{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T23:46:07Z","timestamp":1784331967143,"version":"3.55.0"},"reference-count":39,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,3,23]],"date-time":"2019-03-23T00:00:00Z","timestamp":1553299200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2019,3,23]],"date-time":"2019-03-23T00:00:00Z","timestamp":1553299200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"funder":[{"name":"New York State"},{"DOI":"10.13039\/100006431","name":"Carestream Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006431","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Knowl Inf Syst"],"published-print":{"date-parts":[[2020,1]]},"DOI":"10.1007\/s10115-019-01351-4","type":"journal-article","created":{"date-parts":[[2019,3,23]],"date-time":"2019-03-23T10:02:31Z","timestamp":1553335351000},"page":"317-336","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":54,"title":["Constructing biomedical domain-specific knowledge graph with minimum supervision"],"prefix":"10.1007","volume":"62","author":[{"given":"Jianbo","family":"Yuan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiwei","family":"Jin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongxia","family":"Jin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianchao","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tristram","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiebo","family":"Luo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,3,23]]},"reference":[{"key":"1351_CR1","doi-asserted-by":"crossref","unstructured":"Angeli G, Premkumar MJJ, Manning CD (2015) Leveraging linguistic structure for open domain information extraction. In: Proceedings of the 53rd annual meeting of the association for computational linguistics and the 7th international joint conference on natural language processing of the Asian Federation of Natural Language Processing, July 26\u201331, 2015, vol 1. Long Papers, Beijing, China, pp 344\u2013354","DOI":"10.3115\/v1\/P15-1034"},{"key":"1351_CR2","unstructured":"Arthur D, Vassilvitskii S (2007) k-means++: the advantages of careful seeding. In: Proceedings of the eighteenth annual ACM-SIAM symposium on discrete algorithms. Society for Industrial and Applied Mathematics, Philadelphia, pp 1027\u20131035"},{"issue":"1","key":"1351_CR3","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25(1):25","journal-title":"Nat Genet"},{"key":"1351_CR4","doi-asserted-by":"crossref","unstructured":"Augenstein I, Vlachos A, Maynard D (2015) Extracting relations between non-standard entities using distant supervision and imitation learning. In: Proceedings of the 2015 conference on empirical methods in natural language processing. Association for Computational Linguistics, Florence, pp 747\u2013757","DOI":"10.18653\/v1\/D15-1086"},{"issue":"9","key":"1351_CR5","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1186\/s12859-016-1131-5","volume":"17","author":"T Bai","year":"2016","unstructured":"Bai T, Gong L, Wang Y, Wang Y, Kulikowski CA, Huang L (2016) A method for exploring implicit concept relatedness in biomedical knowledge network. BMC Bioinform 17(9):265","journal-title":"BMC Bioinform"},{"issue":"5","key":"1351_CR6","doi-asserted-by":"publisher","first-page":"706","DOI":"10.1016\/j.jbi.2008.03.004","volume":"41","author":"F Belleau","year":"2008","unstructured":"Belleau F, Nolin M-A, Tourigny N, Rigault P, Morissette J (2008) Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J Biomed Inform 41(5):706\u2013716","journal-title":"J Biomed Inform"},{"key":"1351_CR7","unstructured":"Bojanowski P, Grave E, Joulin A, Mikolov T (2016) Enriching word vectors with subword information. arXiv preprint arXiv:1607.04606"},{"key":"1351_CR8","doi-asserted-by":"crossref","unstructured":"Bollacker K, Evans C, Paritosh P, Sturge T, Taylor J (2008) Freebase: a