{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T10:53:56Z","timestamp":1777460036386,"version":"3.51.4"},"reference-count":92,"publisher":"Elsevier","isbn-type":[{"value":"9780128114322","type":"print"}],"license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019]]},"DOI":"10.1016\/b978-0-12-809633-8.20409-3","type":"book-chapter","created":{"date-parts":[[2018,2,16]],"date-time":"2018-02-16T00:32:23Z","timestamp":1518741143000},"page":"602-611","source":"Crossref","is-referenced-by-count":21,"title":["Text Mining for Bioinformatics Using Biomedical Literature"],"prefix":"10.1016","author":[{"given":"Andre","family":"Lamurias","sequence":"first","affiliation":[]},{"given":"Francisco M.","family":"Couto","sequence":"additional","affiliation":[]}],"member":"78","reference":[{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib1","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/j.tibtech.2010.04.005","article-title":"Event extraction for systems biology by text mining the literature","volume":"28","author":"Ananiadou","year":"2010","journal-title":"Trends in Biotechnology"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib2","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1136\/jamia.2009.002733","article-title":"An overview of MetaMap: Historical perspective and recent advances","volume":"17","author":"Aronson","year":"2010","journal-title":"Journal of the American Medical Informatics Association"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib3","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1186\/1471-2105-13-161","article-title":"Concept annotation in the CRAFT corpus","volume":"13","author":"Bada","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib4","doi-asserted-by":"crossref","first-page":"9977","DOI":"10.1073\/pnas.92.22.9977","article-title":"Models of natural language understanding","volume":"92","author":"Bates","year":"1995","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib5","unstructured":"Bethard, S., Ogren, P., Becker, L., 2014. ClearTK 2.0: Design patterns for machine learning in UIMA. In: Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC\u05f314), European Language Resources Association (ELRA), Reykjavik, Iceland. pp. 3289\u20133293. Available at: http:\/\/www.lrec-conf.org\/proceedings\/lrec2014\/pdf\/218_Paper.pdf."},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib6","doi-asserted-by":"crossref","unstructured":"Bethard, S., Savova, G., Chen, W.T., et al., 2016. Semeval-2016 task 12: Clinical tempeval. Proceedings of SemEval, 1052\u20131062.","DOI":"10.18653\/v1\/S16-1165"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib7","series-title":"Natural Language Processing With Python: Analyzing Text With the Natural Language Toolkit","author":"Bird","year":"2009"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib8","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1111\/j.1467-8640.2011.00399.x","article-title":"Extracting contextualized complex biological events with rich graph-based feature sets","volume":"27","author":"Bj\u00f6rne","year":"2011","journal-title":"Computational Intelligence"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib9","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1145\/2133806.2133826","article-title":"Probabilistic topic models","volume":"55","author":"Blei","year":"2012","journal-title":"Communications of the ACM"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib10","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1007\/978-3-540-74851-9_35","article-title":"Investigating document triage on paper and electronic media","author":"Buchanan","year":"2007","journal-title":"Research and Advanced Technology for Digital Libraries"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib11","first-page":"9","article-title":"Using encyclopedic knowledge for named entity disambiguation","author":"Bunescu","year":"2006","journal-title":"Eacl"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib12","doi-asserted-by":"crossref","first-page":"S7","DOI":"10.1186\/1758-2946-7-S1-S7","article-title":"A document processing pipeline for annotating chemical entities in scientific documents","volume":"7","author":"Campos","year":"2015","journal-title":"Journal of Cheminformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib13","first-page":"2017","article-title":"Impact of translation on named-entity recognition in radiology texts","author":"Campos","year":"2017","journal-title":"Database"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib14","first-page":"249","article-title":"Assessing agreement on classification tasks: The kappa statistic","volume":"22","author":"Carletta","year":"1996","journal-title":"Computational Linguistics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib15","unstructured":"Carpenter, B., 2007. LingPipe for 99.99% recall of gene mentions. In: Proceedings of the Second BioCreative Challenge Evaluation Workshop, pp. 307\u2013309."