{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T13:07:34Z","timestamp":1761743254717,"version":"3.37.0"},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"S8","license":[{"start":{"date-parts":[[2009,8,1]],"date-time":"2009-08-01T00:00:00Z","timestamp":1249084800000},"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":[[2009,8]]},"DOI":"10.1186\/1471-2105-10-s8-s1","type":"journal-article","created":{"date-parts":[[2009,8,27]],"date-time":"2009-08-27T18:14:41Z","timestamp":1251396881000},"source":"Crossref","is-referenced-by-count":27,"title":["Extraction of human kinase mutations from literature, databases and genotyping studies"],"prefix":"10.1186","volume":"10","author":[{"given":"Martin","family":"Krallinger","sequence":"first","affiliation":[]},{"given":"Jose MG","family":"Izarzugaza","sequence":"additional","affiliation":[]},{"given":"Carlos","family":"Rodriguez-Penagos","sequence":"additional","affiliation":[]},{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,8,27]]},"reference":[{"key":"3341_CR1","doi-asserted-by":"publisher","first-page":"1912","DOI":"10.1126\/science.1075762","volume":"298","author":"G Manning","year":"2002","unstructured":"Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S: The Protein Kinase Complement of the Human Genome. Science 2002, 298: 1912\u20131934.","journal-title":"Science"},{"key":"3341_CR2","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1038\/nature02062","volume":"425","author":"JA Ubersax","year":"2003","unstructured":"Ubersax JA, Woodbury EL, Quang PN, Paraz M, Blethrow JD, Shah K, Shokat KM, Morgan DO: Targets of the Cyclin-dependent Kinase Cdk1. Nature 2003, 425: 859\u2013864.","journal-title":"Nature"},{"key":"3341_CR3","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1038\/nature04187","volume":"438","author":"J Ptacek","year":"2005","unstructured":"Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee SJ, Mah AS, Meng L, Stark MJR, Stern DF, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki PF, Snyder M: Global Analysis of Protein Phosphorylation in Yeast. Nature 2005, 438: 679\u2013684.","journal-title":"Nature"},{"issue":"3","key":"3341_CR4","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1016\/S0092-8674(02)00741-9","volume":"109","author":"M Huse","year":"2002","unstructured":"Huse M, Kuriyan J: The conformational plasticity of protein kinases. Cell 2002, 109(3):275\u201382.","journal-title":"Cell"},{"issue":"5","key":"3341_CR5","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1080\/08977190802312844","volume":"26","author":"AW Burgess","year":"2008","unstructured":"Burgess AW: EGFR family: structure physiology signalling and therapeutic targets. Growth Factors 2008, 26(5):263\u201374.","journal-title":"Growth Factors"},{"key":"3341_CR6","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1007\/978-0-387-78885-2_3","volume":"631","author":"S Yamada","year":"2008","unstructured":"Yamada S, Shiro Y: Structural basis of the signal transduction in the two-component system. Adv Exp Med Biol 2008, 631: 22\u201339.","journal-title":"Adv Exp Med Biol"},{"issue":"5","key":"3341_CR7","doi-asserted-by":"publisher","first-page":"478","DOI":"10.2174\/138920308785915254","volume":"9","author":"P Sanz","year":"2008","unstructured":"Sanz P: AMP-activated protein kinase: structure and regulation. Curr Protein Pept Sci 2008, 9(5):478\u201392.","journal-title":"Curr Protein Pept Sci"},{"issue":"5","key":"3341_CR8","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1002\/humu.20166","volume":"25","author":"C Ortutay","year":"2005","unstructured":"Ortutay C, V\u00e4liaho J, Stenberg K, Vihinen M: KinMutBase: a registry of disease-causing mutations in protein kinase domains. Hum Mutat 2005, 25(5):435\u201342.","journal-title":"Hum Mutat"},{"key":"3341_CR9","doi-asserted-by":"publisher","first-page":"D824","DOI":"10.1093\/nar\/gkn832","volume":"37","author":"CJ Richardson","year":"2009","unstructured":"Richardson CJ, Gao Q, Mitsopoulous C, Zvelebil M, Pearl LH, Pearl FMG: MoKCa Database-mutations of Kinases in Cancer. Nucleic Acids Res 2009, 37: D824-D831.","journal-title":"Nucleic Acids Res"},{"key":"3341_CR10","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res 2000, 28: 235\u201342.","journal-title":"Nucleic Acids Res"},{"key":"3341_CR11","first-page":"D281","volume-title":"Nucleic Acids Res","author":"RD Finn","year":"2008","unstructured":"Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer ELL, Bateman A: The Pfam protein families database. Nucleic Acids Res 2008, (36 Database):D281\u20138."