GnpIS: an information system to integrate genetic and genomic data from plants and fungi.
Identifieur interne : 000169 ( PubMed/Curation ); précédent : 000168; suivant : 000170GnpIS: an information system to integrate genetic and genomic data from plants and fungi.
Auteurs : Delphine Steinbach [France] ; Michael Alaux ; Joelle Amselem ; Nathalie Choisne ; Sophie Durand ; Raphaël Flores ; Aminah-Olivia Keliet ; Erik Kimmel ; Nicolas Lapalu ; Isabelle Luyten ; Célia Michotey ; Nacer Mohellibi ; Cyril Pommier ; Sébastien Reboux ; Dorothée Valdenaire ; Daphné Verdelet ; Hadi QuesnevilleSource :
- Database : the journal of biological databases and curation [ 1758-0463 ] ; 2013.
English descriptors
- KwdEn :
- MESH :
- genetics : Fungi, Genome, Fungal, Genome, Plant, Plants, Triticum.
- Databases, Genetic, Genomics, International Cooperation, Search Engine.
Abstract
Data integration is a key challenge for modern bioinformatics. It aims to provide biologists with tools to explore relevant data produced by different studies. Large-scale international projects can generate lots of heterogeneous and unrelated data. The challenge is to integrate this information with other publicly available data. Nucleotide sequencing throughput has been improved with new technologies; this increases the need for powerful information systems able to store, manage and explore data. GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research. Here, we illustrate its use. Database URL: http://urgi.versailles.inra.fr/gnpis.
DOI: 10.1093/database/bat058
PubMed: 23959375
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Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, Versailles, 78026, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, UR1164 URGI - Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, Versailles, 78026</wicri:regionArea></affiliation></author><author><name sortKey="Alaux, Michael" sort="Alaux, Michael" uniqKey="Alaux M" first="Michael" last="Alaux">Michael Alaux</name></author><author><name sortKey="Amselem, Joelle" sort="Amselem, Joelle" uniqKey="Amselem J" first="Joelle" last="Amselem">Joelle Amselem</name></author><author><name sortKey="Choisne, Nathalie" sort="Choisne, Nathalie" uniqKey="Choisne N" first="Nathalie" last="Choisne">Nathalie Choisne</name></author><author><name sortKey="Durand, Sophie" sort="Durand, Sophie" uniqKey="Durand S" first="Sophie" last="Durand">Sophie Durand</name></author><author><name sortKey="Flores, Raphael" sort="Flores, Raphael" uniqKey="Flores R" first="Raphaël" last="Flores">Raphaël Flores</name></author><author><name sortKey="Keliet, Aminah Olivia" sort="Keliet, Aminah Olivia" uniqKey="Keliet A" first="Aminah-Olivia" last="Keliet">Aminah-Olivia Keliet</name></author><author><name sortKey="Kimmel, Erik" sort="Kimmel, Erik" uniqKey="Kimmel E" first="Erik" last="Kimmel">Erik Kimmel</name></author><author><name sortKey="Lapalu, Nicolas" sort="Lapalu, Nicolas" uniqKey="Lapalu N" first="Nicolas" last="Lapalu">Nicolas Lapalu</name></author><author><name sortKey="Luyten, Isabelle" sort="Luyten, Isabelle" uniqKey="Luyten I" first="Isabelle" last="Luyten">Isabelle Luyten</name></author><author><name sortKey="Michotey, Celia" sort="Michotey, Celia" uniqKey="Michotey C" first="Célia" last="Michotey">Célia Michotey</name></author><author><name sortKey="Mohellibi, Nacer" sort="Mohellibi, Nacer" uniqKey="Mohellibi N" first="Nacer" last="Mohellibi">Nacer Mohellibi</name></author><author><name sortKey="Pommier, Cyril" sort="Pommier, Cyril" uniqKey="Pommier C" first="Cyril" last="Pommier">Cyril Pommier</name></author><author><name sortKey="Reboux, Sebastien" sort="Reboux, Sebastien" uniqKey="Reboux S" first="Sébastien" last="Reboux">Sébastien Reboux</name></author><author><name sortKey="Valdenaire, Dorothee" sort="Valdenaire, Dorothee" uniqKey="Valdenaire D" first="Dorothée" last="Valdenaire">Dorothée Valdenaire</name></author><author><name sortKey="Verdelet, Daphne" sort="Verdelet, Daphne" uniqKey="Verdelet D" first="Daphné" last="Verdelet">Daphné Verdelet</name></author><author><name sortKey="Quesneville, Hadi" sort="Quesneville, Hadi" uniqKey="Quesneville H" first="Hadi" last="Quesneville">Hadi Quesneville</name></author></analytic><series><title level="j">Database : the journal of biological databases and curation</title><idno type="eISSN">1758-0463</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Databases, Genetic</term><term>Fungi (genetics)</term><term>Genome, Fungal (genetics)</term><term>Genome, Plant (genetics)</term><term>Genomics</term><term>International Cooperation</term><term>Plants (genetics)</term><term>Search Engine</term><term>Triticum (genetics)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fungi</term><term>Genome, Fungal</term><term>Genome, Plant</term><term>Plants</term><term>Triticum</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Genomics</term><term>International Cooperation</term><term>Search Engine</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Data integration is a key challenge for modern bioinformatics. It aims to provide biologists with tools to explore relevant data produced by different studies. Large-scale international projects can generate lots of heterogeneous and unrelated data. The challenge is to integrate this information with other publicly available data. Nucleotide sequencing throughput has been improved with new technologies; this increases the need for powerful information systems able to store, manage and explore data. GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research. Here, we illustrate its use. Database URL: http://urgi.versailles.inra.fr/gnpis.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23959375</PMID><DateCreated><Year>2013</Year><Month>08</Month><Day>20</Day></DateCreated><DateCompleted><Year>2013</Year><Month>10</Month><Day>21</Day></DateCompleted><DateRevised><Year>2015</Year><Month>04</Month><Day>23</Day></DateRevised><Article PubModel="Electronic-Print"><Journal><ISSN IssnType="Electronic">1758-0463</ISSN><JournalIssue CitedMedium="Internet"><Volume>2013</Volume><PubDate><Year>2013</Year></PubDate></JournalIssue><Title>Database : the journal of biological databases and curation</Title><ISOAbbreviation>Database (Oxford)</ISOAbbreviation></Journal><ArticleTitle>GnpIS: an information system to integrate genetic and genomic data from plants and fungi.</ArticleTitle><Pagination><MedlinePgn>bat058</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/database/bat058</ELocationID><Abstract><AbstractText>Data integration is a key challenge for modern bioinformatics. It aims to provide biologists with tools to explore relevant data produced by different studies. Large-scale international projects can generate lots of heterogeneous and unrelated data. The challenge is to integrate this information with other publicly available data. Nucleotide sequencing throughput has been improved with new technologies; this increases the need for powerful information systems able to store, manage and explore data. GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research. Here, we illustrate its use. Database URL: http://urgi.versailles.inra.fr/gnpis.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Steinbach</LastName><ForeName>Delphine</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>INRA, UR1164 URGI - Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, Versailles, 78026, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Alaux</LastName><ForeName>Michael</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Amselem</LastName><ForeName>Joelle</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Choisne</LastName><ForeName>Nathalie</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Durand</LastName><ForeName>Sophie</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Flores</LastName><ForeName>Raphaël</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Keliet</LastName><ForeName>Aminah-Olivia</ForeName><Initials>AO</Initials></Author><Author ValidYN="Y"><LastName>Kimmel</LastName><ForeName>Erik</ForeName><Initials>E</Initials></Author><Author ValidYN="Y"><LastName>Lapalu</LastName><ForeName>Nicolas</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Luyten</LastName><ForeName>Isabelle</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>Michotey</LastName><ForeName>Célia</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Mohellibi</LastName><ForeName>Nacer</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Pommier</LastName><ForeName>Cyril</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Reboux</LastName><ForeName>Sébastien</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Valdenaire</LastName><ForeName>Dorothée</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Verdelet</LastName><ForeName>Daphné</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Quesneville</LastName><ForeName>Hadi</ForeName><Initials>H</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>08</Month><Day>19</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Database (Oxford)</MedlineTA><NlmUniqueID>101517697</NlmUniqueID><ISSNLinking>1758-0463</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Bioinformatics. 2001 Sep;17(9):847-8</RefSource><PMID Version="1">11590104</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2012 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