pubmed2ensembl A Resource for Mining the Biological Literature on Genes 英文参考文献.docVIP

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pubmed2ensembl A Resource for Mining the Biological Literature on Genes 英文参考文献.doc

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pubmed2ensembl A Resource for Mining the Biological Literature on Genes 英文参考文献

pubmed2ensembl:AResourceforMiningtheBiological LiteratureonGenes JoachimBaran1¤a,MartinGerner1,MaximilianHaeussler1¤b,GoranNenadic2,CaseyM.Bergman1* 1FacultyofLifeSciences,UniversityofManchester,Manchester,UnitedKingdom,2SchoolofComputerScience,UniversityofManchester,Manchester,UnitedKingdom Abstract Background: The last two decades have witnessed a dramatic acceleration in the production of genomic sequence informationandpublicationofbiomedicalarticles.Despitethefactthatgenomesequencedataandpublicationsaretwoof themostheavilyrelied-uponsourcesofinformationformanybiologists,verylittleefforthasbeenmadetosystematically integratedatafromgenomicsequencesdirectly withthebiologicalliterature. Foralimitednumberofmodelorganisms dedicated teams manually curate publications about genes; however for species with no such dedicated staff many thousandsofarticlesarenevermappedtogenesorgenomicregions. Methodology/PrincipalFindings:Toovercomethelackofintegrationbetweengenomicdataandbiologicalliterature,we havedevelopedpubmed2ensembl(),anextensiontotheBioMartsystemthatlinksover 2,000,000articlesinPubMedtonearly150,000genesinEnsemblfrom50species.Weuseseveralsourcesofcurated(e.g., EntrezGene)andautomaticallygenerated(e.g.,genenamesextractedthroughtext-miningonMEDLINErecords)sourcesof gene-publication links, allowing users to filter and combine different data sources to suit their individual needs for information extraction and biological discovery. In addition to extending the Ensembl BioMart database to include published information on genes, we also implemented a scripting language for automated BioMart construction and a novelBioMartinterfacethatallowstext-basedqueriestobeperformedagainstPubMedandPubMedCentraldocumentsin conjunctionwithconstraintsongenomicfeatures.Finally,weillustratethepotentialofpubmed2ensemblthroughtypical usecasesthatinvolveintegratedqueriesacrossthebiomedicalliteratureandgenomicdata. Conclusion/Significance: By allowing biologists to find the relevant li