{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T11:29:11Z","timestamp":1742383751580},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"S15","license":[{"start":{"date-parts":[[2009,12,1]],"date-time":"2009-12-01T00:00:00Z","timestamp":1259625600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2009,12]]},"DOI":"10.1186\/1471-2105-10-s15-s9","type":"journal-article","created":{"date-parts":[[2009,12,3]],"date-time":"2009-12-03T20:27:09Z","timestamp":1259872029000},"source":"Crossref","is-referenced-by-count":11,"title":["HypertenGene: extracting key hypertension genes from biomedical literature with position and automatically-generated template features"],"prefix":"10.1186","volume":"10","author":[{"given":"Richard Tzong-Han","family":"Tsai","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Po-Ting","family":"Lai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hong-Jie","family":"Dai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chi-Hsin","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yue-Yang","family":"Bow","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yen-Ching","family":"Chang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wen-Harn","family":"Pan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wen-Lian","family":"Hsu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,12,3]]},"reference":[{"key":"3454_CR1","volume-title":"Proceedings of Second International Workshop on Active Mining (AM'03)","author":"M Shimbo","year":"2003","unstructured":"Shimbo M, Yamasaki T, Matsumoto Y: Using sectioning information for text retrieval: a case study with the MEDLINE abstracts. Proceedings of Second International Workshop on Active Mining (AM'03) 2003."},{"key":"3454_CR2","volume-title":"Proceedings of the 21st International Conference on Data Engineering: 2005","author":"Y Yamamoto","year":"2005","unstructured":"Yamamoto Y, Takagi T: A Sentence Classification System for Multi Biomedical Literature Summarization. Proceedings of the 21st International Conference on Data Engineering: 2005 2005."},{"issue":"2-3","key":"3454_CR3","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/j.ijmedinf.2006.05.002","volume":"76","author":"P Ruch","year":"2007","unstructured":"Ruch P, Boyer C, Chichester C, Tbahriti I, Geissbuhler A, Fabry P, Gobeill J, Pillet V, Rebholz-Schuhmann D, Lovis C: Using argumentation to extract key sentences from biomedical abstracts. International Journal of Medical Informatics 2007, 76(2\u20133):195\u2013200. 10.1016\/j.ijmedinf.2006.05.002","journal-title":"International Journal of Medical Informatics"},{"key":"3454_CR4","volume-title":"Proceedings of the 2003 Conference of the North American Chapter of the Association for Computational Linguistics on Human Language Technology","author":"F Sha","year":"2003","unstructured":"Sha F, Pereira F: Shallow parsing with conditional random fields. In Proceedings of the 2003 Conference of the North American Chapter of the Association for Computational Linguistics on Human Language Technology. Volume 1. Edmonton, Canada: Association for Computational Linguistics; 2003."},{"issue":"2","key":"3454_CR5","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1093\/bioinformatics\/17.2.155","volume":"17","author":"T Ono","year":"2001","unstructured":"Ono T, Hishigaki H, Tanigami A, Takagi T: Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics 2001, 17(2):155\u2013161. 10.1093\/bioinformatics\/17.2.155","journal-title":"Bioinformatics"},{"issue":"5","key":"3454_CR6","doi-asserted-by":"publisher","first-page":"R40","DOI":"10.1186\/gb-2005-6-5-r40","volume":"6","author":"AK Ramani","year":"2005","unstructured":"Ramani AK, Bunescu RC, Mooney RJ, Marcotte EM: Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol 2005, 6(5):R40. 10.1186\/gb-2005-6-5-r40","journal-title":"Genome Biol"},{"key":"3454_CR7","volume-title":"NIPS-05","author":"RC Bunescu","year":"2005","unstructured":"Bunescu RC, Mooney RJ: Subsequence Kernels for Relation Extraction. NIPS-05 2005."},{"key":"3454_CR8","first-page":"60","volume-title":"Proc Int Conf Intell Syst Mol Biol","author":"C Blaschke","year":"1999","unstructured":"Blaschke C, Andrade MA, Ouzounis C, Valencia A: Automatic extraction of biological information from scientific text: protein-protein interactions. Proc Int Conf Intell Syst Mol Biol 1999, 60\u201367."},{"issue":"1","key":"3454_CR9","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/j.jbi.2003.10.001","volume":"37","author":"A Rzhetsky","year":"2004","unstructured":"Rzhetsky A, Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, Yu H, Duboue PA, Weng W, Wilbur WJ, et al.: GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform 2004, 37(1):43\u201353. 