BioRegistry : a structured metadata repository for bioinformatic databases
Identifieur interne : 004520 ( Hal/Checkpoint ); précédent : 004519; suivant : 004521BioRegistry : a structured metadata repository for bioinformatic databases
Auteurs : Malika Smaïl-Tabbone [France] ; Shazia Osman [France] ; Nizar Messai [France] ; Amedeo Napoli [France] ; Marie-Dominique Devignes [France]Source :
English descriptors
Abstract
One of the major challenges in the post genomic era consists in exploiting the vast amounts of biological data stored in the numerous heterogeneous biological databases distributed worldwide. Most research projects in bioinformatics start with data retrieval from selected sources. However, identifying appropriate data sources is not trivial and requires the representation of the knowledge about data sources. We present here the BioRegistry project which aims at providing means to represent and exploit knowledge associated with biological databases. As a first step, a repository structure has been designed to organise metadata associated with databases consisting of five metadata categories: database identification, topics covered, quality information, access/availability, and tracking of the metadata. The BioRegistry model and its relationships with the DCMI (Dublin Core Metadata Initiative) are described. Prototypes with various functionalities to feed, maintain and exploit the repository are presented.
Url:
Links toward previous steps (curation, corpus...)
Links to Exploration step
Hal:inria-00000418Le document en format XML
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key="FR"></country></address></desc></org></tutelle><tutelle active="#struct-2496" type="direct"><org type="laboratory" xml:id="struct-2496" status="OLD"><orgName>INRIA Lorraine</orgName><desc><address><addrLine>615 rue du Jardin Botanique 54600 Villers-lès-Nancy</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/centre-de-recherche-inria/nancy-grand-est</ref></desc><listRelation><relation active="#struct-300009" type="direct"></relation></listRelation></org></tutelle></tutelles></hal:affiliation><country>France</country><placeName><settlement type="city">Nancy</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName><orgName type="university">Université Nancy 2</orgName><orgName type="institution" wicri:auto="newGroup">Université de Lorraine</orgName><placeName><settlement type="city">Nancy</settlement><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region></placeName><orgName type="university">Institut national polytechnique de Lorraine</orgName><orgName type="institution" wicri:auto="newGroup">Université de Lorraine</orgName></affiliation></author></analytic></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="mix" xml:lang="en"><term>bioinformatic data sources</term><term>metadata</term><term>ontology</term><term>registry</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">One of the major challenges in the post genomic era consists in exploiting the vast amounts of biological data stored in the numerous heterogeneous biological databases distributed worldwide. Most research projects in bioinformatics start with data retrieval from selected sources. However, identifying appropriate data sources is not trivial and requires the representation of the knowledge about data sources. We present here the BioRegistry project which aims at providing means to represent and exploit knowledge associated with biological databases. As a first step, a repository structure has been designed to organise metadata associated with databases consisting of five metadata categories: database identification, topics covered, quality information, access/availability, and tracking of the metadata. The BioRegistry model and its relationships with the DCMI (Dublin Core Metadata Initiative) are described. Prototypes with various functionalities to feed, maintain and exploit the repository are presented.</div></front></TEI><hal api="V3"><titleStmt><title xml:lang="en">BioRegistry : a structured metadata repository for bioinformatic databases</title><author role="aut"><persName><forename type="first">Malika</forename><surname>Smaïl-Tabbone</surname></persName><email>malika@loria.fr</email><idno type="idhal">malika-smail-tabbone</idno><idno type="halauthor">62326</idno><affiliation ref="#struct-2358"></affiliation></author><author role="aut"><persName><forename type="first">Shazia</forename><surname>Osman</surname></persName><email></email><idno type="halauthor">54312</idno><affiliation ref="#struct-2358"></affiliation></author><author role="aut"><persName><forename type="first">Nizar</forename><surname>Messai</surname></persName><email></email><idno type="idhal">nizar-messai</idno><idno type="halauthor">62327</idno><affiliation ref="#struct-2358"></affiliation></author><author role="aut"><persName><forename type="first">Amedeo</forename><surname>Napoli</surname></persName><email></email><idno type="halauthor">52676</idno><affiliation ref="#struct-2358"></affiliation></author><author role="aut"><persName><forename type="first">Marie-Dominique</forename><surname>Devignes</surname></persName><email>devignes@loria.fr</email><idno type="halauthor">52674</idno><affiliation ref="#struct-2358"></affiliation></author><editor role="depositor"><persName><forename>Malika</forename><surname>Smail-Tabbone</surname></persName><email>Malika.Smail@loria.fr</email></editor></titleStmt><editionStmt><edition n="v1" type="current"><date type="whenSubmitted">2005-10-10 16:44:44</date><date type="whenModified">2016-05-18 08:55:49</date><date type="whenReleased">2005-10-10 16:44:44</date><date