{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,22]],"date-time":"2026-02-22T19:25:37Z","timestamp":1771788337532,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,5,10]],"date-time":"2022-05-10T00:00:00Z","timestamp":1652140800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004663","name":"Ministry of Science and Technology, Taiwan","doi-asserted-by":"publisher","award":["109-2221-E-002-161-MY3"],"award-info":[{"award-number":["109-2221-E-002-161-MY3"]}],"id":[{"id":"10.13039\/501100004663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>With the proliferation of genomic sequence data for biomedical research, the exploration of human genetic information by domain experts requires a comprehensive interrogation of large numbers of scientific publications in PubMed. However, a query in PubMed essentially provides search results sorted only by the date of publication. A search engine for retrieving and interpreting complex relations between biomedical concepts in scientific publications remains lacking. Here, we present pubmedKB, a web server designed to extract and visualize semantic relationships between four biomedical entity types: variants, genes, diseases, and chemicals. pubmedKB uses state-of-the-art natural language processing techniques to extract semantic relations from the large number of PubMed abstracts. Currently, over 2 million semantic relations between biomedical entity pairs are extracted from over 33 million PubMed abstracts in pubmedKB. pubmedKB has a user-friendly interface with an interactive semantic graph, enabling the user to easily query entities and explore entity relations. Supporting sentences with the highlighted snippets allow to easily navigate the publications. Combined with a new explorative approach to literature mining and an interactive interface for researchers, pubmedKB thus enables rapid, intelligent searching of the large biomedical literature to provide useful knowledge and insights. pubmedKB is available at https:\/\/www.pubmedkb.cc\/.<\/jats:p>","DOI":"10.1093\/nar\/gkac310","type":"journal-article","created":{"date-parts":[[2022,4,18]],"date-time":"2022-04-18T11:10:21Z","timestamp":1650280221000},"page":"W616-W622","source":"Crossref","is-referenced-by-count":19,"title":["pubmedKB: an interactive web server for exploring biomedical entity relations in the biomedical literature"],"prefix":"10.1093","volume":"50","author":[{"given":"Peng-Hsuan","family":"Li","sequence":"first","affiliation":[{"name":"Taiwan AI Labs , Taipei 10351, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ting-Fu","family":"Chen","sequence":"additional","affiliation":[{"name":"Taiwan AI Labs , Taipei 10351, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jheng-Ying","family":"Yu","sequence":"additional","affiliation":[{"name":"Taiwan AI Labs , Taipei 10351, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shang-Hung","family":"Shih","sequence":"additional","affiliation":[{"name":"Taiwan AI Labs , Taipei 10351, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chan-Hung","family":"Su","sequence":"additional","affiliation":[{"name":"Taiwan AI Labs , Taipei 10351, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yin-Hung","family":"Lin","sequence":"additional","affiliation":[{"name":"Taiwan AI Labs , Taipei 10351, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4200-8137","authenticated-orcid":false,"given":"Huai-Kuang","family":"Tsai","sequence":"additional","affiliation":[{"name":"Taiwan AI Labs , Taipei 10351, Taiwan"},{"name":"Institute of Information Science , Academia Sinica, Taipei, 11529, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4876-3309","authenticated-orcid":false,"given":"Hsueh-Fen","family":"Juan","sequence":"additional","affiliation":[{"name":"Taiwan AI Labs , Taipei 10351, Taiwan"},{"name":"Department of Life Science, National Taiwan University , Taipei 10617, Taiwan"},{"name":"Center for Computational and Systems Biology, National Taiwan University , Taipei 10617, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6940-6389","authenticated-orcid":false,"given":"Chien-Yu","family":"Chen","sequence":"additional","affiliation":[{"name":"Taiwan AI Labs , Taipei 10351, Taiwan"},{"name":"Center for Computational and Systems Biology, National Taiwan University , Taipei 10617, Taiwan"},{"name":"Department of Biomechatronics Engineering, National Taiwan University , Taipei, 10617, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5910-5419","authenticated-orcid":false,"given":"Jia-Hsin","family":"Huang","sequence":"additional","affiliation":[{"name":"Taiwan AI Labs , Taipei 10351, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,5,10]]},"reference":[{"key":"2022070423585747500_B1","doi-asserted-by":"crossref","first-page":"bbab134","DOI":"10.1093\/bib\/bbab134","article-title":"Knowledge bases and software support for variant interpretation in precision oncology","volume":"22","author":"Borchert","year":"2021","journal-title":"Briefings Bioinf."