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Journal Article 2017

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

Autor: Cooper, L. Meier, A. Laporte, M-A. Elser, J.L. Mungall, C. Sinn, B.T. Cavaliere, D. Carbon, S. Dunn, N.A. Smith, B. Qu, B. Preece, J. Zhang, E. Todorovic, S. Gkouto, G. Doonan, J.H. Stevenson, D.W. Arnaud, Elizabeth Jaiswal, P.

The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics ...

Enlace original: https://cgspace.cgiar.org/handle/10568/89498

Investigación en Agricultura

KNOWLEDGE ORGANIZATION SYSTEM

ONTOLOGY

RELATIONSHIP SCHEME

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Cooper, L. , Meier, A. , Laporte, M-A. , Elser, J.L. , Mungall, C. , Sinn, B.T. , Cavaliere, D. , Carbon, S. , Dunn, N.A. , Smith, B. , Qu, B. , Preece, J. , Zhang, E. , Todorovic, S. , Gkouto, G. , Doonan, J.H. , Stevenson, D.W. , Arnaud, Elizabeth , Jaiswal, P. , [The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics] , The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

Report 2018

Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species. Workshop Report

Autor: Matentzoglu, N. Balhoff, J. Bello, S. Boerkoel, C. Bradford, Y. Carmody, L. Cooper, L. Grove, C. Harris, N. Köhler, S. Laporte, M-A. Laulederkind, S. Lee, R. Mazandu, G. McMurry, J. Mungall, C. Osumi-Sutherland, D. Pilgrim, C. Rageth, K. Robb, S. Robinson, P. Segerdell, E. Thessen, A. Vasilevsky, N. Zhang, X. Haendel, M.

Logical definitions, in particular those following the Entity-Quality approach, are increasingly used to drive automated classification of phenotypes and integrate phenotypes across species semantically. Over the years, the lack of consistent and widespread use of common standards resulted in con...

Enlace original: https://cgspace.cgiar.org/handle/10568/100816

Investigación en Agricultura

ONTOLOGY

PHENOTYPES

DATA PROCESSING

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Matentzoglu, N. , Balhoff, J. , Bello, S. , Boerkoel, C. , Bradford, Y. , Carmody, L. , Cooper, L. , Grove, C. , Harris, N. , Köhler, S. , Laporte, M-A. , Laulederkind, S. , Lee, R. , Mazandu, G. , McMurry, J. , Mungall, C. , Osumi-Sutherland, D. , Pilgrim, C. , Rageth, K. , Robb, S. , Robinson, P. , Segerdell, E. , Thessen, A. , Vasilevsky, N. , Zhang, X. , Haendel, M. , [Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species. Workshop Report] , Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species. Workshop Report

Conference Paper 2016

Planteome: A resource for common reference ontologies and applications for plant biology

Autor: Jaiswal, P. Cooper, L. Elser, J.L. Meier, A. Laporte, M-A. Mungall, C. Smith, B. Johnson, E.K.S. Seymour, M. Preece, J. Xu, X. Kitchen, R.S. Qu, B. Zhang, E. Arnaud, Elizabeth Carbon, S. Todorovic, S. Stevenson, D.W.

Around the world, a small number of plant species serve as the primary source of food for the human population, yet these crops are vulnerable to multiple stressors, such as diseases, nutrient deficiencies and unfavorable environmental conditions. Traditional breeding methods for plant improvemen...

Enlace original: https://cgspace.cgiar.org/handle/10568/78564

Investigación en Agricultura

CROPS

ONTOLOGY

DATA

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Jaiswal, P. , Cooper, L. , Elser, J.L. , Meier, A. , Laporte, M-A. , Mungall, C. , Smith, B. , Johnson, E.K.S. , Seymour, M. , Preece, J. , Xu, X. , Kitchen, R.S. , Qu, B. , Zhang, E. , Arnaud, Elizabeth , Carbon, S. , Todorovic, S. , Stevenson, D.W. , [Planteome: A resource for common reference ontologies and applications for plant biology] , Planteome: A resource for common reference ontologies and applications for plant biology

Journal Article 2017

Developing data interoperability using standards: A wheat community use case

Autor: Dzale-Yeumo, E. Alaux, M. Arnaud, Elizabeth Aubin, S. Baumann, U. Buche, P. Cooper, L. Cwiek-Kupczynska, H. Davey, R.P. Fulss, R.A. Jonquet, C. Laporte, M-A. Larmande, Pierre Pommier, C. Protonotarios, V. Reverte, C. Shrestha, R. Subirats, I. Venkatesan, A. Whan, A. Quesneville, H.

