Mar 15th, 2016 Ontology Working Group Meeting: Difference between revisions

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=Agenda=
=Agenda=


==Update and report on the visit to IRRI by Austin, Marie-Angelic and Leo==
= Upcoming Meetings and Workshops=
** Austin: annotations- progress report and issues with webservices and dbxref urls
==[https://www.isb-sib.ch/events/biocuration2016/home Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland]==
** Test files on dev.planteome see awn color: http://dev.planteome.org/amigo/search/bioentity?q=awn%20color
* MAL is going
** [https://www.isb-sib.ch/events/biocuration2016/key-dates key dates]
** Abstract submitted: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703
 
==[http://blog.garnetcommunity.org.uk/garnetegenis-workshop-integrating-large-data-plant-science-big-data-discovery/ 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: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/home]
 
 
==DivSeek Partner Assembly, Friday, June 17th, Saskatoon, Canada==
 
 
==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 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
 
== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589


==AmiGO2 issues continued..==
==AmiGO2 issues continued..==

Revision as of 15:20, 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

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


Agenda

Upcoming Meetings and Workshops

Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland

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

AmiGO2 issues continued..

Update on the plans for the Meeting in Montpellier, 9-13 May 2016

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


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:

http://www.ebi.ac.uk/ols/beta/ontologies/oba/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0000017

Upcoming Meetings and Workshops

Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland

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

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