{"id":321194,"date":"2016-11-14T12:35:14","date_gmt":"2016-11-14T20:35:14","guid":{"rendered":"https:\/\/www.microsoft.com\/en-us\/research\/?post_type=msr-research-item&#038;p=321194"},"modified":"2018-10-16T20:18:46","modified_gmt":"2018-10-17T03:18:46","slug":"literome-pubmed-scale-genomic-knowledge-base-cloud","status":"publish","type":"msr-research-item","link":"https:\/\/www.microsoft.com\/en-us\/research\/publication\/literome-pubmed-scale-genomic-knowledge-base-cloud\/","title":{"rendered":"Literome: PubMed-scale Genomic Knowledge Base in the Cloud"},"content":{"rendered":"<p><strong>Motivation:<\/strong> 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.<\/p>\n<div id=\"pageid-content\" class=\"hw-gen-page pagetype-content hw-pub-id-article\">\n<div id=\"content-block\" class=\"10.1093bioinformaticsbtu38310.1093bioinformaticsbtu383\">\n<div class=\"article abstract-view \">\n<div id=\"abstract-1\" class=\"section abstract\">\n<p id=\"p-3\"><strong>Results:<\/strong> 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.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<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 [&hellip;]<\/p>\n","protected":false},"featured_media":0,"template":"","meta":{"msr-url-field":"","msr-podcast-episode":"","msrModifiedDate":"","msrModifiedDateEnabled":false,"ep_exclude_from_search":false,"_classifai_error":"","footnotes":""},"msr-content-type":[3],"msr-research-highlight":[],"research-area":[13553],"msr-publication-type":[193716],"msr-product-type":[],"msr-focus-area":[],"msr-platform":[],"msr-download-source":[],"msr-locale":[268875],"msr-post-option":[],"msr-field-of-study":[],"msr-conference":[],"msr-journal":[],"msr-impact-theme":[],"msr-pillar":[],"class_list":["post-321194","msr-research-item","type-msr-research-item","status-publish","hentry","msr-research-area-medical-health-genomics","msr-locale-en_us"],"msr_publishername":"","msr_edition":"Bioinformatics 2014","msr_affiliation":"","msr_published_date":"2014-05-01","msr_host":"","msr_duration":"","msr_version":"","msr_speaker":"","msr_other_contributors":"","msr_booktitle":"","msr_pages_string":"2840-2842","msr_chapter":"","msr_isbn":"","msr_journal":"","msr_volume":"30","msr_number":"","msr_editors":"","msr_series":"","msr_issue":"19","msr_organization":"","msr_how_published":"","msr_notes":"","msr_highlight_text":"","msr_release_tracker_id":"","msr_original_fields_of_study":"","msr_download_urls":"","msr_external_url":"","msr_secondary_video_url":"","msr_longbiography":"","msr_microsoftintellectualproperty":1,"msr_main_download":"","msr_publicationurl":"https:\/\/academic.oup.com\/bioinformatics\/article-lookup\/doi\/10.1093\/bioinformatics\/btu383","msr_doi":"10.1093\/bioinformatics\/btu383","msr_publication_uploader":[{"type":"url","title":"https:\/\/academic.oup.com\/bioinformatics\/article-lookup\/doi\/10.1093\/bioinformatics\/btu383","viewUrl":false,"id":false,"label_id":0},{"type":"doi","title":"10.1093\/bioinformatics\/btu383","viewUrl":false,"id":false,"label_id":0}],"msr_related_uploader":"","msr_attachments":[{"id":0,"url":"https:\/\/academic.oup.com\/bioinformatics\/article-lookup\/doi\/10.1093\/bioinformatics\/btu383"}],"msr-author-ordering":[{"type":"text","value":"Hoifung Poon","user_id":0,"rest_url":false},{"type":"text","value":"Chris Quirk","user_id":0,"rest_url":false},{"type":"text","value":"Charlie DeZiel","user_id":0,"rest_url":false},{"type":"user_nicename","value":"heckerma","user_id":31991,"rest_url":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/microsoft-research\/v1\/researchers?person=heckerma"}],"msr_impact_theme":[],"msr_research_lab":[],"msr_event":[],"msr_group":[952050],"msr_project":[393227],"publication":[],"video":[],"download":[],"msr_publication_type":"inproceedings","related_content":{"projects":[{"ID":393227,"post_title":"Biomedical Natural Language Processing","post_name":"biomedical-nlp","post_type":"msr-project","post_date":"2017-07-06 09:30:15","post_modified":"2017-07-14 12:37:01","post_status":"publish","permalink":"https:\/\/www.microsoft.com\/en-us\/research\/project\/biomedical-nlp\/","post_excerpt":"The biomedical sciences are beginning to undergo a major transformation. Precision medicine has the potential to make treatments much more effective by better understanding patients, biological mechanisms, and therapeutic effects. However, current approaches only reach a small fraction of the patient population.\u00a0 Consider the molecular tumor board: dozens of highly paid specialists create a custom treatment plan for an individual patient, combing the research literature for research advances that are relevant to the cancer of&hellip;","_links":{"self":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-project\/393227"}]}}]},"_links":{"self":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-research-item\/321194"}],"collection":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-research-item"}],"about":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/types\/msr-research-item"}],"version-history":[{"count":2,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-research-item\/321194\/revisions"}],"predecessor-version":[{"id":394712,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-research-item\/321194\/revisions\/394712"}],"wp:attachment":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/media?parent=321194"}],"wp:term":[{"taxonomy":"msr-content-type","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-content-type?post=321194"},{"taxonomy":"msr-research-highlight","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-research-highlight?post=321194"},{"taxonomy":"msr-research-area","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/research-area?post=321194"},{"taxonomy":"msr-publication-type","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-publication-type?post=321194"},{"taxonomy":"msr-product-type","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-product-type?post=321194"},{"taxonomy":"msr-focus-area","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-focus-area?post=321194"},{"taxonomy":"msr-platform","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-platform?post=321194"},{"taxonomy":"msr-download-source","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-download-source?post=321194"},{"taxonomy":"msr-locale","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-locale?post=321194"},{"taxonomy":"msr-post-option","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-post-option?post=321194"},{"taxonomy":"msr-field-of-study","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-field-of-study?post=321194"},{"taxonomy":"msr-conference","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-conference?post=321194"},{"taxonomy":"msr-journal","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-journal?post=321194"},{"taxonomy":"msr-impact-theme","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-impact-theme?post=321194"},{"taxonomy":"msr-pillar","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-pillar?post=321194"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}