Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization
Identifieur interne : 000312 ( Main/Exploration ); précédent : 000311; suivant : 000313Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization
Auteurs : Sofie Van Landeghem [Belgique] ; Jari Björne [Finlande] ; Chih-Hsuan Wei [États-Unis, Taïwan] ; Kai Hakala [Finlande] ; Sampo Pyysalo [Royaume-Uni] ; Sophia Ananiadou [Royaume-Uni] ; Hung-Yu Kao [Taïwan] ; Zhiyong Lu [États-Unis] ; Tapio Salakoski [Finlande] ; Yves Van De Peer [Belgique] ; Filip Ginter [Finlande]Source :
- PLoS ONE [ 1932-6203 ] ; 2013.
English descriptors
- KwdEn :
- MESH :
Abstract
Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (
Url:
DOI: 10.1371/journal.pone.0055814
PubMed: 23613707
PubMed Central: 3629104
Affiliations:
- Belgique, Finlande, Royaume-Uni, Taïwan, États-Unis
- Angleterre, Finlande occidentale, Grand Manchester, Maryland
- Manchester, Turku
- Université de Manchester, Université de Turku
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000416
- to stream Pmc, to step Curation: 000416
- to stream Pmc, to step Checkpoint: 000265
- to stream PubMed, to step Corpus: 000044
- to stream PubMed, to step Curation: 000044
- to stream PubMed, to step Checkpoint: 000044
- to stream Ncbi, to step Merge: 000174
- to stream Ncbi, to step Curation: 000174
- to stream Ncbi, to step Checkpoint: 000174
- to stream Main, to step Merge: 000312
- to stream Main, to step Curation: 000312
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization</title><author><name sortKey="Van Landeghem, Sofie" sort="Van Landeghem, Sofie" uniqKey="Van Landeghem S" first="Sofie" last="Van Landeghem">Sofie Van Landeghem</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Plant Systems Biology, VIB, Gent, Belgium</addr-line></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Systems Biology, VIB, Gent</wicri:regionArea><wicri:noRegion>Gent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium</addr-line></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent</wicri:regionArea><wicri:noRegion>Gent</wicri:noRegion></affiliation></author><author><name sortKey="Bjorne, Jari" sort="Bjorne, Jari" uniqKey="Bjorne J" first="Jari" last="Björne">Jari Björne</name><affiliation wicri:level="3"><nlm:aff id="aff3"><addr-line>Turku Centre for Computer Science, Turku, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Turku Centre for Computer Science, Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="aff4"><addr-line>Department of Information Technology, University of Turku, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Information Technology, University of Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName><orgName type="university">Université de Turku</orgName></affiliation></author><author><name sortKey="Wei, Chih Hsuan" sort="Wei, Chih Hsuan" uniqKey="Wei C" first="Chih-Hsuan" last="Wei">Chih-Hsuan Wei</name><affiliation wicri:level="2"><nlm:aff id="aff5"><addr-line>National Center for Biotechnology Information, Bethesda, Maryland, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Center for Biotechnology Information, Bethesda, Maryland</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="aff6"><addr-line>Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan</wicri:regionArea><wicri:noRegion>Tainan</wicri:noRegion></affiliation></author><author><name sortKey="Hakala, Kai" sort="Hakala, Kai" uniqKey="Hakala K" first="Kai" last="Hakala">Kai Hakala</name><affiliation wicri:level="4"><nlm:aff id="aff4"><addr-line>Department of Information Technology, University of Turku, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Information Technology, University of Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName><orgName type="university">Université de Turku</orgName></affiliation></author><author><name sortKey="Pyysalo, Sampo" sort="Pyysalo, Sampo" uniqKey="Pyysalo S" first="Sampo" last="Pyysalo">Sampo Pyysalo</name><affiliation