},{"key":"2022070423585747500_B2","doi-asserted-by":"crossref","first-page":"D1062","DOI":"10.1093\/nar\/gkx1153","article-title":"ClinVar: improving access to variant interpretations and supporting evidence","volume":"46","author":"Landrum","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2022070423585747500_B3","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1007\/978-1-62703-435-7_20","article-title":"PharmGKB: the pharmacogenomics knowledge base","volume":"1015","author":"Thorn","year":"2013","journal-title":"Methods Mol. Biol."},{"key":"2022070423585747500_B4","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1007\/978-1-4939-3167-5_2","article-title":"UniProtKB\/Swiss-Prot, the manually annotated section of the uniprot knowledgebase: how to use the entry view","volume":"1374","author":"Boutet","year":"2016","journal-title":"Methods Mol. Biol."},{"key":"2022070423585747500_B5","doi-asserted-by":"crossref","first-page":"3454","DOI":"10.1093\/bioinformatics\/btx439","article-title":"On expert curation and scalability: uniprotkb\/Swiss-Prot as a case study","volume":"33","author":"Poux","year":"2017","journal-title":"Bioinformatics"},{"key":"2022070423585747500_B6","doi-asserted-by":"crossref","first-page":"i41","DOI":"10.1093\/bioinformatics\/btm229","article-title":"Manual curation is not sufficient for annotation of genomic databases","volume":"23","author":"Baumgartner","year":"2007","journal-title":"Bioinformatics"},{"key":"2022070423585747500_B7","doi-asserted-by":"crossref","first-page":"bbaa142","DOI":"10.1093\/bib\/bbaa142","article-title":"Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature","volume":"22","author":"Lee","year":"2021","journal-title":"Briefings Bioinf."},{"key":"2022070423585747500_B8","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1038\/s41588-020-0603-8","article-title":"A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer","volume":"52","author":"Wagner","year":"2020","journal-title":"Nat. Genet."},{"key":"2022070423585747500_B9","doi-asserted-by":"crossref","first-page":"bbaa057","DOI":"10.1093\/bib\/bbaa057","article-title":"Recent advances in biomedical literature mining","volume":"22","author":"Zhao","year":"2021","journal-title":"Briefings Bioinf."},{"key":"2022070423585747500_B10","doi-asserted-by":"crossref","first-page":"W530","DOI":"10.1093\/nar\/gky355","article-title":"LitVar: a semantic search engine for linking genomic variant data in pubmed and PMC","volume":"46","author":"Allot","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2022070423585747500_B11","doi-asserted-by":"crossref","DOI":"10.1101\/583450","article-title":"variant2literature: full text literature search for genetic variants","author":"Lin","year":"2019"},{"key":"2022070423585747500_B12","first-page":"63","article-title":"NLTK: the natural language toolkit","volume-title":"Proceedings of the ACL-02 Workshop on Effective tools and methodologies for teaching natural language processing and computational linguistics - Volume 1, ETMTNLP \u201902","author":"Loper","year":"2002"},{"key":"2022070423585747500_B13","doi-asserted-by":"crossref","first-page":"1234","DOI":"10.1093\/bioinformatics\/btz682","article-title":"BioBERT: a pre-trained biomedical language representation model for biomedical text mining","volume":"36","author":"Lee","year":"2020","journal-title":"Bioinformatics"},{"key":"2022070423585747500_B14","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1109\/ITME.2019.00022","article-title":"BioBERT based named entity recognition in electronic medical record","volume-title":"2019 10th International Conference on Information Technology in Medicine and Education (ITME)","author":"Yu","year":"2019"},{"key":"2022070423585747500_B15","doi-asserted-by":"crossref","first-page":"73729","DOI":"10.1109\/ACCESS.2019.2920708","article-title":"A neural named entity recognition and multi-type normalization tool for biomedical text mining","volume":"7","author":"Kim","year":"2019","journal-title":"IEEE Access"},{"key":"2022070423585747500_B16","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1093\/bioinformatics\/btx541","article-title":"tmVar 2.0: integrating genomic variant information from literature with dbSNP and clinvar for precision medicine","volume":"34","author":"Wei","year":"2018","journal-title":"Bioinformatics"},{"key":"2022070423585747500_B17","doi-asserted-by":"crossref","first-page":"e918710","DOI":"10.1155\/2015\/918710","article-title":"GNormPlus: an integrative approach for tagging genes, gene families, and protein domains","volume":"2015","author":"Wei","year":"2015","journal-title":"Biomed. Res. Int."