Apr. 26th, 2016 Ontology Working Group Meeting: Difference between revisions
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** annotations by species | ** annotations by species | ||
== Update from [https://www.isb-sib.ch/events/biocuration2016/home Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland]== | |||
* MAL attended and presented a talk | |||
** [https://www.isb-sib.ch/events/biocuration2016/key-dates key dates] | |||
** Abstract: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703 | |||
==Plant Trait Ontology updates== | |||
* Recent revisions and changes to the equivalence axioms etc | |||
* Planning to do release soon- by end of this month | |||
==Other Items== | |||
===OBA development- Chris Mungall=== | ===OBA development- Chris Mungall=== | ||
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* Together these are used to build the ontology with equivalence axioms, with the entire ontology hierarchy being inferred automatically, e.g: | * Together these are used to build the ontology with equivalence axioms, with the entire ontology hierarchy being inferred automatically, e.g: | ||
http://www.ebi.ac.uk/ols/beta/ontologies/oba/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0000017 | http://www.ebi.ac.uk/ols/beta/ontologies/oba/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0000017 | ||
= Upcoming Meetings and Workshops= | = Upcoming Meetings and Workshops= |
Revision as of 16:48, 22 April 2016
Planteome Ontology WG Zoom Meeting
- Date: Tuesday Apr. 26th, 2016
- Time: 8:15am PDT (GMT-7)
- Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/762470789
- attendees:
Agenda
Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016
- Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home
- http://tinyurl.com/hzsho6v
- About 70+ Participants are signed up:
- Still finalizing the agenda, final version TBA
- First day- Plenary sessions, tool demos
- GG will give an ontology 101 session
- Following days hands-on sessions
ICBO 2016 Call for Papers is open
- ICBO call for papers is open- http://icbo.cgrb.oregonstate.edu/ICBO_submission
http://icbo.cgrb.oregonstate.edu/ICBO_submission
Deadline is May 5th
Proposed Topics, with suggested lead:
- Planteome paper- LC
- Mappings- MAL
- Annotations project on rice, cassava and lentil, etc - AM
Formats:
- Extended Abstract- up to 2 pages
- Short Papers- up to 4 pages
- Full Papers- up to 6 pages
https://easychair.org/conferences/?conf=icbo2016
Papers will be published in a book of proceedings, not in a journal
AmiGO2 Update:
- New version of AmiGO is in the works- you can preview it here: http://dev.planteome.org/amigo/dd_browse
- GO version: http://tomodachi.berkeleybop.org/amigo/landing
- Significant changes:
- Actual browser functionality
- Neighborhood tab (was ancestors and children)
- All relations will be displayed..?????
- annotations by species
Update from Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland
- MAL attended and presented a talk
Plant Trait Ontology updates
- Recent revisions and changes to the equivalence axioms etc
- Planning to do release soon- by end of this month
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
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]
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