wicri:level="4"><nlm:aff id="aff7"><addr-line>National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester</wicri:regionArea><placeName><settlement type="city">Manchester</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Manchester</region></placeName><orgName type="university">Université de Manchester</orgName></affiliation></author><author><name sortKey="Ananiadou, Sophia" sort="Ananiadou, Sophia" uniqKey="Ananiadou S" first="Sophia" last="Ananiadou">Sophia Ananiadou</name><affiliation wicri:level="4"><nlm:aff id="aff7"><addr-line>National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester</wicri:regionArea><placeName><settlement type="city">Manchester</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Manchester</region></placeName><orgName type="university">Université de Manchester</orgName></affiliation></author><author><name sortKey="Kao, Hung Yu" sort="Kao, Hung Yu" uniqKey="Kao H" first="Hung-Yu" last="Kao">Hung-Yu Kao</name><affiliation wicri:level="1"><nlm:aff id="aff6"><addr-line>Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan</wicri:regionArea><wicri:noRegion>Tainan</wicri:noRegion></affiliation></author><author><name sortKey="Lu, Zhiyong" sort="Lu, Zhiyong" uniqKey="Lu Z" first="Zhiyong" last="Lu">Zhiyong Lu</name><affiliation wicri:level="2"><nlm:aff id="aff5"><addr-line>National Center for Biotechnology Information, Bethesda, Maryland, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Center for Biotechnology Information, Bethesda, Maryland</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Salakoski, Tapio" sort="Salakoski, Tapio" uniqKey="Salakoski T" first="Tapio" last="Salakoski">Tapio Salakoski</name><affiliation wicri:level="3"><nlm:aff id="aff3"><addr-line>Turku Centre for Computer Science, Turku, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Turku Centre for Computer Science, Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="aff4"><addr-line>Department of Information Technology, University of Turku, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Information Technology, University of Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName><orgName type="university">Université de Turku</orgName></affiliation></author><author><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Plant Systems Biology, VIB, Gent, Belgium</addr-line></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Systems Biology, VIB, Gent</wicri:regionArea><wicri:noRegion>Gent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium</addr-line></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent</wicri:regionArea><wicri:noRegion>Gent</wicri:noRegion></affiliation></author><author><name sortKey="Ginter, Filip" sort="Ginter, Filip" uniqKey="Ginter F" first="Filip" last="Ginter">Filip Ginter</name><affiliation wicri:level="4"><nlm:aff id="aff4"><addr-line>Department of Information Technology, University of Turku, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Information Technology, University of Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName><orgName type="university">Université de Turku</orgName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23613707</idno><idno type="pmc">3629104</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3629104</idno><idno type="RBID">PMC:3629104</idno><idno type="doi">10.1371/journal.pone.0055814</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000416</idno><idno type="wicri:Area/Pmc/Curation">000416</idno><idno type="wicri:Area/Pmc/Checkpoint">000265</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">000044</idno><idno type="wicri:Area/PubMed/Curation">000044</idno><idno type="wicri:Area/PubMed/Checkpoint">000044</idno><idno type="wicri:Area/Ncbi/Merge">000174</idno><idno type="wicri:Area/Ncbi/Curation">000174</idno><idno type="wicri:Area/Ncbi/Checkpoint">000174</idno><idno type="wicri:Area/Main/Merge">000312</idno><idno type="wicri:Area/Main/Curation">000312</idno><idno