{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T15:57:46Z","timestamp":1777651066016,"version":"3.51.4"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Advances in sequencing technology have led to an exponential growth of genomics data, yet it remains a formidable challenge to interpret such data for identifying disease genes and drug targets. There has been increasing interest in adopting a systems approach that incorporates prior knowledge such as gene networks and genotype\u2013phenotype associations. The majority of such knowledge resides in text such as journal publications, which has been undergoing its own exponential growth. It has thus become a significant bottleneck to identify relevant knowledge for genomic interpretation as well as to keep up with new genomics findings.<\/jats:p><jats:p>Results: In the Literome project, we have developed an automatic curation system to extract genomic knowledge from PubMed articles and made this knowledge available in the cloud with a Web site to facilitate browsing, searching and reasoning. Currently, Literome focuses on two types of knowledge most pertinent to genomic medicine: directed genic interactions such as pathways and genotype\u2013phenotype associations. Users can search for interacting genes and the nature of the interactions, as well as diseases and drugs associated with a single nucleotide polymorphism or gene. Users can also search for indirect connections between two entities, e.g. a gene and a disease might be linked because an interacting gene is associated with a related disease.<\/jats:p><jats:p>Availability and implementation: Literome is freely available at literome.azurewebsites.net. Download for non-commercial use is available via Web services.<\/jats:p><jats:p>Contact: \u00a0hoifung@microsoft.com<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu383","type":"journal-article","created":{"date-parts":[[2014,6,18]],"date-time":"2014-06-18T06:14:23Z","timestamp":1403072063000},"page":"2840-2842","source":"Crossref","is-referenced-by-count":48,"title":["Literome: PubMed-scale genomic knowledge base in the cloud"],"prefix":"10.1093","volume":"30","author":[{"given":"Hoifung","family":"Poon","sequence":"first","affiliation":[{"name":"Microsoft Research, One Microsoft Way, Redmond, WA 98052, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris","family":"Quirk","sequence":"additional","affiliation":[{"name":"Microsoft Research, One Microsoft Way, Redmond, WA 98052, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charlie","family":"DeZiel","sequence":"additional","affiliation":[{"name":"Microsoft Research, One Microsoft Way, Redmond, WA 98052, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Heckerman","sequence":"additional","affiliation":[{"name":"Microsoft Research, One Microsoft Way, Redmond, WA 98052, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,6,17]]},"reference":[{"key":"2023041303472688500_","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1186\/1471-2105-5-147","article-title":"Content-rich biological network constructed by mining PubMed abstracts","volume":"5","author":"Chen","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023041303472688500_","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","article-title":"Hallmarks of cancer: the next generation","volume":"144","author":"Hanahan","year":"2011","journal-title":"Cell"},{"key":"2023041303472688500_","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1016\/j.cell.2011.03.007","article-title":"Boosting signal-to-noise in complex biology: prior knowledge is power","volume":"144","author":"Ideker","year":"2011","journal-title":"Cell"},{"key":"2023041303472688500_","doi-asserted-by":"crossref","first-page":"e55814","DOI":"10.1371\/journal.pone.0055814","article-title":"Large-scale event extraction from literature with multi-level gene normalization","volume":"8","author":"Landeghem","year":"2013","journal-title":"PLoS One"},{"key":"2023041303472688500_","doi-asserted-by":"crossref","first-page":"D940","DOI":"10.1093\/nar\/gkr972","article-title":"Disease ontology: a backbone for disease semantic integration","volume":"40","author":"Schriml","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023041303472688500_","doi-asserted-by":"crossref","first-page":"W585","DOI":"10.1093\/nar\/gks563","article-title":"Geneview: a comprehensive semantic search engine for PubMed","volume":"40","author":"Thomas","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023041303472688500_","doi-asserted-by":"crossref","first-page":"bas041","DOI":"10.1093\/database\/bas041","article-title":"Accelerating literature curation with text-mining tools: a case study of using pubtator to curate genes in PubMed abstracts","volume":"2012","author":"Wei","year":"2012","journal-title":"Database"},{"key":"2023041303472688500_","doi-asserted-by":"crossref","first-page":"D1001","DOI":"10.1093\/nar\/gkt1229","article-title":"The NHGRI GWAS catalog, a curated resource of SNP-trait associations","volume":"42","author":"Welter","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023041303472688500_","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1038\/clpt.2012.96","article-title":"Pharmacogenomics knowledge for personalized medicine","volume":"92","author":"Whirl-Carrillo","year":"2012","journal-title":"Clin. 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