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Journal Article 2017

Autor: Jonquet, C. Toulet, A. Arnaud, Elizabeth Aubin, S. Dzale-Yeumo, E. Emonet, V. Graybeal, J. Laporte, M-A. Musen, M.A. Pesce, V. Larmande, Pierre

Many vocabularies and ontologies are produced to represent and annotate agronomic data. However, those ontologies are spread out, in different formats, of different size, with different structures and from overlapping domains. Therefore, there is need for a common platform to receive and host the...

Enlace original: https://cgspace.cgiar.org/handle/10568/89904

Investigación en Agricultura
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Jonquet, C. ,  Toulet, A. ,  Arnaud, Elizabeth ,  Aubin, S. ,  Dzale-Yeumo, E. ,  Emonet, V. ,  Graybeal, J. ,  Laporte, M-A. ,  Musen, M.A. ,  Pesce, V. ,  Larmande, Pierre ,  [AgroPortal: a vocabulary and ontology repository for agronomy] ,  AgroPortal: a vocabulary and ontology repository for agronomy
Journal Article 2017

Autor: Garnier, E. Stahl, U. Laporte, M-A. Kattge, J. Mougenot, I. Kuhn, I. Laporte, B. Amiaud, B. Ahrestani, F.S. Bonisch, G. Bunker, D.E. Cornelissen, J.H.C. Díaz, S. Enquist, B.J. Gachet, S. Jaureguiberry, P. Kleyer, M. Lavorel, S. Maicher, L. Pérez Harguindeguy, N. Poorter, H. Schildhauer, M. Shipley, B. Violle, C. Weiher, E. Wirth, C. Wright, I.J. Klotz, S.
Enlace original: https://cgspace.cgiar.org/handle/10568/79467

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Garnier, E. ,  Stahl, U. ,  Laporte, M-A. ,  Kattge, J. ,  Mougenot, I. ,  Kuhn, I. ,  Laporte, B. ,  Amiaud, B. ,  Ahrestani, F.S. ,  Bonisch, G. ,  Bunker, D.E. ,  Cornelissen, J.H.C. ,  Díaz, S. ,  Enquist, B.J. ,  Gachet, S. ,  Jaureguiberry, P. ,  Kleyer, M. ,  Lavorel, S. ,  Maicher, L. ,  Pérez Harguindeguy, N. ,  Poorter, H. ,  Schildhauer, M. ,  Shipley, B. ,  Violle, C. ,  Weiher, E. ,  Wirth, C. ,  Wright, I.J. ,  Klotz, S. ,  [Towards a thesaurus of plant characteristics: an ecological contribution] ,  Towards a thesaurus of plant characteristics: an ecological contribution
Journal Article 2017

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
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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

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
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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 2018

Autor: Endara L. Burleigh G. Cooper L. Jaiswal, P. Laporte, M-A.

Assembling large-scale phenotypic datasets for evolutionary and biodiversity studies of plants can be extremely difficult and time consuming. New semi-automated Natural Language Processing (NLP) pipelines can extract phenotypic data from taxonomic descriptions, and their performance can be enhanc...

Enlace original: https://cgspace.cgiar.org/handle/10568/100813

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Endara L. ,  Burleigh G. ,  Cooper L. ,  Jaiswal, P. ,  Laporte, M-A. ,  [A Natural Language Processing Pipeline to extract phenotypic data from formal taxonomic descriptions with a focus on flagellate plants] ,  A Natural Language Processing Pipeline to extract phenotypic data from formal taxonomic descriptions with a focus on flagellate plants
Conference Paper 2016

Autor: Valette, L. Pietragalla, J. Laporte, M-A. Afolabi, A. Boukar, O. Cannon, Steven B. Diers, D.W. Dreher, K.A. Gaur, Pooran M. Guerrero, A.F. Hash, C.T. Hualla, V. Inoussa, D. Kalberer, S.R. Kondombo-Barro, C.P. Kumar, S. López Montes, A. Menda, N. Nelson, R. Ofodile, S. Patil, S. Prasad, P. Rajendran, K. Rami, J.F. Rathore, A. Sackville Hamilton, N.R. Reinhard Simon, Guvener Selim Teme, N. Weltzien, Eva Arnaud, Elizabeth Shrestha, R.

The Crop Ontology (CO, http://www.cropontology.org/) is a resource of the Integrated Breeding Platform (IBP, http://integratedbreeding.net/) providing breeders with crop specific terms for fieldbook edition and data annotation. Until Mai 2015, a plant phenotype was annotated with 3 CO identifiers...