type="wicri:Area/Main/Exploration">000312</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization</title><author><name sortKey="Van Landeghem, Sofie" sort="Van Landeghem, Sofie" uniqKey="Van Landeghem S" first="Sofie" last="Van Landeghem">Sofie Van Landeghem</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Plant Systems Biology, VIB, Gent, Belgium</addr-line></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Systems Biology, VIB, Gent</wicri:regionArea><wicri:noRegion>Gent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium</addr-line></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent</wicri:regionArea><wicri:noRegion>Gent</wicri:noRegion></affiliation></author><author><name sortKey="Bjorne, Jari" sort="Bjorne, Jari" uniqKey="Bjorne J" first="Jari" last="Björne">Jari Björne</name><affiliation wicri:level="3"><nlm:aff id="aff3"><addr-line>Turku Centre for Computer Science, Turku, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Turku Centre for Computer Science, Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="aff4"><addr-line>Department of Information Technology, University of Turku, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Information Technology, University of Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName><orgName type="university">Université de Turku</orgName></affiliation></author><author><name sortKey="Wei, Chih Hsuan" sort="Wei, Chih Hsuan" uniqKey="Wei C" first="Chih-Hsuan" last="Wei">Chih-Hsuan Wei</name><affiliation wicri:level="2"><nlm:aff id="aff5"><addr-line>National Center for Biotechnology Information, Bethesda, Maryland, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Center for Biotechnology Information, Bethesda, Maryland</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="aff6"><addr-line>Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan</wicri:regionArea><wicri:noRegion>Tainan</wicri:noRegion></affiliation></author><author><name sortKey="Hakala, Kai" sort="Hakala, Kai" uniqKey="Hakala K" first="Kai" last="Hakala">Kai Hakala</name><affiliation wicri:level="4"><nlm:aff id="aff4"><addr-line>Department of Information Technology, University of Turku, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Information Technology, University of Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName><orgName type="university">Université de Turku</orgName></affiliation></author><author><name sortKey="Pyysalo, Sampo" sort="Pyysalo, Sampo" uniqKey="Pyysalo S" first="Sampo" last="Pyysalo">Sampo Pyysalo</name><affiliation wicri:level="4"><nlm:aff id="aff7"><addr-line>National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester</wicri:regionArea><placeName><settlement type="city">Manchester</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Manchester</region></placeName><orgName type="university">Université de Manchester</orgName></affiliation></author><author><name sortKey="Ananiadou, Sophia" sort="Ananiadou, Sophia" uniqKey="Ananiadou S" first="Sophia" last="Ananiadou">Sophia Ananiadou</name><affiliation wicri:level="4"><nlm:aff id="aff7"><addr-line>National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester</wicri:regionArea><placeName><settlement type="city">Manchester</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Manchester</region></placeName><orgName type="university">Université de Manchester</orgName></affiliation></author><author><name sortKey="Kao, Hung Yu" sort="Kao, Hung Yu" uniqKey="Kao H" first="Hung-Yu" last="Kao">Hung-Yu Kao</name><affiliation wicri:level="1"><nlm:aff id="aff6"><addr-line>Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan</addr-line></nlm:aff><country xml:lang="fr">Taïwan</country><wicri:regionArea>Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan</wicri:regionArea><wicri:noRegion>Tainan</wicri:noRegion></affiliation></author><author><name sortKey="Lu, Zhiyong" sort="Lu, Zhiyong" uniqKey="Lu Z" first="Zhiyong" last="Lu">Zhiyong Lu</name><affiliation