LINNAEUS: A species name identification system for biomedical literature
Identifieur interne : 000603 ( Main/Exploration ); précédent : 000602; suivant : 000604LINNAEUS: A species name identification system for biomedical literature
Auteurs : Martin Gerner [Royaume-Uni] ; Goran Nenadic [Royaume-Uni] ; Casey M. Bergman [Royaume-Uni]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2010.
Abstract
The task of recognizing and identifying species names in biomedical literature has recently been regarded as critical for a number of applications in text and data mining, including gene name recognition, species-specific document retrieval, and semantic enrichment of biomedical articles.
In this paper we describe an open-source species name recognition and normalization software system, LINNAEUS, and evaluate its performance relative to several automatically generated biomedical corpora, as well as a novel corpus of full-text documents manually annotated for species mentions. LINNAEUS uses a dictionary-based approach (implemented as an efficient deterministic finite-state automaton) to identify species names and a set of heuristics to resolve ambiguous mentions. When compared against our manually annotated corpus, LINNAEUS performs with 94% recall and 97% precision at the mention level, and 98% recall and 90% precision at the document level. Our system successfully solves the problem of disambiguating uncertain species mentions, with 97% of all mentions in PubMed Central full-text documents resolved to unambiguous NCBI taxonomy identifiers.
LINNAEUS is an open source, stand-alone software system capable of recognizing and normalizing species name mentions with speed and accuracy, and can therefore be integrated into a range of bioinformatics and text-mining applications. The software and manually annotated corpus can be downloaded freely at
Url:
DOI: 10.1186/1471-2105-11-85
PubMed: 20149233
PubMed Central: 2836304
Affiliations:
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Bergman</name><affiliation wicri:level="4"><nlm:aff id="I1">Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT</wicri:regionArea><orgName type="university">Université de Manchester</orgName><placeName><settlement type="city">Manchester</settlement><region type="nation">Angleterre</region><region nuts="2" type="region">Grand Manchester</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">20149233</idno><idno type="pmc">2836304</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836304</idno><idno type="RBID">PMC:2836304</idno><idno type="doi">10.1186/1471-2105-11-85</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000148</idno><idno type="wicri:Area/Pmc/Curation">000148</idno><idno type="wicri:Area/Pmc/Checkpoint">000145</idno><idno type="wicri:Area/Ncbi/Merge">000078</idno><idno type="wicri:Area/Ncbi/Curation">000078</idno><idno type="wicri:Area/Ncbi/Checkpoint">000078</idno><idno type="wicri:Area/Main/Merge">000608</idno><idno type="wicri:Area/Main/Curation">000603</idno><idno type="wicri:Area/Main/Exploration">000603</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">LINNAEUS: A species name identification system for biomedical literature</title><author><name sortKey="Gerner, Martin" sort="Gerner, Martin" uniqKey="Gerner M" first="Martin" last="Gerner">Martin Gerner</name><affiliation wicri:level="4"><nlm:aff id="I1">Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT</wicri:regionArea><orgName type="university">Université de Manchester</orgName><placeName><settlement type="city">Manchester</settlement><region type="nation">Angleterre</region><region nuts="2" type="region">Grand Manchester</region></placeName></affiliation></author><author><name sortKey="Nenadic, Goran" sort="Nenadic, Goran" uniqKey="Nenadic G" first="Goran" last="Nenadic">Goran Nenadic</name><affiliation wicri:level="4"><nlm:aff id="I2">School of Computer Science, University of Manchester, Manchester, M13 9PL, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>School of Computer Science, University of Manchester, Manchester, M13 9PL</wicri:regionArea><orgName type="university">Université de Manchester</orgName><placeName><settlement type="city">Manchester</settlement><region type="nation">Angleterre</region><region nuts="2" type="region">Grand Manchester</region></placeName></affiliation></author><author><name sortKey="Bergman, Casey M" sort="Bergman, Casey M" uniqKey="Bergman C" first="Casey M" last="Bergman">Casey M. Bergman</name><affiliation wicri:level="4"><nlm:aff id="I1">Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT</wicri:regionArea><orgName type="university">Université de Manchester</orgName><placeName><settlement type="city">Manchester</settlement><region type="nation">Angleterre</region><region nuts="2" type="region">Grand Manchester</region></placeName></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The task of recognizing and identifying species names in biomedical literature has recently been regarded as critical for a number of applications in text and data mining, including gene name recognition, species-specific document retrieval, and semantic enrichment of biomedical articles.