11:30 Set priorities and ordering of the listed discussion topics. <br />
<br />
12:00 Lunch<br />
<br />
13:00 Discussion of topics<br />
<br />
15:00 break<br />
<br />
15:30 Discussion of topics<br />
<br />
17:30 Done for the day<br />
<br />
19:30 dinner<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
8:30 Discussion of topics<br />
<br />
10:30 break<br />
<br />
11:00 Discussion of topics<br />
<br />
12:00 lunch<br />
<br />
1:30 Discussion of topics<br />
<br />
2:30 Suzi Lewis: Summary of the meeting, action items, resolutions, and future plans.<br />
<br />
3:30 Departures<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
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]. <br />
<br />
Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
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].<br />
<br />
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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6756OntologyRelations2008-04-09T21:26:01Z<p>Suzi: /* Goals */</p>
<hr />
<div>== Workshop on the Relationship Ontology ==<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
The goals of this workshop are to develop the content of the relationship ontology. The agenda is still a work in progess, and topics discussed will depend on progress made in preliminary discussions which will be documented on this wiki. Possible areas for discussion are:<br />
<br />
# What new relationships should be added to the RO: [[RO:Main_Page | Current Proposals for new relations ]]<br />
## The relations that are required for anatomies and development (David O-S, Melissa H, Fabian N can you expand on this?)<br />
## The relations that are required for describing phenotypic data (Chris can you expand on this?)<br />
## The relations that are required for cross-products between anatomy and biological process<br />
## Idiosyncratic relationships in the FMA<br />
## The Larry Hunter "agent", or epistemic relations<br />
## The Larry Hunter & Mike Bada relationships to ChEBI<br />
# To consolidate the methodology for doing so<br />
<br />
== Draft Agenda ==<br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
8:30 Suzi Lewis: Logistics and protocols<br />
<br />
8:45 Introductions: why you attended, background and expertise<br />
<br />
9:00 Barry Smith (moderator): Discussion of methodology for creating new relations (e.g. some-part question)<br />
<br />
10:00 break<br />
<br />
10:30 (continued) Discussion of methodology for creating new relations (e.g. all-some question)<br />
<br />
11:30 Set priorities and ordering of the listed discussion topics. <br />
<br />
12:00 Lunch<br />
<br />
13:00 Discussion of topics<br />
<br />
15:00 break<br />
<br />
15:30 Discussion of topics<br />
<br />
17:30 Done for the day<br />
<br />
19:30 dinner<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
8:30 Discussion of topics<br />
<br />
10:30 break<br />
<br />
11:00 Discussion of topics<br />
<br />
12:00 lunch<br />
<br />
1:30 Discussion of topics<br />
<br />
2:30 Suzi Lewis: Summary of the meeting, action items, resolutions, and future plans.<br />
<br />
3:30 Departures<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
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]. <br />
<br />
Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
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].<br />
<br />
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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6754OntologyRelations2008-04-07T19:28:56Z<p>Suzi: /* Invited */</p>
<hr />
<div>== Workshop on the Relationship Ontology ==<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
The goals of this workshop are to develop the content of the relationship ontology. The agenda is still a work in progess, and topics discussed will depend on progress made in preliminary discussions which will be documented on this wiki. Possible areas for discussion are:<br />
<br />
# What new relationships should be added to the RO: [[RO:Main_Page | Current Proposals for new relations ]]<br />
## The relations that are required for anatomies and development (David O-S, Melissa H, Fabian N can you expand on this?)<br />
## The relations that are required for describing phenotypic data (Chris can you expand on this?)<br />
## The relations that are required for cross-products between anatomy and biological process<br />
## Idiosyncratic relationships in the FMA<br />
#* The Larry Hunter "agent", or epistemic relations<br />
## The Larry Hunter & Mike Bada relationships to ChEBI<br />
# To consolidate the methodology for doing so<br />
<br />
== Draft Agenda ==<br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
8:30 Suzi Lewis: Logistics and protocols<br />
<br />
8:45 Introductions: why you attended, background and expertise<br />
<br />
9:00 Barry Smith (moderator): Discussion of methodology for creating new relations (e.g. some-part question)<br />
<br />
10:00 break<br />
<br />
10:30 (continued) Discussion of methodology for creating new relations (e.g. all-some question)<br />
<br />
11:30 Set priorities and ordering of the listed discussion topics. <br />
<br />
12:00 Lunch<br />
<br />
13:00 Discussion of topics<br />
<br />
15:00 break<br />
<br />
15:30 Discussion of topics<br />
<br />
17:30 Done for the day<br />
<br />
19:30 dinner<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
8:30 Discussion of topics<br />
<br />
10:30 break<br />
<br />
11:00 Discussion of topics<br />
<br />
12:00 lunch<br />
<br />
1:30 Discussion of topics<br />
<br />
2:30 Suzi Lewis: Summary of the meeting, action items, resolutions, and future plans.<br />
<br />
3:30 Departures<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
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]. <br />
<br />
Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
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].<br />
<br />
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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6753OntologyRelations2008-04-07T19:28:33Z<p>Suzi: /* Confirmed */</p>
<hr />
<div>== Workshop on the Relationship Ontology ==<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
The goals of this workshop are to develop the content of the relationship ontology. The agenda is still a work in progess, and topics discussed will depend on progress made in preliminary discussions which will be documented on this wiki. Possible areas for discussion are:<br />
<br />
# What new relationships should be added to the RO: [[RO:Main_Page | Current Proposals for new relations ]]<br />
## The relations that are required for anatomies and development (David O-S, Melissa H, Fabian N can you expand on this?)<br />
## The relations that are required for describing phenotypic data (Chris can you expand on this?)<br />
## The relations that are required for cross-products between anatomy and biological process<br />
## Idiosyncratic relationships in the FMA<br />
#* The Larry Hunter "agent", or epistemic relations<br />
## The Larry Hunter & Mike Bada relationships to ChEBI<br />
# To consolidate the methodology for doing so<br />
<br />
== Draft Agenda ==<br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
8:30 Suzi Lewis: Logistics and protocols<br />
<br />
8:45 Introductions: why you attended, background and expertise<br />
<br />
9:00 Barry Smith (moderator): Discussion of methodology for creating new relations (e.g. some-part question)<br />
<br />
10:00 break<br />
<br />
10:30 (continued) Discussion of methodology for creating new relations (e.g. all-some question)<br />
<br />
11:30 Set priorities and ordering of the listed discussion topics. <br />
<br />
12:00 Lunch<br />
<br />
13:00 Discussion of topics<br />
<br />
15:00 break<br />
<br />
15:30 Discussion of topics<br />
<br />
17:30 Done for the day<br />
<br />
19:30 dinner<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
8:30 Discussion of topics<br />
<br />
10:30 break<br />
<br />
11:00 Discussion of topics<br />
<br />
12:00 lunch<br />
<br />
1:30 Discussion of topics<br />
<br />
2:30 Suzi Lewis: Summary of the meeting, action items, resolutions, and future plans.<br />
<br />
3:30 Departures<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
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]. <br />
<br />
Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
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].<br />
<br />
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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Tanya Berardini (TAIR / Stanford, CA)<br />
