Literature-based Discovery

When Don Swanson hypothesized a connection between Raynaud’s phenomenon anddietary?shoil,the?eldofliterature-baseddiscovery(LBD)wasborn. During thesubsequenttwodecadesasteadystreamofresearchershavepublishedarticles aboutLBDandthe?eldhasmadesteadyprogressinlayingfoundationsandc- ating an identity. It is curiously signi?cant that LBD is not “owned” by any p- ticulardiscipline,forexample, knowledge discoveryortextmining. Rather,LBD researchersoriginatefromarangeof?eldsincludinginformationscience,infor- tionretrieval,logic,andthebiomedicalsciences. Thisre?ectsthefactLBDisan inherentlymulti-disciplinaryenterprisewherecollaborationsbetweentheinfor- tionandbiomedicalsciencesarereadilyencountered. Thismulti-disciplinaryaspect ofLBDhasmadeitharderforthe?eldtoplanta?ag,sotospeak. Thepresentv- umecanbeseenasanattempttoredressthis. Itpresentschaptersprovidingabroad brushstrokeofLBDbyleadingresearchersprovidinganoverviewofthestateofthe art,themodelsandtheoriesused,experimentalstudies,lessonslearnt,application areas,andfuturechallenges. Inshort,itattemptstoconveyalearnedimpressionof whereandhowLBDisbeingdeployed. DonSwansonhaskindlyagreedtoprovide theintroductorychapter. Itisthehopeandintentionthatthisvolumewillplanta ?aginthegroundandinspirenewresearcherstotheLBDchallenge. PeterBruza July2007 MarcWeeber v Contents Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix Part I General Outlook and Possibilities Literature-Based Discovery? The Very Idea . . . . . . . . . . . . . . . . . . . . . . . . . 3 D. R. Swanson The Place of Literature-Based Discovery in Contemporary Scienti?c Practice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 NeilR. SmalheiserandVetleI. Torvik The Tip of the Iceberg: The Quest for Innovation at the Base of the Pyramid. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 M. D. GordonandN. F. Awad The ‘Open Discovery’ Challenge. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 JonathanD. Wren Where is the Discovery in Literature-Based Discovery?. . . . . . . . . . . . . . . . 57 R. N. Kostoff Part II Methodology and Applications Analyzing LBD Methods using a General Framework. . . . . . . . . . . . . . . . . 75 A. K. Sehgal,X. Y. Qiu,andP. Srinivasan Evaluation of Literature-Based Discovery Systems. . . . . . . . . . . . . . . . . . . . 101 M. Yetisgen-YildizandW. Pratt vii viii Contents Factor Analytic Approach to Transitive Text Mining using Medline Descriptors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115 J. StegmannandG. Grohmann Literature-Based Knowledge Discovery using Natural Language Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133 D. Hristovski,C. Friedman,T. C. Rind?esch,andB. Peterlin Information Retrieval in Literature-Based Discovery. . . . . . . . . . . . . . . . . . 153 W. Hersh Biomedical Application of Knowledge Discovery . . . . . . . . . . . . . . . . . . . . . 173 A. Koike Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193 Contributors NeveenFaragAwad SchoolofBusiness,WayneStateUniversity,USA CarolFriedman DepartmentofBiomedicalInformatics,ColumbiaUniversity,622West168St, NewYork,NY10032,USA MichaelD. Gordon RossSchoolofBusiness,UniversityofMichigan,USA mdgordon@umich. edu GuenterGrohmann Charite-Institute ´ ofMedicalInformatics,12203Berlin,Germany guenter. grohmann@charite. de WilliamHersh DepartmentofMedicalInformaticsandClinicalEpidemiology, SchoolofMedicine,OregonHealthandScienceUniversity, 3181SWSamJacksonParkRd. ,Portland,OR97239,USA hersh@ohsu. edu DimitarHristovski InstituteofBiomedicalInformatics,MedicalFaculty,UniversityofLjubljana, Vrazovtrg2/2,1104Ljubljana,Slovenia dimitar. hristovski@mf. uni-lj. si AsakoKoike CentralResearchLaboratory,HitachiLtd.