Applications of Natural Language Processing in Biodiversity Science
Identifieur interne : 000269 ( Main/Exploration ); précédent : 000268; suivant : 000270Applications of Natural Language Processing in Biodiversity Science
Auteurs : Anne E. Thessen [États-Unis] ; Hong Cui [États-Unis] ; Dmitry Mozzherin [États-Unis]Source :
- Advances in Bioinformatics [ 1687-8027 ] ; 2012.
Abstract
Centuries of biological knowledge are contained in the massive body of scientific literature, written for human-readability but too big for any one person to consume. Large-scale mining of information from the literature is necessary if biology is to transform into a data-driven science. A computer can handle the volume but cannot make sense of the language. This paper reviews and discusses the use of natural language processing (NLP) and machine-learning algorithms to extract information from systematic literature. NLP algorithms have been used for decades, but require special development for application in the biological realm due to the special nature of the language. Many tools exist for biological information extraction (cellular processes, taxonomic names, and morphological characters), but none have been applied life wide and most still require testing and development. Progress has been made in developing algorithms for automated annotation of taxonomic text, identification of taxonomic names in text, and extraction of morphological character information from taxonomic descriptions. This manuscript will briefly discuss the key steps in applying information extraction tools to enhance biodiversity science.
Url:
DOI: 10.1155/2012/391574
PubMed: 22685456
PubMed Central: 3364545
Affiliations:
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Thessen</name><affiliation wicri:level="2"><nlm:aff id="I1">Center for Library and Informatics, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Library and Informatics, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Cui, Hong" sort="Cui, Hong" uniqKey="Cui H" first="Hong" last="Cui">Hong Cui</name><affiliation wicri:level="2"><nlm:aff id="I2">School of Information Resources and Library Science, University of Arizona, Tucson, AZ 85719, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Information Resources and Library Science, University of Arizona, Tucson, AZ 85719</wicri:regionArea><placeName><region type="state">Arizona</region></placeName></affiliation></author><author><name sortKey="Mozzherin, Dmitry" sort="Mozzherin, Dmitry" uniqKey="Mozzherin D" first="Dmitry" last="Mozzherin">Dmitry Mozzherin</name><affiliation wicri:level="2"><nlm:aff id="I1">Center for Library and Informatics, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Library and Informatics, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22685456</idno><idno type="pmc">3364545</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3364545</idno><idno type="RBID">PMC:3364545</idno><idno type="doi">10.1155/2012/391574</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000210</idno><idno type="wicri:Area/Pmc/Curation">000210</idno><idno type="wicri:Area/Pmc/Checkpoint">000112</idno><idno type="wicri:Area/Ncbi/Merge">000133</idno><idno type="wicri:Area/Ncbi/Curation">000133</idno><idno type="wicri:Area/Ncbi/Checkpoint">000133</idno><idno type="wicri:doubleKey">1687-8027:2012:Thessen A:applications:of:natural</idno><idno type="wicri:Area/Main/Merge">000272</idno><idno type="wicri:Area/Main/Curation">000269</idno><idno type="wicri:Area/Main/Exploration">000269</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Applications of Natural Language Processing in Biodiversity Science</title><author><name sortKey="Thessen, Anne E" sort="Thessen, Anne E" uniqKey="Thessen A" first="Anne E." last="Thessen">Anne E. Thessen</name><affiliation wicri:level="2"><nlm:aff id="I1">Center for Library and Informatics, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Library and Informatics, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Cui, Hong" sort="Cui, Hong" uniqKey="Cui H" first="Hong" last="Cui">Hong Cui</name><affiliation wicri:level="2"><nlm:aff id="I2">School of Information Resources and Library Science, University of Arizona, Tucson, AZ 85719, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Information Resources and Library Science, University of Arizona, Tucson, AZ 85719</wicri:regionArea><placeName><region type="state">Arizona</region></placeName></affiliation></author><author><name sortKey="Mozzherin, Dmitry" sort="Mozzherin, Dmitry" uniqKey="Mozzherin D" first="Dmitry" last="Mozzherin">Dmitry Mozzherin</name><affiliation wicri:level="2"><nlm:aff id="I1">Center for Library and Informatics, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Library and Informatics, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author></analytic><series><title level="j">Advances in Bioinformatics</title><idno type="ISSN">1687-8027</idno><idno type="eISSN">1687-8035</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Centuries of biological knowledge are contained in the massive body of scientific literature, written for human-readability but too big for any one person to consume. Large-scale mining of information from the literature is necessary if biology is to transform into a data-driven science.
