{"id":2773,"date":"2023-06-13T01:08:23","date_gmt":"2023-06-13T00:08:23","guid":{"rendered":"https:\/\/archive.belbi.bg.ac.rs\/2023\/?post_type=abstract&#038;p=2773"},"modified":"2023-06-14T18:37:24","modified_gmt":"2023-06-14T17:37:24","slug":"semantic-unification-and-search-of-bioinformatics-databases","status":"publish","type":"abstract","link":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/semantic-unification-and-search-of-bioinformatics-databases\/","title":{"rendered":"Semantic unification and search of bioinformatics databases"},"content":{"rendered":"\n<p>A. Veljkovi\u0107<sup>1*<\/sup>, and N. Miti\u0107<sup>1<\/sup><\/p>\n\n\n\n<p class=\"affiliation-para\"><sup>1<\/sup>Faculty of Mathematics, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia<\/p>\n\n\n\n<p>aleksandar.veljkovic [at] matf.bg.ac.rs<\/p>\n\n\n\n<p><strong>Abstract<\/strong><\/p>\n\n\n\n<p class=\"abstract-para\">Analyzing biological data from various sources offers a comprehensive perspective of a domain, facilitating the identification of patterns that would otherwise be challenging or impossible to observe when focusing solely on individual biological entities. The process of linking data from different databases can present challenges due to inconsistencies in properties and identifiers assigned to the same entity across databases. Although certain databases include a range of identifiers from multiple sources, the search capabilities are restricted to exact property matching, preventing the execution of complex queries involving multiple metadata attributes.<\/p>\n\n\n\n<p class=\"abstract-para\">We designed a novel data framework that aims to address these challenges by facilitating the linkage and retrieval of information from diverse interconnected biological data sources. To evaluate the effectiveness of the model, we conducted tests and created a knowledge graph using metadata extracted from five separate public datasets: DisProt, HGNC, Tantigen 2.0, IEDB, and DisGeNET. The resulting graph establishes connections between more than 17 million nodes, comprising 2.5 million distinct biological entity objects, and encompasses over 4 million relationships.<\/p>\n\n\n\n<p class=\"abstract-para\">Additionally, we designed and implemented a general-purpose procedure for extracting new relationships based on semantic similarity from data transformed into the BioGraph data model.<\/p>\n\n\n\n<p class=\"abstract-para\"><strong>Keywords:<\/strong> Bioinformatics database, semantic search, unification, BioGraph<\/p>\n","protected":false},"excerpt":{"rendered":"<p>A. Veljkovi\u0107<sup>1*<\/sup>, and N. Miti\u0107<sup>1<\/sup><\/p>\n<p class=\"affiliation-para\"><sup>1<\/sup>Faculty of Mathematics, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia<\/p>\n<p> <a class=\"continue-reading-link\" href=\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/semantic-unification-and-search-of-bioinformatics-databases\/\"><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>Semantic unification and search of bioinformatics databases - 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=\"Semantic unification and search of bioinformatics databases - BelBi 2023\" \/>\n<meta property=\"og:description\" content=\"A. Veljkovi\u01071*, and N. Miti\u010711Faculty of Mathematics, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia Continue reading\" \/>\n<meta property=\"og:url\" content=\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/semantic-unification-and-search-of-bioinformatics-databases\/\" \/>\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\/semantic-unification-and-search-of-bioinformatics-databases\/\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/semantic-unification-and-search-of-bioinformatics-databases\/\",\"name\":\"Semantic unification and search of bioinformatics databases - BelBi 2023\",\"isPartOf\":{\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#website\"},\"datePublished\":\"2023-06-13T00:08:23+00:00\",\"dateModified\":\"2023-06-14T17:37:24+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/semantic-unification-and-search-of-bioinformatics-databases\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/semantic-unification-and-search-of-bioinformatics-databases\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/semantic-unification-and-search-of-bioinformatics-databases\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Semantic unification and search of bioinformatics databases\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#website\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/\",\"name\":\"BelBi 2023\",\"description\":\"\",\"publisher\":{\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/?s={search_term_string}\"},\"query-input\":\"required name=search_term_string\"}],\"inLanguage\":\"en-US\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#organization\",\"name\":\"Belgrade Bioinformatics Conference\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#\/schema\/logo\/image\/\",\"url\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-content\/uploads\/2023\/02\/145_97_171.png\",\"contentUrl\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-content\/uploads\/2023\/02\/145_97_171.png\",\"width\":278,\"height\":500,\"caption\":\"Belgrade Bioinformatics Conference\"},\"image\":{\"@id\":\"https:\/\/archive.belbi.bg.ac.rs\/2023\/#\/schema\/logo\/image\/\"}}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Semantic unification and search of bioinformatics databases - BelBi 2023","robots":{"index":"noindex","follow":"follow"},"og_locale":"en_US","og_type":"article","og_title":"Semantic unification and search of bioinformatics databases - BelBi 2023","og_description":"A. Veljkovi\u01071*, and N. Miti\u010711Faculty of Mathematics, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia Continue reading","og_url":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/semantic-unification-and-search-of-bioinformatics-databases\/","og_site_name":"BelBi 2023","article_modified_time":"2023-06-14T17:37:24+00:00","twitter_card":"summary_large_image","twitter_misc":{"Est. reading time":"1 minute"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/semantic-unification-and-search-of-bioinformatics-databases\/","url":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/semantic-unification-and-search-of-bioinformatics-databases\/","name":"Semantic unification and search of bioinformatics databases - BelBi 2023","isPartOf":{"@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#website"},"datePublished":"2023-06-13T00:08:23+00:00","dateModified":"2023-06-14T17:37:24+00:00","breadcrumb":{"@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/semantic-unification-and-search-of-bioinformatics-databases\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/semantic-unification-and-search-of-bioinformatics-databases\/"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/abstract\/semantic-unification-and-search-of-bioinformatics-databases\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/archive.belbi.bg.ac.rs\/2023\/"},{"@type":"ListItem","position":2,"name":"Semantic unification and search of bioinformatics databases"}]},{"@type":"WebSite","@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#website","url":"https:\/\/archive.belbi.bg.ac.rs\/2023\/","name":"BelBi 2023","description":"","publisher":{"@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#organization"},"potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/archive.belbi.bg.ac.rs\/2023\/?s={search_term_string}"},"query-input":"required name=search_term_string"}],"inLanguage":"en-US"},{"@type":"Organization","@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#organization","name":"Belgrade Bioinformatics Conference","url":"https:\/\/archive.belbi.bg.ac.rs\/2023\/","logo":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#\/schema\/logo\/image\/","url":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-content\/uploads\/2023\/02\/145_97_171.png","contentUrl":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-content\/uploads\/2023\/02\/145_97_171.png","width":278,"height":500,"caption":"Belgrade Bioinformatics Conference"},"image":{"@id":"https:\/\/archive.belbi.bg.ac.rs\/2023\/#\/schema\/logo\/image\/"}}]}},"_links":{"self":[{"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/abstract\/2773"}],"collection":[{"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/abstract"}],"about":[{"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/types\/abstract"}],"author":[{"embeddable":true,"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/users\/162"}],"wp:attachment":[{"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/media?parent=2773"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/categories?post=2773"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/archive.belbi.bg.ac.rs\/2023\/wp-json\/wp\/v2\/tags?post=2773"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}