Author: "Larmande, Pierre" - Searchworks@Jio Institute Digital Library Search Results

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276 results on '"Larmande, Pierre"'

51. Rice Galaxy: an open resource for plant science

Author: Juanillas, Venice, primary, Dereeper, Alexis, additional, Beaume, Nicolas, additional, Droc, Gaetan, additional, Dizon, Joshua, additional, Mendoza, John Robert, additional, Perdon, Jon Peter, additional, Mansueto, Locedie, additional, Triplett, Lindsay, additional, Lang, Jillian, additional, Zhou, Gabriel, additional, Ratharanjan, Kunalan, additional, Plale, Beth, additional, Haga, Jason, additional, Leach, Jan E, additional, Ruiz, Manuel, additional, Thomson, Michael, additional, Alexandrov, Nickolai, additional, Larmande, Pierre, additional, Kretzschmar, Tobias, additional, and Mauleon, Ramil P, additional
Published: 2019
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52. Benchmarking Database Systems for Genomic Selection Implementation

Author: Nti-Addae, Yaw, primary, Matthews, Dave, additional, Ulat, Victor Jun, additional, Syed, Raza, additional, Sempéré, Guil-hem, additional, Pétel, Adrien, additional, Renner, Jon, additional, Larmande, Pierre, additional, Guignon, Valentin, additional, Jones, Elizabeth, additional, and Robbins, Kelly, additional
Published: 2019
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53. Agronomic Linked Data (AgroLD): a Knowledge-based System to Enable Integrative Biology in Agronomy

Author: Larmande, Pierre, El Hassouni, Nordine, Venkatesan, Aravind, Jonquet, Clément, Ruiz, Manuel, Larmande, Pierre, El Hassouni, Nordine, Venkatesan, Aravind, Jonquet, Clément, and Ruiz, Manuel
Abstract: Plant science is a multi-disciplinary scientific discipline that includes research areas such as -omics, physiology, genetics, plant breeding, systems biology and the interaction of plants with the environment to name a few. Among other things, agronomic research aims to improve crop health, production and study the environmental impact on crops. Researchers need to understand deeply the implications and interactions of the various biological processes, by linking data at di↵erent scales (e.g., genomics, proteomics and phenomics). Recent advances in high-throughput technologies have resulted in a tremendous increase in the amount of genomics or phenomics data produced in plant science. This increase, in conjunction with the heterogeneity and variability of the data, presents a major challenge to adopt an integrative research approach. We are facing an urgent need to e↵ectively integrate and assimilate complementary datasets to understand the biological system as a whole. The Semantic Web o↵ers technologies for the integration of heterogeneous data and its transformation into explicitly knowledge thanks to ontologies. We have developed AgroLD (the Agronomic Linked Data – www.agrold.org), a knowledge-based system that exploits the Semantic Web technology and some of the relevant standard domain ontologies, to integrate genome to phenome information on plant species widely studied by the plant science community. We present some integration results of the project, which initially focused on genomics, proteomics and phenomics. Currently, AgroLD contains hundreds millions of triples created by annotating more than 50 datasets coming from 10 data sources such as Gramene.org [1] and TropGeneDB [2] with 10 ontologies such as Gene Ontology [3] and Plant Trait Ontology [4]. Our objective is to o↵er a domain specific
Published: 2018

54. South Green, une plateforme de bioinformatique tournée vers l'agriculture dans les pays du sud

Author: Ravel, Sébastien, Bocs, Stéphanie, Brousseau, Louise, De Lamotte, Frédéric, Dereeper, Alexis, Droc, Gaëtan, Dufayard, Jean François, Guignon, Valentin, Hamelin, Chantal, Larmande, Pierre, Mahé, Frédéric, Martin, Guillaume, Orjuela-Bouniol, Julie, Pitollat, Bertrand, Rouard, Mathieu, Ruiz, Manuel, Sabot, François, Sarah, Gautier, Sempere, Guilhem, Summo, Marilyne, Tando, Ndomassi, Tranchant-Dubreuil, Christine, Ravel, Sébastien, Bocs, Stéphanie, Brousseau, Louise, De Lamotte, Frédéric, Dereeper, Alexis, Droc, Gaëtan, Dufayard, Jean François, Guignon, Valentin, Hamelin, Chantal, Larmande, Pierre, Mahé, Frédéric, Martin, Guillaume, Orjuela-Bouniol, Julie, Pitollat, Bertrand, Rouard, Mathieu, Ruiz, Manuel, Sabot, François, Sarah, Gautier, Sempere, Guilhem, Summo, Marilyne, Tando, Ndomassi, and Tranchant-Dubreuil, Christine
Abstract: South Green (www.southgreen.fr) est une plateforme de bio-informatique dédiée `a la génétique et la génomique des plantes tropicales et méditerranéennes d'intérêt agronomique et de leurs pathogènes. Elle fédère un réseau de bio informaticiens appartenant à différentes unités et instituts de Montpellier (Bioversity International, CIRAD, INRA et IRD) soit environ une vingtaine de personnes en interaction avec les équipes de recherches, avec une expertise multidisciplinaire allant de l'intégration de données et de connaissance au développement de logiciels en bio-informatique, à l'analyse de données de séquençage (détection de polymorphismes et variants structuraux, pangénomique, métagénomique, analyse différentielle de données RNAseq) et le calcul haute performance. Le plateforme South Green a pour objectifs de : Promouvoir des outils originaux issus de la recherche méthodologique. Promouvoir l'interopérabilité des applications développées au sein du réseau. Centraliser l'ensemble des logiciels et systèmes d'information développées au sein d'un portail Web unique (http://www.southgreen.fr) Promouvoir les échanges et les développements collaboratifs Proposer des formations en bio-informatique, bio analyse de données et `a l'utilisation de clusters de calcul Promouvoir la démarche qualité au sein du réseau. Proposer un support pour le calcul à haute performance La plateforme assure le développement de systèmes d'informations et d'outils innovants, nécessaires aux projets scientifiques, réalises au sein de la plateforme et en lien avec l'analyse des données produites par les technologies de séquençage à haut débit (annotation des génomes et de transcriptomes, phylogénie, génotypage) tels que GreenPhylDB, SNiPlay, Gigwa ou AgroLD. Elle propose également des pipelines d'analyses de données de séquençage au travers de deux gestionnaires de workflows : Galaxy et TOGGLe. Enfin, impliquée dans plusieurs projets de séquençage international, elle possède une forte expertise en d
Published: 2018

55. The South Green Bioinformatics platform, a comprehensive resource for crop genomics

Author: Manuel Ruiz, Dereeper, Alexis, Droc, Gaëtan, Sarah, Gautier, Tranchant-Dubreuil, Christine, Dufayard, Jean François, Guignon, Valentin, Hamelin, Chantal, Lamotte, Frédéric, Larmande, Pierre, Sabot, François, Sempere, Guilhem, Summo, Marilyne, Pitollat, Bertrand, This, Dominique, stéphanie bocs, Hueber, Yann, El Hassouni, Nordine, Guillaume Martin, Gkanogiannis, Anestis, Sébastien RAVEL, Monat, Cécile, Tando, Ndomassi, and Rouard, Mathieu
Subjects: ComputingMethodologies_PATTERNRECOGNITION, food and beverages
Abstract: Analysis and visualization of massive genomics datasets are an ongoing trend in plant sciences. The South Green Bioinformatics platform provides an ecosystem of tools that were originally developed as independent entities to fulfill the need for specific projects or crops, but have evolved over time to generic tools to comprehensively study crop genomics. We have built a large panel of public information systems dedicated to specialized datasets (markers, genes, gene families, transcriptomes, genotypes, phenotypes, etc.) and crop-specific resources called Genome Hubs. Target users of bioinformatic analytical workflows are usually divided between people who use command-line and those who do not. We addressed both categories by offering complementary solutions, like Galaxy-based and command-line applications. Various groups used the South Green infrastructure to obtain their data and results, and were able to publish high-quality biological information, on Coffee genome, Banana, Cocoa, African rice or large transcriptome resources. Tools developed for these studies are adaptable to a wide range of other organisms.
Published: 2017