A computer can handle the volume but cannot make sense of the language. This paper reviews and discusses the use of natural language processing (NLP) and machine-learning algorithms to extract information from systematic literature. NLP algorithms have been used for decades, but require special development for application in the biological realm due to the special nature of the language. Many tools exist for biological information extraction (cellular processes, taxonomic names, and morphological characters), but none have been applied life wide and most still require testing and development. Progress has been made in developing algorithms for automated annotation of taxonomic text, identification of taxonomic names in text, and extraction of morphological character information from taxonomic descriptions. This manuscript will briefly discuss the key steps in applying information extraction tools to enhance biodiversity science.
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Friedman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yu, H" uniqKey="Yu H">H Yu</name></author><author><name sortKey="Kim, W" uniqKey="Kim W">W Kim</name></author><author><name sortKey="Hatzivassiloglou, V" uniqKey="Hatzivassiloglou V">V Hatzivassiloglou</name></author><author><name sortKey="Wilbur, Wj" uniqKey="Wilbur W">WJ Wilbur</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chang, Jt" uniqKey="Chang J">JT Chang</name></author><author><name sortKey="Schutze, H" uniqKey="Schutze H">H Schutze</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wren, Jd" uniqKey="Wren J">JD Wren</name></author><author><name sortKey="Garner, Hr" uniqKey="Garner H">HR Garner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lydon, S" uniqKey="Lydon S">S Lydon</name></author><author><name sortKey="Wood, M" uniqKey="Wood M">M Wood</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Taylor, A" uniqKey="Taylor A">A Taylor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Radford, Ae" uniqKey="Radford A">AE Radford</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Diederich, J" uniqKey="Diederich J">J Diederich</name></author><author><name sortKey="Fortuner, R" uniqKey="Fortuner R">R Fortuner</name></author><author><name sortKey="Milton, J" uniqKey="Milton J">J Milton</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wood, M" uniqKey="Wood M">M Wood</name></author><author><name sortKey="Lydon, S" uniqKey="Lydon S">S Lydon</name></author><author><name sortKey="Tablan, V" uniqKey="Tablan V">V Tablan</name></author><author><name sortKey="Maynard, D" uniqKey="Maynard D">D Maynard</name></author><author><name sortKey="Cunningham, H" uniqKey="Cunningham H">H Cunningham</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cui, H" uniqKey="Cui H">H Cui</name></author><author><name sortKey="Heidorn, Pb" uniqKey="Heidorn P">PB Heidorn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wei, Q" uniqKey="Wei Q">Q Wei</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Soderland, S" uniqKey="Soderland S">S Soderland</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cui, H" uniqKey="Cui H">H Cui</name></author><author><name sortKey="Singaram, S" uniqKey="Singaram S">S Singaram</name></author><author><name sortKey="Janning, A" uniqKey="Janning A">A Janning</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mabee, Pm" uniqKey="Mabee P">PM Mabee</name></author><author><name sortKey="Ashburner, M" uniqKey="Ashburner M">M Ashburner</name></author><author><name sortKey="Cronk, Q" uniqKey="Cronk Q">Q Cronk</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Arizona</li><li>Massachusetts</li></region></list><tree><country name="États-Unis"><region name="Massachusetts"><name sortKey="Thessen, Anne E" sort="Thessen, Anne E" uniqKey="Thessen A" first="Anne E." last="Thessen">Anne E. Thessen</name></region><name sortKey="Cui, Hong" sort="Cui, Hong" uniqKey="Cui H" first="Hong" last="Cui">Hong Cui</name><name sortKey="Mozzherin, Dmitry" sort="Mozzherin, Dmitry" uniqKey="Mozzherin D" first="Dmitry" last="Mozzherin">Dmitry Mozzherin</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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