},{"key":"3341_CR12","first-page":"D291","volume-title":"Nucleic Acids Res","author":"LH Greene","year":"2007","unstructured":"Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, Orengo CA: The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res 2007, (35 Database):D291\u20137."},{"issue":"3","key":"3341_CR13","doi-asserted-by":"crossref","first-page":"81","DOI":"10.14712\/fb2006052030081","volume":"52","author":"I Shchemelinin","year":"2006","unstructured":"Shchemelinin I, Sefc L, Necas E: Protein kinases, their function and implication in cancer and other diseases. Folia Biol (Praha) 2006, 52(3):81\u2013100.","journal-title":"Folia Biol (Praha)"},{"issue":"5853","key":"3341_CR14","doi-asserted-by":"publisher","first-page":"1108","DOI":"10.1126\/science.1145720","volume":"318","author":"LD Wood","year":"2007","unstructured":"Wood LD, Parsons DW, Jones S, Lin J, Sj\u00f6blom T, Leary RJ, Shen D, Boca SM, Barber TD, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JKV, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PVK, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B: The genomic landscapes of human breast and colorectal cancers. Science 2007, 318(5853):1108\u201313.","journal-title":"Science"},{"issue":"5797","key":"3341_CR15","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1126\/science.1133427","volume":"314","author":"T Sj\u00f6blom","year":"2006","unstructured":"Sj\u00f6blom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz SD, Willis J, Dawson D, Willson JKV, Gazdar AF, Hartigan J, Wu L, Liu C, Parmigiani G, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE: The consensus coding sequences of human breast and colorectal cancers. Science 2006, 314(5797):268\u201374.","journal-title":"Science"},{"issue":"7132","key":"3341_CR16","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1038\/nature05610","volume":"446","author":"C Greenman","year":"2007","unstructured":"Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C, Edkins S, O'Meara S, Vastrik I, Schmidt EE, Avis T, Barthorpe S, Bhamra G, Buck G, Choudhury B, Clements J, Cole J, Dicks E, Forbes S, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jenkinson A, Jones D, Menzies A, Mironenko T, Perry J, Raine K, Richardson D, Shepherd R, Small A, Tofts C, Varian J, Webb T, West S, Widaa S, Yates A, Cahill DP, Louis DN, Goldstraw P, Nicholson AG, Brasseur F, Looijenga L, Weber BL, Chiew YE, DeFazio A, Greaves MF, Green AR, Campbell P, Birney E, Easton DF, Chenevix-Trench G, Tan MH, Khoo SK, Teh BT, Yuen ST, Leung SY, Wooster R, Futreal PA, Stratton MR: Patterns of somatic mutation in human cancer genomes. Nature 2007, 446(7132):153\u20138.","journal-title":"Nature"},{"key":"3341_CR17","volume-title":"EMBO Rep","author":"A Baudot","year":"2009","unstructured":"Baudot A, Real F, Izarzugaza J, Valencia A: From cancer genomes to cancer models: bridging the gaps. EMBO Rep 2009."},{"issue":"7155","key":"3341_CR18","doi-asserted-by":"publisher","first-page":"811","DOI":"10.1038\/nature06046","volume":"448","author":"D Santamar\u00eda","year":"2007","unstructured":"Santamar\u00eda D, Barri\u00e8re C, Cerqueira A, Hunt S, Tardy C, Newton K, C\u00e1ceres JF, Dubus P, Malumbres M, Barbacid M: Cdk1 is sufficient to drive the mammalian cell cycle. Nature 2007, 448(7155):811\u20135.","journal-title":"Nature"},{"key":"3341_CR19","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1093\/nar\/gkh162","volume":"32","author":"D Rebholz-Schuhmann","year":"2004","unstructured":"Rebholz-Schuhmann D, Marcel S, Albert S, Tolle R, Casari G, Kirsch H: Automatic extraction of mutations from Medline and cross-validation with OMIM. Nucl Acids Res 2004, 32: 135\u2013142.","journal-title":"Nucl Acids Res"},{"key":"3341_CR20","doi-asserted-by":"publisher","first-page":"e16","DOI":"10.1371\/journal.pcbi.0030016","volume":"3","author":"LC Lee","year":"2007","unstructured":"Lee LC, Horn F, Cohen FE: Automatic Extraction of Protein Point Mutations Using a Graph Bigram Association. PLoS Comput Biol 2007, 3: e16-e16.","journal-title":"PLoS Comput Biol"},{"key":"3341_CR21","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1007\/s10796-006-6103-2","volume":"8","author":"CJO Baker","year":"2006","unstructured":"Baker CJO, Witte R: Mutation Mining \u2013 A