10.1016\/j.jbi.2003.10.001","journal-title":"J Biomed Inform"},{"issue":"2","key":"3454_CR10","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/j.artmed.2004.07.016","volume":"33","author":"R Bunescu","year":"2005","unstructured":"Bunescu R, Ge R, Kate RJ, Marcotte EM, Mooney RJ, Ramani AK, Wong YW: Comparative experiments on learning information extractors for proteins and their interactions. Artif Intell Med 2005, 33(2):139\u2013155. 10.1016\/j.artmed.2004.07.016","journal-title":"Artif Intell Med"},{"key":"3454_CR11","doi-asserted-by":"publisher","first-page":"732","DOI":"10.3115\/1220575.1220667","volume-title":"Proceedings of the conference on Human Language Technology and Empirical Methods in Natural Language Processing: 2005","author":"B Rosario","year":"2005","unstructured":"Rosario B, Hearst MA: Multi-way relation classification: application to protein-protein interactions. In Proceedings of the conference on Human Language Technology and Empirical Methods in Natural Language Processing: 2005. Association for Computational Linguistics Morristown, NJ, USA; 2005:732\u2013739. full_text"},{"key":"3454_CR12","first-page":"77","volume-title":"Proc Int Conf Intell Syst Mol Biol","author":"M Craven","year":"1999","unstructured":"Craven M, Kumlien J: Constructing biological knowledge bases by extracting information from text sources. Proc Int Conf Intell Syst Mol Biol 1999, 77\u201386."},{"key":"3454_CR13","first-page":"517","volume-title":"Pac Symp Biocomput","author":"TC Rindflesch","year":"2000","unstructured":"Rindflesch TC, Tanabe L, Weinstein JN, Hunter L: EDGAR: extraction of drugs, genes and relations from the biomedical literature. Pac Symp Biocomput 2000, 517\u2013528."},{"key":"3454_CR14","first-page":"554","volume-title":"Semantic Relations Asserting the Etiology of Genetic Diseases","author":"T Rindflesch","year":"2003","unstructured":"Rindflesch T, Libbus B, Hristovski D, Aronson A, Kilicoglu H: Semantic Relations Asserting the Etiology of Genetic Diseases. American Medical Informatics Association; 2003:554."},{"key":"3454_CR15","first-page":"4","volume-title":"Proceedings of the Pacific Symposium on Biocomputing","author":"H-W Chun","year":"2006","unstructured":"Chun H-W, Tsuruoka Y, Kim J-D, Shiba R, Nagata N, Hishiki T, Tsujii Ji: Extraction of gene-disease relations from Medline using domain dictionaries and machine learning. Proceedings of the Pacific Symposium on Biocomputing 2006, 4\u201315."},{"key":"3454_CR16","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1186\/1471-2105-7-291","volume":"7","author":"M Masseroli","year":"2006","unstructured":"Masseroli M, Kilicoglu H, Lang F-M, Rindflesch TC: Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease. BMC Bioinformatics 2006, 7: 291. 10.1186\/1471-2105-7-291","journal-title":"BMC Bioinformatics"},{"key":"3454_CR17","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1186\/1471-2105-9-207","volume":"9","author":"M Bundschus","year":"2008","unstructured":"Bundschus M, Dejori M, Stetter M, Tresp V, Kriegel H-P: Extraction of semantic biomedical relations from text using conditional random fields. BMC Bioinformatics 2008, 9: 207. 10.1186\/1471-2105-9-207","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 3","key":"3454_CR18","doi-asserted-by":"publisher","first-page":"S4","DOI":"10.1186\/1471-2105-7-S3-S4","volume":"7","author":"HW Chun","year":"2006","unstructured":"Chun HW, Tsuruoka Y, Kim JD, Shiba R, Nagata N, Hishiki T, Tsujii J: Automatic recognition of topic-classified relations between prostate cancer and genes using MEDLINE abstracts. BMC Bioinformatics 2006, 7(Suppl 3):S4. 10.1186\/1471-2105-7-S3-S4","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"3454_CR19","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1016\/j.eswa.2005.09.072","volume":"30","author":"TH Tsai","year":"2006","unstructured":"Tsai TH, Chou WC, Wu SH, Sung TY, Hsiang J, Hsu WL: Integrating linguistic knowledge into a conditional random field framework to identify biomedical named entities. Expert Syst Appl 2006, 30(1):117\u2013128. 10.1016\/j.eswa.2005.09.072","journal-title":"Expert Syst Appl"},{"issue":"Suppl 5","key":"3454_CR20","doi-asserted-by":"publisher","first-page":"S11","DOI":"10.1186\/1471-2105-7-S5-S11","volume":"7","author":"RT Tsai","year":"2006","unstructured":"Tsai RT, Sung CL, Dai HJ, Hung HC, Sung TY, Hsu WL: NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition. BMC Bioinformatics 2006, 7(Suppl 5):S11. 