{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,25]],"date-time":"2023-09-25T23:36:17Z","timestamp":1695684977815},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"S8","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>This article describes the approaches taken by the OntoGene group at the University of Zurich in dealing with two tasks of the BioCreative III competition: classification of articles which contain curatable protein-protein interactions (PPI-ACT) and extraction of experimental methods (PPI-IMT).<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Two main achievements are described in this paper: (a) a system for document classification which crucially relies on the results of an advanced pipeline of natural language processing tools; (b) a system which is capable of detecting all experimental methods mentioned in scientific literature, and listing them with a competitive ranking (AUC iP\/R &gt; 0.5).<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>The results of the BioCreative III shared evaluation clearly demonstrate that significant progress has been achieved in the domain of biomedical text mining in the past few years. Our own contribution, together with the results of other participants, provides evidence that natural language processing techniques have become by now an integral part of advanced text mining approaches.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-s8-s13","type":"journal-article","created":{"date-parts":[[2011,10,5]],"date-time":"2011-10-05T00:44:06Z","timestamp":1317775446000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Detection of interaction articles and experimental methods in biomedical literature"],"prefix":"10.1186","volume":"12","author":[{"given":"Gerold","family":"Schneider","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simon","family":"Clematide","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fabio","family":"Rinaldi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,10,3]]},"reference":[{"issue":"suppl 1","key":"4807_CR1","doi-asserted-by":"publisher","first-page":"D452","DOI":"10.1093\/nar\/gkh052","volume":"32","author":"H Hermjakob","year":"2004","unstructured":"Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H, Armstrong J, Bairoch A, Cesareni G, Sherman D, Apweiler R: IntAct: an open source molecular interaction database. Nucl. Acids Res 2004, 32(suppl 1):D452\u2013455.","journal-title":"Nucl. Acids Res"},{"key":"4807_CR2","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1016\/S0014-5793(01)03293-8","volume":"513","author":"A Zanzoni","year":"2002","unstructured":"Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G: MINT: a Molecular INTeraction database. FEBS Letters 2002, 513: 135\u2013140. 10.1016\/S0014-5793(01)03293-8","journal-title":"FEBS Letters"},{"key":"4807_CR3","doi-asserted-by":"publisher","first-page":"D535","DOI":"10.1093\/nar\/gkj109","volume":"34","author":"C Stark","year":"2006","unstructured":"Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M: BioGRID: A General Repository for Interaction Datasets. Nucleic Acids Research 2006, 34: D535\u20139. 10.1093\/nar\/gkj109","journal-title":"Nucleic Acids Research"},{"issue":"13","key":"4807_CR4","doi-asserted-by":"publisher","first-page":"i41","DOI":"10.1093\/bioinformatics\/btm229","volume":"23","author":"J Baumgartner","year":"2007","unstructured":"Baumgartner J, William A, Cohen KB, Fox LM, Acquaah-Mensah G, Hunter L: Manual curation is not sufficient for annotation of genomic databases. Bioinformatics 2007, 23(13):i41\u201348. 10.1093\/bioinformatics\/btm229","journal-title":"Bioinformatics"},{"key":"4807_CR5","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1186\/1471-2105-9-78","volume":"9","author":"L Hunter","year":"2008","unstructured":"Hunter L, Lu Z, Firby J, Baumgartner W, Johnson H, Ogren P, Cohen KB: OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. BMC Bioinformatics 2008, 9: 78. 10.1186\/1471-2105-9-78","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 2","key":"4807_CR6","doi-asserted-by":"publisher","first-page":"S10","DOI":"10.1186\/gb-2008-9-s2-s10","volume":"9","author":"B Alex","year":"2008","unstructured":"Alex B, Grover C, Haddow B, Kabadjov M, Klein E, Matthews M, Tobin R, Wang X: Automating Curation Using a Natural Language Processing Pipeline. Genome Biology 2008, 9(Suppl 2):S10. 