{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T13:33:20Z","timestamp":1768311200770,"version":"3.49.0"},"reference-count":68,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2010,7,1]],"date-time":"2010-07-01T00:00:00Z","timestamp":1277942400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000837","type":"journal-article","created":{"date-parts":[[2010,7,1]],"date-time":"2010-07-01T21:02:29Z","timestamp":1278018149000},"page":"e1000837","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":110,"title":["A Comprehensive Benchmark of Kernel Methods to Extract Protein\u2013Protein Interactions from Literature"],"prefix":"10.1371","volume":"6","author":[{"given":"Domonkos","family":"Tikk","sequence":"first","affiliation":[]},{"given":"Philippe","family":"Thomas","sequence":"additional","affiliation":[]},{"given":"Peter","family":"Palaga","sequence":"additional","affiliation":[]},{"given":"J\u00f6rg","family":"Hakenberg","sequence":"additional","affiliation":[]},{"given":"Ulf","family":"Leser","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2010,7,1]]},"reference":[{"key":"ref1","first-page":"pe21","article-title":"Text mining for metabolic pathways, signaling cascades, and protein networks.","author":"R Hoffmann","year":"2005","journal-title":"Sci STKE 2005"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2105-9-S8-S2","article-title":"Integrating protein-protein interactions and text mining for protein function prediction.","volume":"9","author":"S Jaeger","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1186\/1471-2105-9-350","article-title":"Integration of relational and hierarchical network information for protein function prediction.","volume":"9","author":"X Jiang","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"12123","DOI":"10.1073\/pnas.2032324100","article-title":"Protein complexes and functional modules in molecular networks.","volume":"100","author":"V Spirin","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1101\/gr.071852.107","article-title":"Protein networks in disease.","volume":"18","author":"T Ideker","year":"2008","journal-title":"Genome Res"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1111\/j.1365-313X.2007.03332.x","article-title":"Molecular and cellular approaches for the detection of protein-protein interactions: latest techniques and current limitations.","volume":"53","author":"S Lalonde","year":"2008","journal-title":"Plant J"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1016\/S0022-2836(03)00239-0","article-title":"How reliable are experimental protein-protein interaction data?","volume":"327","author":"E Sprinzak","year":"2003","journal-title":"J Mol Biol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1111\/j.1365-313X.2007.03316.x","article-title":"Biochemical approaches for discovering protein-protein interactions.","volume":"53","author":"JA Miernyk","year":"2008","journal-title":"Plant J"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"D572","DOI":"10.1093\/nar\/gkl950","article-title":"MINT: the Molecular INTeraction database.","volume":"35","author":"A Chatr-aryamontri","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref10","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":"R Winnenburg","year":"2008","journal-title":"Brief Bioinform"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"i277","DOI":"10.1093\/bioinformatics\/btn182","article-title":"Identifying gene-disease associations using centrality on a literature mined gene-interaction network.","volume":"24","author":"A \u00d6zg\u00fcr","year":"2008","journal-title":"Bioinformatics"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/nbt1295","article-title":"A human phenome-interactome network of protein complexes implicated in genetic disorders.","volume":"25","author":"K Lage","year":"2007","journal-title":"Nat Biotechnol"},{"key":"ref13","first-page":"279","article-title":"A pragmatic information extraction strategy for gathering data on genetic interactions.","volume":"8","author":"D Proux","year":"2000","journal-title":"Proc Int Conf Intell Syst Mol Biol"},{"key":"ref14","article-title":"Biocreative ii.5: Evaluation and ensemble system performance.","author":"F Leitner","year":"2009"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1186\/1471-2105-10-233","article-title":"A realistic assessment of methods for extracting gene\/protein interactions from free text.","volume":"10","author":"R Kabiljo","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"S11","DOI":"10.1186\/1471-2105-9-S9-S11","article-title":"Large-scale directional relationship extraction and resolution.","volume":"9","author":"C Giles","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2105-9-S11-S2","article-title":"All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning.","volume":"9","author":"A Airola","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/j.artmed.2004.07.016","article-title":"Comparative experiments on learning information extractors for proteins and their interactions.","volume":"33","author":"R