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(PDF) Variomes: a high recall search engine to support the curation of genomic variants
<!DOCTYPE html> <html > <head> <meta charset="utf-8"> <meta rel="search" type="application/opensearchdescription+xml" href="/open_search.xml" title="Academia.edu"> <meta content="width=device-width, initial-scale=1" name="viewport"> <meta name="google-site-verification" content="bKJMBZA7E43xhDOopFZkssMMkBRjvYERV-NaN4R6mrs"> <meta name="csrf-param" content="authenticity_token" /> <meta name="csrf-token" content="eG8jUxX_6oU9hOFXHf-KPMlZPpN4wQpwEIUTvP2RLQzx5utsQaeehLFKFmVI4N3DPfy9dGFvCvdvDlSQnIlA_w" /> <meta name="citation_title" content="Variomes: a high recall search engine to support the curation of genomic variants" /> <meta name="citation_publication_date" content="2021" /> <meta name="citation_author" content="Emilie Pasche" /> <meta name="citation_author" content="Anaïs Mottaz" /> <meta name="citation_author" content="Deborah Caucheteur" /> <meta name="citation_author" content="Julien Gobeill" /> <meta name="citation_author" content="Pierre-André Michel" /> <meta name="citation_author" content="Patrick Ruch" /> <meta name="twitter:card" content="summary" /> <meta name="twitter:url" content="https://www.academia.edu/78975880/Variomes_a_high_recall_search_engine_to_support_the_curation_of_genomic_variants" /> <meta name="twitter:title" content="Variomes: a high recall search engine to support the curation of genomic variants" /> <meta name="twitter:description" content="Precision oncology relies on the use of treatments targeting specific genetic variants. However, identifying clinically actionable variants as well as relevant information likely to be used to treat a patient with a given cancer is a labor-intensive" /> <meta name="twitter:image" content="http://a.academia-assets.com/images/twitter-card.jpeg" /> <meta property="fb:app_id" content="2369844204" /> <meta property="og:type" content="article" /> <meta property="og:url" content="https://www.academia.edu/78975880/Variomes_a_high_recall_search_engine_to_support_the_curation_of_genomic_variants" /> <meta property="og:title" content="Variomes: a high recall search engine to support the curation of genomic variants" /> <meta property="og:image" content="http://a.academia-assets.com/images/open-graph-icons/fb-paper.gif" /> <meta property="og:description" content="Precision oncology relies on the use of treatments targeting specific genetic variants. However, identifying clinically actionable variants as well as relevant information likely to be used to treat a patient with a given cancer is a labor-intensive" /> <meta property="article:author" content="https://hes-so.academia.edu/JulienGobeill" /> <meta name="description" content="Precision oncology relies on the use of treatments targeting specific genetic variants. However, identifying clinically actionable variants as well as relevant information likely to be used to treat a patient with a given cancer is a labor-intensive" /> <title>(PDF) Variomes: a high recall search engine to support the curation of genomic variants</title> <link rel="canonical" href="https://www.academia.edu/78975880/Variomes_a_high_recall_search_engine_to_support_the_curation_of_genomic_variants" /> <script async src="https://www.googletagmanager.com/gtag/js?id=G-5VKX33P2DS"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-5VKX33P2DS', { cookie_domain: 'academia.edu', send_page_view: false, }); gtag('event', 'page_view', { 'controller': "single_work", 'action': "show", 'controller_action': 'single_work#show', 'logged_in': 'false', 'edge': 'unknown', // Send nil if there is no A/B test bucket, in case some records get logged // with missing data - that way we can distinguish between the two cases. // ab_test_bucket should be of the form <ab_test_name>:<bucket> 'ab_test_bucket': null, }) </script> <script> var $controller_name = 'single_work'; var $action_name = "show"; var $rails_env = 'production'; var $app_rev = '129f474dbcc8e505390b0f49472dac75fb69884e'; var $domain = 'academia.edu'; var $app_host = "academia.edu"; var $asset_host = "academia-assets.com"; var $start_time = new Date().getTime(); var $recaptcha_key = "6LdxlRMTAAAAADnu_zyLhLg0YF9uACwz78shpjJB"; var $recaptcha_invisible_key = "6Lf3KHUUAAAAACggoMpmGJdQDtiyrjVlvGJ6BbAj"; var $disableClientRecordHit = false; </script> <script> window.require = { config: function() { return function() {} } } </script> <script> window.Aedu = window.Aedu || {}; window.Aedu.hit_data = null; window.Aedu.serverRenderTime = new Date(1740155237000); window.Aedu.timeDifference = new Date().getTime() - 1740155237000; </script> <script type="application/ld+json">{"@context":"https://schema.org","@type":"ScholarlyArticle","abstract":"Precision oncology relies on the use of treatments targeting specific genetic variants. However, identifying clinically actionable variants as well as relevant information likely to be used to treat a patient with a given cancer is a labor-intensive task, which includes searching the literature for a large set of variants. The lack of universally adopted standard nomenclature for variants requires the development of variant-specific literature search engines. We develop a system to perform triage of publications relevant to support an evidence-based decision. Together with providing a ranked list of articles for a given variant, the system is also able to prioritize variants, as found in a Variant Calling Format, assuming that