# Bill Bug (BIRN / San Diego, CA)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Wasila Dahdul (NESCENT)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGD / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
# Judith Blake (JAX / Bar Harbor, ME)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6716OntologyRelations2008-03-31T01:01:33Z<p>Suzi: /* Goals */</p>
<hr />
<div>== Workshop on the Relationship Ontology ==<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
The goals of this workshop are to develop the content of the relationship ontology. In particular we will discuss these areas:<br />
<br />
# To add new relationships to RO: [[RO:Main_Page | Current Proposals for new relations ]]<br />
## The relations that are required for anatomies and development (David O-S, Melissa H, Fabian N)<br />
## The relations that are required for describing phenotypic data (Chris can you expand on this?)<br />
## The relations that are required for cross-products between anatomy and biological process<br />
## Idiosyncratic relationships in the FMA<br />
#* The Larry Hunter "agent", or epistemic relations<br />
## The Larry Hunter & Mike Bada relationships to ChEBI<br />
# To consolidate the methodology for doing so<br />
<br />
== Draft Agenda ==<br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
8:30 Suzi Lewis: Logistics and protocols<br />
<br />
8:45 Introductions: why you attended, background and expertise<br />
<br />
9:00 Barry Smith (moderator): Discussion of methodology for creating new relations (e.g. some-part question)<br />
<br />
10:00 break<br />
<br />
10:30 (continued) Discussion of methodology for creating new relations (e.g. all-some question)<br />
<br />
11:30 Set priorities and ordering of the listed discussion topics. <br />
<br />
12:00 Lunch<br />
<br />
13:00 Discussion of topics<br />
<br />
15:00 break<br />
<br />
15:30 Discussion of topics<br />
<br />
17:30 Done for the day<br />
<br />
19:30 dinner<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
8:30 Discussion of topics<br />
<br />
10:30 break<br />
<br />
11:00 Discussion of topics<br />
<br />
12:00 lunch<br />
<br />
1:30 Discussion of topics<br />
<br />
2:30 Suzi Lewis: Summary of the meeting, action items, resolutions, and future plans.<br />
<br />
3:30 Departures<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
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]. <br />
<br />
Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
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].<br />
<br />
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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
# Judith Blake (JAX / Bar Harbor, ME)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6676OntologyRelations2008-03-25T17:45:09Z<p>Suzi: /* Goals */</p>
<hr />
<div>== Workshop on the Relationship Ontology ==<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
The goals of this workshop are to develop the content of the relationship ontology. In particular we will discuss these areas:<br />
<br />
# To add new relationships to RO: [[RO:Main_Page | Current Proposals for new relations ]]<br />
#* The Larry Hunter "agent", or epistemic relations<br />
#* The Larry Hunter & Mike Bada relationships to ChEBI<br />
#* The relations that are required for anatomies and development (David O-S, Melissa H, Fabian N)<br />
#* The relations that are required for describing phenotypic data (Chris can you expand on this?)<br />
#* The relations that are required for cross-products between anatomy and biological process<br />
#* Idiosyncratic relationships in the FMA<br />
# To consolidate the methodology for doing so<br />
<br />
== Draft Agenda ==<br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
8:30 Suzi Lewis: Logistics and protocols<br />
<br />
8:45 Introductions: why you attended, background and expertise<br />
<br />
9:00 Barry Smith (moderator): Discussion of methodology for creating new relations (e.g. some-part question)<br />
<br />
10:00 break<br />
<br />
10:30 (continued) Discussion of methodology for creating new relations (e.g. some-part question)<br />
<br />
11:30 Set priorities and ordering of the listed discussion topics. <br />
<br />
12:00 Lunch<br />
<br />
13:00 Discussion of topics<br />
<br />
15:00 break<br />
<br />
15:30 Discussion of topics<br />
<br />
17:30 Done for the day<br />
<br />
19:30 dinner<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
8:30 Discussion of topics<br />
<br />
10:30 break<br />
<br />
11:00 Discussion of topics<br />
<br />
12:00 lunch<br />
<br />
1:30 Discussion of topics<br />
<br />
2:30 Suzi Lewis: Summary of the meeting, action items, resolutions, and future plans.<br />
<br />
3:30 Departures<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
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]. <br />
<br />
Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
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].<br />
<br />
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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
# Judith Blake (JAX / Bar Harbor, ME)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6675OntologyRelations2008-03-25T17:40:36Z<p>Suzi: </p>
<hr />
<div>== Workshop on the Relationship Ontology ==<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
The goals of this workshop are to develop the content of the relationship ontology. In particular we will discuss these areas:<br />
<br />
# To add new relationships to RO: [[RO:Main_Page | Current Proposals for new relations ]]<br />
#* The Larry Hunter "agent", or epistemic relations<br />
#* The Larry Hunter & Mike Bada relationships to ChEBI<br />
#* The relations that are required for anatomies and development (David O-S, Melissa H, Fabian N)<br />
#* The relations that are required for describing phenotypic data (Chris can you expand on this?)<br />
#* The relations that are required for cross-products between anatomy and biological process<br />
# To consolidate the methodology for doing so<br />
<br />
== Draft Agenda ==<br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
8:30 Suzi Lewis: Logistics and protocols<br />
<br />
8:45 Introductions: why you attended, background and expertise<br />
<br />
9:00 Barry Smith (moderator): Discussion of methodology for creating new relations (e.g. some-part question)<br />
<br />
10:00 break<br />
<br />
10:30 (continued) Discussion of methodology for creating new relations (e.g. some-part question)<br />
<br />
11:30 Set priorities and ordering of the listed discussion topics. <br />
<br />
12:00 Lunch<br />
<br />
13:00 Discussion of topics<br />
<br />
15:00 break<br />
<br />
15:30 Discussion of topics<br />
<br />
17:30 Done for the day<br />
<br />
19:30 dinner<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
8:30 Discussion of topics<br />
<br />
10:30 break<br />
<br />
11:00 Discussion of topics<br />
<br />
12:00 lunch<br />
<br />
1:30 Discussion of topics<br />
<br />
2:30 Suzi Lewis: Summary of the meeting, action items, resolutions, and future plans.<br />
<br />
3:30 Departures<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
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]. <br />
<br />
Fly in to the [http://www.flydenver.com/ Denver International Airport].<br />
<br />
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].<br />
<br />
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.<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Werner Ceusters (ORG / Buffalo, NY)<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# Chris Mungall (Flybase / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Washington, DC)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Nigam Shah (NCBO / Stanford, CA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (ORG / Buffalo, NY)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
# Judith Blake (JAX / Bar Harbor, ME)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=Phenote:Main_Page&diff=6444Phenote:Main Page2008-01-21T21:22:48Z<p>Suzi: /* ProtocolEditor and matrix view for BIRN */</p>
<hr />
<div>==Phenote - A biomedical annotation tool using ontologies==<br />
<br />
This wiki page currently serves as the public Phenote project page for posting of materials related to its development. In particular, this will be the site used for announcement and posting of working group agendas and reports/transcripts.<br />
<br />
=== What is Phenote? ===<br />
<br />
