SisAgriV1, Main, Exploration, bibRecord, 000000

Mining plant genomic and genetic data using the GnpIS information system

Identifieur interne : 000000 ( Main/Exploration ); suivant : 000001

Mining plant genomic and genetic data using the GnpIS information system

Auteurs : Anne-Francoise Adam-Blondon [France] ; Michael Alaux [France] ; Sophie Durand [France] ; Thomas Letellier [France] ; Guillaume Merceron [France] ; Nacer Mohellibi [France] ; Cyril Pommier [France] ; Delphine Steinbach [France] ; Françoise Alfama-Depauw [France] ; Joëlle Amselem [France] ; Dorothée Charruaud [France] ; Nathalie Choisne [France] ; Raphaël-Gauthier Flores [France] ; Claire Guerche [France] ; Véronique Jamilloux [France] ; Erik Kimmel [France] ; Nicolas Lapalu [France] ; Mikaël Loaec [France] ; Célia Michotey [France] ; Hadi Quesneville [France]

Source :

RBID : Hal:hal-01435388

Descripteurs français

mix :
- architecture génétique, architecture moléculaire, base de données, bioinformatique, génotype, interoperabilité, phénotype, système d'information.

English descriptors

mix :
- GMOD genome browser, GWAS, association genetics, bioinformatics, database, genetic resources, genomes, genotypes, interMine, interoperability, markers, phenotypes, polymorphism.

Abstract

GnpIS is an information system designed to help scientists working on plants and fungi to decipher the molecular and genetic architecture of trait variations by facilitating the navigation through genetic, genomic, and phenotypic information. The purpose of the present chapter is to illustrate how users can (1) explore datasets from phenotyping experiments in order to build new datasets for studying genotype × environment interactions in traits, (2) browse into the results of other genetic analysis data such as GWAS to generate or check working hypothesis about candidate genes or to identify important alleles and germplasms for breeding programs, and (3) explore the polymorphism in specific area of the genome using InterMine, JBrowse tools embedded in the GnpIS information system.

Url:

https://hal.archives-ouvertes.fr/hal-01435388

DOI: 10.1007/978-1-4939-6658-5_5

Affiliations:

France

Links toward previous steps (curation, corpus...)