the clinical actionability of a genetic variant is correlated with the volume of literature published about the variant. Our system searches within three pre-annotated document collections: MEDLINE abstracts, PubMed Central full-text articles and ClinicalTrial...","author":[{"@context":"https://schema.org","@type":"Person","name":"Julien Gobeill","url":"https://hes-so.academia.edu/JulienGobeill"}],"contributor":[],"dateCreated":"2022-05-11","datePublished":"2021-01-01","headline":"Variomes: a high recall search engine to support the curation of genomic variants","image":"https://attachments.academia-assets.com/85852696/thumbnails/1.jpg","inLanguage":"en","keywords":["Biology"],"publisher":{"@context":"https://schema.org","@type":"Organization","name":"Cold Spring Harbor Laboratory"},"sourceOrganization":[{"@context":"https://schema.org","@type":"EducationalOrganization","name":"hes-so"}],"thumbnailUrl":"https://attachments.academia-assets.com/85852696/thumbnails/1.jpg","url":"https://www.academia.edu/78975880/Variomes_a_high_recall_search_engine_to_support_the_curation_of_genomic_variants"}</script><style type="text/css">@media(max-width: 567px){:root{--token-mode: Rebrand;--dropshadow: 0 2px 4px 0 #22223340;--primary-brand: #0645b1;--error-dark: #b60000;--success-dark: #05b01c;--inactive-fill: #ebebee;--hover: #0c3b8d;--pressed: #082f75;--button-primary-fill-inactive: #ebebee;--button-primary-fill: #0645b1;--button-primary-text: #ffffff;--button-primary-fill-hover: #0c3b8d;--button-primary-fill-press: #082f75;--button-primary-icon: #ffffff;--button-primary-fill-inverse: #ffffff;--button-primary-text-inverse: #082f75;--button-primary-icon-inverse: #0645b1;--button-primary-fill-inverse-hover: #cddaef;--button-primary-stroke-inverse-pressed: 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window.loswp.work = {"work":{"id":78975880,"created_at":"2022-05-11T10:52:56.251-07:00","from_world_paper_id":205017992,"updated_at":"2022-05-11T17:19:25.082-07:00","_data":{"abstract":"Precision oncology relies on the use of treatments targeting specific genetic variants. However, identifying clinically actionable variants as well as relevant information likely to be used to treat a patient with a given cancer is a labor-intensive task, which includes searching the literature for a large set of variants. The lack of universally adopted standard nomenclature for variants requires the development of variant-specific literature search engines. We develop a system to perform triage of publications relevant to support an evidence-based decision. Together with providing a ranked list of articles for a given variant, the system is also able to prioritize variants, as found in a Variant Calling Format, assuming that the clinical actionability of a genetic variant is correlated with the volume of literature published about the variant. Our system searches within three pre-annotated document collections: MEDLINE abstracts, PubMed Central full-text articles and ClinicalTrial...","publisher":"Cold Spring Harbor Laboratory","publication_date":"2021,,"},"document_type":"paper","pre_hit_view_count_baseline":null,"quality":"high","language":"en","title":"Variomes: a high recall search engine to support the curation of genomic variants","broadcastable":false,"draft":null,"has_indexable_attachment":true,"indexable":true}}["work"]; window.loswp.workCoauthors = [32463478]; window.loswp.locale = "en"; window.loswp.countryCode = "SG"; window.loswp.cwvAbTestBucket = ""; window.loswp.designVariant = "ds_vanilla"; window.loswp.fullPageMobileSutdModalVariant = "control"; window.loswp.useOptimizedScribd4genScript = false; window.loginModal = {}; window.loginModal.appleClientId = 'edu.academia.applesignon'; window.userInChina = "false";</script><script defer="" src="https://accounts.google.com/gsi/client"></script><div class="ds-loswp-container"><div class="ds-work-card--grid-container"><div class="ds-work-card--container js-loswp-work-card"><div class="ds-work-card--cover"><div class="ds-work-cover--wrapper"><div class="ds-work-cover--container"><button class="ds-work-cover--clickable js-swp-download-button" data-signup-modal="{"location":"swp-splash-paper-cover","attachmentId":85852696,"attachmentType":"pdf"}"><img alt="First page of “Variomes: a high recall search engine to support the curation of genomic variants”" class="ds-work-cover--cover-thumbnail" src="https://0.academia-photos.com/attachment_thumbnails/85852696/mini_magick20220522-21075-2gsna0.png?1653218595" /><img alt="PDF Icon" class="ds-work-cover--file-icon" src="//a.academia-assets.com/images/single_work_splash/adobe_icon.svg" /><div class="ds-work-cover--hover-container"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span><p>Download Free PDF</p></div><div class="ds-work-cover--ribbon-container">Download Free PDF</div><div class="ds-work-cover--ribbon-triangle"></div></button></div></div></div><div class="ds-work-card--work-information"><h1 class="ds-work-card--work-title">Variomes: a high recall search engine to support the curation of genomic variants</h1><div class="ds-work-card--work-authors ds-work-card--detail"><a class="ds-work-card--author js-wsj-grid-card-author ds2-5-body-md ds2-5-body-link" data-author-id="32463478" href="https://hes-so.academia.edu/JulienGobeill"><img alt="Profile image of Julien Gobeill" class="ds-work-card--author-avatar" src="//a.academia-assets.com/images/s65_no_pic.png" />Julien Gobeill</a></div><div class="ds-work-card--detail"><p class="ds-work-card--detail