Phenote is a software application and open-source toolkit to facilitate annotation of biomedical data using ontologies. It is being driven by its development as a phenotype annotation tool, but is generalizable to any tool to be used for annotation using ontologies.<br />
<br />
This is being developed by the [http://berkeleybop.org Core 2] group with the [http://www.bioontology.org National Center for Biomedical Ontology.]<br />
<br />
For more information, please visit the website at [http://www.phenote.org phenote.org]<br />
<br />
=== Who should be interested in Phenote? ===<br />
<br />
Anyone doing annotation using ontologies. Specifically, anyone doing phenotype annotation such as biocurators affiliated with model organism databases, biological/medical image analysts and ontology developers.<br />
<br />
===Request tracker===<br />
<br />
You can use the tracker (currently hosted on sourceforge) to request new items or suggest modifications<br />
<br />
* [https://sourceforge.net/tracker/?group_id=76834&atid=887913 Phenote Request tracker on sourceforge]<br />
<br />
===Mailing List===<br />
<br />
The OBO Phenote list is for discussion of Phenote software, announcements, etc.<br />
<br />
You can subscribe or browse the archives here:<br />
<br />
* [https://lists.sourceforge.net/lists/listinfo/obo-phenote OBO-Phenote Mail List]<br />
<br />
===Phenote Developers Group===<br />
The Phenote Developers Group has regularly scheduled meetings on the ''second and fourth Tuesdays of each month, 10:30am (Pacific time)''. If you are currently developing Phenote code or are interested in contributing, please join us for our next meeting on '''Tuesday, August 14th, 2007'''. These will be conducted by phone by dialing in to 877.208.9784. Please shoot me an email for the passcode.<br />
<br />
===Phenote Working Group===<br />
The Phenote User group has a regularly scheduled meeting on the ''first Thursday of each month, 8:30am (Pacific time)''. Please join us for our next chat on '''Thursday, February 7, 2008'''. These will be conducted by WebEx, although an occasional live telephone conference might be in order.<br />
<br />
The goals of the Phenote Users Group are to:<br />
# drive the development of the software by prioritizing features<br />
# test new beta releases; reporting, and prioritizing bug fixes<br />
# sign off on new releases for the general public<br />
# contributing to documentation<br />
<br />
====Joining the Working Group WebEx Chat====<br />
Webex Instructions:<br />
<br />
Topic: NCBO: Monthly Phenote Users Meeting<br />
Date: The 1st Thursday of every 1 month<br />
Time: 8:30 am, Pacific Daylight Time (GMT -07:00, San Francisco)<br />
Meeting Number: 926 281 546<br />
Meeting Password: phenote<br />
-------------------------------------------------------<br />
To join the online meeting<br />
-------------------------------------------------------<br />
1. Go to https://stanford.webex.com/stanford/j.php?ED=96176737&UID=1007605127&PW=c0245958041d0b180e<br />
2. Enter your name and email address.<br />
3. Enter the meeting password: phenote<br />
4. Click "Join Now".<br />
<br />
*If you have never run Webex on your computer or it has been a while since you have, I suggest clicking the link below to run any necessary software updates well ahead of the meeting time: https://stanford.webex.com/stanford/meetingcenter/mcsetup.php <br />
<br />
<br />
*Other meetings: To join in the IRC chat, you will need to use an [http://www.phenote/org/irc_clients.shtml IRC client] and join the irc.sf.net #phenote channel. Alternatively, you can utilize the Phenote IRC applet through your browser by visiting [http://www.phenote.org/irc_chat http://www.phenote.org/irc_chat]. Please visit this webpage for further instructions.<br />
<br />
====Members====<br />
A dedicated group of users are part of this evaluation team. They include:<br />
<br />
*NCBO: Mark Gibson, Nicole Washington (Developers); Lawrence Berkeley National Labs<br />
*Flybase: Michael Ashburner, David Sutherland; University of Cambridge<br />
*Zfin: Amy Singer, Yvonne Bradford, Melissa Haendel; University of Oregon<br />
*Neuroscholar: Gully Burns; USC<br />
*NESCent: Jim Balhoff, Hilmar Lapp; Duke University<br />
*BIRN: Maryann Martone; UCSD<br />
*Wormbase: Karen Yook, Gary S; CalTech<br />
*Xenbase: Erik Segerdell; University of Calgary<br />
*OME: Will Moore; University of Dundee<br />
<br />
If you'd like to join this group, please add yourself to this list and contact [[mailto:NLWashington@lbl.gov Nicole Washington]]<br />
<br />
Most communications for this group (including announcements of upcoming meetings) will be conducted on the obo-phenote mailing list.<br />
<br />
====Phenote:Agendas & Transcripts====<br />
* [[Phenote:Agenda: October 2, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_webex_100207.html Transcripts]]<br />
<br />
* [[Phenote:Agenda: August 7, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_080707.html Transcripts]]<br />
<br />
* [[Phenote:Minutes: July 3, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_070307.html Transcripts]]<br />
<br />
* [[Phenote:Minutes: June 5, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_060507.html Transcripts]]<br />
<br />
* [[Phenote:Minutes: May 1, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_050107.html Transcripts]]<br />
<br />
* [[Phenote:Minutes: April 10, 2007]] - inaugural meeting<br />
<br />
===Sandbox===<br />
<br />
*Annotation Standards: A collection for OMIM annotation. [[OMIM Annotation Standards]]<br />
*Annotation Standards: A collection from various phenotype annotation resources [[MOD Phenotype Annotation Standards]]<br />
<br />
===ProtocolEditor and matrix view for BIRN===<br />
We are currently collaborating with Will Moore at the OME at Dundee, Scotland on integrating his ProtocolEditor with Phenote.<br />
Here is a nice video of his protocol editor:<br />
<br />
http://users.openmicroscopy.org.uk/~ola/720x540/OMERO.ProtocolEditor-new-omero-movie.mov<br />
<br />
The idea is that one defines "Observables" in the ProtocolEditor in addition to everything about the experiment. The observables will be items one wants to record using Phenote. Some examples (from a non-biologist) might be:<br />
<br />
PE: Dendrite length in microns, Phenote: user enters integer or float<br />
<br />
PE: Brain-cell color, Phenote: user enters from drop down list of colors from pato<br />
<br />
PE: Dendrite shape warped, Phenote: user checks true/false checkbox<br />
<br />
To generalize there are 3 different types of Observables, all require an Entity:<br />
# A measurement of an Entity (including units), value to be recorded by entering it in Phenote<br />
# An attribute of an Entity, value to be recorded by selecting from a pick list in Phenote<br />
# The presence of a certain quality/value, to be recorded in Phenote by a checkbox (true/false) <br />
<br />
For #2, a pato attribute, all of the values below the attribute will be available as a pick list, so color would show all of the color values listed in pato.<br />
<br />
In the matrix view the column headings would be each of the Observables defined beforehand in the PE. A row would be something you were making these statements about, like an image (with an image ID). So a row of the matrix would then contain multiple phenotype statements, capturing all of the phenotype information you want to make about a particular image. The matrix allows you to rapidly go through and characterize images, and allows you to see in one line all the data for an image.<br />
<br />
You can still view the traditional table view of 1 row per phenotypic assertion (with image ID repeated). In this view one can add more information about a particular phenotype, like free text description and such. It should also be possible to add additional Phentoypes that are observed for any image, using one row per Phenotype as usual. Upon returning to the matrix view, these could be displayed in "Additional Phenotype" columns (EQ column pairs - an additional pair of columns for each additional Phenotype), thereby maintaining one image per row.<br />
<br />
Another question is how would BIRN like to take advantage of the protocol editor & matrix. <br />
Would this be helpful for literature curation?<br />
Can this be utilized in the context of Smart Atlas? or JINX?<br />
Or would this be used as an experiment/image annotation tool in its own right?</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=Phenote:Main_Page&diff=6443Phenote:Main Page2008-01-21T21:21:59Z<p>Suzi: /* ProtocolEditor and matrix view for BIRN */</p>