wicri:level="2"><nlm:aff id="aff5"><addr-line>National Center for Biotechnology Information, Bethesda, Maryland, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Center for Biotechnology Information, Bethesda, Maryland</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Salakoski, Tapio" sort="Salakoski, Tapio" uniqKey="Salakoski T" first="Tapio" last="Salakoski">Tapio Salakoski</name><affiliation wicri:level="3"><nlm:aff id="aff3"><addr-line>Turku Centre for Computer Science, Turku, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Turku Centre for Computer Science, Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="aff4"><addr-line>Department of Information Technology, University of Turku, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Information Technology, University of Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName><orgName type="university">Université de Turku</orgName></affiliation></author><author><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Plant Systems Biology, VIB, Gent, Belgium</addr-line></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Systems Biology, VIB, Gent</wicri:regionArea><wicri:noRegion>Gent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium</addr-line></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent</wicri:regionArea><wicri:noRegion>Gent</wicri:noRegion></affiliation></author><author><name sortKey="Ginter, Filip" sort="Ginter, Filip" uniqKey="Ginter F" first="Filip" last="Ginter">Filip Ginter</name><affiliation wicri:level="4"><nlm:aff id="aff4"><addr-line>Department of Information Technology, University of Turku, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Information Technology, University of Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName><orgName type="university">Université de Turku</orgName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Data Mining</term><term>Genes</term><term>Multigene Family</term><term>Publications</term><term>Reference Standards</term><term>Signal Transduction (genetics)</term><term>Statistics as Topic</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Signal Transduction</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Data Mining</term><term>Genes</term><term>Multigene Family</term><term>Publications</term><term>Reference Standards</term><term>Statistics as Topic</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (<ext-link ext-link-type="uri" xlink:href="http://www.evexdb.org/api/v001/">http://www.evexdb.org/api/v001/</ext-link>). Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from <ext-link ext-link-type="uri" xlink:href="http://evexdb.org/download/">http://evexdb.org/download/</ext-link>, under the Creative Commons – Attribution – Share Alike (CC BY-SA) license.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Szklarczyk, D" uniqKey="Szklarczyk D">D Szklarczyk</name></author><author><name sortKey="Franceschini, A" uniqKey="Franceschini A">A Franceschini</name></author><author><name sortKey="Kuhn, M" uniqKey="Kuhn M">M Kuhn</name></author><author><name sortKey="Simonovic, M" uniqKey="Simonovic M">M Simonovic</name></author><author><name sortKey="Roth, A" uniqKey="Roth A">A Roth</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stark, C" uniqKey="Stark C">C Stark</name></author><author><name sortKey="Breitkreutz, Bj" uniqKey="Breitkreutz B">BJ Breitkreutz</name></author><author><name sortKey="Chatr Aryamontri, A" uniqKey="Chatr Aryamontri A">A Chatr-aryamontri</name></author><author><name sortKey="Boucher, L" uniqKey="Boucher L">L Boucher</name></author><author><name sortKey="Oughtred, R" uniqKey="Oughtred R">R Oughtred</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ongenaert, M" uniqKey="Ongenaert M">M Ongenaert</name></author><author><name sortKey="Van Neste, L" uniqKey="Van Neste L">L Van Neste</name></author><author><name sortKey="De Meyer, T" uniqKey="De Meyer T">T De Meyer</name></author><author><name sortKey="Menschaert, G" uniqKey="Menschaert