56. Gigwa - Genotype Investigator for Genome-Wide Analyses. [P0442]

Author: Manuel Ruiz, Sempere, Guilhem, Petel, Adrien, Dereeper, Alexis, Gautier, Sarah, and Larmande, Pierre
Subjects: C30 - Documentation et information, L10 - Génétique et amélioration des animaux, F30 - Génétique et amélioration des plantes
Abstract: Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions. Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single- or multi-user mode. In addition, it provides a wide range of popular export formats. The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers. (Texte integral)
Published: 2017

57. South Green bioinformatics platform : Plateforme collaborative de bioinformatique verte héraultaise

Author: Bocs, Stéphanie, Couvin, David, De Lamotte, Frédéric, Dereeper, Alexis, Droc, Gaëtan, Dufayard, Jean François, El Hassouni, Nordine, Farcy, Cédric, Gkanogiannis, Anestis, Guignon, Valentin, Hamelin, Chantal, Hueber, Yann, Larivière, Delphine, Larmande, Pierre, Martin, Guillaume, Monat, Cécile, Ortega Abboud, Enrique, Pitollat, Bertrand, Pointet, Stéphanie, Ravel, Sébastien, Rouard, Mathieu, This, Patrice, and Tranchant-Dubreuil, Christine
Published: 2017

58. The Agronomic Linked Data (AgroLD) Project. [P0322]

Author: Larmande, Pierre, Manuel Ruiz, El Hassouni, Nordine, and Venkatesan, Aravind
Subjects: C30 - Documentation et information, A50 - Recherche agronomique
Abstract: The drastic growth in data in the recent years, within the Agronomic sciences has brought the concept of knowledge management to the forefront. Some of the factors that contribute to this change include a) conducting high-throughput experiments have become affordable, the time spent in generating data through these experiments are minuscule when compared to its integration and analysis; b) publishing data over the web is fairly trivial and c) multiple databases exist for each type of data (i.e. 'omics' data) with a possible overlap or slight variation in its coverage. In most cases these sources remain autonomous and disconnected. Hence, efficiently managed data and the underlying knowledge in principle will make data analysis straightforward aiding in more efficient decision making. At the Institute of Computational Biology (IBC), we are involved in developing methods to aid data integration and knowledge management within the domain of Agronomic sciences to improve information accessibility and interoperability. To this end, we address the challenge by pursuing several complementary research directions towards: distributed, heterogeneous data integration. This talk will focus mainly on,Agronomic Linked Data (AgroLD) wich is a Semantic Web knowledge base designed to integrate data from various publically available plant centric data sources. These include Gramene, Oryzabase, TAIR and resources from the South Green platform among many others. The aim of AgroLD project is to provide a portal for bioinformaticians and domain experts to exploit the homogenized data towards enabling to bridge the knowledge. (Texte integral)
Published: 2017

59. Evaluating Named-Entity Recognition approaches in plant molecular biology

Author: Do, Huy, primary, Than, Khoat, additional, and Larmande, Pierre, additional
Published: 2018
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60. Rice Galaxy: an open resource for plant science

Author: Juanillas, Venice, primary, Dereeper, Alexis, additional, Beaume, Nicolas, additional, Droc, Gaetan, additional, Dizon, Joshua, additional, Mendoza, John Robert, additional, Perdon, Jon Peter, additional, Mansueto, Locedie, additional, Triplett, Lindsay, additional, Lang, Jillian, additional, Zhou, Gabriel, additional, Ratharanjan, Kunalan, additional, Plale, Beth, additional, Haga, Jason, additional, Leach, Jan E., additional, Ruiz, Manuel, additional, Thomson, Michael, additional, Alexandrov, Nickolai, additional, Larmande, Pierre, additional, Kretzschmar, Tobias, additional, and Mauleon, Ramil P., additional
Published: 2018
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61. Agronomic Linked Data (AgroLD): a Knowledge-based System to Enable Integrative Biology in Agronomy

Author: Venkatesan, Aravind, primary, Tagny, Gildas, additional, El Hassouni, Nordine, additional, Chentli, Imene, additional, Guignon, Valentin, additional, Jonquet, Clement, additional, Ruiz, Manuel, additional, and Larmande, Pierre, additional
Published: 2018
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62. Progress in single-access information systems for wheat and rice crop improvement

Author: Scheben, Armin, primary, Chan, Chon-Kit Kenneth, additional, Mansueto, Locedie, additional, Mauleon, Ramil, additional, Larmande, Pierre, additional, Alexandrov, Nickolai, additional, Wing, Rod A, additional, McNally, Kenneth L, additional, Quesneville, Hadi, additional, and Edwards, David, additional
Published: 2018
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63. The South Green Bioinformatics platform, a comprehensive resource for crop genomics

Author: Ruiz, Manuel, Dereeper, Alexis, Droc, Gaëtan, Sarah, Gautier, Tranchant-Dubreuil, Christine, Dufayard, Jean François, Guignon, Valentin, Hamelin, Chantal, De Lamotte, Frédéric, Larmande, Pierre, Sabot, François, Sempere, Guilhem, Summo, Marilyne, Pitollat, Bertrand, This, Dominique, Bocs, Stéphanie, Hueber, Yann, El Hassouni, Nordine, Martin, Guillaume, Gkanogiannis, Anestis, Ravel, Sébastien, Monat, Cécile, Tando, Ndomassi, Rouard, Mathieu, Ruiz, Manuel, Dereeper, Alexis, Droc, Gaëtan, Sarah, Gautier, Tranchant-Dubreuil, Christine, Dufayard, Jean François, Guignon, Valentin, Hamelin, Chantal, De Lamotte, Frédéric, Larmande, Pierre, Sabot, François, Sempere, Guilhem, Summo, Marilyne, Pitollat, Bertrand, This, Dominique, Bocs, Stéphanie, Hueber, Yann, El Hassouni, Nordine, Martin, Guillaume, Gkanogiannis, Anestis, Ravel, Sébastien, Monat, Cécile, Tando, Ndomassi, and Rouard, Mathieu
Abstract: Analysis and visualization of massive genomics datasets are an ongoing trend in plant sciences. The South Green Bioinformatics platform provides an ecosystem of tools that were originally developed as independent entities to fulfill the need for specific projects or crops, but have evolved over time to generic tools to comprehensively study crop genomics. We have built a large panel of public information systems dedicated to specialized datasets (markers, genes, gene families, transcriptomes, genotypes, phenotypes, etc.) and crop-specific resources called Genome Hubs. Target users of bioinformatic analytical workflows are usually divided between people who use command-line and those who do not. We addressed both categories by offering complementary solutions, like Galaxy-based and command-line applications. Various groups used the South Green infrastructure to obtain their data and results, and were able to publish high-quality biological information, on Coffee genome, Banana, Cocoa, African rice or large transcriptome resources. Tools developed for these studies are adaptable to a wide range of other organisms.
Published: 2017

64. AgroPortal: an ontology repository for agronomy

Author: Jonquet, Clément, Toulet, Anne, Emonet, Vincent, Larmande, Pierre, Jonquet, Clément, Toulet, Anne, Emonet, Vincent, and Larmande, Pierre
Abstract: Many vocabularies and ontologies are produced to represent and annotate agronomic data. Therefore, there is a need of a common platform to identify, host and use them in agro-informatics application. By reusing the NCBO BioPortal technology, we have designed AgroPortal an ontology repository for the agronomy domain. The AgroPortal project aims at reusing the scientific outcomes and experience of the biomedical domain in the context of plant, agronomy, food, and biodiversity. We offer an ontology portal which features ontology hosting, search, versioning, visualization, comment, recommendation, enables semantic annotation, as well as storing and exploiting ontology alignments. All of these within a fully semantic web compliant infrastructure. The AgroPortal specifically pays attention to respect the requirements of the agronomic community in terms of ontology formats (e.g., SKOS, trait dictionaries) or supported features. In this demonstration, we will present our platform currently open and accessible at http://agroportal.lirmm.fr.
Published: 2017

65. The Agronomic Linked Data (AgroLD) project

Author: El Hassouni, Nordine, Ruiz, Manuel, Toulet, Anne, Jonquet, Clément, Larmande, Pierre, El Hassouni, Nordine, Ruiz, Manuel, Toulet, Anne, Jonquet, Clément, and Larmande, Pierre
Abstract: Agronomy is an overarching field that consists of various areas of research such Genetics, Plant Molecular Biology, Ecology and Earth Science. At the Institute of Computational Biology (IBC), we are currently building a RDF knowledge base, Agronomic Linked Data (AgroLD – www.agrold.org). The knowledge base is designed to integrate data from various publically available plant centric data sources. The aim of AgroLD project is to provide a portal for bioinformatics and domain experts to exploit the homogenized data model towards filling the knowledge gaps. To this end, we plan to engage with stakeholders in demonstrating the advantages of SW in answering complex domain relevant questions that were unapproachable using traditional methods, strategically filling knowledge gaps.
Published: 2017