},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib16","doi-asserted-by":"crossref","unstructured":"Chaix, E., Dubreucq, B., Fatihi, A., et al., 2016. Overview of the regulatory network of plant seed development (seedev) task at the bionlp shared task 2016. In: Proceedings of the 4th BioNLP shared task workshop. Berlin: Association for Computational Linguistic, pp. 1\u201311.","DOI":"10.18653\/v1\/W16-3001"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib17","doi-asserted-by":"crossref","first-page":"D239","DOI":"10.1093\/nar\/gkv1258","article-title":"miRTarBase 2016: Updates to the experimentally validated miRNA-target interactions database","volume":"44","author":"Chou","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib18","series-title":"Artificial Intelligence Methods and Tools for Systems Biology","first-page":"147","article-title":"Natural language processing and systems biology","author":"Cohen","year":"2004"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib19","series-title":"2017. MER: A Minimal Named-Entity Recognition Tagger and Annotation Server","author":"Couto","year":"2017"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib20","doi-asserted-by":"crossref","first-page":"1371001","DOI":"10.1142\/S0219720013710017","article-title":"The next generation of similarity measures that fully explore the semantics in biomedical ontologies","volume":"11","author":"Couto","year":"2013","journal-title":"Journal of Bioinformatics and Computational Biology"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib21","doi-asserted-by":"crossref","first-page":"e1002854","DOI":"10.1371\/journal.pcbi.1002854","article-title":"Getting more out of biomedical documents with GATE\u05f3s full lifecycle open source text analytics","volume":"9","author":"Cunningham","year":"2013","journal-title":"PLOS Computational Biology"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib22","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1016\/0002-9343(89)90261-1","article-title":"Fish-oil dietary supplementation in patients with Raynaud\u05f3s phenomenon: A double-blind, controlled, prospective study","volume":"86","author":"DiGiacomo","year":"1989","journal-title":"The American Journal of Medicine"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib23","doi-asserted-by":"crossref","unstructured":"Elhadad, N., Pradhan, S., Chapman, W., Manandhar, S., Savova, G., 2015. Semeval-2015 task 14: Analysis of clinical text. In: Proceedings of Workshop on Semantic Evaluation. Association for Computational Linguistics, pp. 303\u201310.","DOI":"10.18653\/v1\/S15-2051"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib24","unstructured":"Farkas, R., Vincze, V., M\u00f3ra, G., Csirik, J., Szarvas, G., 2010. The CoNLL-2010 shared task: Learning to detect hedges and their scope in natural language text. In: Proceedings of the Fourteenth Conference on Computational Natural Language Learning \u2013 Shared Task, Association for Computational Linguistics. pp. 1\u201312."},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib25","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1016\/S1532-0464(03)00012-1","article-title":"Two biomedical sublanguages: A description based on the theories of Zellig Harris","volume":"35","author":"Friedman","year":"2002","journal-title":"Journal of Biomedical Informatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib26","first-page":"401","article-title":"Exploiting shallow linguistic information for relation extraction from biomedical literature","author":"Giuliano","year":"2006","journal-title":"EACL, Citeseer"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib27","unstructured":"Hakala, K., Van Landeghem, S., Salakoski, T., Van de Peer, Y., Ginter, F., 2013. EVEX in ST\u05f313: Application of a large-scale text mining resource to event extraction and network construction. In: Proceedings of the BioNLP Shared Task 2013 Workshop, Association for Computational Linguistics. pp. 26\u201334."