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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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| * Bioversity Curator position is advertised on the [http://www.bioversityinternational.org/jobs/ Bioversity Jobs page]:
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| 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]
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| * Ontology Curator Position at OSU: In progress....
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| * Ontology Curator Position at NYBG: In progress....
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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: https://github.com/Planteome==
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| * Intro to the GitHub- site for the Planteome
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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 than forking
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| * What is 'Forking': (we probably won't need to be doing this)
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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", OBO works well, OWL not so well suited for this. Possible changes coming to OWL to make this work better.
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| ** Different than doing a check out
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| ==2. Overview and update on the Plant Trait Ontology==
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| - The Trait Ontology can be accessed in various ways:
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| * [http://palea.cgrb.oregonstate.edu/trait_ontology/cgi-bin/trait_amigo/browse.cgi?session_id=1852amigo1337966110 TO-Dev AmiGO Browser]
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| * [http://crop-dev.cgrb.oregonstate.edu/amigo/cgi-bin/crop_amigo/term_details?term=TO:0000387&session_id=6933amigo1423596135 TO-Dev on Planteome Browser]
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| * Link to [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/gramene/traits/trait.obo?view=log TO on SVN]
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| ===Updates on the Trait Ontology:===
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| * Early work (~2005-2011) on the TO was done by PJ and CWT at Gramene, primarily to describe QTLs of rice
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| * Since 2012, the Trait Ontology has not been funded under the PO grant
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| * Large amount of interest from the community drove the TO forward [http://wiki.plantontology.org/index.php/Plant_Ontology_and_Crop_Annotation_Workshop_OSU_2012 Crop Plant Trait Ontology Workshop OSU 2012]
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| * A significant amount of work has been done to make the TO compatible with the PO and other reference ontologies
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| * In Summary:
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| ** Revised def'n of the root term: plant trait
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| ** Many changes to top level classes, new terms added, revised names of others
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| ** Renamed and added new upper level terms to align the anatomy and morphology trait (TO:0000017) class with the plant anatomical entity (PO:0025131) branch of the PO
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| ** Many new child terms added
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| ** Definitions revised to contain references to the entity term and quality term from PATO
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| ** Xrefs added to SF trackers
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| ** Full details of the changes have been documented on the [http://wiki.plantontology.org/index.php/Plant_Trait_Ontology Trait Ontology Wiki page] and the [http://sourceforge.net/p/obo/plant-trait-ontology-to-requests/ Trait Ontology SourceForge tracker]
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| * Changes are currently stored on the [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/gramene/traits/trait.obo?view=markup SVN], with notes as to the nature of the changes.
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| ==Logical Definitions; i.e. Cross Products==
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| * Chris has done some work on setting up logical definitions (also called Cross Products)
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| ** Cross products are a way to 'decompose' the TO terms into the element entities (from PO, GO, ChEBI or other ontology) and qualities (from PATO).
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| ** This allows automatic classification by the reasoner - so the computer can make inferences across the ontology
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| ** Cross product file is currently stored on our SVN: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/gramene/traits/trait_xp.obo?view=markup trait_xp.obo] last updated 16 months ago
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| * Example: ligule length (TO:0000024)
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| id: TO:0000024 ! ligule length
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| intersection_of: BATTO:0000001 ! biological attribute
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| intersection_of: affects_quality PATO:0000122 ! length
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| intersection_of: attribute_of PO:0020105 ! ligule
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| * ligule- PO:0020105 (is_a cardinal organ part; part_of vascular leaf)
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| * length- quality from PATO
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| * BATTO- now called "OBA"- [http://www.ontobee.org/browser/index.php?o=OBA Ontology of Biological Attributes], larger ontology which unifies trait ontologies across all types of life.
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| ==3. Panzea Project: Curating Maize Diversity with MaizeGDB==
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| * Recent work with Mary Schaeffer of MaizeGDB which was presented at the Plant and Animal Genome Conference in January 2015.
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| * Link to [https://pag.confex.com/pag/xxiii/webprogram/Paper14937.html Abstract]
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| * Link to presentation on Google Docs: [https://docs.google.com/presentation/d/1OKlfnd7f51JjUSH-S7Y0tgWQu-ySIVuBVMpa2CelZPI/edit?usp=sharing Curating Maize Diversity]]
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| *
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| =Tuesday, Feb 24th, 2015=
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| Who: PJ, EA, LC, BS, DWS
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