Integration and publication of heterogeneous text-mined relationships on the Semantic Web
Identifieur interne : 001565 ( Main/Exploration ); précédent : 001564; suivant : 001566Integration and publication of heterogeneous text-mined relationships on the Semantic Web
Auteurs : Adrien Coulet [France, États-Unis] ; Yael Garten [États-Unis] ; Michel Dumontier ; Russ B. Altman [États-Unis] ; Mark A. Musen [États-Unis] ; Nigam H. Shah [États-Unis]Source :
- Journal of Biomedical Semantics [ 2041-1480 ] ; 2011.
Abstract
Advances in Natural Language Processing (NLP) techniques enable the extraction of fine-grained relationships mentioned in biomedical text. The variability and the complexity of natural language in expressing similar relationships causes the extracted relationships to be highly heterogeneous, which makes the construction of knowledge bases difficult and poses a challenge in using these for data mining or question answering.
We report on the semi-automatic construction of the PHARE relationship ontology (the PHArmacogenomic RElationships Ontology) consisting of 200 curated relations from over 40,000 heterogeneous relationships extracted via text-mining. These heterogeneous relations are then mapped to the PHARE ontology using synonyms, entity descriptions and hierarchies of entities and roles. Once mapped, relationships can be normalized and compared using the structure of the ontology to identify relationships that have similar semantics but different syntax. We compare and contrast the manual procedure with a fully automated approach using WordNet to quantify the degree of integration enabled by iterative curation and refinement of the PHARE ontology. The result of such integration is a repository of normalized biomedical relationships, named PHARE-KB, which can be queried using Semantic Web technologies such as SPARQL and can be visualized in the form of a biological network.
The PHARE ontology serves as a common semantic framework to integrate more than 40,000 relationships pertinent to pharmacogenomics. The PHARE ontology forms the foundation of a knowledge base named PHARE-KB. Once populated with relationships, PHARE-KB (
Url:
DOI: 10.1186/2041-1480-2-S2-S10
PubMed: 21624156
PubMed Central: 3102890
Affiliations:
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Le document en format XML
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Altman</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Medicine, 300 Pasteur Drive, Mail Code 5110, Stanford University, Stanford, CA, 94305, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, 300 Pasteur Drive, Mail Code 5110, Stanford University, Stanford, CA, 94305</wicri:regionArea><wicri:noRegion>94305</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Department of Genetics, Mail Code 5120, Stanford University, Stanford, CA, 94305, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Mail Code 5120, Stanford University, Stanford, CA, 94305</wicri:regionArea><wicri:noRegion>94305</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I5">Department of Bioengineering, 318 Campus Drive, Mail Code 5444, Stanford University, Stanford, CA, 94305, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering, 318 Campus Drive, Mail Code 5444, Stanford University, Stanford, CA, 94305</wicri:regionArea><wicri:noRegion>94305</wicri:noRegion></affiliation></author><author><name sortKey="Musen, Mark A" sort="Musen, Mark A" uniqKey="Musen M" first="Mark A" last="Musen">Mark A. Musen</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Medicine, 300 Pasteur Drive, Mail Code 5110, Stanford University, Stanford, CA, 94305, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, 300 Pasteur Drive, Mail Code 5110, Stanford University, Stanford, CA, 94305</wicri:regionArea><wicri:noRegion>94305</wicri:noRegion></affiliation></author><author><name sortKey="Shah, Nigam H" sort="Shah, Nigam H" uniqKey="Shah N" first="Nigam H" last="Shah">Nigam H. Shah</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Medicine, 300 Pasteur Drive, Mail Code 5110, Stanford University, Stanford, CA, 94305, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, 300 Pasteur Drive, Mail Code 5110, Stanford University, Stanford, CA, 94305</wicri:regionArea><wicri:noRegion>94305</wicri:noRegion></affiliation></author></analytic><series><title level="j">Journal of Biomedical Semantics</title><idno type="eISSN">2041-1480</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Advances in Natural Language Processing (NLP) techniques enable the extraction of fine-grained relationships mentioned in biomedical text. The variability and the complexity of natural language in expressing similar relationships causes the extracted relationships to be highly heterogeneous, which makes the construction of knowledge bases difficult and poses a challenge in using these for data mining or question answering.