66. Gigwa - Genotype Investigator for Genome-Wide Analyses. [P0442]

Author: Ruiz, Manuel, Sempere, Guilhem, Petel, Adrien, Dereeper, Alexis, Gautier, Sarah, Larmande, Pierre, Ruiz, Manuel, Sempere, Guilhem, Petel, Adrien, Dereeper, Alexis, Gautier, Sarah, and Larmande, Pierre
Abstract: Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions. Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single- or multi-user mode. In addition, it provides a wide range of popular export formats. The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers. (Texte integral)
Published: 2017

67. AgroPortal: an open repository of ontologies and vocabularies for agriculture and nutrition data

Author: Jonquet, Clement, Toulet, Anne, Arnaud, Elizabeth, Aubin, Sophie, Yeumo, Esther Dzalé, Emonet, Vincent, Pesce, Valeria, Larmande, Pierre, Système Multi-agent, Interaction, Langage, Evolution (SMILE), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Bioversity International, Consultative Group on International Agricultural Research [CGIAR], DIST Délégation Information Scientifique et Technique (DV-IST), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Food and Agricultural Organization of the United Nations (FAO), United Nations Organization, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Scientific Data Management (ZENITH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Ben Schaap, ANR-12-JS02-0010,SIFR,Indexation sémantique de ressources biomédicales francophones(2012), ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier(2011), ANR-10-LABX-0020/10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Institut National de la Recherche Agronomique (INRA), Food and Agriculture Organization of the United Nations [Rome, Italie] (FAO), ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), and Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)
Subjects: AgroPortal, Ontologies, [INFO]Computer Science [cs], Agronomy
Abstract: International audience; Similarly to what happens in biomedicine, communities engaged in agronomic research need to access specific sets of ontologies for data annotation and integration. For instance, it has been established that the scientific challenges in plant breeding have switched from genetics to phenotyping and that standard traits/phenotypes vocabularies are necessary to facilitate breeder’s data integration and comparison. In parallel of very specific crop dictionaries, important organizations have produced large reference vocabularies such as AGROVOC (Food and Agriculture Organization), NAL Thesaurus (National Agricultural Library) or the CAB Thesaurus (Centre for Agricultural Bioscience International). The more ontologies are being produced in the domain, the more the need to create, store and retrieve alignments between those ontologies become important. In fact, there exists a need of a one-stop-shop for agronomical, environmental and food related ontologies enabling to identify and select an ontology for a specific task as well as offering generic services to exploit them in search, annotation or other scientific data management processes
Published: 2016

68. Integration and Visualization of Epigenome and Mobilome Data in Crops

Author: Robakowska Hyzorek, Dagmara, Mirouze, Marie, Larmande, Pierre, Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Scientific Data Management (ZENITH), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut de Biologie Computationnelle IBC, Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM)
Subjects: [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: National audience; In the coming years, the study of the interaction between the epigenome and the mobilome is likely to give insights on the role of TEs on genome stability and evolution. In the present project we have created tools to collect epigenetic datasets from different laboratories and databases and translate them to a standard format to be integrated, analyzed and finally visualized.
Published: 2016

69. Construction d’un gold standard pour les données agronomiques

Author: Chentli, Imène, Larmande, Pierre, Todorov, Konstantin, Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Scientific Data Management (ZENITH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), WEB Architecture x Semantic WEB x WEB of Data (WEB3), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle IBC, LIRMM, Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), WEB-CUBE, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Fuzziness, Alignments, Data & Ontologies (FADO)
Subjects: Agronomie, Systèmes Questions-Réponses, Web Sémantique, [INFO.INFO-IR]Computer Science [cs]/Information Retrieval [cs.IR], Interrogation de données, [INFO]Computer Science [cs], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], SPARQL, Données de référence, Traitement de Langage Naturel
Abstract: International audience; Dans le contexte des ressources agronomiques et au jour d’aujourd'hui, il n’existe ni de données de référence ni de questions adaptées au domaine pour évaluer les interfaces dotées de Systèmes à Questions-Réponses (SQR). A cet effet, nous avons construit un étalon-or (gold standard) constitué d’un ensemble de questions de référence formulées en langage naturel et leur correspondance en langage SPARQL. Les ressources d’Agronomic LinkedData constituent le jeu de données de référence pour la grande richesse de la base de connaissances.
Published: 2016

70. AgroPortal : A Proposition for Ontology-Based Services in the Agronomic Domain

Author: Jonquet, Clement, Dzalé-Yeumo, Esther, Arnaud, Elizabeth, Larmande, Pierre, Toulet, Anne, Laporte, Marie-Angélique, Système Multi-agent, Interaction, Langage, Evolution (SMILE), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Bioversity International, Consultative Group on International Agricultural Research [CGIAR], Scientific Data Management (ZENITH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), German Centre for Integrative Biodiversity Research (iDiv), ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier(2011), ANR-12-JS02-0010,SIFR,Indexation sémantique de ressources biomédicales francophones(2012), ANR-10-LABX-0020/10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [INFO.INFO-WB]Computer Science [cs]/Web, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Abstract: International audience; 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 community. The AgroPortal project aims at reusing the scientific outcomes and experience of the biomedical domain in the context of plant, agronomic and environment sciences. We will offer an ontology portal which features ontology hosting, search, versioning, visualization, comment, but we will also offer services for semantically annotating data with the ontologies, as well as storing and exploiting ontology alignments and data annotations. All of these within a fully semantic web compliant infrastructure. The main objective of this project is to enable straightforward use of agronomic related ontologies, avoiding data managers and researchers the burden to deal with complex knowledge engineering issues to annotate the research data. The AgroPortal project will specifically pay attention to respect the requirements of the agronomic community and the specificities of the crop domain. We will first focus on the outputs of a few existing driving agronomic use cases related to rice and wheat, with the goal of generalizing to other Crop Ontology related use cases. AgroPortal will offer a robust and stable platform that we anticipate will be highly valued by the community.
Published: 2016

71. Benchmarcking Application main portal

Author: Le Ngoc, Luyen, Tireau, Anne, Venkatesen, Aravind, Neveu, Pascal, Larmande, Pierre, and ProdInra, Migration
Subjects: [INFO.INFO-OH] Computer Science [cs]/Other [cs.OH]
Published: 2016

72. Une architecture orientée services pour l'extraction de connaissances dans la base de données liées AgroLD

Author: Tagny Ngompé, Gildas, Venkatesan, Aravind, El Hassouni, Nordine, Ruiz, Manuel, and Larmande, Pierre
Subjects: Méthodologie, U10 - Informatique, mathématiques et statistiques, Analyse de données, gestion de l'information, 000 - Autres thèmes, Secteur agricole, Sciences végétales, Projet de recherche, Bioinformatique, C30 - Documentation et information, Système d'information, Collecte de données, U30 - Méthodes de recherche
Abstract: L'agronomie est un domaine important constitué de divers domaines de recherche tels que la génétique, la biologie moléculaire des plantes, l'écologie et les sciences de la terre. Les dernières décennies ont vu le succès du développement de technologies à haut débit qui ont révolutionné et transformé la recherche agronomique. L'application de ces technologies a généré de grandes quantités de données et de ressources sur le web. Dans la plupart des cas, ces sources restent autonomes et déconnectées. Le projet Agronomic Linked Data (AgroLD) est une base de connaissances du web sémantique conçue pour intégrer des données provenant de diverses sources publiques de données centrées sur des plantes. L'objectif du projet AgroLD est de fournir un portail web pour les bioinformaticiens et les experts du domaine aﬁn d'exploiter les données homogénéisées et permettre de connecter les connaissances dans ce domaine.
Published: 2016

73. ICBO : International Conference on Biomedical Ontologies

Author: Jonquet, C., Toulet, A., Arnaud, E., Aubin, S., Dzalé Yeumo, E., Emonet, V., Pesce, V., Larmande, Pierre, Jaiswal, P. (ed.), Hoehndorf, R. (ed.), Arighi, C. (ed.), and Meier, A. (ed.)
Abstract: Many vocabularies and ontologies are produced to represent and annotate agronomic data. By reusing the NCBO BioPortal technology, we have already designed and implemented an advanced prototype ontology repository for the agronomy domain. We plan to turn that prototype into a real service to the community. The AgroPortal project aims at reusing the scientific outcomes and experience of the biomedical domain in the context of plant, agronomic, food, environment (perhaps animal) sciences. We offer an ontology portal which features ontology hosting, search, versioning, visualization, comment, recommendation, enables semantic annotation, as well as storing and exploiting ontology alignments. All of these within a fully semantic web compliant infrastructure. The AgroPortal specifically pays attention to respect the requirements of the agronomic community in terms of ontology formats (e.g., SKOS, trait dictionaries) or supported features. In this paper, we present our prototype as well as preliminary outputs of four driving agronomic use cases. With the experience acquired in the biomedical domain and building atop of an already existing technology, we think that AgroPortal offers a robust and stable reference repository that will become highly valuable for the agronomic domain.
Published: 2016

74. Gigwa - Genotype investigator for genome-wide analyses [+ erratum]

Author: Sempéré, G., Philippe, Florian, Dereeper, Alexis, Ruiz, M., Sarah, G., and Larmande, Pierre
Subjects: Genomic variations, HapMap, MongoDB, VCF, SNP, NoSQL, INDEL, Web interface
Abstract: Background: Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions. Description: Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single-or multi-user mode. In addition, it provides a wide range of popular export formats. Conclusions: The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers.
Published: 2016

75. Wheat Data Interoperability Guidelines, Ontologies and User Cases. Recommendations from the RDA Wheat Data Interoperability Working Group

Author: Dzalé Yeumo, Esther, Fulss, Richard, Alaux, Michael, Aubin, Sophie, Arnaud, Elizabeth, Baumann, Ute, Cooper, Laurel, Davey, Richard, Laporte, Marie-Angélique, Larmande, Pierre, Letellier, Thomas, Pommier, Cyril, Protonotarios, Vassilis, Shrestha, Rosemary, Subirats, Imma, Venkatesan, Aravind, and Whan, Alex
Subjects: wheat research, data interoperability
Abstract: The International Wheat Initiative (http://www.wheatinitiative.org) has identified the easy access and interoperability of all wheat related data as a top priority for the wheat research community. An important goal is to make the best use of existing genetic, genomic, and phenotypic data in fundamental and applied wheat science. Hence, data interoperability has become a priority in this community, given the ever-growing data deluge coming from improvements in technologies and numeric methods for DNA (Deoxyribonucleic acid) and RNA (Ribonucleic acid) sequencing, high throughput genotyping and phenotyping, high throughput imaging and satellite monitoring. The Wheat Data Interoperability working group (WDI-WG) was created in 2014 as a Research Data Alliance (RDA, http://rd-alliance.org) working group under the umbrella of Wheat Information System (WheatIS, http://wheatis.org/) expert working group, which is endorsed by the International Wheat Initiative to build an international information system for genetic, genomic, and phenomic data. The primary mission of the WDI-WG is to provide a common framework for describing and representing data with respect to existing open standards. The WDI-WG is formed by data and information practitioners and scientists from different organizations and countries. The standpoint of the WDI-WG was to avoid the creation of new standards. Therefore, the WDI-WG started by surveying the practices of the wheat research community, then converged and agreed on specific recommendations. The proposed recommendations have been endorsed by the RDA and the WheatIS expert working group.
Published: 2016
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76. Developing data interoperability using standards: A wheat community use case

Author: Dzale Yeumo, Esther, primary, Alaux, Michael, additional, Arnaud, Elizabeth, additional, Aubin, Sophie, additional, Baumann, Ute, additional, Buche, Patrice, additional, Cooper, Laurel, additional, Ćwiek-Kupczyńska, Hanna, additional, Davey, Robert P., additional, Fulss, Richard Allan, additional, Jonquet, Clement, additional, Laporte, Marie-Angélique, additional, Larmande, Pierre, additional, Pommier, Cyril, additional, Protonotarios, Vassilis, additional, Reverte, Carmen, additional, Shrestha, Rosemary, additional, Subirats, Imma, additional, Venkatesan, Aravind, additional, Whan, Alex, additional, and Quesneville, Hadi, additional
Published: 2017
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77. Ontology-based services and knowledge management in the Agronomic Domain

Author: Larmande, Pierre, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Scientific Data Management (ZENITH), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), and Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Bioinformatic, Metadata, Ontologies, Data integration, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Semantic web, Agronomy
Abstract: International audience; The drastic growth in data in the recent years, within the Agronomic sciences has brought the concept of knowledge management to the forefront. Some of the factors that contribute to this change include a) conducting high-throughput experiments have become affordable, the time spent in generating data through these experiments are minuscule when compared to its integration and analysis; b) publishing data over the web is fairly trivial and c) multiple databases exist for each type of data (i.e. ‘omics’ data) with a possible overlap or slight variation in its coverage. In most cases these sources remain autonomous and disconnected. Hence, efficiently managed data and the underlying knowledge in principle will make data analysis straightforward aiding in more efficient decision making. At the Institute of Computational Biology (IBC), we are involved in developing methods to aid data integration and knowledge management within the domain of Agronomic sciences to improve information accessibility and interoperability. To this end, we address the challenge by pursuing several complementary research directions towards: distributed, heterogeneous data integration.This talk will focus mainly on, ongoing projects at IBC:a) The AgroPortal project aims at developing a reference ontology repository for the agronomic domain. By reusing the NCBO BioPortal technology, we will offer an ontology portal which features ontology hosting, search, versioning, visualization, comment, but we will also offer services for semantically annotating data with the ontologies, as well as storing and exploiting ontology alignments and data annotations. b) Agronomic Linked Data (AgroLD): is a Semantic Web knowledge base designed to integrate data from various publically available plant centric data sources. These include Gramene, Oryzabase, TAIR and resources from the South Green platform among many others. The aim of AgroLD project is to provide a portal for bioinformaticians and domain experts to exploit the homogenized data towards enabling to bridge the knowledge.
Published: 2015

78. Development of a generic indexing tool to optimize the use of biological data

Author: Le Ngoc, Luyen, Jouannic, Stéphane, Gantet, Pascal, Larmande, Pierre, Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Scientific Data Management (ZENITH), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM)
Subjects: Database applications, Bioinformatic application, Agronomic data, Distributed application, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: National audience; This application is developed in the context of studies of genetic and phenotypic diversity in Asian and African rice (Oryza sativa and Oryza glaberrima). The objective of these studies is to identify by association genetics approaches some genes of interest in order to understand biological processes related to plant development and plasticity or disease resistance and their exploitation by breeding programs. These studies require handling large volumes of data that are heterogeneous and stored in different formats (Excel file, structured or semi-structured text, images, etc.). The volume and diversity of data can be a challenge for researchers for their optimal exploitation. The design of relational databases appears limited and not scalable. In this context, we have developed a tool for integration and generic indexing to navigate, share and annotate these data in order to exploit them. For this purpose, the project is based on a NoSQL management system Document-oriented - MongoDB, allowing data to be dynamically organized and modeled. The innovative aspect of this project is the development of a scalable system that allows users to perform all the steps from data integration to the query formulation.
Published: 2015