Prospector's Tale. Information Systems Frontiers (ISF) 2006, 8: 47\u201357.","journal-title":"Information Systems Frontiers (ISF)"},{"issue":"6","key":"3341_CR22","doi-asserted-by":"publisher","first-page":"1339","DOI":"10.1142\/S0219720007003193","volume":"5","author":"R Witte","year":"2007","unstructured":"Witte R, Baker CJO: Towards A Systematic Evaluation of Protein Mutation Extraction Systems. J Bioinform Comput Biol 2007, 5(6):1339\u20131359.","journal-title":"J Bioinform Comput Biol"},{"key":"3341_CR23","doi-asserted-by":"publisher","first-page":"1862","DOI":"10.1093\/bioinformatics\/btm235","volume":"23","author":"JG Caporaso","year":"2007","unstructured":"Caporaso JG, Baumgartner WA, Randolph DA, Cohen KB, Hunter L: MutationFinder: a High-performance System for Extracting Point Mutation Mentions from text. Bioinformatics 2007, 23: 1862\u20131865.","journal-title":"Bioinformatics"},{"key":"3341_CR24","doi-asserted-by":"publisher","first-page":"1261","DOI":"10.1142\/S021972000700317X","volume":"5","author":"M Erdogmus","year":"2007","unstructured":"Erdogmus M, Sezerman OU: Application of Automatic Mutation-gene pair Extraction to Diseases. J Bioinform Comput Biol 2007, 5: 1261\u20131275.","journal-title":"J Bioinform Comput Biol"},{"key":"3341_CR25","doi-asserted-by":"publisher","first-page":"957","DOI":"10.1002\/humu.20363","volume":"27","author":"R McDonald","year":"2006","unstructured":"McDonald R, Scott Winters R, Ankuda CK, Murphy JA, Rogers AE, Pereira F, Greenblatt MS, White PS: An Automated Procedure to Identify Biomedical Articles that Contain Cancer-associated gene Variants. Hum Mutat 2006, 27: 957\u2013964.","journal-title":"Hum Mutat"},{"key":"3341_CR26","doi-asserted-by":"publisher","first-page":"3249","DOI":"10.1093\/bioinformatics\/bth350","volume":"20","author":"RT McDonald","year":"2004","unstructured":"McDonald RT, Winters RS, Mandel M, Jin Y, White PS, Pereira F: An Entity Tagger for Recognizing Acquired Genomic Variations in Cancer Literature. Bioinformatics 2004, 20: 3249\u20133251.","journal-title":"Bioinformatics"},{"key":"3341_CR27","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1093\/bioinformatics\/btg449","volume":"20","author":"F Horn","year":"2004","unstructured":"Horn F, Lau AL, Cohen FE: Automated Extraction of Mutation data from the Literature: Application of MuteXt to G Protein-coupled Receptors and Nuclear Hormone Receptors. Bioinformatics 2004, 20: 557\u2013568.","journal-title":"Bioinformatics"},{"key":"3341_CR28","doi-asserted-by":"publisher","first-page":"1215","DOI":"10.1142\/S021972000700320X","volume":"5","author":"YL Yip","year":"2007","unstructured":"Yip YL, Lachenal N, Pillet V, Veuthey AL: Retrieving Mutation-specific Information for Human Proteins in UniProt\/Swiss-Prot Knowledgebase. J Bioinform Comput Biol 2007, 5: 1215\u20131231.","journal-title":"J Bioinform Comput Biol"},{"key":"3341_CR29","doi-asserted-by":"publisher","first-page":"1319","DOI":"10.1142\/S0219720007003119","volume":"5","author":"R Kanagasabai","year":"2007","unstructured":"Kanagasabai R, Choo KH, Ranganathan S, Baker CJO: A Workflow for Mutation Extraction and Structure Annotation. J Bioinform Comput Biol 2007, 5: 1319\u20131337.","journal-title":"J Bioinform Comput Biol"},{"key":"3341_CR30","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1002\/humu.20671","volume":"29","author":"YL Yip","year":"2008","unstructured":"Yip YL, Famiglietti M, Gos A, Duek PD, David FPA, Gateau A, Bairoch A: Annotating Single Amino acid Polymorphisms in the UniProt\/Swiss-Prot Knowledgebase. Hum Mutat 2008, 29: 361\u2013366.","journal-title":"Hum Mutat"},{"issue":"5","key":"3341_CR31","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1002\/humu.20021","volume":"23","author":"YL Yip","year":"2004","unstructured":"Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E, Bairoch A: The Swiss-Prot variant page and the ModSNP database: A resource for sequence and structure information on human protein variants. Human Mutation 2004, 23(5):464\u2013470.","journal-title":"Human Mutation"},{"issue":"2","key":"3341_CR32","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/sj.bjc.6601894","volume":"91","author":"S Bamford","year":"2004","unstructured":"Bamford S, Dawson E, Forbes S, Clements J, Pettett R, Dogan A, Flanagan A, Teague J, Futreal PA, Stratton MR, Wooster R: The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer 2004, 91(2):355\u20138.","journal-title":"Br J Cancer"},{"key":"3341_CR33","volume-title":"Hum Mutat","author":"J Hurst","year":"2009","unstructured":"Hurst J, McMillan L, Porter C, Allen J, Fakorede A, Martin A: The SAAPdb web resource: A large-scale structural analysis of mutant proteins. Hum Mutat 2009."