</p></sec><sec><title>Results</title><p>We report on the semi-automatic construction of the PHARE relationship ontology (the PHArmacogenomic RElationships Ontology) consisting of 200 curated relations from over 40,000 heterogeneous relationships extracted via text-mining. These heterogeneous relations are then mapped to the PHARE ontology using synonyms, entity descriptions and hierarchies of entities and roles. Once mapped, relationships can be normalized and compared using the structure of the ontology to identify relationships that have similar semantics but different syntax. We compare and contrast the manual procedure with a fully automated approach using WordNet to quantify the degree of integration enabled by iterative curation and refinement of the PHARE ontology. The result of such integration is a repository of normalized biomedical relationships, named PHARE-KB, which can be queried using Semantic Web technologies such as SPARQL and can be visualized in the form of a biological network.</p></sec><sec><title>Conclusions</title><p>The PHARE ontology serves as a common semantic framework to integrate more than 40,000 relationships pertinent to pharmacogenomics. The PHARE ontology forms the foundation of a knowledge base named PHARE-KB. Once populated with relationships, PHARE-KB (<italic>i</italic>) can be visualized in the form of a biological network to guide human tasks such as database curation and (<italic>ii</italic>) can be queried programmatically to guide bioinformatics applications such as the prediction of molecular interactions. PHARE is available at <ext-link ext-link-type="uri" xlink:href="http://purl.bioontology.org/ontology/PHARE">http://purl.bioontology.org/ontology/PHARE</ext-link>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Groth, P" uniqKey="Groth P">P Groth</name></author><author><name sortKey="Gibson, A" uniqKey="Gibson A">A Gibson</name></author><author><name sortKey="Velterop, J" uniqKey="Velterop J">J Velterop</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Klein, T" uniqKey="Klein T">T Klein</name></author><author><name sortKey="Chang, J" uniqKey="Chang J">J Chang</name></author><author><name sortKey="Cho, M" uniqKey="Cho M">M Cho</name></author><author><name sortKey="Easton, K" uniqKey="Easton K">K Easton</name></author><author><name sortKey="Fergerson, K" uniqKey="Fergerson K">K Fergerson</name></author><author><name sortKey="Hewett, M" uniqKey="Hewett M">M Hewett</name></author><author><name 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Rosse</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Ciccarese, P" uniqKey="Ciccarese P">P Ciccarese</name></author><author><name sortKey="Ocana, M" uniqKey="Ocana M">M Ocana</name></author><author><name sortKey="Castro, Ljg" uniqKey="Castro L">LJG Castro</name></author><author><name sortKey="Das, S" uniqKey="Das S">S Das</name></author><author><name sortKey="Clark, T" uniqKey="Clark T">T Clark</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Garten, Y" uniqKey="Garten Y">Y Garten</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>France</li><li>États-Unis</li></country><region><li>Grand Est</li><li>Lorraine (région)</li></region><settlement><li>Vandoeuvre-lès-Nancy</li></settlement></list><tree><noCountry><name sortKey="Dumontier, Michel" sort="Dumontier, Michel" uniqKey="Dumontier M" first="Michel" last="Dumontier">Michel Dumontier</name></noCountry><country name="France"><region name="Grand Est"><name sortKey="Coulet, Adrien" sort="Coulet, Adrien" uniqKey="Coulet A" first="Adrien" last="Coulet">Adrien Coulet</name></region></country><country name="États-Unis"><noRegion><name sortKey="Coulet, Adrien" sort="Coulet, Adrien" uniqKey="Coulet A" first="Adrien" last="Coulet">Adrien Coulet</name></noRegion><name sortKey="Altman, Russ B" sort="Altman, Russ B" uniqKey="Altman R" first="Russ B" last="Altman">Russ B. Altman</name><name sortKey="Altman, Russ B" sort="Altman, Russ B" uniqKey="Altman R" first="Russ B" last="Altman">Russ B. Altman</name><name sortKey="Altman, Russ B" sort="Altman, Russ B" uniqKey="Altman R" first="Russ B" last="Altman">Russ B. Altman</name><name sortKey="Coulet, Adrien" sort="Coulet, Adrien" uniqKey="Coulet A" first="Adrien" last="Coulet">Adrien Coulet</name><name sortKey="Garten, Yael" sort="Garten, Yael" uniqKey="Garten Y" first="Yael" last="Garten">Yael Garten</name><name sortKey="Garten, Yael" sort="Garten, Yael" uniqKey="Garten Y" first="Yael" last="Garten">Yael Garten</name><name sortKey="Musen, Mark A" sort="Musen, Mark A" uniqKey="Musen M" first="Mark A" last="Musen">Mark A. Musen</name><name sortKey="Shah, Nigam H" sort="Shah, Nigam H" uniqKey="Shah N" first="Nigam H" last="Shah">Nigam H. Shah</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/ParkinsonFranceV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001565 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 001565 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Sante
|area= ParkinsonFranceV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:3102890
|texte= Integration and publication of heterogeneous text-mined relationships on the Semantic Web
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:21624156" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a ParkinsonFranceV1
| This area was generated with Dilib version V0.6.29. |  |