<hr />
<div>==Phenote - A biomedical annotation tool using ontologies==<br />
<br />
This wiki page currently serves as the public Phenote project page for posting of materials related to its development. In particular, this will be the site used for announcement and posting of working group agendas and reports/transcripts.<br />
<br />
=== What is Phenote? ===<br />
<br />
Phenote is a software application and open-source toolkit to facilitate annotation of biomedical data using ontologies. It is being driven by its development as a phenotype annotation tool, but is generalizable to any tool to be used for annotation using ontologies.<br />
<br />
This is being developed by the [http://berkeleybop.org Core 2] group with the [http://www.bioontology.org National Center for Biomedical Ontology.]<br />
<br />
For more information, please visit the website at [http://www.phenote.org phenote.org]<br />
<br />
=== Who should be interested in Phenote? ===<br />
<br />
Anyone doing annotation using ontologies. Specifically, anyone doing phenotype annotation such as biocurators affiliated with model organism databases, biological/medical image analysts and ontology developers.<br />
<br />
===Request tracker===<br />
<br />
You can use the tracker (currently hosted on sourceforge) to request new items or suggest modifications<br />
<br />
* [https://sourceforge.net/tracker/?group_id=76834&atid=887913 Phenote Request tracker on sourceforge]<br />
<br />
===Mailing List===<br />
<br />
The OBO Phenote list is for discussion of Phenote software, announcements, etc.<br />
<br />
You can subscribe or browse the archives here:<br />
<br />
* [https://lists.sourceforge.net/lists/listinfo/obo-phenote OBO-Phenote Mail List]<br />
<br />
===Phenote Developers Group===<br />
The Phenote Developers Group has regularly scheduled meetings on the ''second and fourth Tuesdays of each month, 10:30am (Pacific time)''. If you are currently developing Phenote code or are interested in contributing, please join us for our next meeting on '''Tuesday, August 14th, 2007'''. These will be conducted by phone by dialing in to 877.208.9784. Please shoot me an email for the passcode.<br />
<br />
===Phenote Working Group===<br />
The Phenote User group has a regularly scheduled meeting on the ''first Thursday of each month, 8:30am (Pacific time)''. Please join us for our next chat on '''Thursday, February 7, 2008'''. These will be conducted by WebEx, although an occasional live telephone conference might be in order.<br />
<br />
The goals of the Phenote Users Group are to:<br />
# drive the development of the software by prioritizing features<br />
# test new beta releases; reporting, and prioritizing bug fixes<br />
# sign off on new releases for the general public<br />
# contributing to documentation<br />
<br />
====Joining the Working Group WebEx Chat====<br />
Webex Instructions:<br />
<br />
Topic: NCBO: Monthly Phenote Users Meeting<br />
Date: The 1st Thursday of every 1 month<br />
Time: 8:30 am, Pacific Daylight Time (GMT -07:00, San Francisco)<br />
Meeting Number: 926 281 546<br />
Meeting Password: phenote<br />
-------------------------------------------------------<br />
To join the online meeting<br />
-------------------------------------------------------<br />
1. Go to https://stanford.webex.com/stanford/j.php?ED=96176737&UID=1007605127&PW=c0245958041d0b180e<br />
2. Enter your name and email address.<br />
3. Enter the meeting password: phenote<br />
4. Click "Join Now".<br />
<br />
*If you have never run Webex on your computer or it has been a while since you have, I suggest clicking the link below to run any necessary software updates well ahead of the meeting time: https://stanford.webex.com/stanford/meetingcenter/mcsetup.php <br />
<br />
<br />
*Other meetings: To join in the IRC chat, you will need to use an [http://www.phenote/org/irc_clients.shtml IRC client] and join the irc.sf.net #phenote channel. Alternatively, you can utilize the Phenote IRC applet through your browser by visiting [http://www.phenote.org/irc_chat http://www.phenote.org/irc_chat]. Please visit this webpage for further instructions.<br />
<br />
====Members====<br />
A dedicated group of users are part of this evaluation team. They include:<br />
<br />
*NCBO: Mark Gibson, Nicole Washington (Developers); Lawrence Berkeley National Labs<br />
*Flybase: Michael Ashburner, David Sutherland; University of Cambridge<br />
*Zfin: Amy Singer, Yvonne Bradford, Melissa Haendel; University of Oregon<br />
*Neuroscholar: Gully Burns; USC<br />
*NESCent: Jim Balhoff, Hilmar Lapp; Duke University<br />
*BIRN: Maryann Martone; UCSD<br />
*Wormbase: Karen Yook, Gary S; CalTech<br />
*Xenbase: Erik Segerdell; University of Calgary<br />
*OME: Will Moore; University of Dundee<br />
<br />
If you'd like to join this group, please add yourself to this list and contact [[mailto:NLWashington@lbl.gov Nicole Washington]]<br />
<br />
Most communications for this group (including announcements of upcoming meetings) will be conducted on the obo-phenote mailing list.<br />
<br />
====Phenote:Agendas & Transcripts====<br />
* [[Phenote:Agenda: October 2, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_webex_100207.html Transcripts]]<br />
<br />
* [[Phenote:Agenda: August 7, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_080707.html Transcripts]]<br />
<br />
* [[Phenote:Minutes: July 3, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_070307.html Transcripts]]<br />
<br />
* [[Phenote:Minutes: June 5, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_060507.html Transcripts]]<br />
<br />
* [[Phenote:Minutes: May 1, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_050107.html Transcripts]]<br />
<br />
* [[Phenote:Minutes: April 10, 2007]] - inaugural meeting<br />
<br />
===Sandbox===<br />
<br />
*Annotation Standards: A collection for OMIM annotation. [[OMIM Annotation Standards]]<br />
*Annotation Standards: A collection from various phenotype annotation resources [[MOD Phenotype Annotation Standards]]<br />
<br />
===ProtocolEditor and matrix view for BIRN===<br />
We are currently collaborating with Will Moore at the OME at Dundee, Scotland on integrating his ProtocolEditor with Phenote.<br />
Here is a nice video of his protocol editor:<br />
<br />
http://users.openmicroscopy.org.uk/~ola/720x540/OMERO.ProtocolEditor-new-omero-movie.mov<br />
<br />
The idea is that one defines "Observables" in the ProtocolEditor in addition to everything about the experiment. The observables will be items one wants to record using Phenote. Some examples (from a non-biologist) might be:<br />
<br />
PE: Dendrite length in microns, Phenote: user enters integer or float<br />
PE: Brain-cell color, Phenote: user enters from drop down list of colors from pato<br />
PE: Dendrite shape warped, Phenote: user checks true/false checkbox<br />
<br />
To generalize there are 3 different types of Observables, all require an Entity:<br />
# A measurement of an Entity (including units), value to be recorded by entering it in Phenote<br />
# An attribute of an Entity, value to be recorded by selecting from a pick list in Phenote<br />
# The presence of a certain quality/value, to be recorded in Phenote by a checkbox (true/false) <br />
<br />
For #2, a pato attribute, all of the values below the attribute will be available as a pick list, so color would show all of the color values listed in pato.<br />
<br />
In the matrix view the column headings would be each of the Observables defined beforehand in the PE. A row would be something you were making these statements about, like an image (with an image ID). So a row of the matrix would then contain multiple phenotype statements, capturing all of the phenotype information you want to make about a particular image. The matrix allows you to rapidly go through and characterize images, and allows you to see in one line all the data for an image.<br />
<br />
You can still view the traditional table view of 1 row per phenotypic assertion (with image ID repeated). In this view one can add more information about a particular phenotype, like free text description and such. It should also be possible to add additional Phentoypes that are observed for any image, using one row per Phenotype as usual. Upon returning to the matrix view, these could be displayed in "Additional Phenotype" columns (EQ column pairs - an additional pair of columns for each additional Phenotype), thereby maintaining one image per row.<br />