79. Data integration in the agronomic domain : national and international data discovery system

Author: Philippe, Florian, Venkatesan, Aravind, El Hassouni, Nordine, Pommier, Cyril, Ruiz, Manuel, Larmande, Pierre, Steinbach, Delphine, Quesneville, Hadi, Krimmel, Erik, Flores, Raphaël-Gauthier, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Scientific Data Management (ZENITH), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), and Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Database applications, Bioinformatic application, Indexing applications, Distributed applications, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: National audience; Current research in Agronomy has produced a vast amount of genomic, genetic and phenomic data. To deal with the Volume, Variety and Velocity of those data, it is necessary to first refine to candidate datasets through data discovery then to integrate them through semantic web technologies. Data discovery is an approach that allows to easily search for datasets based on keywords and metadata. The plant bioinformatic node of the Institut Français de Bioinformatique (IFB) gives access to several public information systems hosting domain specific data. It is composed of five bioinformatics platforms : the South Green platform, the LIPM platform, the Roscoff platform ABiMS, the platform for Arthopods for Agroecosystems Arthropods and the URGI platform. The later one plays a key role in several national an international projects like the Whea Initiative. Those platforms integrate several plant genomic, genetic and phenomic data, which they need to expose in data discovery and integration systems. The distributed data discovery system need an ETL (Extraction, Transformation and Loading) based integration pipeline implemented on each platform. This ETL can either be developed from scratch or be based on existing technologies such as KarmaWeb, Talend or Open Refine. The pipeline is being developed at the URGI, and will be deployed on all IFB plant nodes. The data discovery system is based on SolR (implemented in the Transplant portal http://www.transplantdb.eu) which uses the Lucene search framework at its core for full-text indexing. Here, we will present the data discovery system architecture and the ETL solutions evaluation and comparison. Work funded by IFB investment for the future infrastructure project, IFB_Plant node.
Published: 2015

80. AgroPortal : a proposition for ontology-based services in the agronomic domain

Author: Jonquet, Clement, Dzalé-Yeumo, Esther, Arnaud, Elizabeth, Larmande, Pierre, Système Multi-agent, Interaction, Langage, Evolution (SMILE), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de Biologie Computationnelle (IBC), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Scientific Data Management (ZENITH), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), ANR-12-JS02-01001,ANR-11-BINF-0002/11-BINF-0002,ANR-10-LABX-0020/10-LABX-0020, ANR-12-JS02-0010,SIFR,Indexation sémantique de ressources biomédicales francophones(2012), ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Bioversity International, Consultative Group on International Agricultural Research [CGIAR], ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier(2011), and ANR-10-LABX-0020/10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010)
Subjects: TRAITEMENT DE DONNEES, SEMANTIQUE, ONTOLOGIE, agronomic sciences, [INFO.INFO-WB]Computer Science [cs]/Web, RESEAU INFORMATIQUE, semantic annotation, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], TERMINOLOGIE, INTERFACE, [INFO.INFO-TT]Computer Science [cs]/Document and Text Processing, [INFO.INFO-MA]Computer Science [cs]/Multiagent Systems [cs.MA], ontology management, [INFO.INFO-IR]Computer Science [cs]/Information Retrieval [cs.IR], ontology mapping, AGRONOMIE, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], INTERNET
Abstract: National audience; 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 community. The AgroPortal project aims at reusing the scientific outcomes and experience of the biomedical domain in the context of plant, agronomic and environment sciences. We will offer an ontology portal which features ontology hosting, search, versioning, visualization, comment, but we will also offer services for semantically annotating data with the ontologies, as well as storing and exploiting ontology alignments and data annotations. All of these within a fully semantic web compliant infrastructure. The main objective of this project is to enable straightforward use of agronomic related ontologies, avoiding data managers and researchers the burden to deal with complex knowledge engineering issues to annotate the research data. The AgroPortal project will specifically pay attention to respect the requirements of the agronomic community and the specificities of the crop domain. We will first focus on the outputs of a few existing driving agronomic use cases related to rice and wheat, with the goal of generalizing to other Crop Ontology related use cases. AgroPortal will offer a robust and stable platform that we anticipate will be highly valued by the community.
Published: 2015

81. South Green bioinformatics platform: Update 2015

Author: Armero, A., Baurens, Franc-Christophe, stéphanie bocs, Breil, A., Lamotte, Frédéric, Dereeper, Alexis, Droc, Gaëtan, Dufayard, Jean François, El Hassouni, Nordine, Farcy, Cédric, Olivier Garsmeur, Guignon, Valentin, Hamelin, Chantal, Hueber, Yann, Kougbeadjo, Ayite, Larivière, Delphine, Larmande, Pierre, Lorenzo, Jonathan, Guillaume Martin, Monat, Cécile, Ndomassi, T., Ortega Abboud, Enrique, Pitollat, Bertrand, Sébastien RAVEL, Ranwez, Vincent, Rouard, Mathieu, Ruiz, E., Sabot, François, Sarah, Gautier, Sempere, Guilhem, Summo, Marilyne, This, Dominique, Tranchant-Dubreuil, Christine, Vallier, Félix, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Biodiversity International, Université de Yaoundé I, Institut de Recherche pour le Développement (IRD), Université de Montpellier (UM), Institut National de la Recherche Agronomique (INRA), and Université de Lyon (COMUE)
Subjects: C30 - Documentation et information, U10 - Informatique, mathématiques et statistiques, [SCCO.COMP]Cognitive science/Computer science, U30 - Méthodes de recherche, F30 - Génétique et amélioration des plantes
Abstract: International audience; In 2015, the South Green Bioinformatics Platform http://www.southgreen.fr/ is a network of 35 bioinformaticians from five biology research institutes working with two High - Performance Computing Data Centres to develop and use new tools for NGS/ Omic analytics of tropical and Mediterranean crops under projects studying relationsh ip between genetic diversity, agronomic performance and response to selection. South Green is affiliated to the South regional centre of the French Institute of Bioinformatics (the French node of the European research infrastructure, ELIXIR). This communit y and the HPC data centres are all located in Montpellier, which facilitates close collaboration and significant pooling to best meet the biologists' demands of our research units. Since 2004, we developed web - based applications with both generic and in - ho use components, for databases, analysis workflows and web interfaces, in order to: manage genetic and phenotypic information ( e.g. TropGeneDB), analyse molecular markers and genetic diversity ( e.g. SNiPlay), assemble transcriptomes ( e.g. ESTtik) map RNA - Se q ( e.g. ARCAD), annotate and compare genomes ( e.g. GNPAnnot), reconstruct evolutionary history of gene families by phylogenomics ( e.g. GreenPhyl). We also participate to the analysis of numerous crop species, that requires computing and storage facilities as well as interoperable information systems, such as rice ( e.g. OryGenesDB), wheat, sorghum, sugarcane, banana (Banana Genome Hub), palms, yam, coffee (CGH), rubber, cacao (CocoaGenDB), cotton, apple, grapevine, olive, eucalyptus, cassava. To face the dat a deluge, we must increase our analytics capabilities. We document our operation at both, administrator/ developer and user/ scientist level, to provide high quality services and reproducible research. We pool into working groups on key themes such as GBS, at both, developer (extreme pair programming) and user (interdisciplinary knowledge exchange) level. We provide training sessions each year. Finally, we implemented several instances of the Galaxy workflow manager and encapsulated our tools. These instanc es serve as a catalyst for massive NGS analyses but it remains to increase storage capacity and improve data management plans. (Résumé d'auteur)
Published: 2015

82. Enabling knowledge management in the agronomic domain. W448

Author: Larmande, Pierre, Venkatesan, Aravind, Manuel Ruiz, Sempere, Guilhem, and Valduriez, Patrick
Subjects: C30 - Documentation et information, A50 - Recherche agronomique, U10 - Informatique, mathématiques et statistiques
Abstract: The drastic growth in data in the recent years, within the Agronomic sciences has brought the concept of knowledge management to the forefront. Some of the factors that contribute to this change include a) conducting high-throughput experiments have become affordable, the time spent in generating data through these experiments are minuscule when compared to its integration and analysis; b) publishing data over the web is fairly trivial and c) multiple databases exist for each type of data (i.e. 'omics' data) with a possible overlap or slight variation in its coverage [1, 2]. In most cases these sources remain autonomous and disconnected. Hence, efficiently managed data and the underlying knowledge in principle will make data analysis straightforward aiding in more efficient decision making. At the Institute of Computational Biology (IBC), we are involved in developing methods to aid data integration and knowledge management within the domain of Agronomic sciences to improve information accessibility and interoperability. To this end, we address the challenge by pursuing several complementary research directions towards: distributed, heterogeneous data integration. This talk will focus mainly on, ongoing projects at IBC: a) Agronomic Linked Data (AgroLD): is a Semantic Web knowledge base designed to integrate data from various publically available plant centric data sources. These include Gramene, Oryzabase, TAIR and resources from the South Green platform among many others. The aim of AgroLD project is to provide a portal for bioinformaticians and domain experts to exploit the homogenized data towards enabling to bridge the knowledge. b) GIGwA: is a tool developed to manage genomic, transcriptomic and genotyping large data resulting from NGS analyses. Often biologists are required to handle large VCF files to filter, query and extract data for their research. The existing tools are mainly targeted for experienced users by providing command line APIs. With GIGwA, we aim to provide a web user interface to make the system accessible to users from the biological field.
Published: 2015

