InforLorV4, PubMed, Curation, bibRecord, 000141

Ontology-guided data preparation for discovering genotype-phenotype relationships.

Identifieur interne : 000141 ( PubMed/Curation ); précédent : 000140; suivant : 000142

Ontology-guided data preparation for discovering genotype-phenotype relationships.

Auteurs : Adrien Coulet [France] ; Malika Smaïl-Tabbone ; Pascale Benlian ; Amedeo Napoli ; Marie-Dominique Devignes

Source :

BMC bioinformatics [ 1471-2105 ] ; 2008.

RBID : pubmed:18460176

Descripteurs français

KwdFr :
- Algorithmes, Bases de données génétiques, Gènes (génétique), Génotype, Logiciel, Phénotype, Périodiques comme sujet, Systèmes de gestion de bases de données, Sémantique, Terminologie comme sujet, Traitement du langage naturel.
MESH :
- génétique : Gènes.
- Algorithmes, Bases de données génétiques, Génotype, Logiciel, Phénotype, Périodiques comme sujet, Systèmes de gestion de bases de données, Sémantique, Terminologie comme sujet, Traitement du langage naturel.

English descriptors

KwdEn :
- Algorithms, Database Management Systems, Databases, Genetic, Genes (genetics), Genotype, Natural Language Processing, Periodicals as Topic, Phenotype, Semantics, Software, Terminology as Topic.
MESH :
- genetics : Genes.
- Algorithms, Database Management Systems, Databases, Genetic, Genotype, Natural Language Processing, Periodicals as Topic, Phenotype, Semantics, Software, Terminology as Topic.

Abstract

Complexity and amount of post-genomic data constitute two major factors limiting the application of Knowledge Discovery in Databases (KDD) methods in life sciences. Bio-ontologies may nowadays play key roles in knowledge discovery in life science providing semantics to data and to extracted units, by taking advantage of the progress of Semantic Web technologies concerning the understanding and availability of tools for knowledge representation, extraction, and reasoning.

DOI: 10.1186/1471-2105-9-S4-S3
PubMed: 18460176

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pubmed:18460176

Le document en format XML

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<author><name sortKey="Coulet, Adrien" sort="Coulet, Adrien" uniqKey="Coulet A" first="Adrien" last="Coulet">Adrien Coulet</name>
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<country xml:lang="fr">France</country>
<wicri:regionArea>KIKA Medical, Paris, F-75012</wicri:regionArea>
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<author><name sortKey="Smail Tabbone, Malika" sort="Smail Tabbone, Malika" uniqKey="Smail Tabbone M" first="Malika" last="Smaïl-Tabbone">Malika Smaïl-Tabbone</name>
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<author><name sortKey="Benlian, Pascale" sort="Benlian, Pascale" uniqKey="Benlian P" first="Pascale" last="Benlian">Pascale Benlian</name>
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<author><name sortKey="Napoli, Amedeo" sort="Napoli, Amedeo" uniqKey="Napoli A" first="Amedeo" last="Napoli">Amedeo Napoli</name>
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<author><name sortKey="Devignes, Marie Dominique" sort="Devignes, Marie Dominique" uniqKey="Devignes M" first="Marie-Dominique" last="Devignes">Marie-Dominique Devignes</name>
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<term>Natural Language Processing</term>
<term>Periodicals as Topic</term>
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<term>Software</term>
<term>Terminology as Topic</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term>
<term>Bases de données génétiques</term>
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<term>Terminologie comme sujet</term>
<term>Traitement du langage naturel</term>
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<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Database Management Systems</term>
<term>Databases, Genetic</term>
<term>Genotype</term>
<term>Natural Language Processing</term>
<term>Periodicals as Topic</term>
<term>Phenotype</term>
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<term>Terminology as Topic</term>
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<front><div type="abstract" xml:lang="en">Complexity and amount of post-genomic data constitute two major factors limiting the application of Knowledge Discovery in Databases (KDD) methods in life sciences. Bio-ontologies may nowadays play key roles in knowledge discovery in life science providing semantics to data and to extracted units, by taking advantage of the progress of Semantic Web technologies concerning the understanding and availability of tools for knowledge representation, extraction, and reasoning.</div>
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<ArticleTitle>Ontology-guided data preparation for discovering genotype-phenotype relationships.</ArticleTitle>
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<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Complexity and amount of post-genomic data constitute two major factors limiting the application of Knowledge Discovery in Databases (KDD) methods in life sciences. Bio-ontologies may nowadays play key roles in knowledge discovery in life science providing semantics to data and to extracted units, by taking advantage of the progress of Semantic Web technologies concerning the understanding and availability of tools for knowledge representation, extraction, and reasoning.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">This paper presents a method that exploits bio-ontologies for guiding data selection within the preparation step of the KDD process. We propose three scenarios in which domain knowledge and ontology elements such as subsumption, properties, class descriptions, are taken into account for data selection, before the data mining step. Each of these scenarios is illustrated within a case-study relative to the search of genotype-phenotype relationships in a familial hypercholesterolemia dataset. The guiding of data selection based on domain knowledge is analysed and shows a direct influence on the volume and significance of the data mining results.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The method proposed in this paper is an efficient alternative to numerical methods for data selection based on domain knowledge. In turn, the results of this study may be reused in ontology modelling and data integration.</AbstractText>
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<CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Clin Pharmacol Ther. 2007 Mar;81(3):328-45</RefSource>
<PMID Version="1">17339863</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites"><RefSource>Bioinformatics. 2003 Jan;19(1):79-86</RefSource>
<PMID Version="1">12499296</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites"><RefSource>Bioinformatics. 2003 Dec 12;19(18):2420-7</RefSource>
<PMID Version="1">14668226</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites"><RefSource>Bioinformatics. 2005 Jan 15;21(2):263-5</RefSource>
<PMID Version="1">15297300</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites"><RefSource>Brief Bioinform. 2006 Sep;7(3):256-74</RefSource>
<PMID Version="1">16899495</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites"><RefSource>Bioinformatics. 2005 Sep 1;21 Suppl 2:ii54-8</RefSource>
<PMID Version="1">16204125</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites"><RefSource>Clin Genet. 2006 Jul;70(1):20-8</RefSource>
<PMID Version="1">16813599</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites"><RefSource>BMC Bioinformatics. 2006;7:258</RefSource>
<PMID Version="1">16709248</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites"><RefSource>OMICS. 2006 Summer;10(2):185-98</RefSource>
<PMID Version="1">16901225</PMID>
</CommentsCorrections>
<CommentsCorrections RefType="Cites"><RefSource>Nat Struct Mol Biol. 2005 Jan;12(1):54-9</RefSource>
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Ontology-guided data preparation for discovering genotype-phenotype relationships.

Ontology-guided data preparation for discovering genotype-phenotype relationships.

Source :

Descripteurs français

English descriptors

Abstract

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

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki