View source for Ontology Working Group meeting: Tuesday, Feb 10th, 2015

Who: PJ, EA, LC, JE, CM, BS 

Link to audio recording: 
[[File:Planteome ontologies 2-10-15.m4a|thumbnail|Planteome ontologies 2-10-15.m4a]]

* Meetings will be held using Zoom (https://www.zoom.us/) - we are in the process of getting it set up
* Wiki is set up and notes will be kept here, need to login to access

== 1. Coordination between the species-specific Crop Ontologies and the reference ontologies- PO, TO, GO etc==
PJ: Initial goal will be to work on improving and updating the TO

EA provided an overview of the Crop Ontology curation tool (http://www.cropontology.org/) and some background information about the ontologies and platform.

Long term goal is to integrate the CO vocabularies with the reference ontologies.
* Part of the Integrated Breeding Platform
* Common vocabularies are used to integrate data from breeders field book
* Was started as part of the Generation Challenge Program (GCP), which has run out of funding.  The GCP Pantheon webiste (http://pantheon.generationcp.org/index.php) will be shut down soon and so that information needs to be moved somewhere else. Could perhaps go the the [http://genesys.cgxchange.org/gcp-crop-ontology GCP Wiki] page?  

* 18 crops (http://www.cropontology.org/) represented in five sections:
** General Germplasm Ontology
** Phenotype and Trait Ontology
** Structural and Functional Genomic Ontology
** Location and Environmental Ontology
** Plant Anatomy & Development Ontology

Cassava Example: http://www.cropontology.org/ontology/CO_334/Cassava
* Based on OBO-Edit
* Excel-based template
* Visualized by the tool

Common Trait Classes (e.g.) : Maize Ontology (http://www.cropontology.org/ontology/CO_322/Maize)
* "Agronomic/Agronomical" 
* Morphological
* Stress (Abiotic/Biotic Stresses)
* Phenological
* Quality
* Unit

Relations: 
* is_a
* part _of
* method_of
* scale _of
* derived_from

Availability and Formats:
* Download from www.cropontology.org
* API- http://www.cropontology.org/api
* make 'Permalink' to individual terms pages
* Formats include csv, OBO, SKOS, RDF, Trait Template v4
* Ones in blue are OBO based
* Terms are translated into various languages, as synonyms 

Terms have a unique identifier:
* CO_###:#######

===Questions and Discussion: ===
* Goal is to keep the web-based tool for user access, in some form.
* Database behind it is No-SQL based
* Integration with future versions of Term Genie
* We will need a technical call as we we move towards integration at GitHub
* The Trait Ontology is not displayed here as it was confusing to the users.  
* Identified an issue where curators/users can upload an ontology without any quality control.

==2. Prioritizing the work on the species-specific Crop Ontologies- Rice, Wheat and Maize==
* At the PAG meeting- Rice, wheat and Maize were identified as the best candidates to start on
* The PO is well set up to provide entity terms for these as they are important crop/model species 
* The TO has some of the needed terms, but will need additional work

''Fill in some details of the Rice, Wheat and Maize vocabs here:''

==3. Transition to GitHub Repository==
[https://github.com/Planteome Planteome Ontologies on GitHub]
* This will be very useful for editting and versioning, then the relased version can be pushed out to Crop Ontology site

==4. Hiring at Bioversity, OSU and NYBG==
* Bioversity Curator position is advertised on the [http://www.bioversityinternational.org/jobs/ Bioversity Jobs page]: 
You can view it here: [https://hr4u.bioversity.cgiar.org/recruitment/Attachments%5CVA_Post%20Doc_CropOntology_NSF_MPL_Final.pdf Position Description: Post Doctoral Fellow, Crop Ontology, MPL]

* Ontology Curator Position at OSU: In progress....


* Ontology Curator Position at NYBG: In progress....

==5.  Possible Ontology development workshop this spring==
Time is quite short, maybe consider a web-conferencing strategy to start, new people are being added to project at OSU, NYBG, CO

==6.  White paper on plant phenotyping standards==
See details on [http://wiki.planteome.org/index.php/Thursday_Feb_6th,_2015#F._Position_Paper_or_.22White_Paper.22 All Hands Call Feb 6th]

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