Apr. 5th, 2016 Ontology Working Group Meeting: Difference between revisions
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=Planteome Ontology WG Zoom Meeting= | =Planteome Ontology WG Zoom Meeting= | ||
* Date: Tuesday | * Date: Tuesday Apr. 6th, 2016 | ||
* 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, CM, BS | - attendees: AM, MAL, LC, PJ, JE, CM, BS | ||
[[File:Ontology WG Meeting 4-6-16 video.mp4|thumbnail|Ontology WG Meeting 4-6-16 video]] | |||
[[File:Ontology WG Meeting 4-6-16 audio.m4a|thumbnail|Ontology WG Meeting 4-6-16 audio]] | |||
=Agenda= | =Agenda= | ||
==Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016== | ==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: | |||
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/list-of-participants PhenoHarmonIS_List-of-participants] | |||
===Agenda=== | |||
* Still finalizing the agenda, meeting weds, final version TBA | |||
** https://docs.google.com/a/cgxchange.org/document/d/1rRVEu8X-E_a5tgTFYMrC10Ag-cGE0mqUf_yICrU26QY/edit?usp=sharing | |||
* First day- Plenary sessions, tool demos | |||
** GG will give an ontology 101 session | |||
* Following days hands-on sessions | |||
===Agronomy Ontology- Medha Devare and Celine Aubert=== | |||
* meta analysis across platforms for agronomic trials | |||
* trials, variables, measurements, farming practices | |||
* Modeled after traits in trait dictionaries- is it crop specific then? | |||
* Goal is to develop it in Owl using protege- currently not available | |||
* CM: should coordinate with the Food Ontology folks- they will be having a workshop at ICBO | |||
== Progress on developing the rice annotation files from IRRI== | == Progress on developing the rice annotation files from IRRI== | ||
* Austin and Marie-Angelique | * Austin and Marie-Angelique | ||
** Problems- linking to the GRIMS database or linking to Genesys | |||
** Using the institute code in Geneysis might allow for direct links to accession numbers | |||
* taxon is not showing up as it is not in our slim yet | |||
* awnless is a type of awn color???? | |||
* add accession # to label | |||
* | |||
== ICBO 2016 Call for Papers is open== | == ICBO 2016 Call for Papers is open== | ||
| Line 55: | Line 65: | ||
==AmiGO2 issues continued.. == | ==AmiGO2 issues continued.. == | ||
http://tomodachi.berkeleybop.org/amigo/landing | * New version of AmiGO is in the works- you can preview it here: 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 | |||
* | ==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- Tabled for next meeting== | ||
* Presentation for Biocuration meeting- Marie-Angelique | |||
* Progress on the development of the V. 5 trait dictionaries- Marie-Angelique and/or Leo | |||
* | * OBA development- Chris Mungall- moved to April 26th | ||
= Upcoming Meetings and Workshops= | = Upcoming Meetings and Workshops= | ||
Latest revision as of 16:18, 22 April 2016
Planteome Ontology WG Zoom Meeting
- Date: Tuesday Apr. 6th, 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, CM, BS
File:Ontology WG Meeting 4-6-16 video.mp4
File:Ontology WG Meeting 4-6-16 audio.m4a
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:
Agenda
- Still finalizing the agenda, meeting weds, final version TBA
- First day- Plenary sessions, tool demos
- GG will give an ontology 101 session
- Following days hands-on sessions
Agronomy Ontology- Medha Devare and Celine Aubert
- meta analysis across platforms for agronomic trials
- trials, variables, measurements, farming practices
- Modeled after traits in trait dictionaries- is it crop specific then?
- Goal is to develop it in Owl using protege- currently not available
- CM: should coordinate with the Food Ontology folks- they will be having a workshop at ICBO
Progress on developing the rice annotation files from IRRI
- Austin and Marie-Angelique
- Problems- linking to the GRIMS database or linking to Genesys
- Using the institute code in Geneysis might allow for direct links to accession numbers
- taxon is not showing up as it is not in our slim yet
- awnless is a type of awn color????
- add accession # to label
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 April 25th
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 issues continued..
- New version of AmiGO is in the works- you can preview it here: 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
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- Tabled for next meeting
- Presentation for Biocuration meeting- Marie-Angelique
- Progress on the development of the V. 5 trait dictionaries- Marie-Angelique and/or Leo
- OBA development- Chris Mungall- moved to April 26th
Upcoming Meetings and Workshops
Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland
- MAL is going and will be presenting a talk
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