{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T11:10:02Z","timestamp":1768475402795,"version":"3.49.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,11,11]],"date-time":"2021-11-11T00:00:00Z","timestamp":1636588800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Public service platform for artificial intelligence aided diagnosis in medical and health industry"},{"name":"Ministry of Industry and Information Technology of the Peoples Republic of China","award":["2020-0103-3-1"],"award-info":[{"award-number":["2020-0103-3-1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>DeepKG is an end-to-end deep learning-based workflow that helps researchers automatically mine valuable knowledge in biomedical literature. Users can utilize it to establish customized knowledge graphs in specified domains, thus facilitating in-depth understanding on disease mechanisms and applications on drug repurposing and clinical research. To improve the performance of DeepKG, a cascaded hybrid information extraction framework is developed for training model of 3-tuple extraction, and a novel AutoML-based knowledge representation algorithm (AutoTransX) is proposed for knowledge representation and inference. The system has been deployed in dozens of hospitals and extensive experiments strongly evidence the effectiveness. In the context of 144\u2009900 COVID-19 scholarly full-text literature, DeepKG generates a high-quality knowledge graph with 7980 entities and 43\u2009760 3-tuples, a candidate drug list, and relevant animal experimental studies are being carried out. To accelerate more studies, we make DeepKG publicly available and provide an online tool including the data of 3-tuples, potential drug list, question answering system, visualization platform.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>All the results are publicly available at the website (http:\/\/covidkg.ai\/).<\/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\/btab767","type":"journal-article","created":{"date-parts":[[2021,11,5]],"date-time":"2021-11-05T12:23:59Z","timestamp":1636115039000},"page":"1477-1479","source":"Crossref","is-referenced-by-count":26,"title":["DeepKG: an end-to-end deep learning-based workflow for biomedical knowledge graph extraction, optimization and applications"],"prefix":"10.1093","volume":"38","author":[{"given":"Zongren","family":"Li","sequence":"first","affiliation":[{"name":"Medical Big Data Research Center, Chinese PLA General Hospital , Beijing 100039, China"},{"name":"Medical Artificial Intelligence Research Center, Chinese PLA General Hospital , Beijing 100853, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qin","family":"Zhong","sequence":"additional","affiliation":[{"name":"The Medical School of Chinese PLA, Chinese PLA General Hospital , Beijing 100039, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jing","family":"Yang","sequence":"additional","affiliation":[{"name":"The Medical School of Chinese PLA, Chinese PLA General Hospital , Beijing 100039, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yongjie","family":"Duan","sequence":"additional","affiliation":[{"name":"The Medical School of Chinese PLA, Chinese PLA General Hospital , Beijing 100039, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenjun","family":"Wang","sequence":"additional","affiliation":[{"name":"Bio-engineering Research Center, Chinese PLA General Hospital , Beijing 100039, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9688-5311","authenticated-orcid":false,"given":"Chengkun","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of High-Performance Computing, School of Computer Science, National University of Defense Technology, Hunan, Changsha, 410073, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0246-7048","authenticated-orcid":false,"given":"Kunlun","family":"He","sequence":"additional","affiliation":[{"name":"Medical Big Data Research Center, Chinese PLA General Hospital , Beijing 100039, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,11,11]]},"reference":[{"key":"2023020108541566700_btab767-B1","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1186\/s12859-021-04082-y","article-title":"Application of network link prediction in drug discovery","volume":"22","author":"Abbas","year":"2021","journal-title":"BMC Bioinform"},{"key":"2023020108541566700_btab767-B2","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1093\/bib\/bbaa379","article-title":"A comprehensive drug repurposing study for COVID19 treatment: novel putative dihydroorotate dehydrogenase inhibitors show association to serotonin\u2013dopamine receptors","volume":"22","author":"Berber","year":"2021","journal-title":"Brief. 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