ds2-5-body-sm">2021</p><div class="ds-work-card--work-metadata"><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">visibility</span><p class="ds2-5-body-sm" id="work-metadata-view-count">…</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">description</span><p class="ds2-5-body-sm">12 pages</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">link</span><p class="ds2-5-body-sm">1 file</p></div></div><script>(async () => { const workId = 78975880; 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However, identifying clinically actionable variants as well as relevant information likely to be used to treat a patient with a given cancer is a labor-intensive task, which includes searching the literature for a large set of variants. The lack of universally adopted standard nomenclature for variants requires the development of variant-specific literature search engines. We develop a system to perform triage of publications relevant to support an evidence-based decision. Together with providing a ranked list of articles for a given variant, the system is also able to prioritize variants, as found in a Variant Calling Format, assuming that the clinical actionability of a genetic variant is correlated with the volume of literature published about the variant. Our system searches within three pre-annotated document collections: MEDLINE abstracts, PubMed Central full-text articles and ClinicalTrial...</p><div class="ds-work-card--button-container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--work-card","attachmentId":85852696,"attachmentType":"pdf","workUrl":"https://www.academia.edu/78975880/Variomes_a_high_recall_search_engine_to_support_the_curation_of_genomic_variants"}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--work-card","attachmentId":85852696,"attachmentType":"pdf","workUrl":"https://www.academia.edu/78975880/Variomes_a_high_recall_search_engine_to_support_the_curation_of_genomic_variants"}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div><div class="ds-signup-banner-trigger-container"><div class="ds-signup-banner-trigger ds-signup-banner-trigger-control"></div></div><div class="ds-signup-banner ds-signup-banner-control"><div id="ds-signup-banner-close-button"><button class="ds2-5-button ds2-5-button--secondary ds2-5-button--inverse"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">close</span></button></div><div class="ds-signup-banner-ctas"><img src="//a.academia-assets.com/images/academia-logo-capital-white.svg" /><h4 class="ds2-5-heading-serif-sm">Sign up for access to the world's latest research</h4><button class="ds2-5-button ds2-5-button--inverse ds2-5-button--full-width js-swp-download-button" data-signup-modal="{"location":"signup-banner"}">Sign up for free<span class="material-symbols-outlined" style="font-size: 20px" translate="no">arrow_forward</span></button></div><div class="ds-signup-banner-divider"></div><div class="ds-signup-banner-reasons"><div class="ds-signup-banner-reasons-item"><span class="material-symbols-outlined" style="font-size: 24px" translate="no">check</span><span>Get notified about relevant papers</span></div><div class="ds-signup-banner-reasons-item"><span class="material-symbols-outlined" style="font-size: 24px" translate="no">check</span><span>Save papers to use in your research</span></div><div class="ds-signup-banner-reasons-item"><span class="material-symbols-outlined" style="font-size: 24px" translate="no">check</span><span>Join the discussion with peers</span></div><div class="ds-signup-banner-reasons-item"><span class="material-symbols-outlined" style="font-size: 24px" translate="no">check</span><span>Track your impact</span></div></div></div><script>(() => { // Set up signup banner show/hide behavior: // 1. 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Schafer</a></div><p class="ds-related-work--metadata ds2-5-body-xs">BMC Bioinformatics</p><p class="ds-related-work--abstract ds2-5-body-sm">Background: Diagnosis and treatment decisions in cancer increasingly depend on a detailed analysis of the mutational status of a patient's genome. This analysis relies on previously published information regarding the association of variations to disease progression and possible interventions. Clinicians to a large degree use biomedical search engines to obtain such information; however, the vast majority of scientific publications focus on basic science and have no direct clinical impact. We develop the Variant-Information Search Tool (VIST), a search engine designed for the targeted search of clinically relevant publications given an oncological mutation profile. Results: VIST indexes all PubMed abstracts and content from ClinicalTrials.gov. It applies advanced text mining to identify mentions of genes, variants and drugs and uses machine learning based scoring to judge the clinical relevance of indexed abstracts. Its functionality is available through a fast and intuitive web interface. We perform several evaluations, showing that VIST's ranking is superior to that of PubMed or a pure vector space model with regard to the clinical relevance of a document's content. Conclusion: Different user groups search repositories of scientific publications with different intentions. This diversity is not adequately reflected in the standard search engines, often leading to poor performance in specialized settings. We develop a search engine for the specific case of finding documents that are clinically relevant in the course of cancer treatment. We believe that the architecture of our engine, heavily relying on machine learning algorithms, can also act as a blueprint for search engines in other, equally specific domains. VIST is freely available at https://vist. informatik.hu-berlin.de/</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"VIST - a Variant-Information Search Tool for precision oncology","attachmentId":78134287,"attachmentType":"pdf","work_url":"https://www.academia.edu/67245179/VIST_a_Variant_Information_Search_Tool_for_precision_oncology","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/67245179/VIST_a_Variant_Information_Search_Tool_for_precision_oncology"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="1" data-entity-id="21882898" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/21882898/An_automated_procedure_to_identify_biomedical_articles_that_contain_cancer_associated_gene_variants">An automated procedure to identify biomedical articles that contain cancer-associated gene variants</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="43121048" href="https://independent.academia.edu/MarcGreenblatt">Marc Greenblatt</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Human Mutation, 2006</p><p class="ds-related-work--abstract ds2-5-body-sm">The proliferation of biomedical literature makes it increasingly difficult for researchers to find and manage relevant information. However, identifying research articles containing mutation data, a requisite first step in integrating large and complex mutation data sets, is currently tedious, time-consuming and imprecise. More effective mechanisms for identifying articles containing mutation information would be beneficial both for the curation of mutation databases and for individual researchers. We developed an automated method that uses information extraction, classifier, and relevance ranking techniques to determine the likelihood of MEDLINE abstracts containing mentions of genomic variation data suitable for inclusion in mutation databases. We targeted the CDKN2A (p16) gene and the procedure for document identification currently used by CDKN2A Database curators as a measure of feasibility. A set of abstracts was manually identified from a MEDLINE search as potentially containing specific CDKN2A mutation events. A subset of these abstracts was used as a training set for a maximum entropy classifier to identify text features distinguishing "relevant" from "not relevant" abstracts. Each document was represented as a set of indicative word, word pair, and entity tagger-derived genomic variation features. When applied to a test set of 200 candidate abstracts, the classifier predicted 88 articles as being relevant; of these, 29 of 32 manuscripts in which manual curation found CDKN2A sequence variants were positively predicted. Thus, the set of potentially useful articles that a manual curator would have to review was reduced by 56%, maintaining 91% recall (sensitivity) and more than doubling precision (positive predictive value). Subsequent expansion of the training set to 494 articles yielded similar precision and recall rates, and comparison of the original and expanded trials demonstrated that the average precision improved with the larger data set. Our results show that automated systems can effectively identify article subsets relevant to a given task and may prove to be powerful tools for the broader research community. This procedure can be readily adapted to any or all genes, organisms, or set of documents.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"An automated procedure to identify biomedical articles that contain cancer-associated gene variants","attachmentId":42620617,"attachmentType":"pdf","work_url":"https://www.academia.edu/21882898/An_automated_procedure_to_identify_biomedical_articles_that_contain_cancer_associated_gene_variants","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/21882898/An_automated_procedure_to_identify_biomedical_articles_that_contain_cancer_associated_gene_variants"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="2" data-entity-id="91107223" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/91107223/CIViCdb_2022_evolution_of_an_open_access_cancer_variant_interpretation_knowledgebase">CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="104825544" href="https://independent.academia.edu/SeanDelong">Sean Delong</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Nucleic Acids Research</p><p class="ds-related-work--abstract ds2-5-body-sm">CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management, the need for cancer variant interpretation has grown beyond the capability of any single institution. CIViC contains peer-reviewed, published literature curated and expertly-moderated into structured data units (Evidence Items) that can be accessed globally and in real time, reducing barriers to clinical variant knowledge sharing. We have extended CIViC’s functionality to support emergent variant interpretation guidelines, increase interoperability with other variant resources, and promote widespread dissemination of structured curated data. To support the full breadth of variant interpretation from basic to translational, including integration of somatic and germline variant knowledge and inference of drug r...