{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,8]],"date-time":"2025-09-08T05:36:15Z","timestamp":1757309775590},"reference-count":49,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,5,18]],"date-time":"2015-05-18T00:00:00Z","timestamp":1431907200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Biomed Semant"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s13326-015-0023-3","type":"journal-article","created":{"date-parts":[[2015,5,6]],"date-time":"2015-05-06T07:59:10Z","timestamp":1430899150000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Sequential pattern mining for discovering gene interactions and their contextual information from biomedical texts"],"prefix":"10.1186","volume":"6","author":[{"given":"Peggy","family":"Cellier","sequence":"first","affiliation":[]},{"given":"Thierry","family":"Charnois","sequence":"additional","affiliation":[]},{"given":"Marc","family":"Plantevit","sequence":"additional","affiliation":[]},{"given":"Christophe","family":"Rigotti","sequence":"additional","affiliation":[]},{"given":"Bruno","family":"Cr\u00e9milleux","sequence":"additional","affiliation":[]},{"given":"Olivier","family":"Gandrillon","sequence":"additional","affiliation":[]},{"given":"Ji\u0159\u00ed","family":"Kl\u00e9ma","sequence":"additional","affiliation":[]},{"given":"Jean-Luc","family":"Manguin","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2015,5,18]]},"reference":[{"key":"23_CR1","unstructured":"PubMed. http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/ ."},{"key":"23_CR2","unstructured":"BioGRID. http:\/\/thebiogrid.org\/ ."},{"key":"23_CR3","unstructured":"STRING. http:\/\/string-db.org\/ ."},{"key":"23_CR4","unstructured":"Giuliano C, Lavelli A, Romano L. Exploiting shallow linguistic information for relation extraction from biomedical literature. In: Conference of the European Chapter of the Association for Computational Linguistics. Trento, Italy: 2006. p. 401\u20138."},{"issue":"Suppl 3","key":"23_CR5","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1186\/1471-2105-7-S3-S3","volume":"7","author":"F Rinaldi","year":"2006","unstructured":"Rinaldi F, Schneider G, Kaljurand K, Hess M, Romacker M. An environment for relation mining over richly annotated corpora: the case of genia. BMC Bioinformatics. 2006; 7(Suppl 3):S3.","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"23_CR6","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/bioinformatics\/btl616","volume":"23","author":"K Fundel","year":"2007","unstructured":"Fundel K, K\u00fcffner R, Zimmer R. RelEx - relation extraction using dependency parse trees. Bioinformatics. 2007; 23(3):365\u201371.","journal-title":"Bioinformatics"},{"key":"23_CR7","volume-title":"Handbook of Natural Language Processing, Second Edition","author":"JR Hobbs","year":"2010","unstructured":"Hobbs JR, Riloff E. Information extraction In: Indurkhya N, Damerau FJ, editors. Handbook of Natural Language Processing, Second Edition. Boca Raton, FL: CRC: 2010."},{"issue":"Suppl 2","key":"23_CR8","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/gb-2008-9-s2-s4","volume":"9","author":"M Krallinger","year":"2008","unstructured":"Krallinger M, Leitner F, Rodriguez-Penagos C, Valencia A. Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol. 2008; 9(Suppl 2):S4.","journal-title":"Genome Biol"},{"issue":"6","key":"23_CR9","doi-asserted-by":"crossref","first-page":"1086","DOI":"10.1016\/j.jbi.2011.08.011","volume":"44","author":"Y Zhang","year":"2011","unstructured":"Zhang Y, Lin H, Yang Z, Li Y. Neighborhood hash graph kernel for protein-protein interaction extraction. J Biomed Inform. 