Enlace original: https://cgspace.cgiar.org/handle/10568/78758

Investigación en Agricultura
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Valette, L. ,  Pietragalla, J. ,  Laporte, M-A. ,  Afolabi, A. ,  Boukar, O. ,  Cannon, Steven B. ,  Diers, D.W. ,  Dreher, K.A. ,  Gaur, Pooran M. ,  Guerrero, A.F. ,  Hash, C.T. ,  Hualla, V. ,  Inoussa, D. ,  Kalberer, S.R. ,  Kondombo-Barro, C.P. ,  Kumar, S. ,  López Montes, A. ,  Menda, N. ,  Nelson, R. ,  Ofodile, S. ,  Patil, S. ,  Prasad, P. ,  Rajendran, K. ,  Rami, J.F. ,  Rathore, A. ,  Sackville Hamilton, N.R. ,  Reinhard Simon, Guvener Selim ,  Teme, N. ,  Weltzien, Eva ,  Arnaud, Elizabeth ,  Shrestha, R. ,  [Crop ontology: integration of standard variables] ,  Crop ontology: integration of standard variables
Conference Paper 2016

Autor: Jonquet, C. Dzale-Yeumo, E. Arnaud, Elizabeth Larmande, Pierre Toulet, A. Laporte, M-A.

Our project is to develop and support a reference ontology repository for the agronomic domain. By reusing the NCBO BioPortal technology, we have already designed and implemented a prototype ontology repository for plants and a few crops. We plan to turn that prototype into a real service to the ...

Enlace original: https://cgspace.cgiar.org/handle/10568/78753

Investigación en Agricultura
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Jonquet, C. ,  Dzale-Yeumo, E. ,  Arnaud, Elizabeth ,  Larmande, Pierre ,  Toulet, A. ,  Laporte, M-A. ,  [AgroPortal: a proposition for ontology-based services in the agronomic domain] ,  AgroPortal: a proposition for ontology-based services in the agronomic domain
Poster 2016

Autor: Valette, L. Pietragalla, J. Laporte, M-A. Afolabi, A. Boukar, O. Cannon, Steven B. Diers, D.W. Dreher, K.A. Gaur, Pooran M. Guerrero, A.F. Hash, C.T. Hualla, V. Inoussa, D. Kalberer, S.R. Kondombo-Barro, C.P. Kumar, S. López Montes, A. Menda, N. Nelson, R. Ofodile, S. Patil, S. Prasad, P. Rajendran, K. Rami, J.F. Rathore, A. Sackville Hamilton, N.R. Reinhard Simon, Guvener Selim Teme, N. Weltzien, Eva Arnaud, Elizabeth Shrestha, R.
Enlace original: https://cgspace.cgiar.org/handle/10568/78763

Investigación en Agricultura
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Valette, L. ,  Pietragalla, J. ,  Laporte, M-A. ,  Afolabi, A. ,  Boukar, O. ,  Cannon, Steven B. ,  Diers, D.W. ,  Dreher, K.A. ,  Gaur, Pooran M. ,  Guerrero, A.F. ,  Hash, C.T. ,  Hualla, V. ,  Inoussa, D. ,  Kalberer, S.R. ,  Kondombo-Barro, C.P. ,  Kumar, S. ,  López Montes, A. ,  Menda, N. ,  Nelson, R. ,  Ofodile, S. ,  Patil, S. ,  Prasad, P. ,  Rajendran, K. ,  Rami, J.F. ,  Rathore, A. ,  Sackville Hamilton, N.R. ,  Reinhard Simon, Guvener Selim ,  Teme, N. ,  Weltzien, Eva ,  Arnaud, Elizabeth ,  Shrestha, R. ,  [Crop ontology: integration of standard variables] ,  Crop ontology: integration of standard variables
Poster 2016

Autor: Jonquet, C. Dzale-Yeumo, E. Arnaud, Elizabeth Larmande, Pierre Toulet, A. Laporte, M-A.
Enlace original: https://cgspace.cgiar.org/handle/10568/78752

Investigación en Agricultura
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Jonquet, C. ,  Dzale-Yeumo, E. ,  Arnaud, Elizabeth ,  Larmande, Pierre ,  Toulet, A. ,  Laporte, M-A. ,  [AgroPortal: a proposition for ontology-based services in the agronomic domain] ,  AgroPortal: a proposition for ontology-based services in the agronomic domain
Report 2019

Autor: Matentzoglu, N Balhoff, J.P. Bello, S.M. Bradford, Y.M. Carmody, L.C. Cooper, L.D. Laporte, M-A.

The central purpose of this workshop was to bring together users and developers of phenotype ontologies and to provide them with a forum to share, learn and debate. The second edition of the workshop further aimed to address two of the fundamental bottlenecks identified in the course of these com...

Enlace original: https://cgspace.cgiar.org/handle/10568/106627

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Matentzoglu, N ,  Balhoff, J.P. ,  Bello, S.M. ,  Bradford, Y.M. ,  Carmody, L.C. ,  Cooper, L.D. ,  Laporte, M-A. ,  [Phenotype Ontologies Traversing All the Organisms (POTATO) workshop: 2nd edition.] ,  Phenotype Ontologies Traversing All the Organisms (POTATO) workshop: 2nd edition.

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