G">G Menschaert</name></author><author><name sortKey="Bekaert, S" uniqKey="Bekaert S">S Bekaert</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Haibe Kains, B" uniqKey="Haibe Kains B">B Haibe-Kains</name></author><author><name sortKey="Olsen, C" uniqKey="Olsen C">C Olsen</name></author><author><name sortKey="Djebbari, A" uniqKey="Djebbari A">A Djebbari</name></author><author><name sortKey="Bontempi, G" uniqKey="Bontempi G">G Bontempi</name></author><author><name sortKey="Correll, M" uniqKey="Correll M">M Correll</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Rebholz Schuhmann, D" uniqKey="Rebholz Schuhmann D">D Rebholz-Schuhmann</name></author><author><name sortKey="Kirsch, H" uniqKey="Kirsch H">H Kirsch</name></author><author><name sortKey="Arregui, M" uniqKey="Arregui M">M Arregui</name></author><author><name sortKey="Gaudan, S" uniqKey="Gaudan S">S Gaudan</name></author><author><name sortKey="Riethoven, M" uniqKey="Riethoven M">M Riethoven</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hearst, Ma" uniqKey="Hearst M">MA Hearst</name></author><author><name sortKey="Divoli, A" uniqKey="Divoli A">A Divoli</name></author><author><name sortKey="Guturu, H" uniqKey="Guturu H">H Guturu</name></author><author><name sortKey="Ksikes, A" uniqKey="Ksikes A">A Ksikes</name></author><author><name sortKey="Nakov, P" uniqKey="Nakov P">P Nakov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ohta, T" uniqKey="Ohta T">T Ohta</name></author><author><name sortKey="Matsuzaki, T" uniqKey="Matsuzaki T">T Matsuzaki</name></author><author><name sortKey="Okazaki, N" uniqKey="Okazaki N">N Okazaki</name></author><author><name sortKey="Miwa, M" uniqKey="Miwa M">M Miwa</name></author><author><name sortKey="Saetre, R" uniqKey="Saetre R">R Saetre</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Agarwal, S" uniqKey="Agarwal S">S Agarwal</name></author><author><name sortKey="Yu, H" uniqKey="Yu H">H Yu</name></author><author><name sortKey="Kohane, I" uniqKey="Kohane I">I Kohane</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Landeghem, S" uniqKey="Van Landeghem S">S Van Landeghem</name></author><author><name sortKey="Ginter, F" uniqKey="Ginter F">F Ginter</name></author><author><name sortKey="Van De Peer, Y" uniqKey="Van De Peer Y">Y Van de Peer</name></author><author><name sortKey="Salakoski, T" uniqKey="Salakoski T">T Salakoski</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Hucka, M" uniqKey="Hucka M">M Hucka</name></author><author><name sortKey="Finney, A" uniqKey="Finney A">A Finney</name></author><author><name sortKey="Sauro, H" uniqKey="Sauro H">H Sauro</name></author><author><name sortKey="Bolouri, H" uniqKey="Bolouri H">H Bolouri</name></author><author><name sortKey="Doyle, J" uniqKey="Doyle J">J Doyle</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Demir, E" uniqKey="Demir E">E Demir</name></author><author><name sortKey="Cary, M" uniqKey="Cary M">M Cary</name></author><author><name sortKey="Paley, S" uniqKey="Paley S">S Paley</name></author><author><name sortKey="Fukuda, K" uniqKey="Fukuda K">K Fukuda</name></author><author><name sortKey="Lemer, C" uniqKey="Lemer C">C Lemer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ananiadou, S" uniqKey="Ananiadou S">S Ananiadou</name></author><author><name sortKey="Pyysalo, S" uniqKey="Pyysalo S">S Pyysalo</name></author><author><name sortKey="Tsujii, J" uniqKey="Tsujii J">J Tsujii</name></author><author><name sortKey="Kell, Db" uniqKey="Kell D">DB Kell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, J" uniqKey="Kim J">J Kim</name></author><author><name sortKey="Ohta, T" uniqKey="Ohta T">T Ohta</name></author><author><name sortKey="Pyysalo, S" uniqKey="Pyysalo S">S Pyysalo</name></author><author><name sortKey="Kano, Y" uniqKey="Kano Y">Y Kano</name></author><author><name sortKey="Tsujii, J" uniqKey="Tsujii J">J Tsujii</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, Jd" uniqKey="Kim