<br />
Another question is how would BIRN like to take advantage of the protocol editor & matrix. <br />
Would this be helpful for literature curation?<br />
Can this be utilized in the context of Smart Atlas? or JINX?<br />
Or would this be used as an experiment/image annotation tool in its own right?</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=Phenote:Main_Page&diff=6442Phenote:Main Page2008-01-21T21:21:34Z<p>Suzi: /* ProtocolEditor and matrix view for BIRN */</p>
<hr />
<div>==Phenote - A biomedical annotation tool using ontologies==<br />
<br />
This wiki page currently serves as the public Phenote project page for posting of materials related to its development. In particular, this will be the site used for announcement and posting of working group agendas and reports/transcripts.<br />
<br />
=== What is Phenote? ===<br />
<br />
Phenote is a software application and open-source toolkit to facilitate annotation of biomedical data using ontologies. It is being driven by its development as a phenotype annotation tool, but is generalizable to any tool to be used for annotation using ontologies.<br />
<br />
This is being developed by the [http://berkeleybop.org Core 2] group with the [http://www.bioontology.org National Center for Biomedical Ontology.]<br />
<br />
For more information, please visit the website at [http://www.phenote.org phenote.org]<br />
<br />
=== Who should be interested in Phenote? ===<br />
<br />
Anyone doing annotation using ontologies. Specifically, anyone doing phenotype annotation such as biocurators affiliated with model organism databases, biological/medical image analysts and ontology developers.<br />
<br />
===Request tracker===<br />
<br />
You can use the tracker (currently hosted on sourceforge) to request new items or suggest modifications<br />
<br />
* [https://sourceforge.net/tracker/?group_id=76834&atid=887913 Phenote Request tracker on sourceforge]<br />
<br />
===Mailing List===<br />
<br />
The OBO Phenote list is for discussion of Phenote software, announcements, etc.<br />
<br />
You can subscribe or browse the archives here:<br />
<br />
* [https://lists.sourceforge.net/lists/listinfo/obo-phenote OBO-Phenote Mail List]<br />
<br />
===Phenote Developers Group===<br />
The Phenote Developers Group has regularly scheduled meetings on the ''second and fourth Tuesdays of each month, 10:30am (Pacific time)''. If you are currently developing Phenote code or are interested in contributing, please join us for our next meeting on '''Tuesday, August 14th, 2007'''. These will be conducted by phone by dialing in to 877.208.9784. Please shoot me an email for the passcode.<br />
<br />
===Phenote Working Group===<br />
The Phenote User group has a regularly scheduled meeting on the ''first Thursday of each month, 8:30am (Pacific time)''. Please join us for our next chat on '''Thursday, February 7, 2008'''. These will be conducted by WebEx, although an occasional live telephone conference might be in order.<br />
<br />
The goals of the Phenote Users Group are to:<br />
# drive the development of the software by prioritizing features<br />
# test new beta releases; reporting, and prioritizing bug fixes<br />
# sign off on new releases for the general public<br />
# contributing to documentation<br />
<br />
====Joining the Working Group WebEx Chat====<br />
Webex Instructions:<br />
<br />
Topic: NCBO: Monthly Phenote Users Meeting<br />
Date: The 1st Thursday of every 1 month<br />
Time: 8:30 am, Pacific Daylight Time (GMT -07:00, San Francisco)<br />
Meeting Number: 926 281 546<br />
Meeting Password: phenote<br />
-------------------------------------------------------<br />
To join the online meeting<br />
-------------------------------------------------------<br />
1. Go to https://stanford.webex.com/stanford/j.php?ED=96176737&UID=1007605127&PW=c0245958041d0b180e<br />
2. Enter your name and email address.<br />
3. Enter the meeting password: phenote<br />
4. Click "Join Now".<br />
<br />
*If you have never run Webex on your computer or it has been a while since you have, I suggest clicking the link below to run any necessary software updates well ahead of the meeting time: https://stanford.webex.com/stanford/meetingcenter/mcsetup.php <br />
<br />
<br />
*Other meetings: To join in the IRC chat, you will need to use an [http://www.phenote/org/irc_clients.shtml IRC client] and join the irc.sf.net #phenote channel. Alternatively, you can utilize the Phenote IRC applet through your browser by visiting [http://www.phenote.org/irc_chat http://www.phenote.org/irc_chat]. Please visit this webpage for further instructions.<br />
<br />
====Members====<br />
A dedicated group of users are part of this evaluation team. They include:<br />
<br />
*NCBO: Mark Gibson, Nicole Washington (Developers); Lawrence Berkeley National Labs<br />
*Flybase: Michael Ashburner, David Sutherland; University of Cambridge<br />
*Zfin: Amy Singer, Yvonne Bradford, Melissa Haendel; University of Oregon<br />
*Neuroscholar: Gully Burns; USC<br />
*NESCent: Jim Balhoff, Hilmar Lapp; Duke University<br />
*BIRN: Maryann Martone; UCSD<br />
*Wormbase: Karen Yook, Gary S; CalTech<br />
*Xenbase: Erik Segerdell; University of Calgary<br />
*OME: Will Moore; University of Dundee<br />
<br />
If you'd like to join this group, please add yourself to this list and contact [[mailto:NLWashington@lbl.gov Nicole Washington]]<br />
<br />
Most communications for this group (including announcements of upcoming meetings) will be conducted on the obo-phenote mailing list.<br />
<br />
====Phenote:Agendas & Transcripts====<br />
* [[Phenote:Agenda: October 2, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_webex_100207.html Transcripts]]<br />
<br />
* [[Phenote:Agenda: August 7, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_080707.html Transcripts]]<br />
<br />
* [[Phenote:Minutes: July 3, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_070307.html Transcripts]]<br />
<br />
* [[Phenote:Minutes: June 5, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_060507.html Transcripts]]<br />
<br />
* [[Phenote:Minutes: May 1, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_050107.html Transcripts]]<br />
<br />
* [[Phenote:Minutes: April 10, 2007]] - inaugural meeting<br />
<br />
===Sandbox===<br />
<br />
*Annotation Standards: A collection for OMIM annotation. [[OMIM Annotation Standards]]<br />
*Annotation Standards: A collection from various phenotype annotation resources [[MOD Phenotype Annotation Standards]]<br />
<br />
===ProtocolEditor and matrix view for BIRN===<br />
We are currently collaborating with Will Moore at the OME at Dundee, Scotland on integrating his ProtocolEditor with Phenote.<br />
Here is a nice video of his protocol editor:<br />
<br />
http://users.openmicroscopy.org.uk/~ola/720x540/OMERO.ProtocolEditor-new-omero-movie.mov<br />
<br />
The idea is that one defines "Observables" in the ProtocolEditor in addition to everything about the experiment. The observables will be items one wants to record using Phenote. Some examples (from a non-biologist) might be:<br />
<br />
PE: Dendrite length in microns, Phenote: user enters integer or float<br />
PE: Brain-cell color, Phenote: user enters from drop down list of colors from pato<br />
PE: Dendrite shape warped, Phenote: user checks true/false checkbox<br />
<br />
To generalize there are 3 different types of Observables, all require an Entity:<br />
# A measurement of an Entity (including units), value to be recorded by entering it in Phenote<br />
# An attribute of an Entity, value to be recorded by selecting from a pick list in Phenote<br />
# The precense of a certain quality/value, to be recorded in Phenote by a checkbox (true/false) <br />
<br />
For #2, a pato attribute, all of the values below the attribute will be available as a pick list, so color would show all of the color values listed in pato.<br />
<br />
In the matrix view the column headings would be each of the Observables defined beforehand in the PE. A row would be something you were making these statements about, like an image (with an image ID). So a row of the matrix would then contain multiple phenotype statements, capturing all of the phenotype information you want to make about a particular image. The matrix allows you to rapidly go through and characterize images, and allows you to see in one line all the data for an image.<br />
<br />