10.1186\/1471-2105-7-S5-S11","journal-title":"BMC Bioinformatics"},{"key":"3454_CR21","first-page":"282","volume-title":"International Conference on Machine Learning (ICML)","author":"J Lafferty","year":"2001","unstructured":"Lafferty J, McCallum A, Pereira F: Conditional random fields: Probabilistic models for segmenting and labeling sequence data. International Conference on Machine Learning (ICML) 2001, 282\u2013289."},{"key":"3454_CR22","volume-title":"Proceedings of 3rd International Joint Conference of Natural Language Processing (IJCNLP2008). Hyderabad, India","author":"K Hirohata","year":"2008","unstructured":"Hirohata K, Okazaki N, Ananiadou S, Ishizuka M: Identifying Sections in Scientific Abstracts using Conditional Random Fields. Proceedings of 3rd International Joint Conference of Natural Language Processing (IJCNLP2008). Hyderabad, India 2008."},{"key":"3454_CR23","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1109\/IRI.2008.4583016","volume-title":"Proceedings of the IEEE International Conference on Information Reuse and Integration (IEEE IRI 2008): July, 13-15 2008; Las Vegas, Nevada, USA","author":"RTK Lin","year":"2008","unstructured":"Lin RTK, Dai H-J, Bow Y-Y, Day M-Y, Tsai RT-H, Hsu W-L: Result Identification for Biomedical Abstracts Using Conditional Random Fields. Proceedings of the IEEE International Conference on Information Reuse and Integration (IEEE IRI 2008): July, 13\u201315 2008; Las Vegas, Nevada, USA 2008, 122\u2013126."},{"key":"3454_CR24","volume-title":"Writing up research: experimental research report writing for students of English","author":"R Weissberg","year":"1990","unstructured":"Weissberg R, Buker S: Writing up research: experimental research report writing for students of English. Prentice Hall Regents; 1990."},{"key":"3454_CR25","volume-title":"The Annals of Mathematical Statistics","author":"JN Darroch","year":"1972","unstructured":"Darroch JN, Ratcliff D: Generalized Iterative Scaling for Log-Linear Models. The Annals of Mathematical Statistics 1972."},{"key":"3454_CR26","doi-asserted-by":"publisher","DOI":"10.1007\/b98874","volume-title":"Numerical Optimization","author":"J Nocedal","year":"1999","unstructured":"Nocedal J, Wright SJ: Numerical Optimization. Springer; 1999."},{"key":"3454_CR27","first-page":"427","volume-title":"Proceedings of the 43rd Annual Meeting on Association for Computational Linguistics","author":"Z GuoDong","year":"2005","unstructured":"GuoDong Z, Jian S, Jie Z, Min Z: Exploring Various Knowledge in Relation Extraction. In Proceedings of the 43rd Annual Meeting on Association for Computational Linguistics. Ann Arbor, Michigan: Association for Computational Linguistics; 2005:427\u2013434."},{"key":"3454_CR28","volume-title":"Proceedings of the ACL 2004 on Interactive poster and demonstration sessions","author":"N Kambhatla","year":"2004","unstructured":"Kambhatla N: Combining lexical, syntactic, and semantic features with maximum entropy models for extracting relations. In Proceedings of the ACL 2004 on Interactive poster and demonstration sessions. Barcelona, Spain: Association for Computational Linguistics; 2004."},{"key":"3454_CR29","first-page":"51","volume-title":"Proceedings of the First International Symposium on Semantic Mining in Biomedicine (SMBM)","author":"J Xiao","year":"2005","unstructured":"Xiao J, Su J, Zhou G, Tan C: Protein-Protein Interaction Extraction: A Supervised Learning Approach. Proceedings of the First International Symposium on Semantic Mining in Biomedicine (SMBM) 2005, 51\u201359."},{"key":"3454_CR30","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"TF Smith","year":"1981","unstructured":"Smith TF, Waterman MS: Identification of common molecular subsequences. Journal of Molecular Biology 1981, 147: 195\u2013197. 10.1016\/0022-2836(81)90087-5","journal-title":"Journal of Molecular Biology"},{"issue":"5","key":"3454_CR31","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1038\/ng0504-431","volume":"36","author":"K Becker","year":"2004","unstructured":"Becker K, Barnes K, Bright T, Wang S: The Genetic Association Database. Nature Genetics 2004, 36(5):431\u2013432. 10.1038\/ng0504-431","journal-title":"Nature Genetics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-S15-S9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-10-S15-S9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-S15-S9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T10:36:48Z","timestamp":1548153408000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-S15-S9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,12]]},"references-count":31,"journal-issue":{"issue":"S15","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["3454"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-s15-s9","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,12]]},"article-number":"S9"}}