J">JD Kim</name></author><author><name sortKey="Nguyen, N" uniqKey="Nguyen N">N Nguyen</name></author><author><name sortKey="Wang, Y" uniqKey="Wang Y">Y Wang</name></author><author><name sortKey="Tsujii, J" uniqKey="Tsujii J">J Tsujii</name></author><author><name sortKey="Takagi, T" uniqKey="Takagi T">T Takagi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pyysalo, S" uniqKey="Pyysalo S">S Pyysalo</name></author><author><name sortKey="Ohta, T" uniqKey="Ohta T">T Ohta</name></author><author><name sortKey="Rak, R" uniqKey="Rak R">R Rak</name></author><author><name sortKey="Sullivan, D" uniqKey="Sullivan D">D Sullivan</name></author><author><name sortKey="Mao, C" uniqKey="Mao C">C Mao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, L" uniqKey="Chen L">L Chen</name></author><author><name sortKey="Liu, H" uniqKey="Liu H">H Liu</name></author><author><name sortKey="Friedman, C" uniqKey="Friedman C">C Friedman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sayers, Ew" uniqKey="Sayers E">EW Sayers</name></author><author><name sortKey="Barrett, T" uniqKey="Barrett T">T Barrett</name></author><author><name sortKey="Benson, Da" uniqKey="Benson D">DA Benson</name></author><author><name sortKey="Bolton, E" uniqKey="Bolton E">E Bolton</name></author><author><name sortKey="Bryant, Sh" uniqKey="Bryant S">SH Bryant</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="The Uniprot, Consortium" uniqKey="The Uniprot C">Consortium The UniProt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kanehisa, M" uniqKey="Kanehisa M">M Kanehisa</name></author><author><name sortKey="Goto, S" uniqKey="Goto S">S Goto</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rose, Pw" uniqKey="Rose P">PW Rose</name></author><author><name sortKey="Beran, B" uniqKey="Beran B">B Beran</name></author><author><name sortKey="Bi, C" uniqKey="Bi C">C Bi</name></author><author><name sortKey="Bluhm, Wf" uniqKey="Bluhm W">WF Bluhm</name></author><author><name sortKey="Dimitropoulos, D" uniqKey="Dimitropoulos D">D Dimitropoulos</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hirschman, L" uniqKey="Hirschman L">L Hirschman</name></author><author><name sortKey="Yeh, A" uniqKey="Yeh A">A Yeh</name></author><author><name sortKey="Blaschke, C" uniqKey="Blaschke C">C Blaschke</name></author><author><name sortKey="Valencia, A" uniqKey="Valencia A">A Valencia</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Krallinger, M" uniqKey="Krallinger M">M Krallinger</name></author><author><name sortKey="Morgan, A" uniqKey="Morgan A">A Morgan</name></author><author><name sortKey="Smith, L" uniqKey="Smith L">L Smith</name></author><author><name sortKey="Leitner, F" uniqKey="Leitner F">F Leitner</name></author><author><name sortKey="Tanabe, L" uniqKey="Tanabe L">L Tanabe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Leitner, F" uniqKey="Leitner F">F Leitner</name></author><author><name sortKey="Mardis, S" uniqKey="Mardis S">S Mardis</name></author><author><name sortKey="Krallinger, M" uniqKey="Krallinger M">M Krallinger</name></author><author><name sortKey="Cesareni, G" uniqKey="Cesareni G">G Cesareni</name></author><author><name sortKey="Hirschman, L" uniqKey="Hirschman L">L Hirschman</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Stenetorp, P" uniqKey="Stenetorp P">P Stenetorp</name></author><author><name sortKey="Topi, G" uniqKey="Topi G">G Topić</name></author><author><name sortKey="Pyysalo, S" uniqKey="Pyysalo S">S Pyysalo</name></author><author><name sortKey="Ohta, T" uniqKey="Ohta T">T Ohta</name></author><author><name sortKey="Kim, Jd" uniqKey="Kim J">JD Kim</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Bjorne, J" uniqKey="Bjorne J">J Björne</name></author><author><name sortKey="Ginter, F" uniqKey="Ginter F">F Ginter</name></author><author><name sortKey="Salakoski, T" uniqKey="Salakoski T">T Salakoski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kazama, J" uniqKey="Kazama J">J