},{"key":"3341_CR34","doi-asserted-by":"publisher","first-page":"1233","DOI":"10.1142\/S0219720007003144","volume":"5","author":"JG Caporaso","year":"2007","unstructured":"Caporaso JG, Baumgartner WA, Randolph DA, Cohen KB, Hunter L: Rapid Pattern Development for Concept Recognition Systems: Application to Point Mutations. J Bioinform Comput Biol 2007, 5: 1233\u20131259.","journal-title":"J Bioinform Comput Biol"},{"issue":"Suppl 2","key":"3341_CR35","doi-asserted-by":"publisher","first-page":"S3","DOI":"10.1186\/gb-2008-9-s2-s3","volume":"9","author":"AA Morgan","year":"2008","unstructured":"Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, Divoli A, Fundel K, Leaman R, Hakenberg J, Sun C, Liu Hh, Torres R, Krauthammer M, Lau WW, Liu H, Hsu CN, Schuemie M, Cohen KB, Hirschman L: Overview of BioCreative II gene Normalization. Genome Biol 2008, 9(Suppl 2):S3-S3.","journal-title":"Genome Biol"},{"issue":"5","key":"3341_CR36","doi-asserted-by":"publisher","first-page":"1647","DOI":"10.1158\/1078-0432.CCR-05-1981","volume":"12","author":"IYS Tam","year":"2006","unstructured":"Tam IYS, Chung LP, Suen WS, Wang E, Wong MCM, Ho KK, Lam WK, Chiu SW, Girard L, Minna JD, Gazdar AF, Wong MP: Distinct epidermal growth factor receptor and KRAS mutation patterns in non-small cell lung cancer patients with different tobacco exposure and clinicopathologic features. Clin Cancer Res 2006, 12(5):1647\u201353.","journal-title":"Clin Cancer Res"},{"issue":"17","key":"3341_CR37","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Sch\u00e4ffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389\u2013402.","journal-title":"Nucleic Acids Res"},{"key":"3341_CR38","volume-title":"Curr Protoc Hum Genet","author":"JT den Dunnen","year":"2003","unstructured":"den Dunnen JT, Antonarakis SE: Mutation Nomenclature. Curr Protoc Hum Genet 2003., Chapter 7(Unit 7.13):"},{"key":"3341_CR39","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1145\/318723.318728","volume-title":"Proceedings of SIGDOC-86: 5th International Conference on Systems Documentation","author":"M Lesk","year":"1986","unstructured":"Lesk M: Automatic sense disambiguation using machine readable dictionaries: How to tell a pine cone from an ice cream cone. Proceedings of SIGDOC-86: 5th International Conference on Systems Documentation 1986, 24\u201326."},{"key":"3341_CR40","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4615-0907-3","volume-title":"Learning to Classify Text using Support Vector Machines","author":"T Joachims","year":"2002","unstructured":"Joachims T:Learning to Classify Text using Support Vector Machines. Kluwer; 2002. [ http:\/\/www.cs.cornell.edu\/People\/tj\/ ]"},{"key":"3341_CR41","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1002\/humu.20629","volume":"29","author":"RE Saunders","year":"2008","unstructured":"Saunders RE, Perkins SJ: CoagMDB: a Database Analysis of Missense Mutations Within four Conserved Domains in five Vitamin K-dependent Coagulation Serine Proteases Using a Text-mining tool. Hum Mutat 2008, 29: 333\u2013344.","journal-title":"Hum Mutat"},{"key":"3341_CR42","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1186\/1471-2105-9-84","volume":"9","author":"LI Furlong","year":"2008","unstructured":"Furlong LI, Dach H, Hofmann-Apitius M, Sanz F: OSIRISv1.2: a Named Entity Recognition System for Sequence Variants of Genes in Biomedical Literature. BMC Bioinformatics 2008, 9: 84\u201384.","journal-title":"BMC Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-S8-S1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-10-S8-S1\/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-S8-S1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,11]],"date-time":"2025-02-11T22:02:25Z","timestamp":1739311345000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-S8-S1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,8]]},"references-count":42,"journal-issue":{"issue":"S8","published-print":{"date-parts":[[2009,8]]}},"alternative-id":["3341"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-s8-s1","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2009,8]]},"article-number":"S1"}}