collaboratively created graph database for structuring human knowledge. In: Proceedings of the 2008 ACM SIGMOD international conference on management of data. ACM, New York City, pp 1247\u20131250","DOI":"10.1145\/1376616.1376746"},{"key":"1351_CR9","unstructured":"Bordes A, Usunier N, Garcia-Duran A, Weston J, Yakhnenko O (2013) Translating embeddings for modeling multi-relational data. In: Advances in neural information processing systems 26: 27th Annual Conference on Neural Information Processing Systems 2013. Proceedings of a meeting held December 5\u20138, 2013, Lake Tahoe, Nevada, United States, pp 2787\u20132795"},{"key":"1351_CR10","unstructured":"Broder AZ (1997) On the resemblance and containment of documents. In: Proceedings compression and complexity of sequences. IEEE, Piscataway, pp 21\u201329"},{"issue":"D1","key":"1351_CR11","first-page":"D158","volume":"45","author":"U Consortium","year":"2016","unstructured":"Consortium U (2016) Uniprot: the universal protein knowledgebase. Nucleic Acids Res 45(D1):D158\u2013D169","journal-title":"Nucleic Acids Res"},{"key":"1351_CR12","first-page":"19","volume-title":"Deeplife: an entity-aware search, analytics and exploration platform for health and life sciences","author":"P Ernst","year":"2016","unstructured":"Ernst P, Siu A, Milchevski D, Hoffart J, Weikum G (2016) Deeplife: an entity-aware search, analytics and exploration platform for health and life sciences. ACL, Vancouver, p 19"},{"issue":"1","key":"1351_CR13","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1186\/s12859-015-0549-5","volume":"16","author":"P Ernst","year":"2015","unstructured":"Ernst P, Siu A, Weikum G (2015) Knowlife: a versatile approach for constructing a large knowledge graph for biomedical sciences. BMC Bioinform 16(1):157","journal-title":"BMC Bioinform"},{"key":"1351_CR14","doi-asserted-by":"crossref","unstructured":"Finkel JR, Grenager T, Manning C (2005) Incorporating non-local information into information extraction systems by Gibbs sampling. In: Proceedings of the 43rd annual meeting on association for computational linguistics. Association for Computational Linguistics, Florence, pp 363\u2013370","DOI":"10.3115\/1219840.1219885"},{"key":"1351_CR15","doi-asserted-by":"crossref","unstructured":"Gal\u00e1rraga L, Heitz G, Murphy K, Suchanek FM (2014) Canonicalizing open knowledge bases. In: Proceedings of the 23rd ACM international conference on information and knowledge management. ACM, New York City, pp 1679\u20131688","DOI":"10.1145\/2661829.2662073"},{"key":"1351_CR16","unstructured":"Hoffmann R, Zhang C, Ling X, Zettlemoyer L, Weld DS (2011) Knowledge-based weak supervision for information extraction of overlapping relations. In: Proceedings of the 49th annual meeting of the association for computational linguistics: human language technologies, vol 1. Association for Computational Linguistics, Florence, pp 541\u2013550"},{"issue":"4","key":"1351_CR17","doi-asserted-by":"publisher","first-page":"976","DOI":"10.1007\/s10618-014-0396-4","volume":"29","author":"M Ji","year":"2015","unstructured":"Ji M, He Q, Han J, Spangler S (2015) Mining strong relevance between heterogeneous entities from unstructured biomedical data. Data Min Knowl Discov 29(4):976\u2013998","journal-title":"Data Min Knowl Discov"},{"key":"1351_CR18","unstructured":"Kilicoglu H, Fiszman M, Rodriguez A, Shin D, Ripple A, Rindflesch TC (2008) Semantic medline: a web application for managing the results of pubmed searches. In: Proceedings of the third international symposium for semantic mining in biomedicine, vol 2008. Citeseer, Princeton, pp 69\u201376"},{"issue":"2","key":"1351_CR19","doi-asserted-by":"publisher","first-page":"167","DOI":"10.3233\/SW-140134","volume":"6","author":"J Lehmann","year":"2015","unstructured":"Lehmann J, Isele R, Jakob M, Jentzsch A, Kontokostas