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Automatic Conceptual Indexing of French Pharmaceutical

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AutomaticConceptualIndexingofFrench

Pharmaceuticaltheses

VincentMARY†,BrunoPOULIQUEN‡,FranckLEDUFF†

StefanJ.DARMONI󰀂,AlainSEGUI∝,PierreLEBEUX†

†Laboratoired’informatiquem´edicale,Facult´edeM´edecine-Rennes,France

‡EuropeanCommission,JointResearchCentre,IPSCIspra,Italie

󰀂Directiondel’InformatiqueetdesR´eseaux,CHU-Rouen,France

∝Laboratoiredemath´ematiquesetdephysiquepharmaceutique

Facult´edePharmacie-Rennes,France

Abstract.Frenchpharmaceuticalthesesarerarelyquoted.Ifthemainobstaclesorig-inatefromlanguageoraccessbarriers,properindexationcouldalsobeblamed.Man-uallyextractedkeywordsdon’tnecessarycomefromastructuredthesaurus.Inthefollowingwork,thismanualindexingmethodiscomparedtoanautomatedone,”No-mindex”,basedonUMLS.Theautomatedmethodisimprovedbytheadditionofarelevancescoringsystem.Thefirstindexingstepconsistsofdownloading,adaptingandindexingthesesinelectronicformat.Resultswillthenbeanalyzedandsortedbyrelevance,bycomparingclassicstatisticalindices(noise/silence/relevance).Itwasassumedthatthemanuallyobtainedkeywordswerealwaysrelevant.Thesilenceofmanualindexingisneverthelesshigh:sevennewkeywordsareproposedbyNomin-dex,whoseresultsaremixed(10%ofsilence,but50%ofnoise).Thesesresultsarepromisingforthefirstexperiment:pharmaceuticaldocumentwithoutlexiconim-provement.Theindexing,ifitiscurrentlyinsufficientforareallifeuse,couldeasilybeimprovedbyspecificupdatesofthelexicon.

1Introduction

OverathousandpharmaceuticalthesesarepublishedeveryyearinFrance,whichrepresents

averylargeamountofacademicwork.Thesepublicationscanbebasedonbibliography,

laboratoryorresearchwork,andarevalidatedbyapprovedprofessors.Itcouldthereforebe

referredtoonthesamegroundasapublicationintheclassicsense.Pharmacyisinvolved

inmanyaspectsofmodernmedicine.However,pharmaceuticalthesesarerarelyreferredto

inFrenchorinternationalpublications.Thethesescatalogueisupdatedevery6month,and

thesesareonlyexceptionallyavailableonline.Thisaddstotheproblemofthelanguage.

Anewautomatedindexingmethod,”Nomindex”[1],isproposedhere,whichcombinesa

conceptualautomaticindexingmethod,viatheUMLSmetathesaurus[2][3],andasimplified

searchthroughthemetathesaurussemanticnetworkandthecomputationoftherelevance

scoreTFIDF[4].Theindexingisalsomadeavailableonlinewithawebbrowser.

2Objective

Themainobjectiveofthisworkistocomparethemanualindexingsystemtoitsautomated

counterpart,onasampleofthesesdownloadedfromtheinternet.Thefirststepconsistsin2VincentMARYandal.

downloading,adaptingandindexingthesesinelectronicformat.Resultswillthenbeanalyzed

andsortedbyrelevance,byusingclassicstatisticalmeasures(noise/silence/relevance).

3StateoftheArt

3.1Docth`ese/Sudoc

Docthesewas,uptorecently,thesystemholdingthecatalogueofFrenchtheses.Itwasup-

datedbyCDROMevery6monthsandwasavailableatuniversitylibraries.Sudoc1(managedbyABES2)wasdevelopedinparallelandaimedtoreplaceDocthese.Availableonline,SU-

DOCoffersthesesdetailssuchasauthor’sname,title,director’snameand,usually,fouror

fiverelevantkeywords.ThesekeywordsarenotnecessarilyconsistentwiththeMeSH[5],

orwithanotherthesaurus.Thisindexingisperformedbytheauthorandthedirector,andis

validatedbyalibrarian.SUDOCisupdatedaccordingtothepublicationofnewtheses.

3.2IndexingEngine

Thepurposeoftheindexingengineistorecognizeconceptsfromatextandtousethemto

createadatabaseallowingtosearchdocuments.

TheengineusealocallexiconextractedfromtheADM[6]knowledgebase.Keywordsare

groupedbyconceptsconsideringassociatedwords,coumpoundwords,prefixesandsuffixes.

EachconceptcorrespondstoanotionfromtheFrenchMeSH.Weidentifyeachconceptusing

theUMLSCUI(ConceptUniqueIdentifier).

Arelevancescore,TFIDF[7],isattachedtoeachconceptofoundintoadocument.This

scoreweightstheconceptsaccordingtotheirfrequencyinthedocument,relativelytotheir

frequencyinthewholecorpus.Afterafirstsearch,itispossibletolookforthebroaderand

narrowconcepts,ortolookforthesimilardocuments(i.e.thedocumentssharingthesame

concepts).

4MaterialandMethod

4.1Downloadingthetheses,convertingtoHTML,indexing.

Pharmaceuticalthesesareavailableonlyintheirhardcopyforms,makingitdifficulttocon-

vertbacktoanelectronicformat.Ourcatalogueofthesesisthereforecomposedoftheses

downloadedfrompersonalsitesorwiththehelpofprofessorsofpharmaceuticaluniversities.

Theyareusuallyintwodifferentformats:MSWorddocumentorPDF.

TheindexingengineonlyworkswithHTMLformateddocuments.Word97allowsadirect

conversionbetweenworddocumentsandHTML.TwomodulesareofferedbyAdobetodeal

withthePDFdocuments:makeaccessiblepluginandsaveasXMLplugin.Thetheseswere

savedinHTML3.2format,withoutCSS(CascadingStyleSheets).Thisformatretainsthe

H1andH2tags,usedbytheenginetoweighttheconcepts.Thethesesarefedtotheengine,

whichextractstheconcepts.Therelevancescoreiscomputedonceallthetheseshavebeen

1Syst`emeUniversitairedeDocumentation2AgenceBibliographiquedel’EnseignementSup´erieur:http://corail.abes.sudoc.fr