{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,19]],"date-time":"2026-04-19T05:31:30Z","timestamp":1776576690411,"version":"3.51.2"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2019,2,15]],"date-time":"2019-02-15T00:00:00Z","timestamp":1550188800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Bio2Vec"},{"name":"CRG6","award":["3454"],"award-info":[{"award-number":["3454"]}]},{"DOI":"10.13039\/501100004052","name":"King Abdullah University of Science and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004052","name":"KAUST","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004052","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Knowledge graph embeddings (KGEs) have received significant attention in other domains due to their ability to predict links and create dense representations for graphs\u2019 nodes and edges. However, the software ecosystem for their application to bioinformatics remains limited and inaccessible for users without expertise in programing and machine learning. Therefore, we developed BioKEEN (Biological KnowlEdge EmbeddiNgs) and PyKEEN (Python KnowlEdge EmbeddiNgs) to facilitate their easy use through an interactive command line interface. Finally, we present a case study in which we used a novel biological pathway mapping resource to predict links that represent pathway crosstalks and hierarchies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>BioKEEN and PyKEEN are open source Python packages publicly available under the MIT License at https:\/\/github.com\/SmartDataAnalytics\/BioKEEN and https:\/\/github.com\/SmartDataAnalytics\/PyKEEN<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz117","type":"journal-article","created":{"date-parts":[[2019,2,15]],"date-time":"2019-02-15T09:13:55Z","timestamp":1550222035000},"page":"3538-3540","source":"Crossref","is-referenced-by-count":21,"title":["BioKEEN: a library for learning and evaluating biological knowledge graph embeddings"],"prefix":"10.1093","volume":"35","author":[{"given":"Mehdi","family":"Ali","sequence":"first","affiliation":[{"name":"Department of Computer Science, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn , Bonn, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charles Tapley","family":"Hoyt","sequence":"additional","affiliation":[{"name":"Department of Life Science Informatics, Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn , Bonn, Germany"},{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) , Sankt Augustin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Domingo-Fern\u00e1ndez","sequence":"additional","affiliation":[{"name":"Department of Life Science Informatics, Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn , Bonn, Germany"},{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) , Sankt Augustin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jens","family":"Lehmann","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn , Bonn, Germany"},{"name":"Department of Enterprise Information Systems, Fraunhofer Institute for Intelligent Analysis and Information Systems (IAIS) , Sankt Augustin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hajira","family":"Jabeen","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn , Bonn, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,2,15]]},"reference":[{"key":"2023013108050716500_btz117-B1","volume-title":"Translating embeddings for modeling multi-relational data","author":"Bordes","year":"2013"},{"key":"2023013108050716500_btz117-B2","first-page":"01476","article-title":"Convolutional 2d knowledge graph embeddings","volume":"1707","author":"Dettmers","year":"2017","journal-title":"arXiv Preprint arXiv"},{"key":"2023013108050716500_btz117-B3","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1038\/s41540-019-0082-7","article-title":"ComPath: an ecosystem for exploring, analyzing, and curating pathway databases","volume":"5","author":"Domingo-Fern\u00e1ndez","year":"2019","journal-title":"NPJ Syst. Biol. Appl"},{"key":"2023013108050716500_btz117-B4","volume-title":"Deep Learning","author":"Goodfellow","year":"2016"},{"key":"2023013108050716500_btz117-B5","first-page":"01445","article-title":"Embedding logical queries on knowledge graphs","volume":"1806","author":"Hamilton","year":"2018","journal-title":"arXiv Preprint arXiv"},{"key":"2023013108050716500_btz117-B6","doi-asserted-by":"crossref","first-page":"139","DOI":"10.18653\/v1\/D18-2024","article-title":"OpenKE: an open toolkit for knowledge embedding","volume-title":"Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing: System Demonstrations","author":"Han","year":"2018"},{"key":"2023013108050716500_btz117-B7","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1109\/JPROC.2015.2483592","article-title":"A review of relational machine learning for knowledge graphs","author":"Nickel","year":"2016","journal-title":"Proc. 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Knowledge Data Eng."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/18\/3538\/48975186\/bioinformatics_35_18_3538.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/18\/3538\/48975186\/bioinformatics_35_18_3538.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T08:35:16Z","timestamp":1675154116000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/18\/3538\/5320556"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,2,15]]},"references-count":10,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2019,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz117","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/475202","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,9,15]]},"published":{"date-parts":[[2019,2,15]]}}}