{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T08:57:09Z","timestamp":1715331429495},"reference-count":34,"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-s4","type":"journal-article","created":{"date-parts":[[2009,8,27]],"date-time":"2009-08-27T18:14:03Z","timestamp":1251396843000},"source":"Crossref","is-referenced-by-count":20,"title":["Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb"],"prefix":"10.1186","volume":"10","author":[{"given":"Kevin","family":"Nagel","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antonio","family":"Jimeno-Yepes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dietrich","family":"Rebholz-Schuhmann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,8,27]]},"reference":[{"issue":"13","key":"3344_CR1","doi-asserted-by":"publisher","first-page":"1644","DOI":"10.1093\/bioinformatics\/btg226","volume":"19","author":"JA Barker","year":"2003","unstructured":"Barker JA, Thornton JM: An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics 2003, 19(13):1644\u20139.","journal-title":"Bioinformatics"},{"issue":"4","key":"3344_CR2","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1002\/prot.10221","volume":"49","author":"TJ Oldfield","year":"2002","unstructured":"Oldfield TJ: Data mining the protein data bank: residue interactions. Proteins 2002, 49(4):510\u201328.","journal-title":"Proteins"},{"key":"3344_CR3","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1186\/1471-2105-8-321","volume":"8","author":"JC Nebel","year":"2007","unstructured":"Nebel JC, Herzyk P, Gilbert DR: Automatic generation of 3D motifs for classification of protein binding sites. BMC Bioinformatics 2007, 8: 321.","journal-title":"BMC Bioinformatics"},{"key":"3344_CR4","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1186\/1471-2105-9-17","volume":"9","author":"DM Kristensen","year":"2008","unstructured":"Kristensen DM, Ward RM, Lisewski AM, Erdin S, Chen BY, Fofanov VY, Kimmel M, Kavraki LE, Lichtarge O: Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BMC Bioinformatics 2008, 9: 17.","journal-title":"BMC Bioinformatics"},{"issue":"6","key":"3344_CR5","doi-asserted-by":"publisher","first-page":"723","DOI":"10.1093\/bioinformatics\/btk038","volume":"22","author":"BJ Polacco","year":"2006","unstructured":"Polacco BJ, Babbitt PC: Automated discovery of 3D motifs for protein function annotation. Bioinformatics 2006, 22(6):723\u201330.","journal-title":"Bioinformatics"},{"issue":"Suppl 4","key":"3344_CR6","doi-asserted-by":"publisher","first-page":"S10","DOI":"10.1186\/1471-2105-8-S4-S10","volume":"8","author":"S Yoon","year":"2007","unstructured":"Yoon S, Ebert JC, Chung EY, Micheli GD, Altman RB: Clustering protein environments for function prediction: finding PROSITE motifs in 3D. BMC Bioinformatics 2007, 8(Suppl 4):S10.","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"3344_CR7","doi-asserted-by":"publisher","first-page":"1307","DOI":"10.1016\/S0022-2836(03)00045-7","volume":"326","author":"A Stark","year":"2003","unstructured":"Stark A, Sunyaev S, Russell RB: A model for statistical significance of local similarities in structure. J Mol Biol 2003, 326(5):1307\u201316.","journal-title":"J Mol Biol"},{"issue":"4","key":"3344_CR8","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1093\/bioinformatics\/18.4.641","volume":"18","author":"MM Babu","year":"2002","unstructured":"Babu MM, Sankaran K: DOLOP-database of bacterial lipoproteins. Bioinformatics 2002, 18(4):641\u20133.","journal-title":"Bioinformatics"},{"key":"3344_CR9","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1093\/nar\/gkg020","volume":"31","author":"M Ikeda","year":"2003","unstructured":"Ikeda M, Arai M, Okuno T, Shimizu T: TMPDB: a database of experimentally-characterized transmembrane topologies. Nucleic Acids Res 2003, 31: 406\u20139.