83. Towards efficient data integration and knowledge management in the Agronomic domain

Author: Venkatesan, Aravind, El Hassouni, Nordine, Philippe, Florian, Pommier, Cyril, Quesneville, Hadi, Manuel Ruiz, Larmande, Pierre, Institut de Biologie Computationnelle (IBC), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Scientific Data Management (ZENITH), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut National de Recherche en Informatique et en Automatique (INRIA). FRA., Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: Bioinformatic application, Knowledge management, [INFO.INFO-WB]Computer Science [cs]/Web, 000 - Autres thèmes, Agronomic research, RDF, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], C30 - Documentation et information, A50 - Recherche agronomique, Data interoperability, Data integration, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], U30 - Méthodes de recherche, Semantic Web
Abstract: International audience; Today, the revolution in empirical technologies has generated vast amounts of data. This data deluge has created an urgent need to assimilate it with a panoramic view. To this end, information systems play a central role in managing and integrating these data, aiding the biologists in exploiting this integrated information for the extraction of new knowledge. The plant bioinformatics node of the Institut Français de Bioinformatique (IFB) maintains public information systems where a variety of domain specific data are integrated. Currently, efforts are being taken to expose the IFB plant bioinformatics resources as RDF, utilising domain specific ontologies and metadata. Here, we present the overview and the progress of the project.
Published: 2015

84. Progress in single-access information systems for wheat and rice crop improvement.

Author: Scheben, Armin, Chan, Chon-Kit Kenneth, Mansueto, Locedie, Mauleon, Ramil, Larmande, Pierre, Alexandrov, Nickolai, Wing, Rod A, McNally, Kenneth L, Quesneville, Hadi, and Edwards, David
Subjects: CROP improvement, INFORMATION storage & retrieval systems, WHEAT, RICE, CULTIVARS, FOOD crops
Abstract: Improving productivity of the staple crops wheat and rice is essential to feed the growing global population, particularly in the context of a changing climate. However, current rates of yield gain are insufficient to support the predicted population growth. New approaches are required to accelerate the breeding process, and many of these are driven by the application of large-scale crop data. To leverage the substantial volumes and types of data that can be applied for precision breeding, the wheat and rice research communities are working towards the development of integrated systems to access and standardize the dispersed, heterogeneous available data. Here, we outline the initiatives of the International Wheat Information System (WheatIS) and the International Rice Informatics Consortium (IRIC) to establish Web-based single-access systems and data mining tools to make the available resources more accessible, drive discovery and accelerate the production of new crop varieties. We discuss the progress of WheatIS and IRIC towards unifying specialized wheat and rice databases and building custom software platforms to manage and interrogate these data. Single-access crop information systems will strengthen scientific collaboration, optimize the use of public research funds and help achieve the required yield gains in the two most important global food crops. [ABSTRACT FROM AUTHOR]
Published: 2019
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85. The South Green portal: A comprehensive resource for tropical and Mediterranean crop genomics

Author: Guignon, Valentin, Hueber, Yann, Rouard, Mathieu, Bocs, Stéphanie, Couvin, David, De Lamotte, Frédéric, Droc, Gaëtan, Dufayard, Jean François, El Hassouni, Nordine, Farcy, Cédric, Gkanogiannis, Anestis, Hamelin, Chantal, Larivière, Delphine, Martin, Guillaume, Ortega, Enrique, Pitollat, Bertrand, Pointet, Stéphanie, Ruiz, Manuel, Gautier, Sarah, Summo, Marilyne, This, Dominique, Ravel, Sébastien, Larmande, Pierre, Monat, Cécile, Sabot, François, Tando, Ndomassi, Tranchant-Dubreuil, Christine, Sempere, Guilhem, Dereeper, Alexis, Guignon, Valentin, Hueber, Yann, Rouard, Mathieu, Bocs, Stéphanie, Couvin, David, De Lamotte, Frédéric, Droc, Gaëtan, Dufayard, Jean François, El Hassouni, Nordine, Farcy, Cédric, Gkanogiannis, Anestis, Hamelin, Chantal, Larivière, Delphine, Martin, Guillaume, Ortega, Enrique, Pitollat, Bertrand, Pointet, Stéphanie, Ruiz, Manuel, Gautier, Sarah, Summo, Marilyne, This, Dominique, Ravel, Sébastien, Larmande, Pierre, Monat, Cécile, Sabot, François, Tando, Ndomassi, Tranchant-Dubreuil, Christine, Sempere, Guilhem, and Dereeper, Alexis
Abstract: The South Green Web portal (http://www.southgreen.fr/) provides access to a large panel of public databases, analytical workflows and bioinformatics resources dedicated to the genomics of tropical and Mediterranean crops. The portal contains currently about 20 information systems and tools and targets a broad range of crops such as Banana, Cacao, Cassava, Coconut, Coffee, Grape, Rice and Sugarcane.
Published: 2016

86. Gigwa—Genotype investigator for genome-wide analyses

Author: Sempere, Guilhem, Philippe, Florian, Dereeper, Alexis, Ruiz, Manuel, Sarah, Gautier, Larmande, Pierre, Sempere, Guilhem, Philippe, Florian, Dereeper, Alexis, Ruiz, Manuel, Sarah, Gautier, and Larmande, Pierre
Abstract: Background Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions. Description Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single- or multi-user mode. In addition, it provides a wide range of popular export formats. Conclusions The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers.
Published: 2016

87. Facilitating efficient knowledge management and discovery in the Agronomic Sciences

Author: Venkatesan, Aravind, Larmande, Pierre, Jonquet, Clement, Ruiz, Manuel, Valduriez, Patrick, Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Système Multi-agent, Interaction, Langage, Evolution (SMILE), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Scientific Data Management (ZENITH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), IBC, ANR-12-JS02-0010,SIFR,Indexation sémantique de ressources biomédicales francophones(2012), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Jonquet, Clement, JCJC - SIMI 2 - Science informatique et applications - Indexation sémantique de ressources biomédicales francophones - - SIFR2012 - ANR-12-JS02-0010 - JC - VALID, Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM)
Subjects: [INFO.INFO-WB] Computer Science [cs]/Web, [INFO.INFO-WB]Computer Science [cs]/Web, Plant data, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Agronomic linked data, Semantic web, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], RDF
Abstract: International audience; The advancement of empirical and information technologies in the recent years have drastically increased the amount of data in fields of Life Sciences, and Agronomic Sciences. To understand the complexity of a given system it is important to link (integrate) diverse datasets. A promising solution towards data integration challenges is offered by the Semantic Web technologies1. The Semantic Web was proposed, to remedy the fragmentation of all potentially useful information on the web. Currently, the bio-medical domain has accepted the Semantic Web technologies as a means to manage (integrate) knowledge. Although we are witnessing an increased usage of ontologies within the Agronomic Sciences, the data in this domain is highly distributed in nature. Utilizing these data resources more effectively and taking advantage of associated cross-disciplinary research opportunities poses a major challenge to both domain experts and information technologists.
Published: 2014

88. Data standards in the wheat research community

Author: Aubin Sophie, Alaux Michael, Baumann Ute, Cooper Laurel, Fulss Richard Allan, Larmande Pierre, Pommier Cyril, Protonotarios Vassilis, Shresta Rosemary, Subirats Imma, Whan Alex, and Dzale Yeumo Esther
Subjects: Wheat data interoperability
Abstract: This report studies the usage of data standards in the wheat research community through a public web survey. It had been conducted by the Wheat data interoperability working group (https://www.rd-alliance.org/groups/wheat-data-interoperability-wg.html) under the umbrella of the Wheat Information expert working group (http://wheatis.org/) and the Research Data Alliance (https://www.rd-alliance.org/). It allowed the group to identify data formats and controlled vocabularies which are the most used by data producers and data consumers in the wheat research community.
Published: 2014
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89. Semantic Annotation Workflow using Bio-Ontologies