You can still view the traditional table view of 1 row per phenotypic assertion (with image ID repeated). In this view one can add more information about a particular phenotype, like free text description and such. It should also be possible to add additional Phentoypes that are observed for any image, using one row per Phenotype as usual. Upon returning to the matrix view, these could be displayed in "Additional Phenotype" columns (EQ column pairs - an additional pair of columns for each additional Phenotype), thereby maintaining one image per row.<br />
<br />
Another question is how would BIRN like to take advantage of the protocol editor & matrix. <br />
Would this be helpful for literature curation?<br />
Can this be utilized in the context of Smart Atlas? or JINX?<br />
Or would this be used as an experiment/image annotation tool in its own right?</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6441OntologyRelations2008-01-21T20:52:39Z<p>Suzi: /* Invited Participants */</p>
<hr />
<div>== Workshop on the Relationship Ontology ==<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
The goals of this workshop are to develop the content of the relationship ontology. In particular we will discuss these areas:<br />
<br />
# To add new relationships to RO: [[RO:Main_Page | Current Proposals for new relations ]]<br />
#* The "regulates" relationship<br />
#* The relations that are required for anatomies and development<br />
#* The relations that are required for describing phenotypic data<br />
#* The relations that are required for cross-products between anatomy and biological process<br />
# To consolidate the methodology for doing so<br />
<br />
== Draft Agenda ==<br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
8:30 Suzi Lewis: Logistics and protocols<br />
<br />
8:45 Introductions: why you attended, background and expertise<br />
<br />
9:00 Barry Smith (moderator): Discussion of methodology for creating new relations (e.g. some-part question)<br />
<br />
10:00 break<br />
<br />
10:30 (continued) Discussion of methodology for creating new relations (e.g. some-part question)<br />
<br />
11:30 Set priorities and ordering of the listed discussion topics. <br />
<br />
12:00 Lunch<br />
<br />
13:00 Discussion of topics<br />
<br />
15:00 break<br />
<br />
15:30 Discussion of topics<br />
<br />
17:30 Done for the day<br />
<br />
19:30 dinner<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
8:30 Discussion of topics<br />
<br />
10:30 break<br />
<br />
11:00 Discussion of topics<br />
<br />
12:00 lunch<br />
<br />
1:30 Discussion of topics<br />
<br />
2:30 Suzi Lewis: Summary of the meeting, action items, resolutions, and future plans.<br />
<br />
3:30 Departures<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
Details on location, transportation and hotels forthcoming...<br />
<br />
== Invited Participants ==<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Judith Blake (JAX / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (Center for Ontology / Buffalo, NY)<br />
<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
# Chris Mungall (NCBO / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Wash, DC)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6440OntologyRelations2008-01-21T20:52:00Z<p>Suzi: /* Invited Participants */</p>
<hr />
<div>== Workshop on the Relationship Ontology ==<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
The goals of this workshop are to develop the content of the relationship ontology. In particular we will discuss these areas:<br />
<br />
# To add new relationships to RO: [[RO:Main_Page | Current Proposals for new relations ]]<br />
#* The "regulates" relationship<br />
#* The relations that are required for anatomies and development<br />
#* The relations that are required for describing phenotypic data<br />
#* The relations that are required for cross-products between anatomy and biological process<br />
# To consolidate the methodology for doing so<br />
<br />
== Draft Agenda ==<br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
8:30 Suzi Lewis: Logistics and protocols<br />
<br />
8:45 Introductions: why you attended, background and expertise<br />
<br />
9:00 Barry Smith (moderator): Discussion of methodology for creating new relations (e.g. some-part question)<br />
<br />
10:00 break<br />
<br />
10:30 (continued) Discussion of methodology for creating new relations (e.g. some-part question)<br />
<br />
11:30 Set priorities and ordering of the listed discussion topics. <br />
<br />
12:00 Lunch<br />
<br />
13:00 Discussion of topics<br />
<br />
15:00 break<br />
<br />
15:30 Discussion of topics<br />
<br />
17:30 Done for the day<br />
<br />
19:30 dinner<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
8:30 Discussion of topics<br />
<br />
10:30 break<br />
<br />
11:00 Discussion of topics<br />
<br />
12:00 lunch<br />
<br />
1:30 Discussion of topics<br />
<br />
2:30 Suzi Lewis: Summary of the meeting, action items, resolutions, and future plans.<br />
<br />
3:30 Departures<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
Details on location, transportation and hotels forthcoming...<br />
<br />
== Invited Participants ==<br />
<br />
Participants will include:<br />
<br />
=== Confirmed ===<br />
# Mike Bada (host / Denver, CO)<br />
# Judith Blake (JAX / Bar Harbor, ME)<br />
# Larry Hunter (host / Denver, CO)<br />
# Suzi Lewis (NCBO / Berkeley, CA)<br />
# David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
# Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
# Barry Smith (NCBO / Buffalo, NY)<br />
<br />
=== Invited ===<br />
# Thomas Bittner (Center for Ontology / Buffalo, NY)<br />
<br />
# Melissa Haendel (ZFIN / Eugene, OR)<br />
# David Hill (MGI / Bar Harbor, ME)<br />
# Waclaw Kusnierczyk (Bergen, Norway)<br />
# Chris Mungall (NCBO / Berkeley, CA)<br />
# Fabian Neuhaus (NIST / Wash, DC)<br />
# Cornelius Rosse (FMA / Seattle, WA)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6410OntologyRelations2008-01-04T03:42:23Z<p>Suzi: /* Draft Agenda */</p>
<hr />
<div>== Workshop on the Relationship Ontology ==<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
The goals of this workshop are to develop the content of the relationship ontology. In particular we will discuss these areas:<br />
<br />
# To add new relationships to RO: [[RO:Main_Page | Current Proposals for new relations ]]<br />
#* The "regulates" relationship<br />
#* The relations that are required for anatomies and development<br />
#* The relations that are required for describing phenotypic data<br />
#* The relations that are required for cross-products between anatomy and biological process<br />
# To consolidate the methodology for doing so<br />
<br />
== Draft Agenda ==<br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
8:30 Suzi Lewis: Logistics and protocols<br />
<br />
8:45 Introductions: why you attended, background and expertise<br />
<br />
9:00 Barry Smith (moderator): Discussion of methodology for creating new relations (e.g. some-part question)<br />
<br />
10:00 break<br />
<br />
10:30 (continued) Discussion of methodology for creating new relations (e.g. some-part question)<br />
<br />
11:30 Set priorities and ordering of the listed discussion topics. <br />
<br />
12:00 Lunch<br />
<br />
13:00 Discussion of topics<br />
<br />
15:00 break<br />
<br />
15:30 Discussion of topics<br />
<br />
17:30 Done for the day<br />
<br />
19:30 dinner<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
8:30 Discussion of topics<br />
<br />
10:30 break<br />
<br />
11:00 Discussion of topics<br />
<br />
12:00 lunch<br />
<br />
1:30 Discussion of topics<br />
<br />
2:30 Suzi Lewis: Summary of the meeting, action items, resolutions, and future plans.<br />
<br />
3:30 Departures<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
Details on location, transportation and hotels forthcoming...<br />
<br />
== Invited Participants ==<br />
<br />
Participants will include:<br />
<br />
Mike Bada (host / Denver, CO) confirmed<br />
<br />
Thomas Bittner (Center for Ontology / Buffalo, NY)<br />
<br />
Judith Blake (JAX / Bar Harbor, ME) confirmed<br />
<br />
Pierre Grenon (IFOMIS / Saarbruecken, Germany)<br />
<br />
Melissa Haendel (ZFIN / Eugene, OR)<br />
<br />
David Hill (MGI / Bar Harbor, ME)<br />
<br />
Larry Hunter (host / Denver, CO) confirmed<br />
<br />
Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
Suzi Lewis (NCBO / Berkeley, CA) confirmed<br />
<br />
Chris Mungall (NCBO / Berkeley, CA)<br />
<br />
Fabian Neuhaus (NIST / Wash, DC)<br />
<br />