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase","attachmentId":94488230,"attachmentType":"pdf","work_url":"https://www.academia.edu/91107223/CIViCdb_2022_evolution_of_an_open_access_cancer_variant_interpretation_knowledgebase","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/91107223/CIViCdb_2022_evolution_of_an_open_access_cancer_variant_interpretation_knowledgebase"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="3" data-entity-id="20917456" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/20917456/Literature_mining_of_genetic_variants_for_curation_quantifying_the_importance_of_supplementary_material">Literature mining of genetic variants for curation: quantifying the importance of supplementary material</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="11235922" href="https://unimelb.academia.edu/KarinVerspoor">Karin Verspoor</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Database, 2014</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Literature mining of genetic variants for curation: quantifying the importance of supplementary material","attachmentId":41627778,"attachmentType":"pdf","work_url":"https://www.academia.edu/20917456/Literature_mining_of_genetic_variants_for_curation_quantifying_the_importance_of_supplementary_material","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/20917456/Literature_mining_of_genetic_variants_for_curation_quantifying_the_importance_of_supplementary_material"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="4" data-entity-id="21067221" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/21067221/B_E_A_R_GeneInfo_a_tool_for_identifying_gene_related_biomedical_publications_through_user_modifiable_queries">B.E.A.R. GeneInfo: a tool for identifying gene-related biomedical publications through user modifiable queries</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="42288754" href="https://independent.academia.edu/MartinHessner">Martin Hessner</a></div><p class="ds-related-work--metadata ds2-5-body-xs">BMC bioinformatics, 2004</p><p class="ds-related-work--abstract ds2-5-body-sm">Once specific genes are identified through high throughput genomics technologies there is a need to sort the final gene list to a manageable size for validation studies. The triaging and sorting of genes often relies on the use of supplemental information related to gene structure, metabolic pathways, and chromosomal location. Yet in disease states where the genes may not have identifiable structural elements, poorly defined metabolic pathways, or limited chromosomal data, flexible systems for obtaining additional data are necessary. In these situations having a tool for searching the biomedical literature using the list of identified genes while simultaneously defining additional search terms would be useful. We have built a tool, BEAR GeneInfo, that allows flexible searches based on the investigators knowledge of the biological process, thus allowing for data mining that is specific to the scientist&#39;s strengths and interests. This tool allows a user to upload a series of GenBa...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"B.E.A.R. GeneInfo: a tool for identifying gene-related biomedical publications through user modifiable queries","attachmentId":42416873,"attachmentType":"pdf","work_url":"https://www.academia.edu/21067221/B_E_A_R_GeneInfo_a_tool_for_identifying_gene_related_biomedical_publications_through_user_modifiable_queries","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/21067221/B_E_A_R_GeneInfo_a_tool_for_identifying_gene_related_biomedical_publications_through_user_modifiable_queries"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="5" data-entity-id="18344960" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/18344960/A_novel_information_retrieval_model_for_high_throughput_molecular_medicine_modalities">A novel information retrieval model for high-throughput molecular medicine modalities</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="38333328" href="https://independent.academia.edu/DanMasys">Dan Masys</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Cancer informatics, 2009</p><p class="ds-related-work--abstract ds2-5-body-sm">Significant research has been devoted to predicting diagnosis, prognosis, and response to treatment using high-throughput assays. Rapid translation into clinical results hinges upon efficient access to up-to-date and high-quality molecular medicine modalities. We first explain why this goal is inadequately supported by existing databases and portals and then introduce a novel semantic indexing and information retrieval model for clinical bioinformatics. The formalism provides the means for indexing a variety of relevant objects (e.g. papers, algorithms, signatures, datasets) and includes a model of the research processes that creates and validates these objects in order to support their systematic presentation once retrieved.We test the applicability of the model by constructing proof-of-concept encodings and visual presentations of evidence and modalities in molecular profiling and prognosis of: (a) diffuse large B-cell lymphoma (DLBCL) and (b) breast cancer.