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Le document en format XML

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<sourceDesc><biblStruct><analytic><title xml:lang="en">Mining plant genomic and genetic data using the GnpIS information system</title>
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<author><name sortKey="Choisne, Nathalie" sort="Choisne, Nathalie" uniqKey="Choisne N" first="Nathalie" last="Choisne">Nathalie Choisne</name>
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  <orgName type="acronym">INRA</orgName>
  <desc>    <address>      <country key="FR"></country>
    </address>
    <ref type="url">http://www.inra.fr</ref>
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</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Flores, Raphael Gauthier" sort="Flores, Raphael Gauthier" uniqKey="Flores R" first="Raphaël-Gauthier" last="Flores">Raphaël-Gauthier Flores</name>
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  <orgName type="acronym">INRA</orgName>
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    <ref type="url">http://www.inra.fr</ref>
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<country>France</country>
</affiliation>
</author>
<author><name sortKey="Guerche, Claire" sort="Guerche, Claire" uniqKey="Guerche C" first="Claire" last="Guerche">Claire Guerche</name>
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  <orgName type="acronym">URGI</orgName>
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  <orgName type="acronym">INRA</orgName>
  <desc>    <address>      <country key="FR"></country>
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</org>
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</hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Jamilloux, Veronique" sort="Jamilloux, Veronique" uniqKey="Jamilloux V" first="Véronique" last="Jamilloux">Véronique Jamilloux</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-104665" status="VALID">  <orgName>Unité de Recherche Génomique Info</orgName>
  <orgName type="acronym">URGI</orgName>
  <desc>    <address>      <addrLine>INRA, Centre de recherche de Versailles, bat.18 Route de Saint Cyr 78000 Versailles</addrLine>
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  <orgName type="acronym">INRA</orgName>
  <desc>    <address>      <country key="FR"></country>
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    <ref type="url">http://www.inra.fr</ref>
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</org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Kimmel, Erik" sort="Kimmel, Erik" uniqKey="Kimmel E" first="Erik" last="Kimmel">Erik Kimmel</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-104665" status="VALID">  <orgName>Unité de Recherche Génomique Info</orgName>
  <orgName type="acronym">URGI</orgName>
  <desc>    <address>      <addrLine>INRA, Centre de recherche de Versailles, bat.18 Route de Saint Cyr 78000 Versailles</addrLine>
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    </address>
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  <orgName type="acronym">INRA</orgName>
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    <ref type="url">http://www.inra.fr</ref>
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</org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Lapalu, Nicolas" sort="Lapalu, Nicolas" uniqKey="Lapalu N" first="Nicolas" last="Lapalu">Nicolas Lapalu</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-89191" status="VALID">  <orgName>BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes</orgName>
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</hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Loaec, Mikael" sort="Loaec, Mikael" uniqKey="Loaec M" first="Mikaël" last="Loaec">Mikaël Loaec</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-104665" status="VALID">  <orgName>Unité de Recherche Génomique Info</orgName>
  <orgName type="acronym">URGI</orgName>
  <desc>    <address>      <addrLine>INRA, Centre de recherche de Versailles, bat.18 Route de Saint Cyr 78000 Versailles</addrLine>
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  <orgName type="acronym">INRA</orgName>
  <desc>    <address>      <country key="FR"></country>
    </address>
    <ref type="url">http://www.inra.fr</ref>
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</org>
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</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Michotey, Celia" sort="Michotey, Celia" uniqKey="Michotey C" first="Célia" last="Michotey">Célia Michotey</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-104665" status="VALID">  <orgName>Unité de Recherche Génomique Info</orgName>
  <orgName type="acronym">URGI</orgName>
  <desc>    <address>      <addrLine>INRA, Centre de recherche de Versailles, bat.18 Route de Saint Cyr 78000 Versailles</addrLine>
      <country key="FR"></country>
    </address>
    <ref type="url">http://urgi.versailles.inra.fr/</ref>
  </desc>
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<tutelles><tutelle name="UR1164" active="#struct-92114" type="direct"><org type="institution" xml:id="struct-92114" status="VALID">  <orgName>Institut National de la Recherche Agronomique</orgName>
  <orgName type="acronym">INRA</orgName>
  <desc>    <address>      <country key="FR"></country>
    </address>
    <ref type="url">http://www.inra.fr</ref>
  </desc>
</org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Quesneville, Hadi" sort="Quesneville, Hadi" uniqKey="Quesneville H" first="Hadi" last="Quesneville">Hadi Quesneville</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-104665" status="VALID">  <orgName>Unité de Recherche Génomique Info</orgName>
  <orgName type="acronym">URGI</orgName>