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"3344_CR10","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1093\/bioinformatics\/17.4.359","volume":"17","author":"EM Marcotte","year":"2001","unstructured":"Marcotte EM, Xenarios I, Eisenberg D: Mining literature for protein-protein interactions. Bioinformatics 2001, 17(4):359\u201363.","journal-title":"Bioinformatics"},{"key":"3344_CR11","first-page":"60","volume-title":"Proc Int Conf Intell Syst Mol Biol","author":"C Blaschke","year":"1999","unstructured":"Blaschke C, Andrade MA, Ouzounis C, Valencia A: Automatic extraction of biological information from scientific text: protein-protein interactions. Proc Int Conf Intell Syst Mol Biol 1999, 60\u20137."},{"key":"3344_CR12","first-page":"374","volume-title":"Pac Symp Biocomput","author":"BJ Stapley","year":"2002","unstructured":"Stapley BJ, Kelley LA, Sternberg MJE: Predicting the sub-cellular location of proteins from text using support vector machines. Pac Symp Biocomput 2002, 374\u201385."},{"issue":"Suppl 1","key":"3344_CR13","doi-asserted-by":"publisher","first-page":"S74","DOI":"10.1093\/bioinformatics\/17.suppl_1.S74","volume":"17","author":"C Friedman","year":"2001","unstructured":"Friedman C, Kra P, Yu H, Krauthammer M, Rzhetsky A: GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics 2001, 17(Suppl 1):S74\u201382.","journal-title":"Bioinformatics"},{"issue":"Suppl 1","key":"3344_CR14","doi-asserted-by":"publisher","first-page":"S16","DOI":"10.1186\/1471-2105-6-S1-S16","volume":"6","author":"C Blaschke","year":"2005","unstructured":"Blaschke C, Leon EA, Krallinger M, Valencia A: Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinformatics 2005, 6(Suppl 1):S16.","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"3344_CR15","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(2):e16.","journal-title":"PLoS Comput Biol"},{"issue":"6","key":"3344_CR16","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\u201359.","journal-title":"J Bioinform Comput Biol"},{"key":"3344_CR17","first-page":"29","volume-title":"5th CERMM Annual Symposium","author":"CJO Baker","year":"2005","unstructured":"Baker CJO, Witte R: Mutation Miner \u2013 Textual Annotation of Protein Structures. In 5th CERMM Annual Symposium. Concordia University, Montr\u00e9al, Qu\u00e9bec, Canada: Centre for Research in Molecular Modeling; 2005:29."},{"key":"3344_CR18","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. Nucleic Acids Res 2004, 32: 135\u201342.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"3344_CR19","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(4):557\u201368.","journal-title":"Bioinformatics"},{"key":"3344_CR20","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-A Prospector's Tale. Information Systems Frontiers 2006, 8: 47\u201357.","journal-title":"Information Systems Frontiers"},{"issue":"6","key":"3344_CR21","doi-asserted-by":"publisher","first-page":"1319","DOI":"10.1142\/S0219720007003119","volume":"5","author":"R Kanagasabai","year":"2007","unstructured":"Kanagasabai R, Choo K, Ranganathan S, Baker C: A workflow for mutation extraction and structure annotation. J Bioinform Comput Biol 2007, 5(6):1319\u20131337.","journal-title":"J Bioinform Comput Biol"},{"issue":"6","key":"3344_CR22","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(6):1215\u201331.","journal-title":"J Bioinform Comput Biol"},{"issue":"2","key":"3344_CR23","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1093\/bioinformatics\/btm557","volume":"24","author":"D Rebholz-Schuhmann","year":"2008","unstructured":"Rebholz-Schuhmann D, Arregui M, Gaudan S, Kirsch H, Jimeno A: Text processing through Web services: calling Whatizit. Bioinformatics 2008, 24(2):296\u20138.","journal-title":"Bioinformatics"},{"key":"3344_CR24","volume-title":"Building and evaluating resources for biomedical text mining, LREC Workshop","author":"P Pezik","year":"2008","unstructured":"Pezik P, Jimeno Yepes A, Lee V, Rebholz-Schuhmann D: Static dictionary features for term polysemy identification. Building and evaluating resources for biomedical text mining, LREC Workshop 2008."},{"key":"3344_CR25","volume-title":"BMC Bioinformatics","author":"Y Tsuruoka","year":"2008","unstructured":"Tsuruoka Y, Mcnaught J, Ananiadou S: Normalizing biomedical terms by minimizing ambiguity and variability. BMC Bioinformatics 2008., 9(Suppl 3):","edition":"9"},{"key":"3344_CR26","first-page":"D187","volume-title":"Nucleic Acids Res","author":"CH Wu","year":"2006","unstructured":"Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, Suzek B: The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 2006, (34 Database):D187\u201391."