Performance evaluation of unified medical language system®'s synonyms expansion to query PubMed
Identifieur interne : 000E61 ( Ncbi/Checkpoint ); précédent : 000E60; suivant : 000E62Performance evaluation of unified medical language system®'s synonyms expansion to query PubMed
Auteurs : Nicolas Griffon [France] ; Wiem Chebil [France, Tunisie] ; Laetitia Rollin [France] ; Gaetan Kerdelhue [France] ; Benoit Thirion [France] ; Jean-François Gehanno [France] ; Stéfan Jacques Darmoni [France]Source :
- BMC Medical Informatics and Decision Making [ 1472-6947 ] ; 2012.
Abstract
PubMed is the main access to medical literature on the Internet. In order to enhance the performance of its information retrieval tools, primarily non-indexed citations, the authors propose a method: expanding users' queries using Unified Medical Language System' (UMLS) synonyms i.e. all the terms gathered under one unique Concept Unique Identifier.
This method was evaluated using queries constructed to emphasize the differences between this new method and the current PubMed automatic term mapping. Four experts assessed citation relevance.
Using UMLS, we were able to retrieve new citations in 45.5% of queries, which implies a small increase in recall. The new strategy led to a heterogeneous 23.7% mean increase in non-indexed citation retrieved. Of these, 82% have been published less than 4 months earlier. The overall mean precision was 48.4% but differed according to the evaluators, ranging from 36.7% to 88.1% (Inter rater agreement was poor: kappa = 0.34).
This study highlights the need for specific search tools for each type of user and use-cases. The proposed strategy may be useful to retrieve recent scientific advancement.
Url:
DOI: 10.1186/1472-6947-12-12
PubMed: 22376010
PubMed Central: 3309945
Affiliations:
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uniqKey="Rollin L" first="Laetitia" last="Rollin">Laetitia Rollin</name><affiliation wicri:level="3"><nlm:aff id="I2">TIBS, Rouen University, LITIS EA 4108, Rouen, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>TIBS, Rouen University, LITIS EA 4108, Rouen</wicri:regionArea><placeName><region type="region">Région Normandie</region><region type="old region">Haute-Normandie</region><settlement type="city">Rouen</settlement></placeName></affiliation></author><author><name sortKey="Kerdelhue, Gaetan" sort="Kerdelhue, Gaetan" uniqKey="Kerdelhue G" first="Gaetan" last="Kerdelhue">Gaetan Kerdelhue</name><affiliation wicri:level="3"><nlm:aff id="I1">CISMeF, Rouen University Hospital, Cour Leschevin, Porte 21, 3ème étage. 1 rue de Germont, 76031 Rouen Cedex, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>CISMeF, Rouen University Hospital, Cour Leschevin, Porte 21, 3ème étage. 1 rue de Germont, 76031 Rouen 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xml:lang="fr">France</country><wicri:regionArea>CISMeF, Rouen University Hospital, Cour Leschevin, Porte 21, 3ème étage. 1 rue de Germont, 76031 Rouen Cedex</wicri:regionArea><placeName><region type="region" nuts="2">Région Normandie</region><region type="old region" nuts="2">Haute-Normandie</region><settlement type="city">Rouen</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="I2">TIBS, Rouen University, LITIS EA 4108, Rouen, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>TIBS, Rouen University, LITIS EA 4108, Rouen</wicri:regionArea><placeName><region type="region">Région Normandie</region><region type="old region">Haute-Normandie</region><settlement type="city">Rouen</settlement></placeName></affiliation></author><author><name sortKey="Gehanno, Jean Francois" sort="Gehanno, Jean Francois" uniqKey="Gehanno J" first="Jean-François" last="Gehanno">Jean-François Gehanno</name><affiliation wicri:level="3"><nlm:aff id="I2">TIBS, Rouen University, LITIS EA 4108, Rouen, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>TIBS, Rouen University, LITIS EA 4108, Rouen</wicri:regionArea><placeName><region type="region">Région Normandie</region><region type="old region">Haute-Normandie</region><settlement type="city">Rouen</settlement></placeName></affiliation></author><author><name sortKey="Darmoni, Stefan Jacques" sort="Darmoni, Stefan Jacques" uniqKey="Darmoni S" first="Stéfan Jacques" last="Darmoni">Stéfan Jacques Darmoni</name><affiliation wicri:level="3"><nlm:aff id="I1">CISMeF, Rouen University Hospital, Cour Leschevin, Porte 21, 3ème étage. 1 rue de Germont, 76031 Rouen Cedex, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>CISMeF, Rouen University Hospital, Cour Leschevin, Porte 21, 3ème étage. 