In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop wheat data interoperability guidelines. Interoperability is the ability of two or more systems and devices to cooperate and exchange data, and interpret that shared informa...

Enlace original: https://cgspace.cgiar.org/handle/10568/89854

Investigación en Agricultura

ONTOLOGY

STANDARDS

TERMINOLOGY

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Dzale-Yeumo, E. , Alaux, M. , Arnaud, Elizabeth , Aubin, S. , Baumann, U. , Buche, P. , Cooper, L. , Cwiek-Kupczynska, H. , Davey, R.P. , Fulss, R.A. , Jonquet, C. , Laporte, M-A. , Larmande, Pierre , Pommier, C. , Protonotarios, V. , Reverte, C. , Shrestha, R. , Subirats, I. , Venkatesan, A. , Whan, A. , Quesneville, H. , [Developing data interoperability using standards: A wheat community use case] , Developing data interoperability using standards: A wheat community use case

Conference Paper 2013

The species-specific crop ontology (Generation Challenge Programme): Application and integration into the reference plant trait ontology to enable data mining on phenotypes.

Autor: Arnaud, Elizabeth Shrestha, R. Kulakow, P.A. Bakare, M. López Montes, A. Ofodile, S. Reddy T.P. Prasad, P. Shah, Tushaar Hash, C.T. Weltzien, Eva Sissoko, I. Guerrero, A.F. Simon, R. Borja Borja, N.F. Ramil, M. Matteis, L. Skofic, M. Hazekamp, T. McLaren, G. Cooper, L. Jaiswal, P. Menda, N. Nelson, R. Grant, D. Bastow, R. Mueller, L. Rami, J.F.

The Crop Ontology (CO) of the Generation Challenge Program (GCP) (http://cropontology.org/) currently contains eleven crop-specific ontologies and has been developed for the Integrated Breeding Platform (IBP) (https://www.integratedbreeding.net/) by several CGIAR centers. The CO provides validate...

Enlace original: https://cgspace.cgiar.org/handle/10568/57036

Investigación en Agricultura

POTATOES

ONTOLOGY

PHENOTYPES

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Arnaud, Elizabeth , Shrestha, R. , Kulakow, P.A. , Bakare, M. , López Montes, A. , Ofodile, S. , Reddy T.P. , Prasad, P. , Shah, Tushaar , Hash, C.T. , Weltzien, Eva , Sissoko, I. , Guerrero, A.F. , Simon, R. , Borja Borja, N.F. , Ramil, M. , Matteis, L. , Skofic, M. , Hazekamp, T. , McLaren, G. , Cooper, L. , Jaiswal, P. , Menda, N. , Nelson, R. , Grant, D. , Bastow, R. , Mueller, L. , Rami, J.F. , [The species-specific crop ontology (Generation Challenge Programme): Application and integration into the reference plant trait ontology to enable data mining on phenotypes.] , The species-specific crop ontology (Generation Challenge Programme): Application and integration into the reference plant trait ontology to enable data mining on phenotypes.

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Resultados de búsqueda

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

[Planteome_NAR_2017.pdf]

Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species. Workshop Report

[Phenotype_Matentzoglu_2018.pdf]

Planteome: A resource for common reference ontologies and applications for plant biology

Developing data interoperability using standards: A wheat community use case

[DzaleYeumo_2017.pdf]

The species-specific crop ontology (Generation Challenge Programme): Application and integration into the reference plant trait ontology to enable data mining on phenotypes.