{"id":"https://openalex.org/W7100885367","doi":null,"title":"BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btu383 Databases and ontologies Advance Access publication June 17, 2014 Literome: PubMed-scale genomic knowledge base in the cloud","display_name":"BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btu383 Databases and ontologies Advance Access publication June 17, 2014 Literome: PubMed-scale genomic knowledge base in the cloud","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W7100885367"},"language":"en","primary_location":{"id":"pmh:oai:CiteSeerX.psu:10.1.1.995.1059","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.995.1059","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/30/19/2840.full.pdf","raw_type":"text"},"volume":null,"type":"article","indexed_in":[],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019494985","display_name":"Hoifung Poon","orcid":"https://orcid.org/0000-0002-9067-0918","observed_orcids":["https://orcid.org/0000-0002-9067-0918"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hoifung Poon","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Chris Quirk","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chris Quirk","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048593287","display_name":"Charlie DeZiel","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Charlie Deziel","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016386034","display_name":"David E. Heckerman","orcid":"https://orcid.org/0000-0002-4274-6084","observed_orcids":["https://orcid.org/0000-0002-4274-6084"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"David Heckerman","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":null,"display_name":"Jonathan Wren","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jonathan Wren","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.46065122,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":true,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0035000001080334187,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genotype-phenotype-correlation","display_name":"genotype-phenotype correlation","score":0.8960000276565552},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphisms","display_name":"single nucleotide polymorphisms","score":0.9350000023841858},{"id":"https://openalex.org/keywords/genomic-medicine","display_name":"genomic medicine","score":0.593999981880188}],"concepts":[{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.6798999905586243},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.6352999806404114},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.6261000037193298},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5837000012397766},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.5620999932289124},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4580000042915344},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42570000886917114},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.38909998536109924},{"id":"https://openalex.org/C45235069","wikidata":"https://www.wikidata.org/wiki/Q278425","display_name":"Table (database)","level":2,"score":0.37619999051094055},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.3698999881744385},{"id":"https://openalex.org/C2780154274","wikidata":"https://www.wikidata.org/wiki/Q7126717","display_name":"Download","level":2,"score":0.349700003862381},{"id":"https://openalex.org/C65603577","wikidata":"https://www.wikidata.org/wiki/Q3427877","display_name":"Web resource","level":2,"score":0.3409999907016754},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3068999946117401},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.2971000075340271},{"id":"https://openalex.org/C115925183","wikidata":"https://www.wikidata.org/wiki/Q1412694","display_name":"Knowledge-based systems","level":2,"score":0.295199990272522},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.27869999408721924},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2775999903678894},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.2757999897003174},{"id":"https://openalex.org/C35578498","wikidata":"https://www.wikidata.org/wiki/Q193424","display_name":"Web service","level":2,"score":0.26100000739097595},{"id":"https://openalex.org/C141674004","wikidata":"https://www.wikidata.org/wiki/Q1344256","display_name":"Ensembl","level":5,"score":0.259799987077713},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.25769999623298645},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.257099986076355},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.25540000200271606},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25279998779296875},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.25220000743865967}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:CiteSeerX.psu:10.1.1.995.1059","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.995.1059","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/30/19/2840.full.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W7096094942","https://openalex.org/W2108475224","https://openalex.org/W7096066401","https://openalex.org/W2135157583","https://openalex.org/W1991237726","https://openalex.org/W2413738648","https://openalex.org/W4362736376","https://openalex.org/W123056462","https://openalex.org/W2462053388","https://openalex.org/W2118002992"],"abstract_inverted_index":{"Motivation:":[0],"Advances":[1],"in":[2,36,58,120],"sequencing":[3],"technology":[4],"have":[5,102],"led":[6],"to":[7,20,79,89,108,127,143],"an":[8,104,202],"expo-nential":[9],"growth":[10],"of":[11,54,139,165],"genomics":[12,94],"data,":[13],"yet":[14],"it":[15],"remains":[16],"a":[17,38,76,124,176,193,196,208],"formidable":[18],"challenge":[19],"interpret":[21],"such":[22,45,55,60,149],"data":[23],"for":[24,83,159,186,221],"identifying":[25],"disease":[26,197],"genes":[27,161],"and":[28,49,115,131,152,162,172,195,212],"drug":[29],"targets.":[30],"There":[31],"has":[32,65,73],"been":[33,66],"increasing":[34],"interest":[35],"adopting":[37],"systems":[39],"approach":[40],"that":[41],"incorporates":[42],"prior":[43],"knowledge":[44,56,82,111,118,140],"as":[46,61,86,88,150,168,170],"gene":[47,194,204],"networks":[48],"geno-type\u2013phenotype":[50],"associations.":[51,155],"The":[52],"majority":[53],"resides":[57],"text":[59],"journal":[62],"publications,":[63],"which":[64],"undergoing":[67],"its":[68],"own":[69],"exponential":[70],"growth.":[71],"It":[72],"thus":[74],"become":[75],"significant":[77],"bottleneck":[78],"identify":[80],"relevant":[81],"genomic":[84,110,144],"interpretation":[85],"well":[87,169],"keep":[90],"up":[91],"with":[92,123,175,207],"new":[93],"findings.":[95],"Results:":[96],"In":[97],"the":[98,121,163,166],"Literome":[99,134,214],"project,":[100],"we":[101],"developed":[103],"automatic":[105],"curation":[106],"system":[107],"extract":[109],"from":[112],"PubMed":[113],"articles":[114],"made":[116],"this":[117],"available":[119,217],"cloud":[122],"Web":[125,227],"site":[126],"facilitate":[128],"browsing,":[129],"searching":[130],"reasoning.":[132],"Currently,":[133],"focuses":[135],"on":[136],"two":[137,190],"types":[138],"most":[141],"pertinent":[142],"medi-cine:":[145],"directed":[146],"genic":[147],"interactions":[148],"pathways":[151],"genotype\u2013":[153],"phenotype":[154],"Users":[156,182],"can":[157,183],"search":[158,185],"interacting":[160,203],"nature":[164],"interactions,":[167],"diseases":[171],"drugs":[173],"asso-ciated":[174],"single":[177],"nucleotide":[178],"polymorphism":[179],"or":[180],"gene.":[181],"also":[184],"indirect":[187],"connections":[188],"between":[189],"entities,":[191],"e.g.":[192],"might":[198],"be":[199],"linked":[200],"because":[201],"is":[205,215,224],"associated":[206],"related":[209],"disease.":[210],"Availability":[211],"implementation:":[213],"freely":[216],"at":[218],"liter-ome.azurewebsites.net.":[219],"Download":[220],"non-commercial":[222],"use":[223],"avail-able":[225],"via":[226],"services.":[228]},"counts_by_year":[],"updated_date":"2026-10-14T16:39:01.820549","created_date":"2025-10-27T00:00:00"}