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| =Tuesday, Feb 10th, 2015=
| | '''* [[Ontology Working Group meeting: Tuesday, Feb 10th, 2015]]''' |
| Who: PJ, EA, LC, JE, CM, BS
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| * Meetings will be held using Zoom (https://www.zoom.us/) - we are in the process of getting it set up
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| * Wiki is set up and notes will be kept here, need to login to access
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| == 1. Coordination between the species-specific Crop Ontologies and the reference ontologies- PO, TO, GO etc==
| | '''* [[Ontology Working Group Meeting Tuesday, Feb 17th, 2015]]''' |
| PJ: Initial goal will be to work on improving and updating the TO
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| EA provided an overview of the Crop Ontology curation tool (http://www.cropontology.org/) and some background information about the ontologies and platform.
| | '''* [[Ontology Working Group Meeting Tuesday, Feb 24th, 2015]]''' |
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| Long term goal is to integrate the CO vocabularies with the reference ontologies.
| | Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page |
| * Part of the Integrated Breeding Platform
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| * Common vocabularies are used to integrate data from breeders field book
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| * 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?
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| * 18 crops (http://www.cropontology.org/) represented in five sections:
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| ** General Germplasm Ontology
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| ** Phenotype and Trait Ontology
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| ** Structural and Functional Genomic Ontology
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| ** Location and Environmental Ontology
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| ** Plant Anatomy & Development Ontology
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| Cassava Example: http://www.cropontology.org/ontology/CO_334/Cassava
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| * Based on OBO-Edit
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| * Excel-based template
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| * Visualized by the tool
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| Common Trait Classes (e.g.) : Maize Ontology (http://www.cropontology.org/ontology/CO_322/Maize)
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| * "Agronomic/Agronomical"
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| * Morphological
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| * Stress (Abiotic/Biotic Stresses)
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| * Phenological
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| * Quality
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| * Unit
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| Relations:
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| * is_a
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| * part _of
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| * method_of
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| * scale _of
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| * derived_from
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| Availability and Formats:
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| * Download from www.cropontology.org
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| * API- http://www.cropontology.org/api
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| * make 'Permalink' to individual terms pages
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| * Formats include csv, OBO, SKOS, RDF, Trait Template v4
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| * Ones in blue are OBO based
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| * Terms are translated into various languages, as synonyms
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| Terms have a unique identifier:
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| * CO_###:#######
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| ===Questions and Discussion: ===
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| * Goal is to keep the web-based tool for user access, in some form.
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| * Database behind it is No-SQL based
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| * Integration with future versions of Term Genie
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| * We will need a technical call as we we move towards integration at GitHub
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| * The Trait Ontology is not displayed here as it was confusing to the users.
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| * Identified an issue where curators/users can upload an ontology without any quality control.
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| ==2. Prioritizing the work on the species-specific Crop Ontologies- Rice, Wheat and Maize==
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| * At the PAG meeting- Rice, wheat and Maize were identified as the best candidates to start on
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| * The PO is well set up to provide entity terms for these as they are important crop/model species
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| * The TO has some of the needed terms, but will need additional work
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| ''Fill in some details of the Rice, Wheat and Maize vocabs here:''
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| ==3. Transition to GitHub Repository==
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| [https://github.com/Planteome Planteome Ontologies on GitHub]
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| * This will be very useful for editting and versioning, then the relased version can be pushed out to Crop Ontology site
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| ==4. Hiring at Bioversity, OSU and NYBG==
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| ==5. Possible Ontology development workshop this spring==
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| Time is quite short, maybe consider a web-conferencing strategy to start, new people are being added to project at OSU, NYBG, CO
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| ==6. White paper on plant phenotyping standards==
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| 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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| =Tuesday, Feb 17th, 2015=
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| Who: PJ, LC, CM,
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| 1. Discussion of the GitHub Repository:
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| * Forking:
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| - You can copy a version of the ontology into your own user space to make local changes, changes can be made there, and then a make a "pull request"
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| - Administrator can review the pull request and look at the difs, and select the parts that are accepted. Can also be voted on by the project members
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| - Works best if the files are easily "diffable"
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| - Different than doing a check out
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| - Procedure will be to do a check out. Two step commit process: make changes and then commit locally, then do a "push" to synchronize with the server version.
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| * Branching: It is different
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| 2. Overview and update on the Plant Trait Ontology
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| 3. Recent work with Mary Schaeffer of MaizeGDB which was presented at the PAG Conference (https://pag.confex.com/pag/xxiii/webprogram/Paper14937.html)in January.
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| 4. Links to the up-to-date versions (live and dev) of the Plant Trait Ontology:
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| [[Planteome_Ontology_Development_and_Coordination_Working_Group#Ontology_Development_Resources_and_Workshops]] | |