TY - STD TI - OMIM . [http://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM] UR - http://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM ID - ref1 ER - TY - STD TI - BioCreAtIvE . [http://biocreative.sourceforge.net] UR - http://biocreative.sourceforge.net ID - ref2 ER - TY - STD TI - Gene Ontology . [http://www.geneontology.org] UR - http://www.geneontology.org ID - ref3 ER - TY - CHAP AU - Kim, J. AU - Ohta, T. AU - Tsuruoka, Y. AU - Tateisi, Y. AU - Collier, N. PY - 2004 DA - 2004// TI - Introduction to the bio-entity recognition task at JNLPBA BT - Proceedings of the Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA-2004) UR - https://doi.org/10.3115/1567594.1567610 DO - 10.3115/1567594.1567610 ID - Kim2004 ER - TY - JOUR AU - Kim, J. PY - 2003 DA - 2003// TI - GENIA corpus–semantically annotated corpus for bio-textmining JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg1023 DO - 10.1093/bioinformatics/btg1023 ID - Kim2003 ER - TY - CHAP AU - Wilbur, W. J. AU - Hazard, G. F. AU - Divita, G. AU - Mork, J. G. AU - Aronson, A. R. AU - Browne, A. C. PY - 1999 DA - 1999// TI - Analysis of biomedical text for chemical names: a comparison of three methods BT - Proc AMIA Symp ID - Wilbur1999 ER - TY - CHAP AU - Corbett, P. AU - Batchelor, C. AU - Teufel, S. PY - 2007 DA - 2007// TI - Annotation of Chemical Named Entities BT - Biological, translational, and clinical language processing ID - Corbett2007 ER - TY - STD TI - PubChem . [http://pubchem.ncbi.nlm.nih.gov] UR - http://pubchem.ncbi.nlm.nih.gov ID - ref8 ER - TY - STD TI - ChEBI . [http://www.ebi.ac.uk/chebi] UR - http://www.ebi.ac.uk/chebi ID - ref9 ER - TY - JOUR AU - Settles, B. PY - 2005 DA - 2005// TI - ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti475 DO - 10.1093/bioinformatics/bti475 ID - Settles2005 ER - TY - STD TI - LingPipe . [http://www.alias-i.com/lingpipe] UR - http://www.alias-i.com/lingpipe ID - ref11 ER - TY - STD TI - Hersh W, Cohen A, Roberts P, Rekapalli H: TREC 2006 genomics track overview.the Fifteenth Text Retrieval Conference ID - ref12 ER - TY - CHAP AU - Aronson, A. R. PY - 2001 DA - 2001// TI - Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program BT - Proc AMIA Symp ID - Aronson2001 ER - TY - JOUR AU - Rebholz-Schuhmann, D. AU - Arregui, M. AU - Gaudan, S. AU - Kirsch, H. AU - Jimeno, A. PY - 2008 DA - 2008// TI - Text processing through Web services: Calling Whatizit JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btm557 DO - 10.1093/bioinformatics/btm557 ID - Rebholz-Schuhmann2008 ER - TY - CHAP AU - Craven, M. AU - Kumlien, J. PY - 1999 DA - 1999// TI - Constructing Biological Knowledge Bases by Extracting Information from Text Sources BT - Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology ID - Craven1999 ER - TY - CHAP AU - Ray, S. AU - Craven, M. PY - 2001 DA - 2001// TI - Representing Sentence Structure in Hidden Markov Models for Information Extraction BT - Proceedings of the Seventeenth International Joint Conference on Artificial Intelligence PB - Morgan Kaufmann CY - Seattle, WA ID - Ray2001 ER - TY - JOUR AU - Krallinger, M. AU - Malik, R. AU - Valencia, A. PY - 2006 DA - 2006// TI - Text mining and protein annotations: the construction and use of protein description sentences JO - Genome Inform VL - 17 ID - Krallinger2006 ER - TY - CHAP AU - Chun, H. W. AU - Tsuruoka, Y. AU - Kim, J. D. AU - Shiba, R. AU - Nagata, N. AU - Hishiki, T. AU - Tsujii, J. PY - 2006 DA - 2006// TI - Extraction of gene-disease relations from Medline using domain dictionaries and machine learning BT - Pac Symp Biocomput ID - Chun2006 ER - TY - STD TI - NLM MeSH . [http://www.nlm.nih.gov/mesh] UR - http://www.nlm.nih.gov/mesh ID - ref19 ER - TY - STD