Kazama</name></author><author><name sortKey="Tsujii, J" uniqKey="Tsujii J">J Tsujii</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Charniak, E" uniqKey="Charniak E">E Charniak</name></author><author><name sortKey="Johnson, M" uniqKey="Johnson M">M Johnson</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="De Marneffe, Mc" uniqKey="De Marneffe M">MC de Marneffe</name></author><author><name sortKey="Maccartney, B" uniqKey="Maccartney B">B MacCartney</name></author><author><name sortKey="Manning, C" uniqKey="Manning C">C Manning</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bjorne, J" uniqKey="Bjorne J">J Björne</name></author><author><name sortKey="Ginter, F" uniqKey="Ginter F">F Ginter</name></author><author><name sortKey="Pyysalo, S" uniqKey="Pyysalo S">S Pyysalo</name></author><author><name sortKey="Tsujii, J" uniqKey="Tsujii J">J Tsujii</name></author><author><name sortKey="Salakoski, T" uniqKey="Salakoski T">T Salakoski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bjorne, J" uniqKey="Bjorne J">J Björne</name></author><author><name sortKey="Van Landeghem, S" uniqKey="Van Landeghem S">S Van Landeghem</name></author><author><name sortKey="Pyysalo, S" uniqKey="Pyysalo S">S Pyysalo</name></author><author><name sortKey="Ohta, T" uniqKey="Ohta T">T Ohta</name></author><author><name sortKey="Ginter, F" uniqKey="Ginter F">F Ginter</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Flicek, P" uniqKey="Flicek P">P Flicek</name></author><author><name sortKey="Amode, Mr" uniqKey="Amode M">MR Amode</name></author><author><name sortKey="Barrell, D" uniqKey="Barrell D">D Barrell</name></author><author><name sortKey="Beal, K" uniqKey="Beal K">K Beal</name></author><author><name sortKey="Brent, S" uniqKey="Brent S">S Brent</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kersey, Pj" uniqKey="Kersey P">PJ Kersey</name></author><author><name sortKey="Lawson, D" uniqKey="Lawson D">D Lawson</name></author><author><name sortKey="Birney, E" uniqKey="Birney E">E Birney</name></author><author><name sortKey="Derwent, Ps" uniqKey="Derwent P">PS Derwent</name></author><author><name sortKey="Haimel, M" uniqKey="Haimel M">M Haimel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hsu, Cn" uniqKey="Hsu C">CN Hsu</name></author><author><name sortKey="Chang, Ym" uniqKey="Chang Y">YM Chang</name></author><author><name sortKey="Kuo, Cj" uniqKey="Kuo C">CJ Kuo</name></author><author><name sortKey="Lin, Ys" uniqKey="Lin Y">YS Lin</name></author><author><name sortKey="Huang, Hs" uniqKey="Huang H">HS Huang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wei, Ch" uniqKey="Wei C">CH Wei</name></author><author><name sortKey="Kao, Hy" uniqKey="Kao H">HY Kao</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Wei, Ch" uniqKey="Wei C">CH Wei</name></author><author><name sortKey="Kao, Hy" uniqKey="Kao H">HY Kao</name></author><author><name sortKey="Lu, Z" uniqKey="Lu Z">Z Lu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cohen, Kb" uniqKey="Cohen K">KB Cohen</name></author><author><name sortKey="Johnson, H" uniqKey="Johnson H">H Johnson</name></author><author><name sortKey="Verspoor, K" uniqKey="Verspoor K">K Verspoor</name></author><author><name sortKey="Roeder, C" uniqKey="Roeder C">C Roeder</name></author><author><name sortKey="Hunter, L" uniqKey="Hunter L">L Hunter</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Blake, C" uniqKey="Blake C">C Blake</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, Jd" uniqKey="Kim J">JD Kim</name></author><author><name sortKey="Pyysalo, S" uniqKey="Pyysalo S">S Pyysalo</name></author><author><name sortKey="Ohta, T" uniqKey="Ohta T">T Ohta</name></author><author><name sortKey="Bossy, R" uniqKey="Bossy R">R Bossy</name></author><author><name sortKey="Nguyen, N" uniqKey="Nguyen N">N Nguyen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Miwa, M" uniqKey="Miwa M">M Miwa</name></author><author><name sortKey="Thompson, P" uniqKey="Thompson