2011; 44(6):1086\u201392.","journal-title":"J Biomed Inform"},{"key":"23_CR10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/2041-1480-2-1","volume":"2","author":"T Polajnar","year":"2011","unstructured":"Polajnar T, Damoulas T, Girolami M. Protein interaction sentence detection using multiple semantic kernels. J Biomed Semantics. 2011; 2:1.","journal-title":"J Biomed Semantics"},{"issue":"7","key":"23_CR11","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pcbi.1000837","volume":"6","author":"D Tikk","year":"2010","unstructured":"Tikk D, Thomas PE, Palaga P, Hakenberg J, Leser U. A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature. PLoS Comput Biol. 2010; 6(7):1\u201319.","journal-title":"PLoS Comput Biol"},{"key":"23_CR12","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/1471-2105-14-12","volume":"14","author":"D Tikk","year":"2013","unstructured":"Tikk D, Solt I, Thomas PE, Leser U. A detailed error analysis of 13 kernel methods for protein-protein interaction extraction. BMC Bioinformatics. 2013; 14:12.","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"23_CR13","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1093\/bioinformatics\/btn631","volume":"25","author":"Y Miyao","year":"2009","unstructured":"Miyao Y, Sagae K, S\u00e6tre R, Matsuzaki T, Tsujii J. Evaluating contributions of natural language parsers to protein-protein interaction extraction. Bioinformatics. 2009; 25(3):394\u2013400.","journal-title":"Bioinformatics"},{"key":"23_CR14","volume-title":"Text Mining and Its Applications: Results of the NEMIS Launch Conference. Studies in Fuzziness and Soft Computing","author":"C N\u00e9dellec","year":"2004","unstructured":"N\u00e9dellec C. Machine learning for information extraction in genomics - state of the art and perspectives. In: Text Mining and Its Applications: Results of the NEMIS Launch Conference. Studies in Fuzziness and Soft Computing. Berlin Heidelberg: Springer: 2004. p. 99\u2013118."},{"key":"23_CR15","volume-title":"International Conference on Intelligent Text Processing and Computational Linguistics. LNCS, vol. 5449","author":"G Schneider","year":"2009","unstructured":"Schneider G, Kaljurand K, Rinaldi F. Detecting protein-protein interactions in biomedical texts using a parser and linguistic resources. In: International Conference on Intelligent Text Processing and Computational Linguistics. LNCS, vol. 5449. Berlin, Germany: Springer: 2009. p. 406\u201317."},{"issue":"16","key":"23_CR16","doi-asserted-by":"crossref","first-page":"2154","DOI":"10.1093\/bioinformatics\/bts332","volume":"28","author":"M Gerner","year":"2012","unstructured":"Gerner M, Sarafraz F, Bergman CM, Nenadic G. Biocontext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events. Bioinformatics. 2012; 28(16):2154\u201361.","journal-title":"Bioinformatics"},{"key":"23_CR17","volume-title":"Proceedings of the 2010 Workshop on Biomedical Natural Language Processing","author":"J Bj\u00f6rne","year":"2010","unstructured":"Bj\u00f6rne J, Ginter F, Pyysalo S, Tsujii J, Salakoski T. Scaling up biomedical event extraction to the entire pubmed. In: Proceedings of the 2010 Workshop on Biomedical Natural Language Processing. Uppsala, Sweden: Association for Computational Linguistics: 2010. p. 28\u201336. http:\/\/www.aclweb.org\/anthology\/W10-1904 ."},{"issue":"3","key":"23_CR18","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1109\/TCBB.2010.51","volume":"7","author":"J Hakenberg","year":"2010","unstructured":"Hakenberg J, Leaman R, Vo NH, Jonnalagadda S, Sullivan R, Miller C,et al. Efficient extraction of protein-protein interactions from full-text articles. IEEE\/ACM Trans Comput Biol Bioinform. 2010; 7(3):481\u201394.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform."},{"issue":"Suppl 5","key":"23_CR19","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/2041-1480-2-S5-S4","volume":"2","author":"A Ben Abacha","year":"2011","unstructured":"Ben Abacha A, Zweigenbaum P. Automatic extraction of semantic relations between medical entities: a rule based approach. J Biomed Semantics. 2011; 2(Suppl 5):S4.","journal-title":"J Biomed Semantics"},{"key":"23_CR20","doi-asserted-by":"crossref","unstructured":"Hearst MA. Automatic acquisition of hyponyms from large text corpora. In: Proceedings of the 14th Conference on Computational Linguistics - Volume 2. COLING \u201992. Nantes, France: 1992. p. 539\u201345.","DOI":"10.3115\/992133.992154"},{"issue":"Suppl 2","key":"23_CR21","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/gb-2008-9-s2-s14","volume":"9","author":"J Hakenberg","year":"2008","unstructured":"Hakenberg J, Plake C, Royer L, Strobelt H, Leser U, Schroeder M. Gene mention normalization and interaction extraction with context models and sentence motifs. Genome Biol. 2008; 9(Suppl 2):14.","journal-title":"Genome Biol"},{"key":"23_CR22","volume-title":"Proc. of the 12th Int. Conf. on Extending Database Technology: Advances in Database Technology. EDBT \u201909","author":"P Palaga","year":"2009","unstructured":"Palaga P, Nguyen L, Leser U, Hakenberg J. High-performance information extraction with alibaba. In: Proc. of the 12th Int. Conf. on Extending Database Technology: Advances in Database Technology. EDBT \u201909. New York, NY, USA: ACM: 2009. p. 1140\u20131143."},{"key":"23_CR23","unstructured":"Hakenberg J, Schroeder M, Leser U. Consensus pattern alignment to find protein-protein interactions in text. In: Proc. Second BioCreative Challenge Evaluation Workshop. Madrid, Spain: 2007."},{"key":"23_CR24","doi-asserted-by":"crossref","unstructured":"Agrawal R, Srikant R. Mining sequential patterns. In: International Conference on Data Engineering. IEEE Computer Society: 1995. p. 3\u201314.","DOI":"10.1109\/ICDE.1995.380415"},{"key":"23_CR25","volume-title":"Knowledge Discovery in Databases","author":"WJ Frawley","year":"1991","unstructured":"Frawley WJ, Piatetsky-Shapiro G, Matheus CJ. Knowledge discovery in databases: An overview. In: Knowledge Discovery in Databases. Anaheim, CA, USA: AAAI\/MIT Press: 1991. p. 1\u201330."},{"key":"23_CR26","volume-title":"International Conference on Extending Database Technology","author":"R Srikant","year":"1996","unstructured":"Srikant R, Agrawal R. Mining sequential patterns: Generalizations and performance improvements. In: International Conference on Extending Database Technology. London, UK: Springer-Verlag: 1996. p. 3\u201317."},{"key":"23_CR27","volume-title":"International Conference on Data Engineering","author":"J Pei","year":"2001","unstructured":"Pei J, Han B, Mortazavi-Asl B, Pinto H. Prefixspan: Mining sequential patterns efficiently by prefix-projected pattern growth. In: International Conference on Data Engineering. Washington, DC, USA: IEEE Computer Society: 2001. p. 215\u201324."},{"issue":"1\/2","key":"23_CR28","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1023\/A:1007652502315","volume":"42","author":"M Zaki","year":"2001","unstructured":"Zaki M. Spade: An efficient algorithm for mining frequent sequences. Mach Learn. 2001; 42(1\/2):31\u201360.","journal-title":"Mach Learn"},{"key":"23_CR29","volume-title":"Proc. of the 20th Int. Conf. on Data Engineering. ICDE \u201904","author":"J Wang","year":"2004","unstructured":"Wang J, Han J. Bide: Efficient mining of frequent closed sequences. In: Proc. of the 20th Int. Conf. on Data Engineering. ICDE \u201904. Boston, MA, USA: IEEE Computer Society: 2004. p. 79."