Mining protein phosphorylation information from biomedical literature using NLP parsing and Support Vector Machines
Tài liệu tham khảo
Cohen, 2012, The origins of protein phosphorylation, Nat. Cell Biol., 4, E127, 10.1038/ncb0502-e127
Pawson, 2009, Kinome signaling through regulated protein-protein interactions in normal and cancer cells, Curr. Opin. Cell Biol., 21, 147, 10.1016/j.ceb.2009.02.005
Zhang, 2012, Targeting the human kinome for cancer therapy: current perspectives, Crit. Rev. Oncog., 17, 233, 10.1615/CritRevOncog.v17.i2.70
Hu, 2005, Literature mining and database annotation of protein phosphorylation using a rule-based system, Bioinformatics, 21, 2759, 10.1093/bioinformatics/bti390
Apweiler, 2004, UniProt: universal protein knowledgebase, Nucleic Acids Res., 32, D115, 10.1093/nar/gkh131
Holger, 2010, Phospho.ELM: a database of phosphorylation sites-update 2011, Nucleic Acids Res., 39, 1
Kreegipuu, 1999, PhosphoBase, a database of phosphorylation sites: release 2.0, Nucleic Acids Res., 27, 237, 10.1093/nar/27.1.237
Hombeck, 2011, PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse, Nucleic Acids Res., 40
Yang, 2008, PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database, Bioinformatics, 24, i14, 10.1093/bioinformatics/btn297
Torii, 2015, RLIMS-P 2.0: a generalizable rule-based information extraction system for literature mining of protein phosphorylation information, IEEE/ACM Trans. Comput. Biol. Bioinform./IEEE ACM, 12, 17, 10.1109/TCBB.2014.2372765
Xu, 2012, MinePhos: a literature mining system for protein phoshphorylation information extraction, IEEE/ACM Trans. Comput. Biol. Bioinform., 9, 311, 10.1109/TCBB.2011.85
Ananiadou, 2006, Text mining and its potential applications in systems biology, Trends Biotechnol., 24, 571, 10.1016/j.tibtech.2006.10.002
Kabiljo, 2009, A realistic assessment of methods for extracting gene/protein interactions from free text, BMC Bioinform., 10, 233, 10.1186/1471-2105-10-233
Chowdhary, 2009, Bayesian inference of protein-protein interactions from biological literature, Bioinformatics, 25, 1536, 10.1093/bioinformatics/btp245
Bjome, 2010, Complex event extraction at PubMed scale, Bioinformatics, 26, i382, 10.1093/bioinformatics/btq180
Miwa, 2010, Event extraction with complex event classification using rich features, J. Bioinform. Comput. Biology., 8, 131, 10.1142/S0219720010004586
Bui, 2010, A hybrid approach to extract protein-protein interactions, Bioinformatics, 27, 259, 10.1093/bioinformatics/btq620
Klein, 2003, Accurate unlexicalized parsing, 423
Raja, 2013, PPInterFinder—a mining tool for extracting causal relations on human proteins from literature, Database: J. Biol. Databases Curation, 10.1093/database/bas052
Levy, 2006, Tregex and Tsurgeon: tools for querying and manipulating tree data structures, 2231
Dumais, 1998, Inductive learning algorithms and representations for text categorization, 148
Joachims, 1998, Text categorization with support vector machines: learning with many relevant features, 137
Hall, 2009, The Weka data mining software: an update, ACM SIGKDD Explor. Newsl., 11, 10, 10.1145/1656274.1656278
Fayruzov, 2009, Linguistic feature analysis for protein interaction extraction, BMC Bioinform., 10, 374, 10.1186/1471-2105-10-374
Manning, 2002, The protein kinase complement of the human genome, Science, 298, 1912, 10.1126/science.1075762
Milanesi, 2005, Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity, BMC Bioinformatics, 6, S20, 10.1186/1471-2105-6-S4-S20
Kim, 2009, Overview of BioNLP’09 shared task on event extraction, 1
Kim, 2011, Overview of BioNLP shared task 2011, 1
Nedellec, 2013, Overview of BioNLP shared task 2013, 1
Raja, 2013, Template filling, text mining, 2150