{"id":2805,"date":"2023-06-13T01:08:24","date_gmt":"2023-06-13T00:08:24","guid":{"rendered":"https:\/\/archive.belbi.bg.ac.rs\/2023\/?post_type=abstract&#038;p=2805"},"modified":"2023-06-14T18:37:24","modified_gmt":"2023-06-14T17:37:24","slug":"mapping-of-disease-names-to-disease-codes-based-on-natural-language-processing-techniques","status":"publish","type":"abstract","link":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/mapping-of-disease-names-to-disease-codes-based-on-natural-language-processing-techniques\/","title":{"rendered":"Mapping of Disease Names to Disease Codes based on Natural Language Processing Techniques"},"content":{"rendered":"\n<p>An\u0111elka Ze\u010devi\u0107<sup>1*<\/sup>, Jovana Kova\u010devi\u0107<sup>2<\/sup>, and Radoslav Davidovi\u0107<sup>3<\/sup><\/p>\n\n\n\n<p class=\"affiliation-para\"><sup>1<\/sup>Mathematical Institute, Serbian Academy of Sciences and Arts<\/p>\n\n\n\n<p class=\"affiliation-para\"><sup>2<\/sup>Faculty of Mathematics, University of Belgrade<\/p>\n\n\n\n<p class=\"affiliation-para\"><sup>3<\/sup>Institute of Nuclear Sciences Vin\u010da<\/p>\n\n\n\n<p>andjelkaz [at] mi.sanu.ac.rs<\/p>\n\n\n\n<p><strong>Abstract<\/strong><\/p>\n\n\n\n<p class=\"abstract-para\">Information aggregation from various gen, disease, and gen-disease databases such as DisGeNet, COSMIC, HumsaVar, Orphanet, ClinVar, HPO, and Diseases into a unique database would enable researchers to analyze and compare valuable domain findings in a more convenient and systematic way. However, the aggregation poses numerous challenges due to non-uniform information annotation across the databases. In this work, we address the problem of mapping a disease name, when needed, into a standardized disease code (DOID) based on Natural Language Processing text representation techniques. We examine the benefits and limitations of using off-the-shelf embeddings such as Med2vec, and language models such as BioBERT, UmlsBERT, and PubMedBERT in retrieval scenarios with respect to standard full-text search. In addition to qualitative improvements, we elaborate on the technical requirements and computational complexities that come with the embracement of language models and semantic search.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>An\u0111elka Ze\u010devi\u0107<sup>1*<\/sup>, Jovana Kova\u010devi\u0107<sup>2<\/sup>, and Radoslav Davidovi\u0107<sup>3<\/sup><\/p>\n<p class=\"affiliation-para\"><sup>1<\/sup>Mathematical Institute, Serbian Academy of Sciences and Arts<\/p>\n<p class=\"affiliation-para\"><sup>2<\/sup>Faculty of Mathematics, University of Belgrade<\/p>\n<p class=\"affiliation-para\"><sup>3<\/sup>Institute of Nuclear Sciences Vin\u010da<\/p>\n<p> <a class=\"continue-reading-link\" href=\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/mapping-of-disease-names-to-disease-codes-based-on-natural-language-processing-techniques\/\"><span>Continue reading<\/span><i class=\"crycon-right-dir\"><\/i><\/a> <\/p>\n","protected":false},"author":162,"featured_media":0,"template":"","categories":[18],"tags":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.0 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Mapping of Disease Names to Disease Codes based on Natural Language Processing Techniques - BelBi 2023<\/title>\n<meta name=\"robots\" content=\"noindex, follow\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Mapping of Disease Names to Disease Codes based on Natural Language Processing Techniques - BelBi 2023\" \/>\n<meta property=\"og:description\" content=\"An\u0111elka Ze\u010devi\u01071*, Jovana Kova\u010devi\u01072, and Radoslav Davidovi\u010731Mathematical Institute, Serbian Academy of Sciences and Arts2Faculty of Mathematics, University of Belgrade3Institute of Nuclear Sciences Vin\u010da Continue reading\" \/>\n<meta property=\"og:url\" content=\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/mapping-of-disease-names-to-disease-codes-based-on-natural-language-processing-techniques\/\" \/>\n<meta property=\"og:site_name\" content=\"BelBi 2023\" \/>\n<meta property=\"article:modified_time\" content=\"2023-06-14T17:37:24+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/mapping-of-disease-names-to-disease-codes-based-on-natural-language-processing-techniques\/\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/mapping-of-disease-names-to-disease-codes-based-on-natural-language-processing-techniques\/\",\"name\":\"Mapping of Disease Names to Disease Codes based on Natural Language Processing Techniques - 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