Bunescu","year":"2005","journal-title":"Artif Intell Med"},{"key":"ref19","first-page":"171","article-title":"Subsequence kernels for relation extraction.","author":"R Bunescu","year":"2006"},{"key":"ref20","first-page":"625","article-title":"Convolution kernels for natural language.","author":"M Collins","year":"2001"},{"key":"ref21","first-page":"423","article-title":"Dependency tree kernels for relation extraction.","author":"A Culotta","year":"2004"},{"key":"ref22","first-page":"228","article-title":"Semi-supervised classification for extracting protein interaction sentences using dependency parsing.","author":"G Erkan","year":"2007"},{"key":"ref23","first-page":"401","article-title":"Exploiting shallow linguistic information for relation extraction from biomedical literature.","author":"C Giuliano","year":"2006"},{"key":"ref24","first-page":"417","article-title":"A local alignment kernel in the context of NLP.","author":"S Katrenko","year":"2008"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1093\/bioinformatics\/btm544","article-title":"Kernel approaches for genic interaction extraction.","volume":"24","author":"S Kim","year":"2008","journal-title":"Bioinformatics"},{"key":"ref26","first-page":"77","article-title":"Extracting protein-protein interactions from text using rich feature vectors and feature selection.","author":"S Van Landeghem","year":"2008"},{"key":"ref27","first-page":"101","article-title":"Combining multiple layers of syntactic information for protein-protein interaction extraction.","author":"M Miwa","year":"2008"},{"key":"ref28","first-page":"318","article-title":"Efficient convolution kernels for dependency and constituent syntactic trees.","author":"A Moschitti","year":"2006"},{"key":"ref29","article-title":"Extracting Relations from Biomedical Texts Using Syntactic Information.","author":"P Palaga","year":"2009"},{"key":"ref30","first-page":"569","article-title":"Fast kernels for string and tree matching.","author":"SVN Vishwanathan","year":"2002"},{"key":"ref31","first-page":"841","article-title":"A re-examination of dependency path kernels for relation extraction.","author":"M Wang","year":"2008"},{"key":"ref32","first-page":"1083","article-title":"Kernel methods for relation extraction.","volume":"3","author":"D Zelenko","year":"2003","journal-title":"J Mach Learn Res"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1093\/bioinformatics\/btp602","article-title":"Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D.","volume":"26","author":"Y Niu","year":"2010","journal-title":"Bioinformatics"},{"key":"ref34","first-page":"1","article-title":"Overview of BioNLP&apos;09 shared task on event extraction.","author":"JD Kim","year":"2009"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/1471-2105-8-24","article-title":"Benchmarking natural-language parsers for biological applications using dependency graphs.","volume":"8","author":"AB Clegg","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"S6","DOI":"10.1186\/1471-2105-9-S3-S6","article-title":"Comparative analysis of five protein-protein interaction corpora.","volume":"9","author":"S Pyysalo","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1093\/bioinformatics\/btn631","article-title":"Evaluating contributions of natural language parsers to protein-protein interaction extraction.","volume":"25","author":"Y Miyao","year":"2009","journal-title":"Bioinformatics"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1186\/1471-2105-10-374","article-title":"Linguistic feature analysis for protein interaction extraction.","volume":"10","author":"T Fayruzov","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1016\/j.jbi.2007.11.008","article-title":"Extracting interactions between proteins from the literature.","volume":"41","author":"D Zhou","year":"2008","journal-title":"J Biomed Inform"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"S13","DOI":"10.1186\/gb-2008-9-s2-s13","article-title":"OntoGene in BioCreative II.","volume":"9","author":"F Rinaldi","year":"2008","journal-title":"Genome Biol"},{"key":"ref41","first-page":"14","article-title":"The frame-based module of the SUISEKI information extraction system.","volume":"17","author":"C Blaschke","year":"2002","journal-title":"IEEE Intell Syst"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1186\/1471-2105-9-78","article-title":"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.","volume":"9","author":"L Hunter","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/gb-2008-9-s2-s4","article-title":"Overview of the protein-protein interaction annotation extraction task of BioCreative II.","volume":"9","author":"M Krallinger","year":"2008","journal-title":"Genome Biol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"3294","DOI":"10.1093\/bioinformatics\/bti493","article-title":"Discovering patterns to extract protein-protein interactions from the literature: Part II.","volume":"21","author":"Y Hao","year":"2005","journal-title":"Bioinformatics"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"S14","DOI":"10.1186\/gb-2008-9-s2-s14","article-title":"Gene