},{"key":"3344_CR27","first-page":"D13","volume-title":"Nucleic Acids Res","author":"DL Wheeler","year":"2008","unstructured":"Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Ostell J, Pruitt KD, Schuler GD, Shumway M, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2008, (36 Database):D13\u201321."},{"issue":"3","key":"3344_CR28","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/S1532-0464(03)00039-X","volume":"36","author":"G Leroy","year":"2003","unstructured":"Leroy G, Chen H, Martinez JD: A shallow parser based on closed-class words to capture relations in biomedical text. J Biomed Inform 2003, 36(3):145\u201358.","journal-title":"J Biomed Inform"},{"key":"3344_CR29","volume-title":"CIS Bericht-96-100","author":"F Guenthner","year":"1996","unstructured":"Guenthner F: Electronic Lexica and Corpora Research at CIS. CIS Bericht-96\u2013100 1996."},{"key":"3344_CR30","volume-title":"First International Joint Conference on Natural Language Processing In the IJCNLP-04 workshop on Beyond Shallow Analyses","author":"Y Tateisi","year":"2004","unstructured":"Tateisi Y, Ohta T, Tsujii J: Annotation of predicate-argument structure on molecular biology text. First International Joint Conference on Natural Language Processing In the IJCNLP-04 workshop on Beyond Shallow Analyses 2004."},{"key":"3344_CR31","doi-asserted-by":"publisher","first-page":"83","DOI":"10.3115\/1219840.1219851","volume-title":"ACL '05: Proceedings of the 43rd Annual Meeting on Association for Computational Linguistics","author":"Y Miyao","year":"2005","unstructured":"Miyao Y, Tsujii J: Probabilistic disambiguation models for wide-coverage HPSG parsing. In ACL '05: Proceedings of the 43rd Annual Meeting on Association for Computational Linguistics. Morristown, NJ, USA: Association for Computational Linguistics; 2005:83\u201390."},{"key":"3344_CR32","doi-asserted-by":"publisher","first-page":"145","DOI":"10.3115\/990820.990842","volume-title":"Proceedings of the 18th International Conference on Computational Linguistics (COLING)","author":"F Cerbah","year":"2000","unstructured":"Cerbah F: Exogenous and endogenous approaches to semantic categorization of unknown technical terms. Proceedings of the 18th International Conference on Computational Linguistics (COLING) 2000, 145\u2013151."},{"key":"3344_CR33","doi-asserted-by":"publisher","first-page":"15","DOI":"10.3115\/977035.977039","volume-title":"Proceedings of the ninth conference on European chapter of the Association for Computational Linguistics","author":"D Bourigault","year":"1999","unstructured":"Bourigault D, Jacquemin C: Term extraction + term clustering: an integrated platform for computer-aided terminology. In Proceedings of the ninth conference on European chapter of the Association for Computational Linguistics. Morristown, NJ, USA: Association for Computational Linguistics; 1999:15\u201322."},{"key":"3344_CR34","volume-title":"EURASIP journal on bioinformatics & systems biology","author":"S Gaudan","year":"2008","unstructured":"Gaudan S, Jimeno Yepes A, Lee V, Rebholz-Schuhmann D: Combining Evidence, Specificity, and Proximity towards the Normalization of Gene Ontology Terms in Text. EURASIP journal on bioinformatics & systems biology 2008."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-S8-S4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-10-S8-S4\/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-S4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T07:37:34Z","timestamp":1548229054000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-S8-S4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,8]]},"references-count":34,"journal-issue":{"issue":"S8","published-print":{"date-parts":[[2009,8]]}},"alternative-id":["3344"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-s8-s4","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,8]]},"article-number":"S4"}}