10.1186\/gb-2008-9-s2-s10","journal-title":"Genome Biology"},{"key":"4807_CR7","volume-title":"BMC Bioinformatics, special issue on BioCreative III","author":"C Arighi","year":"2011","unstructured":"Arighi C, Roberts P, Agarwal S, Bhattacharya S, Cesareni G, Chatr-aryamontri A, Clematide S, Gaudet P, Giglio MG, Harrow I, Huala E, Krallinger M, Leser U, Li D, Liu F, Lu Z, Maltais L, Okazaki N, Perfetto L, Rinaldi F, Saetre R, Salgado D, Srinivasan P, Thomas PE, Toldo L, Hirschman L, Wu CH: BioCreative III Interactive Task: an Overview. BMC Bioinformatics, special issue on BioCreative III 2011. under review under review"},{"issue":"Suppl 2","key":"4807_CR8","doi-asserted-by":"publisher","first-page":"S13","DOI":"10.1186\/gb-2008-9-s2-s13","volume":"9","author":"F Rinaldi","year":"2008","unstructured":"Rinaldi F, Kappeler T, Kaljurand K, Schneider G, Klenner M, Clematide S, Hess M, von Allmen JM, Parisot P, Romacker M, Vachon T: OntoGene in BioCreative II. Genome Biology 2008, 9(Suppl 2):S13. 10.1186\/gb-2008-9-s2-s13","journal-title":"Genome Biology"},{"issue":"3","key":"4807_CR9","doi-asserted-by":"publisher","first-page":"472","DOI":"10.1109\/TCBB.2010.50","volume":"7","author":"F Rinaldi","year":"2010","unstructured":"Rinaldi F, Schneider G, Kaljurand K, Clematide S, Vachon T, Romacker M: OntoGene in BioCreative II.5. IEEE\/ACM Transactions on Computational Biology and Bioinformatics 2010, 7(3):472\u2013480.","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"key":"4807_CR10","volume-title":"Third International Symposium on Semantic Mining in Biomedicine (SMBM)","author":"T Kappeler","year":"2008","unstructured":"Kappeler T, Clematide S, Kaljurand K, Schneider G, Rinaldi F: Towards Automatic Detection of Experimental Methods from Biomedical Literature. Third International Symposium on Semantic Mining in Biomedicine (SMBM) 2008."},{"key":"4807_CR11","volume-title":"Proceedings of CICLING 2009","author":"G Schneider","year":"2009","unstructured":"Schneider G, Kaljurand K, Kappeler T, Rinaldi F: Detecting protein-protein interactions in biomedical texts using a parser and linguistic resources. Proceedings of CICLING 2009 2009."},{"key":"4807_CR12","doi-asserted-by":"publisher","first-page":"D193","DOI":"10.1093\/nar\/gkl929","volume":"35","author":"UniProt Consortium","year":"2007","unstructured":"UniProt Consortium: The Universal Protein Resource (UniProt). Nucleic Acids Research 2007, 35: D193\u20137.","journal-title":"Nucleic Acids Research"},{"key":"4807_CR13","unstructured":"Entrez Gene[http:\/\/www.ncbi.nlm.nih.gov\/sites\/entrez?db=gene]"},{"key":"4807_CR14","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1038\/nbt926","volume":"22","author":"H Hermjakob","year":"2004","unstructured":"Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, R A: The HUPO PSI\u2019s molecular interaction format - a community standard for the representation of protein interaction data. Nat. Biotechnol 2004, 22: 177\u2013183. 10.1038\/nbt926","journal-title":"Nat. Biotechnol"},{"key":"4807_CR15","unstructured":"[http:\/\/clkb.ncibi.org\/]"},{"key":"4807_CR16","volume-title":"Doctoral Thesis","author":"G Schneider","year":"2008","unstructured":"Schneider G: Hybrid Long-Distance Functional Dependency Parsing. In Doctoral Thesis. Institute of Computational Linguistics, University of Zurich; 2008."},{"issue":"3","key":"4807_CR17","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1109\/TCBB.2010.61","volume":"7","author":"F Leitner","year":"2010","unstructured":"Leitner F, Mardis SA, Krallinger M, Cesareni G, Hirschman LA, Valencia A: An Overview of BioCreative II.5. IEEE\/ACM Transactions on Computational Biology and Bioinformatics 2010, 7(3):385\u2013399.","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"key":"4807_CR18","first-page":"39","volume":"22","author":"AL Berger","year":"1996","unstructured":"Berger AL, Pietra SAD, Pietra VD: A Maximum Entropy Approach to Natural Language Processing. Computational Linguistics 1996, 22: 39\u201371.","journal-title":"Computational Linguistics"},{"key":"4807_CR19","volume-title":"Notes on CG and LM-BFGS Optimization of Logistic Regression","author":"H Daum\u00e9 III","year":"2004","unstructured":"Daum\u00e9 H III: Notes on CG and LM-BFGS Optimization of Logistic Regression. 2004."},{"issue":"Suppl 1","key":"4807_CR20","doi-asserted-by":"publisher","first-page":"S14","DOI":"10.1186\/1471-2105-6-S1-S14","volume":"6","author":"D Hanisch","year":"2005","unstructured":"Hanisch D, Fundel K, Mevissen HT, Zimmer R, Fluck J: ProMiner: rule-based protein and gene entity recognition. BMC Bioinformatics 2005, 6(Suppl 1):S14. 10.1186\/1471-2105-6-S1-S14","journal-title":"BMC Bioinformatics"},{"key":"4807_CR21","first-page":"8","volume-title":"Proceedings of the second meeting of the North American Chapter of the Association for Computational Linguistics on Language technologies (NAACL01)","author":"T Pedersen","year":"2001","unstructured":"Pedersen T: A Decision Tree of Bigrams is an Accurate Predictor of Word Sense. Proceedings of the second meeting of the North American Chapter of the Association for Computational Linguistics on Language technologies (NAACL01) 2001, 8. [http:\/\/arxiv.org\/abs\/cs\/0103026]"},{"key":"4807_CR22","volume-title":"Corpus Linguistics. An International Handbook, article 58","author":"S Evert","year":"2008","unstructured":"Evert S: Corpora and collocations. In Corpus Linguistics. An International Handbook, article 58. Edited by: L\u00fcdeling A, Kyt\u00f6 M. Berlin; 2008."