Mar 15th, 2016 Ontology Working Group Meeting: Difference between revisions
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* Time: 8:15am PDT (GMT-7) | * Time: 8:15am PDT (GMT-7) | ||
* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/762470789 | * Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/762470789 | ||
- attendees: AM, MAL, LC, PJ, JE | |||
* Links to recordings: | * Links to recordings: | ||
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* Planteome Ontology WG Zoom Meeting: | |||
=Agenda= | =Agenda= | ||
Revision as of 17:05, 15 March 2016
Planteome Ontology WG Zoom Meeting
- Date: Tuesday Mar. 15th, 2016
- Time: 8:15am PDT (GMT-7)
- Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/762470789
- attendees: AM, MAL, LC, PJ, JE
- Links to recordings:
- Planteome IRRI meeting Thursday March 10th:
- Planteome Ontology WG Zoom Meeting:
Agenda
Update and report on the visit to IRRI by Austin, Marie-Angelic and Leo
- Austin: annotations- progress report and issues with webservices and dbxref urls
- Test files on dev.planteome see awn color: http://dev.planteome.org/amigo/search/bioentity?q=awn%20color
- MAL/Leo: Update on the revisions to the Rice Trait dictionary
Recent updates on the TO
- revisions to equivalence axioms- occurs_in and composition
- Stem and culm
- anther morphology traits, incl. anther number
- biochemical branch
- Resolving issues between PO and TO- e.g stem/ culm, grain/kernel/caryopsis and fruit, pistil/carpel etc
- revisions to the equivalence axioms etc
AmiGO2 issues continued..
Tabled for next meeting
Other items?
OBA development- Chris Mungall
- CM: If there is time I would like to walk through the procedure we use to develop OBA.
- Part of this was covered in the tutorial on template-based ontology development, but we had to rush this part due to lack of time:
https://github.com/Planteome/protege-tutorial/tree/master/template-examples
- For OBA, the source of the ontology is primarily in TSVs, found here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/modules
- The design patterns are specified here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/patterns
- Together these are used to build the ontology with equivalence axioms, with the entire ontology hierarchy being inferred automatically, e.g:
Upcoming Meetings and Workshops
Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland
- MAL is going
GARNet/Egenis Workshop: Integrating Large Data into Plant Science, April 21st-22nd 2016, Dartington Hall, Totnes, Devon
- Elizabeth and George are going, EA will present Planteome as part of her talk
Meeting in Montpellier, 9-13 May 2016
Link to tentative agenda/website: [1]
DivSeek Partner Assembly, Friday, June 17th, Saskatoon, Canada
BioOntologies SIG of the Intelligent Systems for Molecular Biology (ISMB); July 8-12, 2016, Orlando, Florida
- Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
- Short papers, up to 4 pages (will be published in JBMS)
- Poster abstracts, up to 1 page
- Flash updates, up to 1 page
7th International Conference on Biological Ontology and BioCreative 2016 Aug 1st to 4th, Corvallis, OR
- Link to program: ICBO + BioCreative Program
- Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589
Update on the plans for the Meeting in Montpellier, 9-13 May 2016
Upcoming Meetings and Workshops
Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland
- MAL is going
GARNet/Egenis Workshop: Integrating Large Data into Plant Science, April 21st-22nd 2016, Dartington Hall, Totnes, Devon
- Elizabeth and George are going, EA will present Planteome as part of her talk
Meeting in Montpellier, 9-13 May 2016
Link to tentative agenda/website: [2]
BioOntologies SIG of the Intelligent Systems for Molecular Biology (ISMB); July 8-12, 2016, Orlando, Florida
- Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
- Short papers, up to 4 pages (will be published in JBMS)
- Poster abstracts, up to 1 page
- Flash updates, up to 1 page
7th International Conference on Biological Ontology and BioCreative 2016 Aug 1st to 4th, Corvallis, OR
- Link to program: ICBO + BioCreative Program
- Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589