type="whenProduced">2005-09-27</date></edition><respStmt><resp>contributor</resp><name key="103146"><persName><forename>Malika</forename><surname>Smail-Tabbone</surname></persName><email>Malika.Smail@loria.fr</email></name></respStmt></editionStmt><publicationStmt><distributor>CCSD</distributor><idno type="halId">inria-00000418</idno><idno type="halUri">https://hal.inria.fr/inria-00000418</idno><idno type="halBibtex">smailtabbone:inria-00000418</idno><idno type="halRefHtml">M.R. Berthold, R. Glen, K. Diederichs, O. Kohlbacher, I. Fisher. First International Symposium on Computational Life Science - CompLife 2005, Sep 2005, Konstanz, Germany, Springer, 3695 (3695), pp.46-56, 2005, Lecture Notes in Bioinformatics</idno><idno type="halRef">M.R. Berthold, R. Glen, K. Diederichs, O. Kohlbacher, I. Fisher. First International Symposium on Computational Life Science - CompLife 2005, Sep 2005, Konstanz, Germany, Springer, 3695 (3695), pp.46-56, 2005, Lecture Notes in Bioinformatics</idno></publicationStmt><seriesStmt><idno type="stamp" n="INRIA">INRIA - Institut National de Recherche en Informatique et en Automatique</idno><idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno><idno type="stamp" n="INPL">Institut National Polytechnique de Lorraine</idno><idno type="stamp" n="LORIA2">Publications du LORIA</idno><idno type="stamp" n="INRIA-NANCY-GRAND-EST">INRIA Nancy - Grand Est</idno><idno type="stamp" n="LORIA">LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications</idno><idno type="stamp" n="LORIA-TALC" p="LORIA">Traitement automatique des langues et des connaissances</idno><idno type="stamp" n="INRIA2">INRIA 2</idno><idno type="stamp" n="INRIA-LORRAINE">INRIA Nancy - Grand Est</idno><idno type="stamp" n="LABO-LORIA-SET" p="LORIA">LABO-LORIA-SET</idno><idno type="stamp" n="UNIV-LORRAINE">Université de Lorraine</idno></seriesStmt><notesStmt><note type="audience" n="1">Not set</note><note type="invited" n="0">No</note><note type="popular" n="0">No</note><note type="peer" n="1">Yes</note><note type="proceedings" n="1">Yes</note></notesStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">BioRegistry : a structured metadata repository for bioinformatic databases</title><author role="aut"><persName><forename type="first">Malika</forename><surname>Smaïl-Tabbone</surname></persName><email>malika@loria.fr</email><idno type="idHal">malika-smail-tabbone</idno><idno type="halAuthorId">62326</idno><affiliation ref="#struct-2358"></affiliation></author><author role="aut"><persName><forename type="first">Shazia</forename><surname>Osman</surname></persName><idno type="halAuthorId">54312</idno><affiliation ref="#struct-2358"></affiliation></author><author role="aut"><persName><forename type="first">Nizar</forename><surname>Messai</surname></persName><idno type="idHal">nizar-messai</idno><idno type="halAuthorId">62327</idno><affiliation ref="#struct-2358"></affiliation></author><author role="aut"><persName><forename type="first">Amedeo</forename><surname>Napoli</surname></persName><idno type="halAuthorId">52676</idno><affiliation ref="#struct-2358"></affiliation></author><author role="aut"><persName><forename type="first">Marie-Dominique</forename><surname>Devignes</surname></persName><email>devignes@loria.fr</email><idno type="halAuthorId">52674</idno><affiliation ref="#struct-2358"></affiliation></author></analytic><monogr><meeting><title>First International Symposium on Computational Life Science - CompLife 2005</title><date type="start">2005-09-27</date><settlement>Konstanz, Germany</settlement></meeting><editor>M.R. Berthold, R. Glen, K. Diederichs, O. Kohlbacher, I. Fisher</editor><imprint><publisher>Springer</publisher><biblScope unit="serie">Lecture Notes in Bioinformatics</biblScope><biblScope unit="volume">3695</biblScope><biblScope unit="issue">3695</biblScope><biblScope unit="pp">46-56</biblScope><date type="datePub">2005-09-27</date></imprint></monogr></biblStruct></sourceDesc><profileDesc><langUsage><language ident="en">English</language></langUsage><textClass><keywords scheme="author"><term xml:lang="en">bioinformatic data sources</term><term xml:lang="en">metadata</term><term xml:lang="en">registry</term><term xml:lang="en">ontology</term></keywords><classCode scheme="halDomain" n="info.info-db">Computer Science [cs]/Databases [cs.DB]</classCode><classCode scheme="halDomain" n="info.info-hc">Computer Science [cs]/Human-Computer Interaction [cs.HC]</classCode><classCode scheme="halTypology" n="COMM">Conference papers</classCode></textClass><abstract xml:lang="en">One of the major challenges in the post genomic era consists in exploiting the vast amounts of biological data stored in the numerous heterogeneous biological databases distributed worldwide. Most research projects in bioinformatics start with data retrieval from selected sources. However, identifying appropriate data sources is not trivial and requires the representation of the knowledge about data sources. We present here the BioRegistry project which aims at providing means to represent and exploit knowledge associated with biological databases. As a first step, a repository structure has been designed to organise metadata associated with databases consisting of five metadata categories: database identification, topics covered, quality information, access/availability, and tracking of the metadata. The BioRegistry model and its relationships with the DCMI (Dublin Core Metadata Initiative) are described. Prototypes with various functionalities to feed, maintain and exploit the repository are presented.</abstract></profileDesc></hal></record>Pour manipuler ce document sous Unix (Dilib)
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