David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
<br />
Cornelius Rosse (FMA / Seattle, WA)<br />
<br />
Alan Ruttenberg (Science Commons / Cambridge, MA) confirmed<br />
<br />
Barry Smith (NCBO / Buffalo, NY) confirmed<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6407OntologyRelations2008-01-03T09:11:07Z<p>Suzi: /* Goals */</p>
<hr />
<div>== Workshop on the Relationship Ontology ==<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
The goals of this workshop are to develop the content of the relationship ontology. In particular we will discuss these areas:<br />
<br />
# To add new relationships to RO: [[RO:Main_Page | Current Proposals for new relations ]]<br />
#* The "regulates" relationship<br />
#* The relations that are required for anatomies and development<br />
#* The relations that are required for describing phenotypic data<br />
#* The relations that are required for cross-products between anatomy and biological process<br />
# To consolidate the methodology for doing so<br />
<br />
== Draft Agenda ==<br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
8:30 Suzi Lewis: Logistics and protocols<br />
<br />
9:00 Introductions: why you attended, background and expertise<br />
<br />
9:30 David Hill: Outlining the issues with the "regulates" relationship<br />
<br />
10:00 break<br />
<br />
10:00 Discussion of the "regulates" relationship<br />
<br />
11:30 Melissa Haendel?: Outlining the issues with the relations that are required for anatomies and development<br />
<br />
12:00 Lunch<br />
<br />
13:00 Discussion of the relations that are required for anatomies and development<br />
<br />
15:00 break<br />
<br />
15:30 Chris Mungall: Outlining the issues with the relations that are required for describing phenotypic data<br />
<br />
16:00 Discussion of the relations that are required for describing phenotypic data<br />
<br />
18:00 break<br />
<br />
19:30 dinner<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
9:00 TBD: Outlining the issues with the relations that are required for cross-products between anatomy and biological process<br />
<br />
9:30 Discussion of the relations that are required for cross-products between anatomy and biological process<br />
<br />
12:00 lunch<br />
<br />
1:30 Barry Smith: Discussion of methodology for creating new relations<br />
<br />
2:30 Suzi Lewis: Summary of the meeting, action items, resolutions, and future plans.<br />
<br />
3:30 Departures<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
Details on location, transportation and hotels forthcoming...<br />
<br />
== Invited Participants ==<br />
<br />
Participants will include:<br />
<br />
Mike Bada (host / Denver, CO) confirmed<br />
<br />
Thomas Bittner (Center for Ontology / Buffalo, NY)<br />
<br />
Judith Blake (JAX / Bar Harbor, ME) confirmed<br />
<br />
Pierre Grenon (IFOMIS / Saarbruecken, Germany)<br />
<br />
Melissa Haendel (ZFIN / Eugene, OR)<br />
<br />
David Hill (MGI / Bar Harbor, ME)<br />
<br />
Larry Hunter (host / Denver, CO) confirmed<br />
<br />
Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
Suzi Lewis (NCBO / Berkeley, CA) confirmed<br />
<br />
Chris Mungall (NCBO / Berkeley, CA)<br />
<br />
Fabian Neuhaus (NIST / Wash, DC)<br />
<br />
David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
<br />
Cornelius Rosse (FMA / Seattle, WA)<br />
<br />
Alan Ruttenberg (Science Commons / Cambridge, MA) confirmed<br />
<br />
Barry Smith (NCBO / Buffalo, NY) confirmed<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6406OntologyRelations2008-01-03T09:10:38Z<p>Suzi: /* Goals */</p>
<hr />
<div>== Workshop on the Relationship Ontology ==<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
The goals of this workshop are to develop the content of the relationship ontology. In particular we will discuss these areas:<br />
<br />
# To add new relationships to RO: [[RO:Main_Page | Current Proposals for new relations ]]<br />
#* The "regulates" relationship<br />
#* The relations that are required for anatomies and development<br />
#* The relations that are required for describing phenotypic data<br />
#* The relations that are required for cross-products between anatomy and biological process<br />
# To consolidate the methodology for doing so<br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
8:30 Suzi Lewis: Logistics and protocols<br />
<br />
9:00 Introductions: why you attended, background and expertise<br />
<br />
9:30 David Hill: Outlining the issues with the "regulates" relationship<br />
<br />
10:00 break<br />
<br />
10:00 Discussion of the "regulates" relationship<br />
<br />
11:30 Melissa Haendel?: Outlining the issues with the relations that are required for anatomies and development<br />
<br />
12:00 Lunch<br />
<br />
13:00 Discussion of the relations that are required for anatomies and development<br />
<br />
15:00 break<br />
<br />
15:30 Chris Mungall: Outlining the issues with the relations that are required for describing phenotypic data<br />
<br />
16:00 Discussion of the relations that are required for describing phenotypic data<br />
<br />
18:00 break<br />
<br />
19:30 dinner<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
9:00 TBD: Outlining the issues with the relations that are required for cross-products between anatomy and biological process<br />
<br />
9:30 Discussion of the relations that are required for cross-products between anatomy and biological process<br />
<br />
12:00 lunch<br />
<br />
1:30 Barry Smith: Discussion of methodology for creating new relations<br />
<br />
2:30 Suzi Lewis: Summary of the meeting, action items, resolutions, and future plans.<br />
<br />
3:30 Departures<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
Details on location, transportation and hotels forthcoming...<br />
<br />
== Invited Participants ==<br />
<br />
Participants will include:<br />
<br />
Mike Bada (host / Denver, CO) confirmed<br />
<br />
Thomas Bittner (Center for Ontology / Buffalo, NY)<br />
<br />
Judith Blake (JAX / Bar Harbor, ME) confirmed<br />
<br />
Pierre Grenon (IFOMIS / Saarbruecken, Germany)<br />
<br />
Melissa Haendel (ZFIN / Eugene, OR)<br />
<br />
David Hill (MGI / Bar Harbor, ME)<br />
<br />
Larry Hunter (host / Denver, CO) confirmed<br />
<br />
Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
Suzi Lewis (NCBO / Berkeley, CA) confirmed<br />
<br />
Chris Mungall (NCBO / Berkeley, CA)<br />
<br />
Fabian Neuhaus (NIST / Wash, DC)<br />
<br />
David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
<br />
Cornelius Rosse (FMA / Seattle, WA)<br />
<br />
Alan Ruttenberg (Science Commons / Cambridge, MA) confirmed<br />
<br />
Barry Smith (NCBO / Buffalo, NY) confirmed<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6404OntologyRelations2008-01-02T19:14:20Z<p>Suzi: /* Goals */</p>
<hr />
<div>== Workshop on the Relationship Ontology ==<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
The goals of this workshop are to develop the content of the relationship ontology. In particular we will discuss these areas:<br />
<br />
# To add new relationships to RO: [[RO:Main_Page | Current Proposals for new relations ]]<br />
#* The "regulates" relationship<br />
#* The relations that are required for anatomies and development<br />
#* The relations that are required for describing phenotypic data<br />
#* The relations that are required for cross-products between anatomy and biological process<br />
# To consolidate the methodology for doing so<br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
8:30 Suzi Lewis: Logistics and protocols<br />
<br />
9:00 Introductions: why you attended, background and expertise<br />
<br />
9:30 David Hill: Outlining the issues with the "regulates" relationship<br />
<br />
10:00 break<br />
<br />
10:00 Discussion of the "regulates" relationship<br />
<br />
11:30 Melissa Haendel?: Outlining the issues with the relations that are required for anatomies and development<br />
<br />
12:00 Lunch<br />
<br />
13:00 Discussion of the relations that are required for anatomies and development<br />
<br />
15:00 break<br />
<br />
15:30 Chris Mungall: Outlining the issues with the relations that are required for describing phenotypic data<br />
<br />
16:00 Discussion of the relations that are required for describing phenotypic data<br />
<br />
18:00 break<br />
<br />
19:30 dinner<br />
<br />
=== Tuesday, May 20th 2008 ===<br />
<br />
9:00<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
Details on location, transportation and hotels forthcoming...<br />