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"A novel information retrieval model for high-throughput molecular medicine modalities","attachmentId":40005809,"attachmentType":"pdf","work_url":"https://www.academia.edu/18344960/A_novel_information_retrieval_model_for_high_throughput_molecular_medicine_modalities","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/18344960/A_novel_information_retrieval_model_for_high_throughput_molecular_medicine_modalities"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="6" data-entity-id="61126517" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/61126517/Electronic_Medical_Record_Search_Engine_EMERSE_An_Information_Retrieval_Tool_for_Supporting_Cancer_Research">Electronic Medical Record Search Engine (EMERSE): An Information Retrieval Tool for Supporting Cancer Research</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="4580702" href="https://ucsf.academia.edu/OksanaGologorskaya">Oksana Gologorskaya</a></div><p class="ds-related-work--metadata ds2-5-body-xs">JCO Clinical Cancer Informatics</p><p class="ds-related-work--abstract ds2-5-body-sm">PURPOSE The Electronic Medical Record Search Engine (EMERSE) is a software tool built to aid research spanning cohort discovery, population health, and data abstraction for clinical trials. EMERSE is now live at three academic medical centers, with additional sites currently working on implementation. In this report, we describe how EMERSE has been used to support cancer research based on a variety of metrics. METHODS We identified peer-reviewed publications that used EMERSE through online searches as well as through direct e-mails to users based on audit logs. These logs were also used to summarize use at each of the three sites. Search terms for two of the sites were characterized using the natural language processing tool MetaMap to determine to which semantic types the terms could be mapped. RESULTS We identified a total of 326 peer-reviewed publications that used EMERSE through August 2019, although this is likely an underestimation of the true total based on the use log analys...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Electronic Medical Record Search Engine (EMERSE): An Information Retrieval Tool for Supporting Cancer Research","attachmentId":74275433,"attachmentType":"pdf","work_url":"https://www.academia.edu/61126517/Electronic_Medical_Record_Search_Engine_EMERSE_An_Information_Retrieval_Tool_for_Supporting_Cancer_Research","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/61126517/Electronic_Medical_Record_Search_Engine_EMERSE_An_Information_Retrieval_Tool_for_Supporting_Cancer_Research"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="7" data-entity-id="92947271" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/92947271/A_Review_of_Precision_Oncology_Knowledgebases_for_Determining_the_Clinical_Actionability_of_Genetic_Variants">A Review of Precision Oncology Knowledgebases for Determining the Clinical Actionability of Genetic Variants</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="35068267" href="https://vanderbilt.academia.edu/JeremyWarner">Jeremy Warner</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Frontiers in Cell and Developmental Biology, 2020</p><p class="ds-related-work--abstract ds2-5-body-sm">The increased availability of tumor genetic testing and targeted cancer therapies contributes to the advancement of precision medicine in the field of oncology. Precision oncology knowledgebases provide a way of organizing clinically relevant genetic information in a way that is easily accessible for both oncologists and patients, facilitating the genetic-based clinical decision making. Many organizations and companies have built precision oncology knowledgebases, intended for multiple users. In general, these knowledgebases offer information on cancer-related genetic variants as well as their associated diagnostic, prognostic, and therapeutic implications, but they often differ in their information curations, designs, and user experiences. It is advisable that oncologists use multiple knowledgebases during their practice to have them complement each other. In the future, convergence toward common standards and formats is needed to ensure that the comprehensive knowledge across all sources can be unified to bring the oncology community closer to the achievement of the goal of precision oncology.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"A Review of Precision Oncology Knowledgebases for Determining the Clinical Actionability of Genetic Variants","attachmentId":95821436,"attachmentType":"pdf","work_url":"https://www.academia.edu/92947271/A_Review_of_Precision_Oncology_Knowledgebases_for_Determining_the_Clinical_Actionability_of_Genetic_Variants","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/92947271/A_Review_of_Precision_Oncology_Knowledgebases_for_Determining_the_Clinical_Actionability_of_Genetic_Variants"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="8" data-entity-id="120990098" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/120990098/OncoSearch_cancer_gene_search_engine_with_literature_evidence">OncoSearch: cancer gene search engine with literature evidence</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="199414644" href="https://independent.academia.edu/Ho%C3%A0ng%C4%90%C4%83ngT">Tiến Hoàng Đăng</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Nucleic Acids Research, 2014</p><p class="ds-related-work--abstract ds2-5-body-sm">In order to identify genes that are involved in oncogenesis and to understand how such genes affect cancers, abnormal gene expressions in cancers are actively studied. For an efficient access to the results of such studies that are reported in biomedical literature, the relevant information is accumulated via text-mining tools and made available through the Web. However, current Web tools are not yet tailored enough to allow queries that specify how a cancer changes along with the change in gene expression level, which is an important piece of information to understand an involved gene's role in cancer progression or regression. OncoSearch is a Web-based engine that searches Medline abstracts for sentences that mention gene expression changes in cancers, with queries that specify (i) whether a gene expression level is up-regulated or down-regulated, (ii) whether a certain type of cancer progresses or regresses along with such gene expression change and (iii) the expected role of the gene in the cancer. OncoSearch is available through http://oncosearch.biopathway.org.