},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib28","doi-asserted-by":"crossref","unstructured":"Hearst, M.A., 1999. Untangling text data mining. In: Proceedings of the 37th annual meeting of the Association for Computational Linguistics on Computational Linguistics, Association for Computational Linguistics. pp. 3\u201310.","DOI":"10.3115\/1034678.1034679"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib29","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1016\/j.jbi.2013.07.011","article-title":"The DDI corpus: An annotated corpus with pharmacological substances and drug-drug interactions","volume":"46","author":"Herrero-Zazo","year":"2013","journal-title":"Journal of Biomedical Informatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10791-008-9076-6","article-title":"TREC genomics special issue overview","volume":"12","author":"Hersh","year":"2009","journal-title":"Information Retrieval"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib31","doi-asserted-by":"crossref","unstructured":"Hersh, W.R., Bhupatiraju, R.T., 2003. TREC genomics track overview. TREC. pp. 14\u201323.","DOI":"10.6028\/NIST.SP.500-255.genomics-overview"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib32","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1186\/1471-2105-6-S1-S1","article-title":"Overview of BioCreAtIvE: Critical assessment of information extraction for biology","volume":"6","author":"Hirschman","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib33","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1093\/bib\/bbv024","article-title":"Community challenges in biomedical text mining over 10 years: Success, failure and the future","volume":"17","author":"Huang","year":"2016","journal-title":"Briefings in Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib34","doi-asserted-by":"crossref","unstructured":"Kelly, L., Goeuriot, L., Suominen, H., et al., 2014. Overview of the share\/clef ehealth evaluation lab 2014. In: International Conference of the Cross-Language Evaluation Forum for European Languages, Springer. pp. 172\u2013191.","DOI":"10.1007\/978-3-319-11382-1_17"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib35","doi-asserted-by":"crossref","first-page":"i180","DOI":"10.1093\/bioinformatics\/btg1023","article-title":"GENIA corpus \u2013 A semantically annotated corpus for bio-text mining","volume":"19","author":"Kim","year":"2003","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib36","doi-asserted-by":"crossref","unstructured":"Kim, J.D., Ohta, T., Tsuruoka, Y., Tateisi, Y., Collier, N., 2004. Introduction to the bio-entity recognition task at JNLPBA. In: Proceedings of the international joint workshop on natural language processing in biomedicine and its applications, Association for Computational Linguistics. pp. 70\u201375.","DOI":"10.3115\/1567594.1567610"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib37","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1758-2946-7-S1-S2","article-title":"The CHEMDNER corpus of chemicals and drugs and its annotation principles","volume":"7","author":"Krallinger","year":"2015","journal-title":"Journal of Cheminformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib38","unstructured":"Krallinger, M., Rabal, O., Lourenco, A., et al., 2015b. Overview of the CHEMD-NER patents task, in: Proceedings of the fifth BioCreative challenge evaluation workshop, pp. 63\u201375."},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib39","doi-asserted-by":"crossref","unstructured":"Krithara, A., Nentidis, A., Paliouras, G., Kakadiaris, I., 2016. Results proceedings of the 4th edition of BioASQ challenge. In: Fourth BioASQ Workshop at the Conference of the Association for Computational Linguistics, pp. 1\u20137.","DOI":"10.18653\/v1\/W16-3101"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib40","first-page":"12","article-title":"Extracting microRNA-gene relations from biomedical literature using distant supervision","author":"Lamurias","year":"2017","journal-title":"PLOS ONE"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib41","doi-asserted-by":"crossref","first-page":"2909","DOI":"10.1093\/bioinformatics\/btt474","article-title":"DNorm: Disease name normalization with pairwise learning to rank","volume":"29","author":"Leaman","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib42","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":"10.1016\/B978-0-12-809633-8.20409-3_bib43","doi-asserted-by":"crossref","unstructured":"Leaman, R., Gonzalez, G., 2008. BANNER: An executable survey of advances in biomedical named entity recognition. In: Pacific Symposium on Biocomputing, pp. 652\u2013663.","DOI":"10.1142\/9789812776136_0062"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib44","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/nature14539","article-title":"Deep learning","volume":"521","author":"LeCun","year":"2015","journal-title":"Nature"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib45","doi-asserted-by":"crossref","first-page":"e0164680","DOI":"10.1371\/journal.pone.0164680","article-title":"BEST: Next-generation biomedical entity search tool for knowledge discovery from biomedical literature","volume":"11","author":"Lee","year":"2016","journal-title":"PLOS ONE"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib46","first-page":"42","article-title":"VERSE: Event and relation extraction in the BioNLP 2016 shared task","volume":"2016","author":"Lever","year":"2016","journal-title":"ACL"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib47","doi-asserted-by":"crossref","first-page":"W535","DOI":"10.1093\/nar\/gkv383","article-title":"PolySearch2: A significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more","volume":"43","author":"Liu","year":"2015","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib48","first-page":"2017","article-title":"Identifying human phenotype terms by combining machine learning and validation rules","author":"Lobo","year":"2017","journal-title":"BioMed Research International"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib49","doi-asserted-by":"crossref","unstructured":"Lopez, V., Pasin, M., Motta, E., 2005. Aqualog: An ontology-portable question answering system for the semantic web. In: European Semantic Web Conference, Springer. pp. 546\u2013562.","DOI":"10.1007\/11431053_37"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib50","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1016\/j.jbi.2009.04.002","article-title":"@ note: A workbench for biomedical text mining","volume":"42","author":"Lourenco","year":"2009","journal-title":"Journal of Biomedical Informatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib51","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1093\/bioinformatics\/btv476","article-title":"Large-scale extraction of gene interactions from full-text literature using DeepDive","volume":"32","author":"Mallory","year":"2016","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib52","volume":"999","author":"Manning","year":"1999"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib53","doi-asserted-by":"crossref","first-page":"55","DOI":"10.3115\/v1\/P14-5010","article-title":"The Stanford CoreNLP natural language processing toolkit","author":"Manning","year":"2014","journal-title":"Association for Computational Linguistics (ACL) System Demonstrations"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib54","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1186\/1471-2105-14-175","article-title":"Wide coverage biomedical event extraction using multiple partially overlapping corpora","volume":"14","author":"Miwa","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib55","doi-asserted-by":"crossref","unstructured":"Miwa, M., Bansal, M., 2016. End-to-end relation extraction using LSTMs on sequences and tree structures. In: Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics, Association for Computational Linguistics. p. 10. doi:10.18653\/v1\/P16\u20131105,arXiv:1601.0770.","DOI":"10.18653\/v1\/P16-1105"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib56","doi-asserted-by":"crossref","unstructured":"Miyao, Y., Ohta, T., Masuda, K., et al., 2006. Semantic retrieval for the accurate identification of relational concepts in massive textbases. In: Proceedings of the 21st International Conference on Computational Linguistics and the 44th annual meeting of the Association for Computational Linguistics, Association for Computational Linguistics. pp. 1017\u20131024.","DOI":"10.3115\/1220175.1220303"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib57","doi-asserted-by":"crossref","first-page":"e309","DOI":"10.1371\/journal.pbio.0020309","article-title":"Textpresso: An ontology-based information retrieval and extraction system for biological literature","volume":"2","author":"M\u00fcller","year":"2004","journal-title":"PLOS Biology"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib58","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1075\/li.30.1.03nad","article-title":"A survey of named entity recognition and classification","volume":"30","author":"Nadeau","year":"2007","journal-title":"Lingvisticae Investigationes"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib59","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1093\/bioinformatics\/btt317","article-title":"BeCAS: Biomedical concept recognition services and visualization","volume":"29","author":"Nunes","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib60","unstructured":"Ohta, T., Pyysalo, S., Tsujii, J., 2011. Overview of the epigenetics and post-translational modifications (EPI) task of BioNLP shared task 2011. In: Proceedings of the BioNLP Shared Task 2011 Workshop, Association for Computational Linguistics. pp. 16\u201325."