Author: Castanier, Emmanuel, Jonquet, Clement, Melzi, Soumia, Larmande, Pierre, Ruiz, Manuel, Valduriez, Patrick, Scientific Data Management (ZENITH), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Système Multi-agent, Interaction, Langage, Evolution (SMILE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), ANR-12-JS02-0010, ANR-12-JS02-0010,SIFR,Indexation sémantique de ressources biomédicales francophones(2012), ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier(2011), and Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)
Subjects: web smatch, Bioinformatics, Plant2RDF, [INFO.INFO-WB]Computer Science [cs]/Web, Intelligence artificielle, Web, semantic annotation, schema annotation, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], bio-semantic, bio-ontologies, plant2rdf, Artificial Intelligence, Bio-informatique, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], ontologie
Abstract: International audience; Biologists have adopted ontologies: *To provide canonical representation of scientific knowledge *To annotate experimental data to enable interpretation, comparison, and discovery across databases *To facilitate knowledge-based applications for decisionsupport, natural language processing, and data integration But off-the-shelf solutions for the biologist to use ontologies are rare (versions, format, availability, license, overlap, etc.) Automatically process complex biological resources text content and generate annotations : * Large-scale - to scale up to many resources and ontologies * Automatic - to keep precision and accuracy * Easy to use and to access - web service approach * Customizable - to fit very specific needs * Smart - to leverage the knowledge contained in ontologies There have been success stories to reproduce: GO annotations, PubMed indexing, etc.
Published: 2014

90. Erratum to: Gigwa-Genotype investigator for genome-wide analyses

Author: Sempéré, Guilhem, primary, Philippe, Florian, additional, Dereeper, Alexis, additional, Ruiz, Manuel, additional, Sarah, Gautier, additional, and Larmande, Pierre, additional
Published: 2016
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91. Development of a knowledge system for Big Data

Author: Luyen, LE Ngoc, primary, Tireau, Anne, additional, Venkatesan, Aravind, additional, Neveu, Pascal, additional, and Larmande, Pierre, additional
Published: 2016
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92. Gigwa—Genotype investigator for genome-wide analyses

Author: Sempéré, Guilhem, primary, Philippe, Florian, additional, Dereeper, Alexis, additional, Ruiz, Manuel, additional, Sarah, Gautier, additional, and Larmande, Pierre, additional
Published: 2016
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93. Genotype investigator for Genome Wide Analysis (GIGwA) [P1111]

Author: Larmande, Pierre, Sempere, Guilhem, Philippe, Florian, Dereeper, Alexis, Ruiz, Manuel, Sarah, Gautier, Larmande, Pierre, Sempere, Guilhem, Philippe, Florian, Dereeper, Alexis, Ruiz, Manuel, and Sarah, Gautier
Abstract: Comparing genetic variations in relation to the functional data is essential to understand the adaptation of organisms to their ecosystems. However, now with the data deluge produced by the Next Generation Sequencing (NGS) arise some computational challenges regarding storage, search, sharing, analysis, and visualization of data that redefine some practices in data management. In this domain, the traditional relational databases are widely used approaches to store and query data in various forms. However, their major drawback is the lack of flexibility to design the field structures of the data. In addition, relational databases are not efficient to retrieve Gigabytes of data. In this context, we used the emerging technology called NoSQL for " Not only SQL ", which refers to non-relational database management systems designed for large-scale data storage and massively-parallel data processing. GIGwA was mainly developed to manage genomic, transcriptomic and genotyping data from NGS analysis because biologists need to handle large VCF files to filter, query and extract data for their research. However, most of existing tools are mainly targeted at experienced users by providing command line API. The aim of GIGwA is to provide a Web user interface to make the system accessible to users from the biological field. (Texte intégral)
Published: 2015

94. Proceedings of the 1st International Workshop on Semantics for Biodiversity

Author: Larmande, Pierre, Arnaud, Elizabeth, Mougenot, Isabelle, Jonquet, Clement, Libourel Rouge, Thérèse, Ruiz, Manuel, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), UMR 228 Espace-Dev, Espace pour le développement, Université de Guyane (UG)-Université des Antilles (UA)-Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM), Système Multi-agent, Interaction, Langage, Evolution (SMILE), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ANR-12-JS02-0010, Pierre Larmande, Elizabeth Arnaud, Isabelle Mougenot, Clement Jonquet, Thérèse Libourel, Manuel Ruiz, ANR-12-JS02-0010,SIFR,Indexation sémantique de ressources biomédicales francophones(2012), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Université de Guyane (UG)-Université des Antilles (UA), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Bioversity International, Consultative Group on International Agricultural Research [CGIAR], Université des Antilles (UA)-Université de Guyane (UG)-Université de Montpellier (UM)-Université de La Réunion (UR)-Avignon Université (AU)-Université de Perpignan Via Domitia (UPVD)-Institut de Recherche pour le Développement (IRD), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)
Subjects: Local knowledge about the value of agricultural and wild biodiversity, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], Text mining, Linked data, Plant diseases and plant-pathogen relationships, [INFO.INFO-WB]Computer Science [cs]/Web, Genomics and phenomics, Environment, Agro-ecology and ecosystem services, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Biomass recycling, Ontology engineering and applications, Mobile devices, Remote sensors, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genetic resources, Visualization tools, Knowledge engineering
Abstract: International audience; Semantic web standards, tools, ontologies and related technologies have considerably matured in the recent years. Nowadays, accessing a wide catalogue of biological, social, environmental, and ecological data sources helps stakeholders working on biodiversity to answer their complex questions. Will the real time access to web resources effectively support the definition of strategies to conserve and manage biodiversity? How might semantic web technologies help us to handle the complex and heterogeneous big data related to biodiversity? The workshop aims to identify the key challenges faced by the bioinformatics community, discuss potential solutions and identify the opportunities emerging from the trans-disciplinary interactions between Plant Science and Informatics experts. Therefore, we expect the bioinformatics experts to explain how they apply semantic web standards and tools to their scientific topic, from biology, agriculture, agro-ecology, genomics, environmental studies, to social sciences, citizen sciences. Research papers presenting various aspects of semantic web technologies applied to biodiversity data, ranging from position papers to implemented systems descriptions and their evaluation, will be selected. We are particularly interested in the use of the semantic technologies to design and develop systems that supports research on agricultural and wild biodiversity conservation and management for food security. Examples may include strategies for resilience to climate change pressures, sustainability of productive ecosystems, ecosystems services monitoring or territories management, rather than systems supporting only research on climate patterns or soil erosion.
Published: 2013

95. Semantics for biodiversity (S4BioDiv2013) : proceedings of the first international workshop on semantics for biodiversity

Author: Larmande, Pierre (ed.), Arnaud, E. (ed.), Mougenot, I. (ed.), Jonquet, C. (ed.), Libourel, T. (ed.), and Ruiz, M. (ed.)
Subjects: CONSERVATION DE LA NATURE, BIOLOGIE VEGETALE, TRAITEMENT DE DONNEES, SEMANTIQUE, BIODIVERSITE, ONTOLOGIE, BASE DE DONNEES, WEB SEMANTIQUE, ETUDE PLURIDISCIPLINAIRE, INFORMATIQUE, ETUDE DE CAS, BIOINFORMATIQUE, GESTION DE L'ENVIRONNEMENT, INTERNET, SYSTEME D'INFORMATION, SOURCE D'INFORMATION
Published: 2013