  <desc>    <address>      <addrLine>INRA, Centre de recherche de Versailles, bat.18 Route de Saint Cyr 78000 Versailles</addrLine>
      <country key="FR"></country>
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    <ref type="url">http://urgi.versailles.inra.fr/</ref>
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<tutelles><tutelle name="UR1164" active="#struct-92114" type="direct"><org type="institution" xml:id="struct-92114" status="VALID">  <orgName>Institut National de la Recherche Agronomique</orgName>
  <orgName type="acronym">INRA</orgName>
  <desc>    <address>      <country key="FR"></country>
    </address>
    <ref type="url">http://www.inra.fr</ref>
  </desc>
</org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
</analytic>
<idno type="DOI">10.1007/978-1-4939-6658-5_5</idno>
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</fileDesc>
<profileDesc><textClass><keywords scheme="mix" xml:lang="en"><term>GMOD genome browser</term>
<term>GWAS</term>
<term>association genetics</term>
<term>bioinformatics</term>
<term>database</term>
<term>genetic resources</term>
<term>genomes</term>
<term>genotypes</term>
<term>interMine</term>
<term>interoperability</term>
<term>markers</term>
<term>phenotypes</term>
<term>polymorphism</term>
</keywords>
<keywords scheme="mix" xml:lang="fr"><term>architecture génétique</term>
<term>architecture moléculaire</term>
<term>base de données</term>
<term>bioinformatique</term>
<term>génotype</term>
<term>interoperabilité</term>
<term>phénotype</term>
<term>système d'information</term>
</keywords>
</textClass>
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</teiHeader>
<front><div type="abstract" xml:lang="en">GnpIS is an information system designed to help scientists working on plants and fungi to decipher the molecular and genetic architecture of trait variations by facilitating the navigation through genetic, genomic, and phenotypic information. The purpose of the present chapter is to illustrate how users can (1) explore datasets from phenotyping experiments in order to build new datasets for studying genotype × environment interactions in traits, (2) browse into the results of other genetic analysis data such as GWAS to generate or check working hypothesis about candidate genes or to identify important alleles and germplasms for breeding programs, and (3) explore the polymorphism in specific area of the genome using InterMine, JBrowse tools embedded in the GnpIS information system.</div>
</front>
</TEI>
<affiliations><list><country><li>France</li>
</country>
</list>
<tree><country name="France"><noRegion><name sortKey="Adam Blondon, Anne Francoise" sort="Adam Blondon, Anne Francoise" uniqKey="Adam Blondon A" first="Anne-Francoise" last="Adam-Blondon">Anne-Francoise Adam-Blondon</name>
</noRegion>
<name sortKey="Alaux, Michael" sort="Alaux, Michael" uniqKey="Alaux M" first="Michael" last="Alaux">Michael Alaux</name>
<name sortKey="Alfama Depauw, Francoise" sort="Alfama Depauw, Francoise" uniqKey="Alfama Depauw F" first="Françoise" last="Alfama-Depauw">Françoise Alfama-Depauw</name>
<name sortKey="Amselem, Joelle" sort="Amselem, Joelle" uniqKey="Amselem J" first="Joëlle" last="Amselem">Joëlle Amselem</name>
<name sortKey="Charruaud, Dorothee" sort="Charruaud, Dorothee" uniqKey="Charruaud D" first="Dorothée" last="Charruaud">Dorothée Charruaud</name>
<name sortKey="Choisne, Nathalie" sort="Choisne, Nathalie" uniqKey="Choisne N" first="Nathalie" last="Choisne">Nathalie Choisne</name>
<name sortKey="Durand, Sophie" sort="Durand, Sophie" uniqKey="Durand S" first="Sophie" last="Durand">Sophie Durand</name>
<name sortKey="Flores, Raphael Gauthier" sort="Flores, Raphael Gauthier" uniqKey="Flores R" first="Raphaël-Gauthier" last="Flores">Raphaël-Gauthier Flores</name>
<name sortKey="Guerche, Claire" sort="Guerche, Claire" uniqKey="Guerche C" first="Claire" last="Guerche">Claire Guerche</name>
<name sortKey="Jamilloux, Veronique" sort="Jamilloux, Veronique" uniqKey="Jamilloux V" first="Véronique" last="Jamilloux">Véronique Jamilloux</name>
<name sortKey="Kimmel, Erik" sort="Kimmel, Erik" uniqKey="Kimmel E" first="Erik" last="Kimmel">Erik Kimmel</name>
<name sortKey="Lapalu, Nicolas" sort="Lapalu, Nicolas" uniqKey="Lapalu N" first="Nicolas" last="Lapalu">Nicolas Lapalu</name>
<name sortKey="Letellier, Thomas" sort="Letellier, Thomas" uniqKey="Letellier T" first="Thomas" last="Letellier">Thomas Letellier</name>
<name sortKey="Loaec, Mikael" sort="Loaec, Mikael" uniqKey="Loaec M" first="Mikaël" last="Loaec">Mikaël Loaec</name>
<name sortKey="Merceron, Guillaume" sort="Merceron, Guillaume" uniqKey="Merceron G" first="Guillaume" last="Merceron">Guillaume Merceron</name>
<name sortKey="Michotey, Celia" sort="Michotey, Celia" uniqKey="Michotey C" first="Célia" last="Michotey">Célia Michotey</name>
<name sortKey="Mohellibi, Nacer" sort="Mohellibi, Nacer" uniqKey="Mohellibi N" first="Nacer" last="Mohellibi">Nacer Mohellibi</name>
<name sortKey="Pommier, Cyril" sort="Pommier, Cyril" uniqKey="Pommier C" first="Cyril" last="Pommier">Cyril Pommier</name>
<name sortKey="Quesneville, Hadi" sort="Quesneville, Hadi" uniqKey="Quesneville H" first="Hadi" last="Quesneville">Hadi Quesneville</name>
<name sortKey="Steinbach, Delphine" sort="Steinbach, Delphine" uniqKey="Steinbach D" first="Delphine" last="Steinbach">Delphine Steinbach</name>
</country>
</tree>
</affiliations>
</record>

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Système d'information stratégique et agriculture (serveur d'exploration)

Mining plant genomic and genetic data using the GnpIS information system

Mining plant genomic and genetic data using the GnpIS information system

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