Apr. 26th, 2016 Ontology Working Group Meeting: Difference between revisions

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=Agenda=  
=Agenda=  
==Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016==
==1. 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
 
https://www.isb-sib.ch/events/biocuration2016/oral-presentations#
* Why the world needs phenopacketeers, and how to be one Melissa Haendel
 
* PhenoPackets:  https://github.com/phenopackets- Chris Mungall
 
* Noctua:  http://noctua.berkeleybop.org/
 
* LEGO: expressing complex biological models using the Gene Ontology


==2. 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
* Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home
* http://tinyurl.com/hzsho6v
* http://tinyurl.com/hzsho6v
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* Link to the agenda,  
* Link to the agenda,  
** [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/agenda PhenoHarmonIS Agenda]
** [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/agenda PhenoHarmonIS Agenda]


* First day- Plenary sessions, tool demos
* First day- Plenary sessions, tool demos
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* Following days hands-on sessions
* Following days hands-on sessions


== ICBO 2016 Call for Papers is open==
 
 
==3. ICBO 2016 Call for Papers is open==
* ICBO call for papers is open- http://icbo.cgrb.oregonstate.edu/ICBO_submission
* ICBO call for papers is open- http://icbo.cgrb.oregonstate.edu/ICBO_submission


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Papers will be published in a book of proceedings, not in a journal
Papers will be published in a book of proceedings, not in a journal
== 4. Plant Trait Ontology updates==
* Recent revisions and changes to the equivalence axioms etc
* Planning to do release soon- by end of this month
More details TBA:




==AmiGO2 Update: ==
 
==5. AmiGO2 Update: ==
* New version of AmiGO is being tested on the dev.planteome site- http://dev.planteome.org
* New version of AmiGO is being tested on the dev.planteome site- http://dev.planteome.org


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* Issues of the relations and some things showing up in weird places
* Issues of the relations and some things showing up in weird places


* Significant changes:
* Significant changes:
** Actual browser functionality
** Actual browser functionality
** Neighborhood tab (was ancestors and children)
** Neighborhood tab (was ancestors and children)
** All relations will be displayed..?????
** All relations will be displayed..?????
** 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
https://www.isb-sib.ch/events/biocuration2016/oral-presentations#
* Why the world needs phenopacketeers, and how to be one Melissa Haendel
* PhenoPackets:  https://github.com/phenopackets


* Noctua:  http://noctua.berkeleybop.org/


* LEGO: expressing complex biological models using the Gene Ontology


==Plant Trait Ontology updates==
* Recent revisions and changes to the equivalence axioms etc
* Planning to do release soon- by end of this month
More details TBA:


==Other Items==
==Other Items==

Revision as of 17:38, 25 April 2016

Planteome Ontology WG Zoom Meeting

  • Date: Tuesday Apr. 26th, 2016
  • Time: 8:15am PDT (GMT-7)
  • attendees:
File:Xyz
xyz
File:Xyz
xyz

Agenda

1. Update from Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland

https://www.isb-sib.ch/events/biocuration2016/oral-presentations#

  • Why the world needs phenopacketeers, and how to be one Melissa Haendel
  • LEGO: expressing complex biological models using the Gene Ontology

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

  • First day- Plenary sessions, tool demos
    • GG will give an ontology 101 session
  • Following days hands-on sessions


3. ICBO 2016 Call for Papers is open

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

4. Plant Trait Ontology updates

  • Recent revisions and changes to the equivalence axioms etc
  • Planning to do release soon- by end of this month

More details TBA:


5. AmiGO2 Update:

  • Issues of the relations and some things showing up in weird places
  • Significant changes:
    • Actual browser functionality
    • Neighborhood tab (was ancestors and children)
    • All relations will be displayed..?????
    • annotations by species



Other Items

Tabled from previous meetings:

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

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