},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib61","doi-asserted-by":"crossref","first-page":"3089","DOI":"10.1093\/bioinformatics\/btl534","article-title":"Building an abbreviation dictionary using a term recognition approach","volume":"22","author":"Okazaki","year":"2006","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib62","doi-asserted-by":"crossref","unstructured":"Pershina, M., He, Y., Grishman, R., 2015. Personalized page rank for named entity disambiguation. In: HLT-NAACL, pp. 238\u2013243.","DOI":"10.3115\/v1\/N15-1026"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib63","doi-asserted-by":"crossref","first-page":"i575","DOI":"10.1093\/bioinformatics\/bts407","article-title":"Event extraction across multiple levels of biological organization","volume":"28","author":"Pyysalo","year":"2012","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib64","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2105-16-S10-S2","article-title":"Overview of the cancer genetics and pathway curation tasks of bionlp shared task 2013","volume":"16","author":"Pyysalo","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib65","unstructured":"Pyysalo, S., Ginter, F., Moen, H., Salakoski, T., Ananiadou, S., 2013. Distributional semantics resources for biomedical text processing. In: Proceedings of Languages in Biology and Medicine, LBM."},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib66","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1093\/bioinformatics\/btm557","article-title":"Text processing through web services: Calling Whatizit","volume":"24","author":"Rebholz-Schuhmann","year":"2008","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib67","doi-asserted-by":"crossref","first-page":"S11","DOI":"10.1186\/1755-8794-7-S1-S11","article-title":"Effectively processing medical term queries on the UMLS metathesaurus by layered dynamic programming","volume":"7","author":"Ren","year":"2014","journal-title":"BMC Medical Genomics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib68","unstructured":"S\u00e6tre, R., Yoshida, K., Yakushiji, A., et al., 2007. AKANE system: Protein-protein interaction pairs in BioCreAtIvE2 challenge, PPI-IPS subtask. In: Proceedings of the Second BioCreative Challenge Workshop, Madrid. pp. 209\u2013212."},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib69","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1136\/jamia.2009.001560","article-title":"Mayo clinical text analysis and knowledge extraction system (cTAKES): Architecture, component evaluation and applications","volume":"17","author":"Savova","year":"2010","journal-title":"Journal of the American Medical Informatics Association: JAMIA"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib70","unstructured":"Segura Bedmar, I., Martinez, P., Herrero Zazo, M., 2013. Semeval-2013 task 9: Extraction of drug-drug interactions from biomedical texts (ddiextraction 2013). In: Proceedings of the Seventh International Workshop on Semantic Evaluation, Association for Computational Linguistics."},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib71","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1016\/j.jbi.2011.04.005","article-title":"Using a shallow linguistic kernel for drug-drug interaction extraction","volume":"44","author":"Segura-Bedmar","year":"2011","journal-title":"Journal of Biomedical Informatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib72","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1016\/j.jbi.2014.05.007","article-title":"Lessons learnt from the DDIExtraction-2013 shared task","volume":"51","author":"Segura-Bedmar","year":"2014","journal-title":"Journal of Biomedical Informatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib73","doi-asserted-by":"crossref","first-page":"3191","DOI":"10.1093\/bioinformatics\/bti475","article-title":"ABNER: An open source tool for automatically tagging genes, proteins and other entity names in text","volume":"21","author":"Settles","year":"2005","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib74","doi-asserted-by":"crossref","unstructured":"Smith, L.H., Tanabe, L., Rindflesch, T., Wilbur, W.J., 2005. MedTag: A collection of biomedical annotations. In: Proceedings of the ACL-ISMB workshop on linking biological literature, ontologies and databases: Mining biological semantics, Association for Computational Linguistics. pp. 32\u201337.","DOI":"10.3115\/1641484.1641489"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib75","unstructured":"Stenetorp, P., Pyysalo, S., Tsujii, J., 2011. SimSem: Fast approximate string matching in relation to semantic category disambiguation. In: Proceedings of BioNLP 2011 Workshop, Association for Computational Linguistics, Portland, Oregon, USA. pp. 136\u2013145. Available at: http:\/\/www.aclweb.org\/anthology\/W11-0218."