Linking literature to data in the life sciences

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1、Linkingliteraturetodatainthelifesciences10thInternationalBielefeldConference,24-26April2012Overview•Whatliterature?Whatdata?•Howwemakeliterature-dataconnections•Casestudy•ChallengesandfuturedirectionsWhatliterature?Whatdata?DatadefinitionsLiteratureCurated/thematicMo

2、re[expert]humaneffort!databasesStructured:UnstructuredBythedatageneratorsFundermandatescomputabledatasetsJournalrequirementsMetadataDeposition“primary”databasesStandardsPMC336623Extendedtoseveralotherbiologicaldatatypes45000300EuropeanNucleotideArchive•Bigdata40000En

3、semblandEnsemblGenomes2503500030000200•Thematicdata250001502000015000100•PublicdataGenomes10000505000Nucleotides(millions)•Archiveddata0020012002200320042005200620072008200920102001200220032004200520062007200820092010YearYear1400000025000UniProtInterPro12000000200001

4、0000000•Twopetabytesofdata8000000150006000000Entries10000•Scalesto7pbsrawdisk4000000Entries5000•MajorityisDNA20000000020012002200320042005200620072008200920102001200220032004200520062007200820092010YearYear50000070000450000ArrayExpressPDBe4000006000035000050000300000

5、4000025000020000030000150000Structures20000Hybridisations10000010000500000020012002200320042005200620072008200920102001200220032004200520062007200820092010YearYearFigure2.GrowthofkeyresourcesTwocoreliteraturedatabases•26millionabstracts•Twomillionfulltextarticles(191

6、Karticleswithsuppldata)PubMed,Patents,Agricola•Website•Websiteandwebservices•Citationnetworks•SupplementedbyCiteXplore•Databaselinks•Additionaltextmining•Whatizittextmining•over1.1millionnewrecordsperyear•over150KnewarticlesperyearUKPubMedCentralOverview•Builtincolla

7、borationwithPubMedCentralUSA(+PMCCanada)since2006•LedbytheEuropeanBioinformaticsInstitutesince2011,withtheBritishLibrary,andtheUniversityofManchester•Supportedby16UKand2EuropeanFunders,ledbytheWellcomeTrust.Researchspend:~2billionGBP•Alife-scienceweb-basedrepository•

8、Manuscriptsubmissionservice(selfarchivingbygrantholders)•Databaseofgrantinformation–withdetailsofabout18000PIs•Grantreportingandfun