P">P Thompson</name></author><author><name sortKey="Ananiadou, S" uniqKey="Ananiadou S">S Ananiadou</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Bada, M" uniqKey="Bada M">M Bada</name></author><author><name sortKey="Eckert, M" uniqKey="Eckert M">M Eckert</name></author><author><name sortKey="Evans, D" uniqKey="Evans D">D Evans</name></author><author><name sortKey="Garcia, K" uniqKey="Garcia K">K Garcia</name></author><author><name sortKey="Shipley, K" uniqKey="Shipley K">K Shipley</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Ohta, T" uniqKey="Ohta T">T Ohta</name></author><author><name sortKey="Pyysalo, S" uniqKey="Pyysalo S">S Pyysalo</name></author><author><name sortKey="Tsujii, J" uniqKey="Tsujii J">J Tsujii</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Letunic, I" uniqKey="Letunic I">I Letunic</name></author><author><name sortKey="Bork, P" uniqKey="Bork P">P Bork</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Belgique</li><li>Finlande</li><li>Royaume-Uni</li><li>Taïwan</li><li>États-Unis</li></country><region><li>Angleterre</li><li>Finlande occidentale</li><li>Grand Manchester</li><li>Maryland</li></region><settlement><li>Manchester</li><li>Turku</li></settlement><orgName><li>Université de Manchester</li><li>Université de Turku</li></orgName></list><tree><country name="Belgique"><noRegion><name sortKey="Van Landeghem, Sofie" sort="Van Landeghem, Sofie" uniqKey="Van Landeghem S" first="Sofie" last="Van Landeghem">Sofie Van Landeghem</name></noRegion><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><name sortKey="Van Landeghem, Sofie" sort="Van Landeghem, Sofie" uniqKey="Van Landeghem S" first="Sofie" last="Van Landeghem">Sofie Van Landeghem</name></country><country name="Finlande"><region name="Finlande occidentale"><name sortKey="Bjorne, Jari" sort="Bjorne, Jari" uniqKey="Bjorne J" first="Jari" last="Björne">Jari Björne</name></region><name sortKey="Bjorne, Jari" sort="Bjorne, Jari" uniqKey="Bjorne J" first="Jari" last="Björne">Jari Björne</name><name sortKey="Ginter, Filip" sort="Ginter, Filip" uniqKey="Ginter F" first="Filip" last="Ginter">Filip Ginter</name><name sortKey="Hakala, Kai" sort="Hakala, Kai" uniqKey="Hakala K" first="Kai" last="Hakala">Kai Hakala</name><name sortKey="Salakoski, Tapio" sort="Salakoski, Tapio" uniqKey="Salakoski T" first="Tapio" last="Salakoski">Tapio Salakoski</name><name sortKey="Salakoski, Tapio" sort="Salakoski, Tapio" uniqKey="Salakoski T" first="Tapio" last="Salakoski">Tapio Salakoski</name></country><country name="États-Unis"><region name="Maryland"><name sortKey="Wei, Chih Hsuan" sort="Wei, Chih Hsuan" uniqKey="Wei C" first="Chih-Hsuan" last="Wei">Chih-Hsuan Wei</name></region><name sortKey="Lu, Zhiyong" sort="Lu, Zhiyong" uniqKey="Lu Z" first="Zhiyong" last="Lu">Zhiyong Lu</name></country><country name="Taïwan"><noRegion><name sortKey="Wei, Chih Hsuan" sort="Wei, Chih Hsuan" uniqKey="Wei C" first="Chih-Hsuan" last="Wei">Chih-Hsuan Wei</name></noRegion><name sortKey="Kao, Hung Yu" sort="Kao, Hung Yu" uniqKey="Kao H" first="Hung-Yu" last="Kao">Hung-Yu Kao</name></country><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Pyysalo, Sampo" sort="Pyysalo, Sampo" uniqKey="Pyysalo S" first="Sampo" last="Pyysalo">Sampo Pyysalo</name></region><name sortKey="Ananiadou, Sophia" sort="Ananiadou, Sophia" uniqKey="Ananiadou S" first="Sophia" last="Ananiadou">Sophia Ananiadou</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Belgique/explor/OpenAccessBelV2/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000312 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000312 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Belgique
|area= OpenAccessBelV2
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:3629104
|texte= Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:23613707" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a OpenAccessBelV2
| This area was generated with Dilib version V0.6.25. |  |