<br />
== Invited Participants ==<br />
<br />
Participants will include:<br />
<br />
Mike Bada (host / Denver, CO) confirmed<br />
<br />
Thomas Bittner (Center for Ontology / Buffalo, NY)<br />
<br />
Judith Blake (JAX / Bar Harbor, ME) confirmed<br />
<br />
Pierre Grenon (IFOMIS / Saarbruecken, Germany)<br />
<br />
Melissa Haendel (ZFIN / Eugene, OR)<br />
<br />
David Hill (MGI / Bar Harbor, ME)<br />
<br />
Larry Hunter (host / Denver, CO) confirmed<br />
<br />
Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
Suzi Lewis (NCBO / Berkeley, CA) confirmed<br />
<br />
Chris Mungall (NCBO / Berkeley, CA)<br />
<br />
Fabian Neuhaus (NIST / Wash, DC)<br />
<br />
David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
<br />
Cornelius Rosse (FMA / Seattle, WA)<br />
<br />
Alan Ruttenberg (Science Commons / Cambridge, MA) confirmed<br />
<br />
Barry Smith (NCBO / Buffalo, NY) confirmed<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6403OntologyRelations2008-01-02T18:33:47Z<p>Suzi: /* Goals */</p>
<hr />
<div>== Workshop on the Relationship Ontology ==<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
The goals of this workshop are to develop the content of the relationship ontology. In particular we will discuss these areas:<br />
<br />
# To add new relationships to RO: [[RO:Main_Page | Current Proposals for new relations ]]<br />
#* The "regulates" relationship<br />
#* The relations that are required for anatomies and development<br />
#* The relations that are required for describing phenotypic data<br />
#* The relations that are required for cross-products between anatomy and biological process<br />
# To consolidate the methodology for doing so<br />
<br />
=== Monday, May 19th 2008 ===<br />
<br />
8:30 Suzi Lewis: Logistics and protocols<br />
<br />
9:00 Introductions: why you attended, background and expertise<br />
<br />
9:30 David Hill: Outlining the issues with the "regulates" relationship<br />
<br />
10:00 break<br />
<br />
10:00 Discussion of the "regulates" relationship<br />
<br />
11:30 Melissa Haendel?: Outlining the issues with the relations that are required for anatomies and development<br />
<br />
12:00 Lunch<br />
<br />
13:00 Discussion of the relations that are required for anatomies and development<br />
<br />
15:00 break<br />
<br />
15:30 Chris Mungall: Outlining the issues with the relations that are required for describing phenotypic data<br />
<br />
16:00 Discussion of the relations that are required for describing phenotypic data<br />
<br />
18:00 break<br />
<br />
19:30 dinner<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
Details on location, transportation and hotels forthcoming...<br />
<br />
== Invited Participants ==<br />
<br />
Participants will include:<br />
<br />
Mike Bada (host / Denver, CO) confirmed<br />
<br />
Thomas Bittner (Center for Ontology / Buffalo, NY)<br />
<br />
Judith Blake (JAX / Bar Harbor, ME) confirmed<br />
<br />
Pierre Grenon (IFOMIS / Saarbruecken, Germany)<br />
<br />
Melissa Haendel (ZFIN / Eugene, OR)<br />
<br />
David Hill (MGI / Bar Harbor, ME)<br />
<br />
Larry Hunter (host / Denver, CO) confirmed<br />
<br />
Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
Suzi Lewis (NCBO / Berkeley, CA) confirmed<br />
<br />
Chris Mungall (NCBO / Berkeley, CA)<br />
<br />
Fabian Neuhaus (NIST / Wash, DC)<br />
<br />
David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
<br />
Cornelius Rosse (FMA / Seattle, WA)<br />
<br />
Alan Ruttenberg (Science Commons / Cambridge, MA) confirmed<br />
<br />
Barry Smith (NCBO / Buffalo, NY) confirmed<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6397OntologyRelations2008-01-02T03:15:21Z<p>Suzi: /* Invited Participants */</p>
<hr />
<div>== Workshop on the Relationship Ontology ==<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
The goals of this workshop are to develop the content of the relationship ontology. In particular we will discuss these areas:<br />
<br />
# To add new relationships to RO: [[RO:Main_Page | Current Proposals for new relations ]]<br />
# To consolidate the methodology for doing so<br />
# More specifics??<br />
<br />
There is no formal agenda. We will simply prioritize the above items and move through them one by one.<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
Details on location, transportation and hotels forthcoming...<br />
<br />
== Invited Participants ==<br />
<br />
Participants will include:<br />
<br />
Mike Bada (host / Denver, CO) confirmed<br />
<br />
Thomas Bittner (Center for Ontology / Buffalo, NY)<br />
<br />
Judith Blake (JAX / Bar Harbor, ME) confirmed<br />
<br />
Pierre Grenon (IFOMIS / Saarbruecken, Germany)<br />
<br />
Melissa Haendel (ZFIN / Eugene, OR)<br />
<br />
David Hill (MGI / Bar Harbor, ME)<br />
<br />
Larry Hunter (host / Denver, CO) confirmed<br />
<br />
Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
Suzi Lewis (NCBO / Berkeley, CA) confirmed<br />
<br />
Chris Mungall (NCBO / Berkeley, CA)<br />
<br />
Fabian Neuhaus (NIST / Wash, DC)<br />
<br />
David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
<br />
Cornelius Rosse (FMA / Seattle, WA)<br />
<br />
Alan Ruttenberg (Science Commons / Cambridge, MA) confirmed<br />
<br />
Barry Smith (NCBO / Buffalo, NY) confirmed<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6394OntologyRelations2007-12-29T23:41:24Z<p>Suzi: /* Goals */</p>
<hr />
<div>== Workshop on the Relationship Ontology ==<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
The goals of this workshop are to develop the content of the relationship ontology. In particular we will discuss these areas:<br />
<br />
# To add new relationships to RO<br />
# To consolidate the methodology for doing so<br />
# More specifics??<br />
<br />
There is no formal agenda. We will simply prioritize the above items and move through them one by one.<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
Details on location, transportation and hotels forthcoming...<br />
<br />
== Invited Participants ==<br />
<br />
Participants will include:<br />
<br />
Chris Mungall (NCBO / Berkeley, CA)<br />
<br />
Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
<br />
Larry Hunter (host / Denver, CO)<br />
<br />
Suzi Lewis (NCBO / Berkeley, CA)<br />
<br />
Barry Smith (NCBO / Buffalo, NY)<br />
<br />
Melissa Haendel (ZFIN / Eugene, OR)<br />
<br />
Fabian Neuhaus (NIST / Wash, DC)<br />
<br />
Pierre Grenon ()<br />
<br />
David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
<br />
David Hill (MGI / Bar Harbor, ME)<br />
<br />
Mike Bada (host / Denver, CO)<br />
<br />
Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
Thomas Bittner (Center for Ontology / Buffalo, NY)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzihttps://www.bioontology.org//mediawiki/index.php?title=OntologyRelations&diff=6393OntologyRelations2007-12-29T23:41:03Z<p>Suzi: /* Goals */</p>
<hr />
<div>== Workshop on the Relationship Ontology ==<br />
<br />
== Goals == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.<br />
<br />
The goals of this workshop are to develop the content of the relationship ontology. In particular we will discuss these areas:<br />
<br />
# To add new relationships to RO<br />
# To consolidate the methodology for doing so<br />
<br />
There is no formal agenda. We will simply prioritize the above items and move through them one by one.<br />
<br />
== Dates ==<br />
<br />
'''Monday and Tuesday, May 19-20, 2008''' <br />
<br />
== Logistics ==<br />
<br />
'''University of Colorado Medical School''' <br />
<br />
Details on location, transportation and hotels forthcoming...<br />
<br />
== Invited Participants ==<br />
<br />
Participants will include:<br />
<br />
Chris Mungall (NCBO / Berkeley, CA)<br />
<br />
Alan Ruttenberg (Science Commons / Cambridge, MA)<br />
<br />
Larry Hunter (host / Denver, CO)<br />
<br />
Suzi Lewis (NCBO / Berkeley, CA)<br />
<br />
Barry Smith (NCBO / Buffalo, NY)<br />
<br />
Melissa Haendel (ZFIN / Eugene, OR)<br />
<br />
Fabian Neuhaus (NIST / Wash, DC)<br />
<br />
Pierre Grenon ()<br />
<br />
David Osumi-Sutherland (FlyBase / Cambridge, UK)<br />
<br />
David Hill (MGI / Bar Harbor, ME)<br />
<br />
Mike Bada (host / Denver, CO)<br />
<br />
Waclaw Kusnierczyk (Bergen, Norway)<br />
<br />
Thomas Bittner (Center for Ontology / Buffalo, NY)<br />
<br />
== Background Material ==<br />
<br />
[http://obofoundry.org/ro/ Relation Ontology Home ]<br />
<br />
[[RO:Main_Page | Current Proposals for new relations ]]</div>Suzi