TI - NCI . [http://www.nci.nih.gov/cancerinfo/terminologyresources] UR - http://www.nci.nih.gov/cancerinfo/terminologyresources ID - ref20 ER - TY - STD TI - IHTSDO . [http://www.ihtsdo.org] UR - http://www.ihtsdo.org ID - ref21 ER - TY - STD TI - NLM Unified Medical Language System . [http://www.nlm.nih.gov/pubs/factsheets/umls.html] UR - http://www.nlm.nih.gov/pubs/factsheets/umls.html ID - ref22 ER - TY - JOUR AU - Tsai, R. T. H. AU - Wu, S. H. AU - Chou, W. C. AU - Lin, Y. C. AU - He, D. AU - Hsiang, J. AU - Sung, T. Y. AU - Hsu, W. L. PY - 2006 DA - 2006// TI - Various criteria in the evaluation of biomedical named entity recognition JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-92 DO - 10.1186/1471-2105-7-92 ID - Tsai2006 ER - TY - CHAP AU - Buyko, E. AU - Tomanek, K. AU - Hahn, U. PY - 2007 DA - 2007// TI - Resolution of Coordination Ellipses in Complex Biological Named Entity Mentions Using Conditional Random Fields BT - ISMB BioLink SIG ID - Buyko2007 ER - TY - JOUR AU - Chen, L. AU - Liu, H. AU - Friedman, C. PY - 2005 DA - 2005// TI - Gene name ambiguity of eukaryotic nomenclatures JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bth496 DO - 10.1093/bioinformatics/bth496 ID - Chen2005 ER - TY - JOUR AU - Gaudan, S. AU - Kirsch, H. AU - Rebholz-Schuhmann, D. PY - 2005 DA - 2005// TI - Resolving abbreviations to their senses in Medline JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti586 DO - 10.1093/bioinformatics/bti586 ID - Gaudan2005 ER - TY - STD TI - Index . [ftp://ftp.ebi.ac.uk/pub/software/textmining/corpora/diseases] UR - ftp://ftp.ebi.ac.uk/pub/software/textmining/corpora/diseases ID - ref27 ER - TY - BOOK AU - Jacquemin, C. PY - 2001 DA - 2001// TI - Spotting and Discovering Terms Through Natural Language Processing ID - Jacquemin2001 ER - TY - JOUR AU - Hirschman, L. AU - Colosimo, M. AU - Morgan, A. AU - Yeh, A. PY - 2005 DA - 2005// TI - Overview of BioCreAtIvE task 1B: normalized gene lists JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-S1-S11 DO - 10.1186/1471-2105-6-S1-S11 ID - Hirschman2005 ER - TY - STD TI - SPECIALIST NLP Tools . [http://lexsrv3.nlm.nih.gov/SPECIALIST/index.html] UR - http://lexsrv3.nlm.nih.gov/SPECIALIST/index.html ID - ref30 ER - TY - CHAP AU - Bodenreider, O. PY - 2006 DA - 2006// TI - Lexical, Terminological, and Ontological Resources for Biological Text Mining BT - Text Mining for Biology and Biomedicine PB - Artech House CY - Boston ID - Bodenreider2006 ER - TY - STD TI - TKBG . [http://krono.act.uji.es/publications/techrep/tkbg-ebi-report] UR - http://krono.act.uji.es/publications/techrep/tkbg-ebi-report ID - ref32 ER - TY - STD TI - Filtering the UMLS Metathesaurus for MetaMap . [http://skr.nlm.nih.gov/papers/references/filtering06.pdf] UR - http://skr.nlm.nih.gov/papers/references/filtering06.pdf ID - ref33 ER - TY - STD TI - Ambiguity in the UMLS Metathesaurus . [http://skr.nlm.nih.gov/papers/references/ambiguity06.pdf] UR - http://skr.nlm.nih.gov/papers/references/ambiguity06.pdf ID - ref34 ER - TY - CHAP AU - Rebholz-Schuhmann, D. AU - Kirsch, H. AU - Gaudan, S. AU - Arregui, M. AU - Nenadic, G. PY - 2006 DA - 2006// TI - Annotation and Disambiguation of Semantic Types in Biomedical Text: a Cascaded Approach to Named Entity Recognition BT - Workshop on Multi-Dimensional Markup in NLP, EACL PB - Trente CY - Italy ID - Rebholz-Schuhmann2006 ER - TY - STD TI - monq.jfa . [http://monqjfa.berlios.de] UR - http://monqjfa.berlios.de ID - ref36 ER - TY - CHAP AU - Gaudan, S. AU - Jimeno, A. AU - Lee, V. AU - Rebholz-Schuhmann, D. PY - 2008 DA - 2008// TI - Combining evidence, specificity and proximity towards the normalization of Gene Ontology tems in text BT - EURASIP JBSB ID - Gaudan2008 ER -