},{"key":"23_CR30","volume-title":"Knowledge Discovery in Inductive Databases 5th Int. Workshop KDID\u201906, Revised Selected and Invited Papers","author":"M Nanni","year":"2007","unstructured":"Nanni M, Rigotti C. Extracting trees of quantitative serial episodes. In: Knowledge Discovery in Inductive Databases 5th Int. Workshop KDID\u201906, Revised Selected and Invited Papers. Berlin, Germany: Springer: 2007. p. 170\u201388."},{"key":"23_CR31","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1093\/bib\/bbm045","volume":"8","author":"P Zweigenbaum","year":"2007","unstructured":"Zweigenbaum P, Demner-Fushman D, Yu H, Cohen KB. Frontiers of biomedical text mining: current progress. Brief Bioinform. 2007; 8:358\u2013375.","journal-title":"Brief Bioinform"},{"key":"23_CR32","volume-title":"Proc. of the Int. Conf. on Data Engineering","author":"J Pei","year":"2001","unstructured":"Pei J, Han B, Lakshmanan LVS. Mining frequent itemsets with convertible constraints. In: Proc. of the Int. Conf. on Data Engineering. Washington, DC, USA: IEEE Computer Society: 2001. p. 433\u201342."},{"key":"23_CR33","volume-title":"Discovering Knowledge from Local Patterns in SAGE Data","author":"B Cr\u00e9milleux","year":"2008","unstructured":"Cr\u00e9milleux B, Soulet A, Kl\u00e9ma J, H\u00e9bert C, Gandrillon O. Discovering Knowledge from Local Patterns in SAGE Data. Hershey, Pennsylvania, USA: IGI Publishing; 2008."},{"key":"23_CR34","volume-title":"SIGMOD International Conference on Management of Data","author":"RT Ng","year":"1998","unstructured":"Ng RT, Lakshmanan LVS, Han J, Pang A. Exploratory mining and pruning optimizations of constrained association rules. In: SIGMOD International Conference on Management of Data. New York, NY, USA: ACM Press: 1998. p. 13\u201324."},{"key":"23_CR35","volume-title":"International Symposium on Advances in Intelligent Data Analysis. LNCS, vol 6065","author":"P Cellier","year":"2010","unstructured":"Cellier P, Charnois T, Plantevit M, Cr\u00e9milleux B. Recursive sequence mining to discover named entity relations. In: International Symposium on Advances in Intelligent Data Analysis. LNCS, vol 6065. Berlin, Germany: Springer: 2010. p. 30\u201341."},{"key":"23_CR36","volume-title":"International Conference on Intelligent Text Processing and Computational Linguistics","author":"P Cellier","year":"2010","unstructured":"Cellier P, Charnois T, Plantevit M. Sequential patterns to discover and characterise biological relations. In: International Conference on Intelligent Text Processing and Computational Linguistics. Berlin, Germany: LNCS: 2010. p. 537\u201348."},{"key":"23_CR37","doi-asserted-by":"crossref","unstructured":"Rosario B, Hearst MA. Multi-way relation classification: application to protein-protein interactions. In: Conference on Human Language Technology and Empirical Methods in Natural Language Processing. Vancouver, British Columbia, Canada: 2005. p. 732\u20139.","DOI":"10.3115\/1220575.1220667"},{"key":"23_CR38","unstructured":"Schmid H. Probabilistic part-of-speech tagging using decision trees. In: International Conference on New Methods in Language Processing. Manchester, UK: 1994. p. 44\u20139."},{"key":"23_CR39","unstructured":"DMT, 4SP tool. http:\/\/liris.cnrs.fr\/~crigotti\/dmt4sp.html ."},{"key":"23_CR40","doi-asserted-by":"crossref","first-page":"2046","DOI":"10.1093\/bioinformatics\/btg279","volume":"19","author":"JM Temkin","year":"2003","unstructured":"Temkin JM, Gilder MR. Extraction of protein interaction information from unstructured text using a context-free grammar. Bioinformatics. 2003; 19:2046\u201353.","journal-title":"Bioinformatics"},{"key":"23_CR41","doi-asserted-by":"crossref","unstructured":"Hao Y, Zhu X, Huang M, Ming L. Discovering patterns to extract protein-protein interactions from the literature : Part ii. Bioinformatics. 