D, Mendes PN, Hellmann S, Morsey M, Van Kleef P, Auer S et al (2015) Dbpedia-a large-scale, multilingual knowledge base extracted from wikipedia. Semant Web 6(2):167\u2013195","journal-title":"Semant Web"},{"key":"1351_CR20","doi-asserted-by":"crossref","unstructured":"Lin Y, Shen S, Liu Z, Luan H, Sun M (2016) Neural relation extraction with selective attention over instances. In: Proceedings of ACL, vol 1, pp 2124\u20132133","DOI":"10.18653\/v1\/P16-1200"},{"key":"1351_CR21","unstructured":"Mahdisoltani F, Biega J, Suchanek F (2014) Yago3: a knowledge base from multilingual wikipedias. In: CIDR conference 7th Biennial conference on innovative data systems research"},{"key":"1351_CR22","first-page":"55","volume-title":"The stanford coreNLP natural language processing toolkit","author":"CD Manning","year":"2014","unstructured":"Manning CD, Surdeanu M, Bauer J, Finkel J, Bethard SJ, McClosky D (2014) The stanford coreNLP natural language processing toolkit. ACL, Florence, p 55"},{"key":"1351_CR23","unstructured":"Mikolov T, Sutskever I, Chen K, Corrado GS, Dean J (2013) Distributed representations of words and phrases and their compositionality. In: Advances in neural information processing systems 26: 27th Annual Conference on Neural Information Processing Systems 2013. Proceedings of a meeting held December 5\u20138, 2013, Lake Tahoe, Nevada, United States, pp 3111\u20133119"},{"issue":"1","key":"1351_CR24","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1109\/JPROC.2015.2483592","volume":"104","author":"M Nickel","year":"2016","unstructured":"Nickel M, Murphy K, Tresp V, Gabrilovich E (2016) A review of relational machine learning for knowledge graphs. Proc IEEE 104(1):11\u201333","journal-title":"Proc IEEE"},{"key":"1351_CR25","first-page":"25","volume":"12","author":"F Niu","year":"2012","unstructured":"Niu F, Zhang C, R\u00e9 C, Shavlik JW (2012) Deepdive: web-scale knowledge-base construction using statistical learning and inference. VLDS 12:25\u201328","journal-title":"VLDS"},{"key":"1351_CR26","doi-asserted-by":"crossref","unstructured":"Pennington J, Socher R, Manning C (2014) Glove: global vectors for word representation. In: Proceedings of the 2014 conference on empirical methods in natural language processing (EMNLP), pp 1532\u20131543","DOI":"10.3115\/v1\/D14-1162"},{"key":"1351_CR27","unstructured":"Ren X, Wu Z, He W, Qu M, Voss CR, Ji H, Abdelzaher TF, Han J (2016) Cotype: joint extraction of typed entities and relations with knowledge bases. arXiv preprint arXiv:1610.08763"},{"key":"1351_CR28","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1007\/978-3-642-15939-8_10","volume-title":"Machine Learning and Knowledge Discovery in Databases","author":"Sebastian Riedel","year":"2010","unstructured":"Riedel S, Yao L, McCallum A (2010) Modeling relations and their mentions without labeled text. In: Machine Learning and Knowledge Discovery in Databases, European Conference, Barcelona, Spain, September 20\u201324, 2010, Proceedings, Part III, pp 148\u2013163. https:\/\/doi.org\/10.1007\/978-3-642-15939-8_10"},{"issue":"6","key":"1351_CR29","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1016\/j.jbi.2003.11.003","volume":"36","author":"TC Rindflesch","year":"2003","unstructured":"Rindflesch TC, Fiszman M (2003) The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text. J Biomed Inform 36(6):462\u2013477","journal-title":"J Biomed Inform"},{"key":"1351_CR30","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","volume":"20","author":"PJ Rousseeuw","year":"1987","unstructured":"Rousseeuw PJ (1987) Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Math 20:53\u201365","journal-title":"J Comput Appl Math"},{"key":"1351_CR31","first-page":"72","volume-title":"Disambiguation of entities in medline abstracts by combining mesh terms with knowledge","author":"A