},{"key":"2022070423585747500_B18","first-page":"297","article-title":"Sieve-Based entity linking for the biomedical domain","volume-title":"Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics and the 7th International Joint Conference on Natural Language Processing (Volume 2: Short Papers)","author":"D\u2019Souza","year":"2015"},{"key":"2022070423585747500_B19","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1186\/1758-2946-7-S1-S3","article-title":"tmChem: a high performance approach for chemical named entity recognition and normalization","volume":"7","author":"Leaman","year":"2015","journal-title":"Journal of Cheminformatics"},{"key":"2022070423585747500_B20","first-page":"344","article-title":"Leveraging linguistic structure for open domain information extraction","volume-title":"Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics and the 7th International Joint Conference on Natural Language Processing (Volume 1: Long Papers)","author":"Angeli","year":"2015"},{"key":"2022070423585747500_B21","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1038\/nrg.2017.52","article-title":"Settling the score: variant prioritization and mendelian disease","volume":"18","author":"Eilbeck","year":"2017","journal-title":"Nat. Rev. Genet."},{"key":"2022070423585747500_B22","first-page":"2361","article-title":"Enriching Pre-trained language model with entity information for relation classification","volume-title":"Proceedings of the 28th ACM International Conference on Information and Knowledge Management, CIKM \u201919","author":"Wu","year":"2019"},{"key":"2022070423585747500_B23","first-page":"1","article-title":"Exploring the limits of transfer learning with a unified Text-to-Text transformer","volume":"21","author":"Raffel","year":"2020","journal-title":"Journal of Machine Learning Research"},{"key":"2022070423585747500_B24","doi-asserted-by":"crossref","first-page":"1149","DOI":"10.1145\/3077136.3080744","article-title":"Open relation extraction for support passage retrieval: merit and open issues","volume-title":"Proceedings of the 40th International ACM SIGIR Conference on Research and Development in Information Retrieval","author":"Kadry","year":"2017"},{"key":"2022070423585747500_B25","doi-asserted-by":"crossref","DOI":"10.1109\/CVPR42600.2020.01070","article-title":"Self-training with noisy student improves imagenet classification","author":"Xie","year":"2020"},{"key":"2022070423585747500_B26","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s43586-021-00056-9","article-title":"Genome-wide association studies","volume":"1","author":"Uffelmann","year":"2021","journal-title":"Nat Rev Methods Primers"},{"key":"2022070423585747500_B27","first-page":"D845","article-title":"The DisGeNET knowledge platform for disease genomics: 2019 update","volume":"48","author":"Pi\u00f1ero","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2022070423585747500_B28","doi-asserted-by":"crossref","first-page":"D605","DOI":"10.1093\/nar\/gkaa1074","article-title":"The STRING database in 2021: customizable protein\u2013protein networks, and functional characterization of user-uploaded gene\/measurement sets","volume":"49","author":"Szklarczyk","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022070423585747500_B29","doi-asserted-by":"crossref","first-page":"W585","DOI":"10.1093\/nar\/gks563","article-title":"GeneView: a comprehensive semantic search engine for pubmed","volume":"40","author":"Thomas","year":"2012","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/W1\/W616\/44378353\/gkac310.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/W1\/W616\/44378353\/gkac310.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T10:45:27Z","timestamp":1675334727000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/W1\/W616\/6583235"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,5,10]]},"references-count":29,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2022,5,10]]},"published-print":{"date-parts":[[2022,7,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkac310","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,7,5]]},"published":{"date-parts":[[2022,5,10]]}}}