3294.","DOI":"10.1093\/bioinformatics\/bti493"},{"key":"23_CR42","unstructured":"Farkas R, Vincze V, Mora G, Csirik J, Szarvas G. The conll-2010 shared task: Learning to detect hedges and their scope in natural language text. In: Conference on Computational Natural Language Learning: Shared Task. Uppsala, Sweden: 2010."},{"issue":"2","key":"23_CR43","doi-asserted-by":"crossref","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, et al. Comparative experiments on learning information extractors for proteins and their interactions. Artif Intell Med. 2005; 33(2):139\u201355.","journal-title":"Artif Intell Med"},{"issue":"1","key":"23_CR44","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1186\/1471-2105-8-50","volume":"8","author":"S Pyysalo","year":"2007","unstructured":"Pyysalo S, Ginter F, Heimonen J, Bj\u00f6rne J, Boberg J, J\u00e4rvinen J, et al. Bioinfer: a corpus for information extraction in the biomedical domain. BMC Bioinformatics. 2007; 8(1):50.","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"23_CR45","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/bioinformatics\/btl616","volume":"23","author":"K Fundel","year":"2007","unstructured":"Fundel K, K\u00fcffner R, Zimmer R. Relex\u2014relation extraction using dependency parse trees. Bioinformatics. 2007; 23(3):365\u201371.","journal-title":"Bioinformatics"},{"issue":"Suppl 3","key":"23_CR46","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1471-2105-9-S3-S6","volume":"9","author":"S Pyysalo","year":"2008","unstructured":"Pyysalo S, Airola A, Heimonen J, Bjorne J, Ginter F, Salakoski T. Comparative analysis of five protein-protein interaction corpora. BMC Bioinformatics. 2008; 9(Suppl 3):6. doi:10.1186\/1471-2105-9-s3-s6.","journal-title":"BMC Bioinformatics"},{"key":"23_CR47","unstructured":"HGNC (HUGO Gene Nomenclature Committee). http:\/\/www.genenames.org\/ ."},{"issue":"6","key":"23_CR48","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1016\/j.jbi.2004.08.003","volume":"37","author":"Y Tsuruoka","year":"2004","unstructured":"Tsuruoka Y, Tsujii J. Improving the performance of dictionary-based approaches in protein name recognition. J Biomed Inform. 2004; 37(6):461\u201370.","journal-title":"J Biomed Inform"},{"issue":"Natural Compoun","key":"23_CR49","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1111\/j.1749-6632.2009.04911.x","volume":"1171","author":"BB Aggarwal","year":"2009","unstructured":"Aggarwal BB, Kunnumakkara AB, Harikumar KB, Gupta SR, Tharakan ST, Koca C, et al. Signal transducer and activator of transcription-3, inflammation, and cancer: how intimate is the relationship?Ann NY Acad Sci. 2009; 1171(Natural Compounds and Their Role in Apoptotic Cell Signaling Pathways):59\u201376.","journal-title":"Ann NY Acad Sci"}],"container-title":["Journal of Biomedical Semantics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-015-0023-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s13326-015-0023-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13326-015-0023-3","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,24]],"date-time":"2019-08-24T13:10:30Z","timestamp":1566652230000},"score":1,"resource":{"primary":{"URL":"http:\/\/www.jbiomedsem.com\/content\/6\/1\/27"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,5,18]]},"references-count":49,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["23"],"URL":"https:\/\/doi.org\/10.1186\/s13326-015-0023-3","relation":{},"ISSN":["2041-1480"],"issn-type":[{"value":"2041-1480","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,5,18]]},"article-number":"27"}}