Siu","year":"2016","unstructured":"Siu A, Ernst P, Weikum G (2016) Disambiguation of entities in medline abstracts by combining mesh terms with knowledge. ACL, Florence, p 72"},{"key":"1351_CR32","unstructured":"Siu A, Nguyen DB, Weikum G (2013) Fast entity recognition in biomedical. In: Proceedings of workshop on data mining for healthcare (DMH) at conference on knowledge discovery and data mining (KDD). ACM Press, New York"},{"key":"1351_CR33","unstructured":"Surdeanu M, Tibshirani J, Nallapati R, Manning CD (2012) Multi-instance multi-label learning for relation extraction. In: Proceedings of the 2012 joint conference on empirical methods in natural language processing and computational natural language learning. Association for Computational Linguistics, Florence, pp 455\u2013465"},{"key":"1351_CR34","doi-asserted-by":"crossref","unstructured":"Wang Z, Zhang J, Feng J, Chen Z (2014) Knowledge graph embedding by translating on hyperplanes. In: Proceedings of the Twenty-Eighth AAAI Conference on Artificial Intelligence, July 27\u201331, 2014, Qu\u00e9bec City, Qu\u00e9bec, Canada, pp 1112\u20131119","DOI":"10.1609\/aaai.v28i1.8870"},{"key":"1351_CR35","unstructured":"Xie R, Liu Z, Sun M (2016) Representation learning of knowledge graphs with hierarchical types. In: Proceedings of the twenty-fifth international joint conference on artificial intelligence, pp 2965\u20132971"},{"key":"1351_CR36","doi-asserted-by":"crossref","unstructured":"You Q, Luo J, Jin H, Yang J (2015) Robust image sentiment analysis using progressively trained and domain transferred deep networks. In: Proceedings of the twenty-ninth AAAI conference on artificial intelligence. AAAI Press, Palo Alto, pp 381\u2013388","DOI":"10.1609\/aaai.v29i1.9179"},{"key":"1351_CR37","doi-asserted-by":"crossref","unstructured":"Yuan J, Guo H, Jin Z, Jin H, Zhang X, Luo J (2017) One-shot learning for fine-grained relation extraction via convolutional siamese neural network. In: IEEE international conference on big data. IEEE, Piscataway, pp 2194\u20132199","DOI":"10.1109\/BigData.2017.8258168"},{"issue":"1","key":"1351_CR38","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/s13637-017-0057-1","volume":"2017","author":"J Yuan","year":"2016","unstructured":"Yuan J, Holtz C, Smith T, Luo J (2016) Autism spectrum disorder detection from semi-structured and unstructured medical data. EURASIP J Bioinform Syst Biol 2017(1):3","journal-title":"EURASIP J Bioinform Syst Biol"},{"key":"1351_CR39","doi-asserted-by":"crossref","unstructured":"Zeng D, Liu K, Chen Y, Zhao J (2015) Distant supervision for relation extraction via piecewise convolutional neural networks. In: EMNLP, pp 1753\u20131762","DOI":"10.18653\/v1\/D15-1203"}],"container-title":["Knowledge and Information Systems"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10115-019-01351-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10115-019-01351-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10115-019-01351-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,14]],"date-time":"2022-09-14T07:17:00Z","timestamp":1663139820000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10115-019-01351-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,3,23]]},"references-count":39,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,1]]}},"alternative-id":["1351"],"URL":"https:\/\/doi.org\/10.1007\/s10115-019-01351-4","relation":{},"ISSN":["0219-1377","0219-3116"],"issn-type":[{"value":"0219-1377","type":"print"},{"value":"0219-3116","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,3,23]]},"assertion":[{"value":"4 January 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 February 2019","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 March 2019","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 March 2019","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}]}}