mention normalization and interaction extraction with context models and sentence motifs.","volume":"9","author":"J Hakenberg","year":"2008","journal-title":"Genome Biol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1536","DOI":"10.1093\/bioinformatics\/btp245","article-title":"Bayesian inference of protein-protein interactions from biological literature.","volume":"25","author":"R Chowdhary","year":"2009","journal-title":"Bioinformatics"},{"key":"ref47","first-page":"730","article-title":"Using maximum entropy model to extract protein-protein interaction information from biomedical literature.","author":"C Sun","year":"2007"},{"key":"ref48","first-page":"46","article-title":"Task-oriented evaluation of syntactic parsers and their representations.","author":"Y Miyao","year":"2008"},{"key":"ref49","first-page":"25","article-title":"On the unification of syntactic annotations under the Stanford dependency scheme: A case study on BioInfer and GENIA.","author":"S Pyysalo","year":"2007"},{"key":"ref50","article-title":"Any Domain Parsing: Automatic Domain Adaptation for Natural Language Parsing.","author":"D McClosky","year":"2009"},{"key":"ref51","first-page":"101","article-title":"Self-training for biomedical parsing.","author":"D McClosky","year":"2008"},{"key":"ref52","article-title":"Making large-scale support vector machine learning practical, Advances in kernel methods: support vector learning","author":"T Joachims","year":"1999"},{"key":"ref53","article-title":"Advances in kernel methods: support vector learning","year":"1999"},{"key":"ref54","first-page":"131","article-title":"Regularized least-squares classification.","volume":"190","author":"R Rifkin","year":"2003","journal-title":"Nato Science Series Sub Series III Computer and Systems Sciences"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/1471-2105-7-S2-S4","article-title":"Support vector machine implementations for classification &amp; clustering.","volume":"7","author":"S Winters-Hilt","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref56","article-title":"LIBSVM: a library for support vector machines.","author":"CC Chang","year":"2001"},{"key":"ref57","article-title":"Convolution kernels on discrete structures.","author":"D Haussler","year":"1999"},{"key":"ref58","first-page":"292","article-title":"A spectrum tree kernel.","volume":"2","author":"T Kuboyama","year":"2007","journal-title":"Information and Media Technologies"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1186\/1471-2105-8-50","article-title":"BioInfer: a corpus for information extraction in the biomedical domain.","volume":"8","author":"S Pyysalo","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/bioinformatics\/btl616","article-title":"RelEx \u2013 relation extraction using dependency parse trees.","volume":"23","author":"K Fundel","year":"2007","journal-title":"Bioinformatics"},{"key":"ref61","first-page":"326","article-title":"Mining Medline: abstracts, sentences, or phrases?","author":"J Ding","year":"2002","journal-title":"Pac Symp Biocomput"},{"key":"ref62","first-page":"97","article-title":"Learning language in logic-genic interaction extraction challenge.","author":"C Nedellec","year":"2005"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"e39","DOI":"10.1016\/j.ijmedinf.2009.04.010","article-title":"Protein-protein interaction extraction by leveraging multiple kernels and parsers.","volume":"18","author":"M Miwa","year":"2009","journal-title":"Int J Med Inform"},{"key":"ref64","article-title":"Syntactic features for protein-protein interaction extraction.","author":"R S\u00e6tre","year":"2007"},{"key":"ref65","first-page":"1","article-title":"The terascale challenge.","author":"D Ravichandran","year":"2004"},{"key":"ref66","first-page":"200","article-title":"Transductive inference for text classification using support vector machines.","author":"T Joachims","year":"1999"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1093\/bioinformatics\/bti597","article-title":"Extraction of regulatory gene\/protein networks from medline.","volume":"22","author":"J Saric","year":"2006","journal-title":"Bioinformatics"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"2759","DOI":"10.1093\/bioinformatics\/bti390","article-title":"Literature mining and database annotation of protein phosphorylation using a rule-based system.","volume":"21","author":"ZZ Hu","year":"2005","journal-title":"Bioinformatics"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000837","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T20:59:14Z","timestamp":1540328354000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000837"}},"subtitle":[],"editor":[{"given":"Andrey","family":"Rzhetsky","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2010,7,1]]},"references-count":68,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2010,7,1]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000837","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,7,1]]}}}