},{"issue":"5","key":"4807_CR23","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1093\/bioinformatics\/16.5.412","volume":"16","author":"P Baldi","year":"2000","unstructured":"Baldi P, Brunak S, Chauvin Y, Andersen CAF, Nielsen H: Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 2000, 16(5):412\u2013424. 10.1093\/bioinformatics\/16.5.412","journal-title":"Bioinformatics"},{"issue":"7-8","key":"4807_CR24","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1162\/153244303322753670","volume":"3","author":"G Forman","year":"2003","unstructured":"Forman G: An Extensive Empirical Study of Feature Selection Metrics for Text Classification. Journal of Machine Learning Research 2003, 3(7\u20138):1289\u20131305. 10.1162\/153244303322753670","journal-title":"Journal of Machine Learning Research"},{"issue":"3","key":"4807_CR25","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1109\/TCBB.2010.49","volume":"7","author":"M Lan","year":"2010","unstructured":"Lan M, Su J: Empirical investigations into full-text protein interaction Article Categorization Task (ACT) in the BioCreative II.5 Challenge. IEEEACM transactions on computational biology and bioinformatics IEEE ACM 2010, 7(3):421\u2013427. [http:\/\/www.computer.org\/portal\/web\/csdl\/doi\/10.1109\/TCBB.2010.49]","journal-title":"IEEEACM transactions on computational biology and bioinformatics IEEE ACM"},{"issue":"20","key":"4807_CR26","doi-asserted-by":"publisher","first-page":"2768","DOI":"10.1093\/bioinformatics\/btm393","volume":"23","author":"Y Tsuruoka","year":"2007","unstructured":"Tsuruoka Y, McNaught J, Tsujii J, Ananiadou S: Learning string similarity measures for gene\/protein name dictionary look-up using logistic regression. Bioinformatics 2007, 23(20):2768\u20132774. 10.1093\/bioinformatics\/btm393","journal-title":"Bioinformatics"},{"issue":"6","key":"4807_CR27","doi-asserted-by":"publisher","first-page":"815","DOI":"10.1093\/bioinformatics\/btp071","volume":"25","author":"J Wermter","year":"2009","unstructured":"Wermter J, Tomanek K, Hahn U: High-performance gene name normalization with GENO. Bioinformatics 2009, 25(6):815\u2013821. 10.1093\/bioinformatics\/btp071","journal-title":"Bioinformatics"},{"issue":"2","key":"4807_CR28","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1093\/bioinformatics\/btq620","volume":"27","author":"QC Bui","year":"2010","unstructured":"Bui QC, Katrenko S, Sloot PMA: A hybrid approach to extract protein-protein interactions. Bioinformatics 2010, 27(2):259\u2013265.","journal-title":"Bioinformatics"},{"issue":"3","key":"4807_CR29","doi-asserted-by":"publisher","first-page":"394","DOI":"10.1093\/bioinformatics\/btn631","volume":"25","author":"Y Miyao","year":"2009","unstructured":"Miyao Y, Sagae K, Saetre R, Matsuzaki T, Tsujii J: Evaluating contributions of natural language parsers to protein-protein interaction extraction. Bioinformatics 2009, 25(3):394\u2013400. 10.1093\/bioinformatics\/btn631","journal-title":"Bioinformatics"},{"issue":"5","key":"4807_CR30","doi-asserted-by":"publisher","first-page":"866","DOI":"10.1016\/j.jbi.2009.07.004","volume":"42","author":"M Lan","year":"2009","unstructured":"Lan M, Tan CL, Su J: Feature generation and representations for protein-protein interaction classification. Journal of Biomedical Informatics 2009, 42(5):866\u2013872. 10.1016\/j.jbi.2009.07.004","journal-title":"Journal of Biomedical Informatics"},{"key":"4807_CR31","first-page":"83","volume-title":"Third BioCreative Challenge Workshop","author":"S Kim","year":"2010","unstructured":"Kim S, Wilbur WJ: Improving Protein-Protein Interaction Article Classification Performance by Utilizing Grammatical Relations. Third BioCreative Challenge Workshop 2010, 83\u201388."},{"issue":"Suppl 1","key":"4807_CR32","doi-asserted-by":"publisher","first-page":"S3","DOI":"10.1186\/1471-2105-9-S1-S3","volume":"9","author":"RTH Tsai","year":"2008","unstructured":"Tsai RTH, Hung HC, Dai HJ, Lin YW, Hsu WL: Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles. BMC Bioinformatics 2008, 9(Suppl 1):S3. 10.1186\/1471-2105-9-S1-S3","journal-title":"BMC Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-S8-S13.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T16:51:42Z","timestamp":1630515102000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-S8-S13"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,10,3]]},"references-count":32,"journal-issue":{"issue":"S8","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4807"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-s8-s13","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,10,3]]},"assertion":[{"value":"3 October 2011","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S13"}}