Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family.
Identifieur interne : 000612 ( Ncbi/Curation ); précédent : 000611; suivant : 000613Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family.
Auteurs : Sudhansu Dash [États-Unis] ; Jacqueline D. Campbell [États-Unis] ; Ethalinda K S. Cannon [États-Unis] ; Alan M. Cleary [États-Unis] ; Wei Huang [États-Unis] ; Scott R. Kalberer [États-Unis] ; Vijay Karingula [États-Unis] ; Alex G. Rice [États-Unis] ; Jugpreet Singh [États-Unis] ; Pooja E. Umale [États-Unis] ; Nathan T. Weeks [États-Unis] ; Andrew P. Wilkey [États-Unis] ; Andrew D. Farmer [Grèce] ; Steven B. Cannon [États-Unis]Source :
- Nucleic acids research [ 1362-4962 ] ; 2016.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Plant Proteins.
- classification : Fabaceae.
- genetics : Fabaceae, Plant Proteins.
- Databases, Genetic, Genome, Plant, Genomics, Internet, Multigene Family, Phylogeny, Protein Structure, Tertiary, Quantitative Trait Loci, Synteny.
Abstract
Legume Information System (LIS), at http://legumeinfo.org, is a genomic data portal (GDP) for the legume family. LIS provides access to genetic and genomic information for major crop and model legumes. With more than two-dozen domesticated legume species, there are numerous specialists working on particular species, and also numerous GDPs for these species. LIS has been redesigned in the last three years both to better integrate data sets across the crop and model legumes, and to better accommodate specialized GDPs that serve particular legume species. To integrate data sets, LIS provides genome and map viewers, holds synteny mappings among all sequenced legume species and provides a set of gene families to allow traversal among orthologous and paralogous sequences across the legumes. To better accommodate other specialized GDPs, LIS uses open-source GMOD components where possible, and advocates use of common data templates, formats, schemas and interfaces so that data collected by one legume research community are accessible across all legume GDPs, through similar interfaces and using common APIs. This federated model for the legumes is managed as part of the 'Legume Federation' project (accessible via http://legumefederation.org), which can be thought of as an umbrella project encompassing LIS and other legume GDPs.
DOI: 10.1093/nar/gkv1159
PubMed: 26546515
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Campbell</name><affiliation wicri:level="4"><nlm:affiliation>Dept. of Agronomy, Iowa State University, Ames, IA 50011, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Dept. of Agronomy, Iowa State University, Ames, IA 50011</wicri:regionArea><placeName><region type="state">Iowa</region><settlement type="city">Ames (Iowa)</settlement></placeName><orgName type="university">Université d'État de l'Iowa</orgName></affiliation></author><author><name sortKey="Cannon, Ethalinda K S" sort="Cannon, Ethalinda K S" uniqKey="Cannon E" first="Ethalinda K S" last="Cannon">Ethalinda K S. Cannon</name><affiliation wicri:level="4"><nlm:affiliation>Dept. of Computer Science, Iowa State University, Ames, IA 50011, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Dept. of Computer Science, Iowa State University, Ames, IA 50011</wicri:regionArea><placeName><region type="state">Iowa</region><settlement type="city">Ames (Iowa)</settlement></placeName><orgName type="university">Université d'État de l'Iowa</orgName></affiliation></author><author><name sortKey="Cleary, Alan M" sort="Cleary, Alan M" uniqKey="Cleary A" first="Alan M" last="Cleary">Alan M. Cleary</name><affiliation wicri:level="2"><nlm:affiliation>National Center for Genome Resources, Santa Fe, NM 87505, USA Dept. of Computer Science, Montana State University, Bozeman, MT 59715, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Center for Genome Resources, Santa Fe, NM 87505, USA Dept. of Computer Science, Montana State University, Bozeman, MT 59715</wicri:regionArea><placeName><region type="state">Montana</region></placeName></affiliation></author><author><name sortKey="Huang, Wei" sort="Huang, Wei" uniqKey="Huang W" first="Wei" last="Huang">Wei Huang</name><affiliation wicri:level="4"><nlm:affiliation>Dept. of Agronomy, Iowa State University, Ames, IA 50011, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Dept. of Agronomy, Iowa State University, Ames, IA 50011</wicri:regionArea><placeName><region type="state">Iowa</region><settlement type="city">Ames (Iowa)</settlement></placeName><orgName type="university">Université d'État de l'Iowa</orgName></affiliation></author><author><name sortKey="Kalberer, Scott R" sort="Kalberer, Scott R" uniqKey="Kalberer S" first="Scott R" last="Kalberer">Scott R. Kalberer</name><affiliation wicri:level="4"><nlm:affiliation>USDA-ARS Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011</wicri:regionArea><placeName><region type="state">Iowa</region><settlement type="city">Ames (Iowa)</settlement></placeName><orgName type="university">Université d'État de l'Iowa</orgName></affiliation></author><author><name sortKey="Karingula, Vijay" sort="Karingula, Vijay" uniqKey="Karingula V" first="Vijay" last="Karingula">Vijay Karingula</name><affiliation wicri:level="4"><nlm:affiliation>Dept. of Agronomy, Iowa State University, Ames, IA 50011, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Dept. of Agronomy, Iowa State University, Ames, IA 50011</wicri:regionArea><placeName><region type="state">Iowa</region><settlement type="city">Ames (Iowa)</settlement></placeName><orgName type="university">Université d'État de l'Iowa</orgName></affiliation></author><author><name sortKey="Rice, Alex G" sort="Rice, Alex G" uniqKey="Rice A" first="Alex