96. In-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches

Author: Lorieux, Mathias, Blein, Mélisande, Lozano, Jaime, Bouniol, Mathieu, Droc, Gaétan, Diévart, Anne, Périn, Christophe, Mieulet, Delphine, Lanau, Nadège, Bès, Martine, Rouvière, Claire, Gay, Céline, Piffanelli, Pietro, Larmande, Pierre, Michel, Corinne, Barnola, Isabelle, Biderre-Petit, Corinne, Sallaud, Christophe, Perez, Pascual, Bourgis, Fabienne, Ghesquière, Alain, Gantet, Pascal, Tohme, Joe, Morel, Jean Benoit, Guiderdoni, Emmanuel, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Biologie du développement des espèces pérennes cultivées (UMR BEPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Biogemma, Chappes, France, BIOGEMMA, Biogemma Clermont-Ferrand, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), French plant genomics collaborative programme Genoplante, National Research Agency (ANR) [ANR-GNP-05086G], ANR-05-GPLA-0026,CAGRILL,Characterization of mutants and seed Amplification in the Génoplante Rice Insertion Line Library(2005), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)
Subjects: DNA, Bacterial, Génétique moléculaire, DNA, Plant, Phénotype, Oryza sativa, Descendance, Genes, Plant, F30 - Génétique et amélioration des plantes, reverse genetics, Transformation, Genetic, Expression des gènes, H20 - Maladies des plantes, Gene Library, Plant Diseases, rice, food and beverages, Oryza, Sequence Analysis, DNA, forward genetics, Magnaporthe, Mutagenesis, Insertional, Phenotype, insertion mutagenesis, Collection de matériel génétique, Mutation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Caractère agronomique, Plasmids
Abstract: International audience; We report here the molecular and phenotypic features of a library of 31,562 insertion lines generated in the model japonica cultivar Nipponbare of rice (Oryza sativa L.), called Oryza Tag Line (OTL). Sixteen thousand eight hundred and fourteen T-DNA and 12,410 Tos17 discrete insertion sites have been characterized in these lines. We estimate that 8686 predicted gene intervals--i.e. one-fourth to one-fifth of the estimated rice nontransposable element gene complement--are interrupted by sequence-indexed T-DNA (6563 genes) and/or Tos17 (2755 genes) inserts. Six hundred and forty-three genes are interrupted by both T-DNA and Tos17 inserts. High quality of the sequence indexation of the T2 seed samples was ascertained by several approaches. Field evaluation under agronomic conditions of 27,832 OTL has revealed that 18.2% exhibit at least one morphophysiological alteration in the T1 progeny plants. Screening 10,000 lines for altered response to inoculation by the fungal pathogen Magnaporthe oryzae allowed to observe 71 lines (0.7%) developing spontaneous lesions simulating disease mutants and 43 lines (0.4%) exhibiting an enhanced disease resistance or susceptibility. We show here that at least 3.5% (four of 114) of these alterations are tagged by the mutagens. The presence of allelic series of sequence-indexed mutations in a gene among OTL that exhibit a convergent phenotype clearly increases the chance of establishing a linkage between alterations and inserts. This convergence approach is illustrated by the identification of the rice ortholog of AtPHO2, the disruption of which causes a lesion-mimic phenotype owing to an over-accumulation of phosphate, in nine lines bearing allelic insertions.
Published: 2012
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97. The rice functional genomics (refuge) platform, an international hosting platform for elucidating gene function using rice as a model system

Author: Mieulet, Delphine, Mayonnove, Pauline, Portfaix, Murielle, Larmande, Pierre, Gantet, Pascal, Ghesquière, Alain, and Guiderdoni, Emmanuel
Subjects: C30 - Documentation et information, education, health care economics and organizations, F30 - Génétique et amélioration des plantes
Abstract: REFUGE is an international hosting platform for the elucidation of gene function using rice as a model species. It offers international scientists, notably nonrice specialists, an access to know-how, bioinformatic, biological, and molecular resources, allowing the use of rice as a model system to investigate gene function through functional genomics strategies. PhD and postdoctoral researchers, notably from the South, are the first target beneficiaries of this initiative. Visiting scientists have access to REFUGE's know-how, including bioinformatic searches, preparation of T-DNA vectors, high-throughput production of rice transformants, molecular characterization of transformants, genotyping of insertion lines from local and international collections; growth, crossing, and phenotyping in containment greenhouse; and access to cell imaging and genotyping platforms. Hosted scientists have the opportunity to carry out one to several visits from 1 to 3 months, the REFUGE staff taking care of the materials produced between two visits. The REFUGE platform provides supervision of the hosted scientists or students and covers bench fees. Visitors have to find their own travel and subsistence funds. However, REFUGE can provide assistance to scientists notably from South countries, to find an appropriate funding source for travel and subsistence. Applications should be submitted at http://www.refuge-platform.org and will be readily examined by the REFUGE scientific committee. Funded by Agropolis Fondation, http://www.agropolis-fondation.fr/, REFUGE is a collaborative venture between the joint research unit DAP -INRA, CIRAD and Montpellier University and Agronomy School- and the 'Plant genome and development' laboratory at IRD and Perpignan University. (Texte intégral)
Published: 2010

98. Semantic annotation workflow using bio-ontologies.

Author: Castanier, E., Jonquet, Cécile, Melzi, S., Larmande, Pierre, Ruiz, Manuel, Valduriez, Patrick, Castanier, E., Jonquet, Cécile, Melzi, S., Larmande, Pierre, Ruiz, Manuel, and Valduriez, Patrick
Published: 2014

99. The south green bioinformatics platform : [P988]

Author: Rouard, Mathieu, Dereeper, Alexis, Droc, Gaëtan, Sarah, Gautier, Dufayard, Jean-François, Guignon, Valentin, Hamelin, Chantal, Homa, Félix, De Lamotte, Frédéric, Larmande, Pierre, Larivière, Delphine, Sabot, François, Sempere, Guilhem, Summo, Marilyne, Pitollat, Bertrand, Pointet, Stéphanie, This, Dominique, Bocs, Stéphanie, Ruiz, Manuel, Rouard, Mathieu, Dereeper, Alexis, Droc, Gaëtan, Sarah, Gautier, Dufayard, Jean-François, Guignon, Valentin, Hamelin, Chantal, Homa, Félix, De Lamotte, Frédéric, Larmande, Pierre, Larivière, Delphine, Sabot, François, Sempere, Guilhem, Summo, Marilyne, Pitollat, Bertrand, Pointet, Stéphanie, This, Dominique, Bocs, Stéphanie, and Ruiz, Manuel
Abstract: The South Green platform (http://www.southgreen.fr/) is a local network of scientists gathering Bioinformatics skills based on the Agropolis campus that hosts research institutes such as CIRAD, IRD, INRA, SupAgro and Bioversity international. Based on this strong local community in the field of agriculture, food and biodiversity, various bioinformatics applications and resources dedicated to genomics of tropical and Mediterranean plants has been developed and published. The objectives of South Green are to promote these original tools as well as their interoperability. Exchange and collaborative developments are also fostered through regular hands-on sessions on synergistic themes such as Galaxy, genome annotation or next generation genotyping. Finally, we provide access to computing facilities and hands-on training for both users and developers engaged in the network. The South Green web portal contains currently 20 information systems and tools and targets about 30 plants. As a proof of concept for system interoperability, we recently released the Banana Genome Hub powered by major GMOD components (i.e. Chado, Cmap, Gbrowse, Tripal, Galaxy, Pathway tools) and South Green tools (e.g. GnpAnnot, GreenPhylDB, SNiPlay, TropGeneDB, ESTtik, OryGenesDB). This concept of hub can be extended to other crops as currently done for the Coffee genome. (Texte intégral)
Published: 2014

100. A personalized integrated system for functional genomic analysis

Author: Droc, Gaëtan, Perin, Christophe, Fromentin, Sébastien, Larmande, Pierre, Développement et amélioration des plantes (UMR DAP), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)
Subjects: PLANT FUNCTIONAL GENOMICS, fungi, GENETIC DATABASES, [SDV.IDA]Life Sciences [q-bio]/Food engineering, food and beverages, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, BASES DE DONNEES
Abstract: International audience; Plant functional genomics requires data integration from several sources. A classical example is the need for cross-references between gene location and the corresponding mutant lines, a feature already present in reverse genetic databases like OryGenesDB or T-DNA express. We recently developed three plant databases specifically designed for rice functional genomics: OryGenesDB, OryzaTagLine, and GreenPhylDB. OryGenesDB is a reverse genetics and genomic database and works together with OryzaTagLine, which contains the corresponding phenotypic description of the mutant lines. GreenPhylDB is designed for comparative functional genomics and links the two model plant species Oryza sativa and Arabidopsis thaliana through ortholog predictions. We developed Orylink to run web queries on remote databases. Using Orylink, biologists can speed up information retrieval across these three databases including FST, mutant phenotypes and Arabidopsis orthologs. The interface supports user logins and profiles. Any user can personalize the system using specific forms to display relevant information synthesized from many data sources. Furthermore, we developed and registered some Web services on the BioMOBY registry that can be used to retrieve genomic location, gene information, germplasm name, phenotype description, and information on Arabidopsis thaliana and rice gene orthologs independently of Orylink. The application is available with many other tools at http://orygenesdb.cirad.fr
Published: 2009

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