},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib76","doi-asserted-by":"crossref","unstructured":"Styler IV, W.F., Bethard, S., Finan, S., et al., 2014. Temporal annotation in the clinical domain. Transactions of the Association for Computational Linguistics 2, 143\u2013154.","DOI":"10.1162\/tacl_a_00172"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib77","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1136\/amiajnl-2013-001628","article-title":"Evaluating temporal relations in clinical text: 2012 i2b2 challenge","volume":"20","author":"Sun","year":"2013","journal-title":"Journal of the American Medical Informatics Association"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib78","first-page":"93","article-title":"An introduction to conditional random fields for relational learning","author":"Sutton","year":"2006","journal-title":"Introduction to Statistical Relational Learning"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib79","first-page":"29","article-title":"Medical literature as a potential source of new knowledge","volume":"78","author":"Swanson","year":"1990","journal-title":"Bulletin of the Medical Library Association"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib80","doi-asserted-by":"crossref","first-page":"D380","DOI":"10.1093\/nar\/gkv1277","article-title":"STITCH 5: Augmenting protein-chemical interaction networks with tissue and affinity data","volume":"44","author":"Szklarczyk","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib81","doi-asserted-by":"crossref","first-page":"D362","DOI":"10.1093\/nar\/gkw937","article-title":"The STRING database in 2017: Quality-controlled protein-protein association networks, made broadly accessible","volume":"45","author":"Szklarczyk","year":"2017","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib82","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2105-9-S3-S2","article-title":"Normalizing biomedical terms by minimizing ambiguity and variability","volume":"9","author":"Tsuruoka","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib83","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1093\/bioinformatics\/btr214","article-title":"Discovering and visualizing indirect associations between biomedical concepts","volume":"27","author":"Tsuruoka","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib84","doi-asserted-by":"crossref","unstructured":"Tsuruoka, Y., Tsujii, J., 2005. Bidirectional inference with the easiest-Proceedings of the first strategy for tagging sequence data. In: Conference on human language technology and empirical methods in natural language processing, Association for Computational Linguistics. pp. 467\u2013474.","DOI":"10.3115\/1220575.1220634"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib85","doi-asserted-by":"crossref","first-page":"25","DOI":"10.12688\/wellcomeopenres.10210.1","article-title":"SciLite: A platform for displaying text-mined annotations as a means to link research articles with biological data","volume":"1","author":"Venkatesan","year":"2016","journal-title":"Wellcome Open Research"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib86","first-page":"gkt441","article-title":"PubTator: A web-based text mining tool for assisting biocuration","author":"Wei","year":"2013","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib87","first-page":"2015","article-title":"GNormPlus: An integrative approach for tagging genes, gene families, and protein domains","author":"Wei","year":"2015","journal-title":"BioMed Research International"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib88","first-page":"btt156","article-title":"tmVar: A text mining approach for extracting sequence variants in biomedical literature","author":"Wei","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib89","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1093\/bib\/bbn043","article-title":"Facts from text: Can text mining help to scale-up high-quality manual curation of gene products with ontologies?","volume":"9","author":"Winnenburg","year":"2008","journal-title":"Briefings in Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib90","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1145\/772862.772873","article-title":"Background and overview for KDD cup 2002 task 1: Information extraction from biomedical articles","volume":"4","author":"Yeh","year":"2002","journal-title":"ACM SIGKDD Explorations Newsletter"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib91","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1038\/ng0208-124","article-title":"A navigator for human genome epidemiology","volume":"40","author":"Yu","year":"2008","journal-title":"Nature genetics"},{"key":"10.1016\/B978-0-12-809633-8.20409-3_bib92","unstructured":"Zhang, C., 2015. DeepDive: A data management system for automatic knowledge base construction. PhD Thesis, The University of Wisconsin-Madison."}],"container-title":["Encyclopedia of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338204093?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338204093?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T21:43:26Z","timestamp":1751406206000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/B9780128096338204093"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9780128114322"],"references-count":92,"URL":"https:\/\/doi.org\/10.1016\/b978-0-12-809633-8.20409-3","relation":{},"subject":[],"published":{"date-parts":[[2019]]}}}