</p></sec><sec><title>Results</title><p>In this paper we describe an open-source species name recognition and normalization software system, LINNAEUS, and evaluate its performance relative to several automatically generated biomedical corpora, as well as a novel corpus of full-text documents manually annotated for species mentions. LINNAEUS uses a dictionary-based approach (implemented as an efficient deterministic finite-state automaton) to identify species names and a set of heuristics to resolve ambiguous mentions. When compared against our manually annotated corpus, LINNAEUS performs with 94% recall and 97% precision at the mention level, and 98% recall and 90% precision at the document level. Our system successfully solves the problem of disambiguating uncertain species mentions, with 97% of all mentions in PubMed Central full-text documents resolved to unambiguous NCBI taxonomy identifiers.</p></sec><sec><title>Conclusions</title><p>LINNAEUS is an open source, stand-alone software system capable of recognizing and normalizing species name mentions with speed and accuracy, and can therefore be integrated into a range of bioinformatics and text-mining applications. The software and manually annotated corpus can be downloaded freely at <ext-link ext-link-type="uri" xlink:href="http://linnaeus.sourceforge.net/">http://linnaeus.sourceforge.net/</ext-link>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Jensen, Lj" uniqKey="Jensen L">LJ Jensen</name></author><author><name sortKey="Saric, J" uniqKey="Saric J">J Saric</name></author><author><name sortKey="Bork, P" uniqKey="Bork P">P Bork</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Krallinger, M" uniqKey="Krallinger M">M Krallinger</name></author><author><name sortKey="Hirschman, L" uniqKey="Hirschman L">L Hirschman</name></author><author><name sortKey="Valencia, A" uniqKey="Valencia A">A Valencia</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hanisch, D" uniqKey="Hanisch D">D Hanisch</name></author><author><name 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uniqKey="Coffin J">J Coffin</name></author><author><name sortKey="Haase, A" uniqKey="Haase A">A Haase</name></author><author><name sortKey="Levy, Ja" uniqKey="Levy J">JA Levy</name></author><author><name sortKey="Montagnier, L" uniqKey="Montagnier L">L Montagnier</name></author><author><name sortKey="Oroszlan, S" uniqKey="Oroszlan S">S Oroszlan</name></author><author><name sortKey="Teich, N" uniqKey="Teich N">N Teich</name></author><author><name sortKey="Temin, H" uniqKey="Temin H">H Temin</name></author><author><name sortKey="Toyoshima, K" uniqKey="Toyoshima K">K Toyoshima</name></author><author><name sortKey="Varmus, H" uniqKey="Varmus H">H Varmus</name></author><author><name sortKey="Vogt, P" uniqKey="Vogt P">P Vogt</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Shah, Pk" uniqKey="Shah P">PK Shah</name></author><author><name sortKey="Perez Iratxeta, C" uniqKey="Perez Iratxeta C">C Perez-Iratxeta</name></author><author><name sortKey="Bork, P" uniqKey="Bork P">P Bork</name></author><author><name sortKey="Andrade, Ma" uniqKey="Andrade M">MA Andrade</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schuemie, Mj" uniqKey="Schuemie M">MJ Schuemie</name></author><author><name sortKey="Weeber, M" uniqKey="Weeber M">M Weeber</name></author><author><name sortKey="Schijvenaars, Bj" uniqKey="Schijvenaars B">BJ Schijvenaars</name></author><author><name sortKey="Van Mulligen, Em" uniqKey="Van Mulligen E">EM van Mulligen</name></author><author><name sortKey="Eijk, Cc Van Der" uniqKey="Eijk C">CC van der Eijk</name></author><author><name sortKey="Jelier, R" uniqKey="Jelier R">R Jelier</name></author><author><name sortKey="Mons, B" uniqKey="Mons B">B Mons</name></author><author><name sortKey="Kors, Ja" uniqKey="Kors J">JA Kors</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Corney, Dp" uniqKey="Corney D">DP Corney</name></author><author><name sortKey="Buxton, Bf" uniqKey="Buxton B">BF Buxton</name></author><author><name sortKey="Langdon, Wb" uniqKey="Langdon W">WB Langdon</name></author><author><name sortKey="Jones, Dt" uniqKey="Jones D">DT Jones</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Eales, Jm" uniqKey="Eales J">JM Eales</name></author><author><name sortKey="Pinney, Jw" uniqKey="Pinney J">JW Pinney</name></author><author><name sortKey="Stevens, Rd" uniqKey="Stevens R">RD Stevens</name></author><author><name sortKey="Robertson, Dl" uniqKey="Robertson D">DL Robertson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lin, J" uniqKey="Lin J">J Lin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sarntivijai, S" uniqKey="Sarntivijai S">S Sarntivijai</name></author><author><name sortKey="Ade, As" uniqKey="Ade A">AS Ade</name></author><author><name sortKey="Athey, Bd" uniqKey="Athey B">BD Athey</name></author><author><name sortKey="States, Dj" uniqKey="States D">DJ States</name></author></analytic></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Royaume-Uni</li></country><region><li>Angleterre</li><li>Grand Manchester</li></region><settlement><li>Manchester</li></settlement><orgName><li>Université de Manchester</li></orgName></list><tree><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Gerner, Martin" sort="Gerner, Martin" uniqKey="Gerner M" first="Martin" last="Gerner">Martin Gerner</name></region><name sortKey="Bergman, Casey M" sort="Bergman, Casey M" uniqKey="Bergman C" first="Casey M" last="Bergman">Casey M. Bergman</name><name sortKey="Nenadic, Goran" sort="Nenadic, Goran" uniqKey="Nenadic G" first="Goran" last="Nenadic">Goran Nenadic</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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