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"OncoSearch: cancer gene search engine with literature evidence","attachmentId":115972972,"attachmentType":"pdf","work_url":"https://www.academia.edu/120990098/OncoSearch_cancer_gene_search_engine_with_literature_evidence","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/120990098/OncoSearch_cancer_gene_search_engine_with_literature_evidence"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="9" data-entity-id="126593963" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/126593963/VarSight_Prioritizing_Clinically_Reported_Variants_with_Binary_Classification_Algorithms">VarSight: Prioritizing Clinically Reported Variants with Binary Classification Algorithms</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="232764520" href="https://independent.academia.edu/AlanaGrajewski">Alana Grajewski</a></div><p class="ds-related-work--metadata ds2-5-body-xs">2019</p><p class="ds-related-work--abstract ds2-5-body-sm">MotivationIn genomic medicine for rare disease patients, the primary goal is to identify one or more variants that cause their disease. Typically, this is done through filtering and then prioritization of variants for manual curation. However, prioritization of variants in rare disease patients remains a challenging task due to the high degree of variability in phenotype presentation and molecular source of disease. Thus, methods that can identify and/or prioritize variants to be clinically reported in the presence of such variability are of critical importance.ResultsWe tested the application of classification algorithms that ingest variant predictions along with phenotype information for predicting whether a variant will ultimately be clinically reported and returned to a patient. To test the classifiers, we performed a retrospective study on variants that were clinically reported to 237 patients in the Undiagnosed Diseases Network. We treated the classifiers as variant prioritiza...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"VarSight: Prioritizing Clinically Reported Variants with Binary Classification Algorithms","attachmentId":120448476,"attachmentType":"pdf","work_url":"https://www.academia.edu/126593963/VarSight_Prioritizing_Clinically_Reported_Variants_with_Binary_Classification_Algorithms","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/126593963/VarSight_Prioritizing_Clinically_Reported_Variants_with_Binary_Classification_Algorithms"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div></div></div><div class="ds-sticky-ctas--wrapper js-loswp-sticky-ctas hidden"><div class="ds-sticky-ctas--grid-container"><div class="ds-sticky-ctas--container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--sticky-ctas","attachmentId":85852696,"attachmentType":"pdf","workUrl":null}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--sticky-ctas","attachmentId":85852696,"attachmentType":"pdf","workUrl":null}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div><div class="ds-below-fold--grid-container"><div class="ds-work--container js-loswp-embedded-document"><div class="attachment_preview" data-attachment="Attachment_85852696" style="display: none"><div class="js-scribd-document-container"><div class="scribd--document-loading js-scribd-document-loader" style="display: block;"><img alt="Loading..." src="//a.academia-assets.com/images/loaders/paper-load.gif" /><p>Loading Preview</p></div></div><div style="text-align: center;"><div class="scribd--no-preview-alert js-preview-unavailable"><p>Sorry, preview is currently unavailable. You can download the paper by clicking the button above.</p></div></div></div></div><div class="ds-sidebar--container js-work-sidebar"><div class="ds-related-content--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="0" data-entity-id="59973567" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/59973567/A_harmonized_meta_knowledgebase_of_clinical_interpretations_of_cancer_genomic_variants">A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="36435872" href="https://independent.academia.edu/JordiDeuPons">Jordi Deu-Pons</a></div><div class="ds-related-work--ctas"><button class="ds2-5-text-link 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href="https://independent.academia.edu/RaymondKim25">Raymond Kim</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Genome Medicine, 2019</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Standard operating procedure for curation and clinical interpretation of variants in cancer","attachmentId":97561102,"attachmentType":"pdf","work_url":"https://www.academia.edu/95356089/Standard_operating_procedure_for_curation_and_clinical_interpretation_of_variants_in_cancer","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/95356089/Standard_operating_procedure_for_curation_and_clinical_interpretation_of_variants_in_cancer"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="4" data-entity-id="105636920" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/105636920/Starvar_symptom_based_tool_for_automatic_ranking_of_variants_using_evidence_from_literature_and_genomes">Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="117250500" href="https://independent.academia.edu/MarwaAbdelhakim">Marwa