1 rue de Germont, 76031 Rouen Cedex</wicri:regionArea><placeName><region type="region" nuts="2">Région Normandie</region><region type="old region" nuts="2">Haute-Normandie</region><settlement type="city">Rouen</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="I2">TIBS, Rouen University, LITIS EA 4108, Rouen, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>TIBS, Rouen University, LITIS EA 4108, Rouen</wicri:regionArea><placeName><region type="region">Région Normandie</region><region type="old region">Haute-Normandie</region><settlement type="city">Rouen</settlement></placeName></affiliation></author></analytic><series><title level="j">BMC Medical Informatics and Decision Making</title><idno type="eISSN">1472-6947</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>PubMed is the main access to medical literature on the Internet. In order to enhance the performance of its information retrieval tools, primarily non-indexed citations, the authors propose a method: expanding users' queries using Unified Medical Language System' (UMLS) synonyms i.e. all the terms gathered under one unique Concept Unique Identifier.</p></sec><sec><title>Methods</title><p>This method was evaluated using queries constructed to emphasize the differences between this new method and the current PubMed automatic term mapping. Four experts assessed citation relevance.</p></sec><sec><title>Results</title><p>Using UMLS, we were able to retrieve new citations in 45.5% of queries, which implies a small increase in recall. The new strategy led to a heterogeneous 23.7% mean increase in non-indexed citation retrieved. Of these, 82% have been published less than 4 months earlier. The overall mean precision was 48.4% but differed according to the evaluators, ranging from 36.7% to 88.1% (Inter rater agreement was poor: kappa = 0.34).</p></sec><sec><title>Conclusions</title><p>This study highlights the need for specific search tools for each type of user and use-cases. 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Darmoni</name></author><author><name sortKey="Pereira, S" uniqKey="Pereira S">S Pereira</name></author><author><name sortKey="Neveol, A" uniqKey="Neveol A">A Névéol</name></author><author><name sortKey="Massari, P" uniqKey="Massari P">P Massari</name></author><author><name sortKey="Dahamna, B" uniqKey="Dahamna B">B Dahamna</name></author><author><name sortKey="Letord, C" uniqKey="Letord C">C Letord</name></author><author><name sortKey="Kedelhue, G" uniqKey="Kedelhue G">G Kedelhué</name></author><author><name sortKey="Piot, J" uniqKey="Piot J">J Piot</name></author><author><name sortKey="Derville, A" uniqKey="Derville A">A Derville</name></author><author><name sortKey="Thirion, B" uniqKey="Thirion B">B Thirion</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Islamaj Do An, R" uniqKey="Islamaj Do An R">R Islamaj Doğan</name></author><author><name sortKey="Murray, Gc" uniqKey="Murray G">GC Murray</name></author><author><name sortKey="Neveol, A" uniqKey="Neveol A">A Névéol</name></author><author><name sortKey="Lu, Z" uniqKey="Lu Z">Z Lu</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>France</li><li>Tunisie</li></country><region><li>Haute-Normandie</li><li>Région Normandie</li></region><settlement><li>Rouen</li></settlement></list><tree><country name="France"><region name="Région Normandie"><name sortKey="Griffon, Nicolas" sort="Griffon, Nicolas" uniqKey="Griffon N" first="Nicolas" last="Griffon">Nicolas Griffon</name></region><name sortKey="Chebil, Wiem" sort="Chebil, Wiem" uniqKey="Chebil W" first="Wiem" last="Chebil">Wiem Chebil</name><name sortKey="Chebil, Wiem" sort="Chebil, Wiem" uniqKey="Chebil W" first="Wiem" last="Chebil">Wiem Chebil</name><name sortKey="Darmoni, Stefan Jacques" sort="Darmoni, Stefan Jacques" uniqKey="Darmoni S" first="Stéfan Jacques" last="Darmoni">Stéfan Jacques Darmoni</name><name sortKey="Darmoni, Stefan Jacques" sort="Darmoni, Stefan Jacques" uniqKey="Darmoni S" first="Stéfan Jacques" last="Darmoni">Stéfan Jacques Darmoni</name><name sortKey="Gehanno, Jean Francois" sort="Gehanno, Jean Francois" uniqKey="Gehanno J" first="Jean-François" last="Gehanno">Jean-François Gehanno</name><name sortKey="Griffon, Nicolas" sort="Griffon, Nicolas" uniqKey="Griffon N" first="Nicolas" last="Griffon">Nicolas Griffon</name><name sortKey="Kerdelhue, Gaetan" sort="Kerdelhue, Gaetan" uniqKey="Kerdelhue G" first="Gaetan" last="Kerdelhue">Gaetan Kerdelhue</name><name sortKey="Kerdelhue, Gaetan" sort="Kerdelhue, Gaetan" uniqKey="Kerdelhue G" first="Gaetan" last="Kerdelhue">Gaetan Kerdelhue</name><name sortKey="Rollin, Laetitia" sort="Rollin, Laetitia" uniqKey="Rollin L" first="Laetitia" last="Rollin">Laetitia Rollin</name><name sortKey="Thirion, Benoit" sort="Thirion, Benoit" uniqKey="Thirion B" first="Benoit" last="Thirion">Benoit Thirion</name><name sortKey="Thirion, Benoit" sort="Thirion, Benoit" uniqKey="Thirion B" first="Benoit" last="Thirion">Benoit Thirion</name></country><country name="Tunisie"><noRegion><name sortKey="Chebil, Wiem" sort="Chebil, Wiem" uniqKey="Chebil W" first="Wiem" last="Chebil">Wiem Chebil</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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