G" last="Rice">Alex G. Rice</name><affiliation wicri:level="2"><nlm:affiliation>National Center for Genome Resources, Santa Fe, NM 87505, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Center for Genome Resources, Santa Fe, NM 87505</wicri:regionArea><placeName><region type="state">Nouveau-Mexique</region></placeName></affiliation></author><author><name sortKey="Singh, Jugpreet" sort="Singh, Jugpreet" uniqKey="Singh J" first="Jugpreet" last="Singh">Jugpreet Singh</name><affiliation wicri:level="2"><nlm:affiliation>ORISE Fellow, USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>ORISE Fellow, USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011</wicri:regionArea><placeName><region type="state">Iowa</region></placeName></affiliation></author><author><name sortKey="Umale, Pooja E" sort="Umale, Pooja E" uniqKey="Umale P" first="Pooja E" last="Umale">Pooja E. Umale</name><affiliation wicri:level="2"><nlm:affiliation>National Center for Genome Resources, Santa Fe, NM 87505, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Center for Genome Resources, Santa Fe, NM 87505</wicri:regionArea><placeName><region type="state">Nouveau-Mexique</region></placeName></affiliation></author><author><name sortKey="Weeks, Nathan T" sort="Weeks, Nathan T" uniqKey="Weeks N" first="Nathan T" last="Weeks">Nathan T. Weeks</name><affiliation wicri:level="4"><nlm:affiliation>USDA-ARS Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011</wicri:regionArea><placeName><region type="state">Iowa</region><settlement type="city">Ames (Iowa)</settlement></placeName><orgName type="university">Université d'État de l'Iowa</orgName></affiliation></author><author><name sortKey="Wilkey, Andrew P" sort="Wilkey, Andrew P" uniqKey="Wilkey A" first="Andrew P" last="Wilkey">Andrew P. Wilkey</name><affiliation wicri:level="4"><nlm:affiliation>Dept. of Agronomy, Iowa State University, Ames, IA 50011, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Dept. of Agronomy, Iowa State University, Ames, IA 50011</wicri:regionArea><placeName><region type="state">Iowa</region><settlement type="city">Ames (Iowa)</settlement></placeName><orgName type="university">Université d'État de l'Iowa</orgName></affiliation></author><author><name sortKey="Farmer, Andrew D" sort="Farmer, Andrew D" uniqKey="Farmer A" first="Andrew D" last="Farmer">Andrew D. Farmer</name><affiliation wicri:level="1"><nlm:affiliation>National Center for Genome Resources, Santa Fe, NM 87505, USA adf@ncgr.org.</nlm:affiliation><country wicri:rule="url">Grèce</country><wicri:regionArea>National Center for Genome Resources, Santa Fe, NM 87505</wicri:regionArea><wicri:noRegion>NM 87505</wicri:noRegion></affiliation></author><author><name sortKey="Cannon, Steven B" sort="Cannon, Steven B" uniqKey="Cannon S" first="Steven B" last="Cannon">Steven B. Cannon</name><affiliation wicri:level="4"><nlm:affiliation>Dept. of Agronomy, Iowa State University, Ames, IA 50011, USA USDA-ARS Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011, USA steven.cannon@ars.usda.gov.</nlm:affiliation><orgName type="university">Université d'État de l'Iowa</orgName><country>États-Unis</country><placeName><settlement type="city">Ames (Iowa)</settlement><region type="state">Iowa</region></placeName></affiliation></author></analytic><series><title level="j">Nucleic acids research</title><idno type="eISSN">1362-4962</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Databases, Genetic</term><term>Fabaceae (classification)</term><term>Fabaceae (genetics)</term><term>Genome, Plant</term><term>Genomics</term><term>Internet</term><term>Multigene Family</term><term>Phylogeny</term><term>Plant Proteins (chemistry)</term><term>Plant Proteins (genetics)</term><term>Protein Structure, Tertiary</term><term>Quantitative Trait Loci</term><term>Synteny</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Fabaceae</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fabaceae</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Genome, Plant</term><term>Genomics</term><term>Internet</term><term>Multigene Family</term><term>Phylogeny</term><term>Protein Structure, Tertiary</term><term>Quantitative Trait Loci</term><term>Synteny</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Legume Information System (LIS), at http://legumeinfo.org, is a genomic data portal (GDP) for the legume family. LIS provides access to genetic and genomic information for major crop and model legumes. With more than two-dozen domesticated legume species, there are numerous specialists working on particular species, and also numerous GDPs for these species. LIS has been redesigned in the last three years both to better integrate data sets across the crop and model legumes, and to better accommodate specialized GDPs that serve particular legume species. To integrate data sets, LIS provides genome and map viewers, holds synteny mappings among all sequenced legume species and provides a set of gene families to allow traversal among orthologous and paralogous sequences across the legumes. To better accommodate other specialized GDPs, LIS uses open-source GMOD components where possible, and advocates use of common data templates, formats, schemas and interfaces so that data collected by one legume research community are accessible across all legume GDPs, through similar interfaces and using common APIs. This federated model for the legumes is managed as part of the 'Legume Federation' project (accessible via http://legumefederation.org), which can be thought of as an umbrella project encompassing LIS and other legume GDPs.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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