Abdelhakim</a></div><p class="ds-related-work--metadata ds2-5-body-xs">BMC Bioinformatics</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes","attachmentId":105037501,"attachmentType":"pdf","work_url":"https://www.academia.edu/105636920/Starvar_symptom_based_tool_for_automatic_ranking_of_variants_using_evidence_from_literature_and_genomes","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/105636920/Starvar_symptom_based_tool_for_automatic_ranking_of_variants_using_evidence_from_literature_and_genomes"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="5" data-entity-id="73191563" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/73191563/Evolution_of_the_open_access_CIViC_knowledgebase_is_driven_by_the_needs_of_the_cancer_variant_interpretation_community">Evolution of the open-access CIViC knowledgebase is driven by the needs of the cancer variant interpretation community</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="104825544" href="https://independent.academia.edu/SeanDelong">Sean Delong</a></div><p class="ds-related-work--metadata ds2-5-body-xs">bioRxiv, 2021</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Evolution of the open-access CIViC knowledgebase is driven by the needs of the cancer variant interpretation community","attachmentId":81807259,"attachmentType":"pdf","work_url":"https://www.academia.edu/73191563/Evolution_of_the_open_access_CIViC_knowledgebase_is_driven_by_the_needs_of_the_cancer_variant_interpretation_community","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" 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class="ds-related-work--metadata ds2-5-body-xs">BMC …, 2010</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Concept-based query expansion for retrieving gene related publications from MEDLINE","attachmentId":30990373,"attachmentType":"pdf","work_url":"https://www.academia.edu/648943/Concept_based_query_expansion_for_retrieving_gene_related_publications_from_MEDLINE","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-related-work-grid-card-view-pdf" href="https://www.academia.edu/648943/Concept_based_query_expansion_for_retrieving_gene_related_publications_from_MEDLINE"><span class="ds2-5-text-link__content">View PDF</span><span 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18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="12" data-entity-id="67527515" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/67527515/VarRanker_rapid_prioritization_of_sequence_variations_associated_with_human_disease">VarRanker: rapid prioritization of sequence variations associated with human disease</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="41669875" href="https://independent.academia.edu/ClementK">Mark Clement</a></div><p class="ds-related-work--metadata ds2-5-body-xs">BMC bioinformatics, 2013</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" 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data-collection-position="13" data-entity-id="67131481" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/67131481/PubTermVariants_biomedical_term_variants_and_their_use_for_PubMed_search">PubTermVariants: biomedical term variants and their use for PubMed search</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="49176891" href="https://independent.academia.edu/RezartaDogan">Rezarta Dogan</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Proceedings of the 15th Workshop on Biomedical Natural Language Processing, 2016</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"PubTermVariants: biomedical term variants and their use for PubMed 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href="https://www.academia.edu/78203877/DoCM_a_database_of_curated_mutations_in_cancer">DoCM: a database of curated mutations in cancer</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="58843716" href="https://independent.academia.edu/EMardis">Elaine Mardis</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Nature methods, 2016</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"DoCM: a database of curated mutations in cancer","attachmentId":85332894,"attachmentType":"pdf","work_url":"https://www.academia.edu/78203877/DoCM_a_database_of_curated_mutations_in_cancer","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free 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class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="167824036" href="https://independent.academia.edu/RickyKanak">Ricky Kanak</a></div><p class="ds-related-work--metadata ds2-5-body-xs">arXiv: Quantitative Methods, 2019</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Ask2Me VarHarmonizer: A Python-Based Tool to Harmonize Variants from Cancer Genetic Testing Reports and Map them to the ClinVar Database","attachmentId":90105595,"attachmentType":"pdf","work_url":"https://www.academia.edu/85394592/Ask2Me_VarHarmonizer_A_Python_Based_Tool_to_Harmonize_Variants_from_Cancer_Genetic_Testing_Reports_and_Map_them_to_the_ClinVar_Database","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free 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href="https://ku-dk.academia.edu/CLioma">C. 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