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| Roser Morante - academic web page |
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Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter, 2002 Artificial Intelligence and Molecular Biology Edited by Lawrence Hunter, 1993 General ResourcesBio-NLP tools linked in the Biocreative web page Compendium of BioNLP Resources by Martin Krallinger Corpora for biomedical NLP, bookmarks by Kevin Cohen, Biomedical Text Mining Group, Center for Computational Pharmacology University of Colorado Health Sciences Center BioNLP Resources by Alex Morgan BioNLP Benchmarks by Jörg Hakenberg Resources for Biomedical Terminology and Ontology by Mark A. Mandel BioNLP UIMA Component Repository Named Entity TaggersBANNER CRF based, developed by Arizona State University, Dept. of Computer Science and Dept. of Biomedical Informatics ABNER CRF based, by Burr Settles, Department of Computer Sciences, University of Wisconsin-Madison LINGPIPE Information extraction and data mining tools, developed by Alias-i, Inc. JNET JULIE Lab Named Entity Tagger MetaMap Portal, program developed by Dr. Alan Aronson at the National Library of Medicine (NLM) to map biomedical text to the UMLS Metathesaurus OrganismTagger Organism Tagger by Semantic Software Lab Tokenizers - taggersGENIA tagger Tagger developed at the Tsujii Laboratory of the University of Tokyo, Japan SPECIALIST Text Tools developed by the Lexical Systems Group, NLM, NIH, USA ParsersDavid McClosky's self trained biomedical parser, Brown University, USA ENJU Syntactic parser developed at the Tsujii Laboratory of the University of Tokyo, Japan LRDEP A dpendency parser developed by Kenji Sagae at the Tsujii Laboratory of the University of Tokyo, Japan Parsed MEDLINE developed by the Tsujii Laboratory of the University of Tokyo, Japan Other toolsBioSimplify, Sentence simplification for biomedical texts, Department of Biomedical Informatics, Arizona State University Data IntegrationHanalyzer: a 3R System. Center for Computational Pharmacology, University of Colorado Arrowsmith: linking documents, disciplines, investigators and databases, University of Illinois at Chicago PPI - Information Extraction systemsPPI-learning with all-dependency-paths kernel by Bioinformatics Laboratory, Turku Center for Computer Science, University of Turku, Finland AKANE++PPI Information extraction system for PPI developed at the Tsujii Laboratory of the University of Tokyo, Japan Event Extraction systems / Semantic role labelersStanford Biomedical Event Parser (SBEP) by Bioinformatics Laboratory, The Stanford Natural Language Processing Group, USA BioKIT semantic role labeler by the NUS Natural Language Processing Group Annotation ToolsKNOWTATOR General-purpose text annotation tool, CCP Center for Computational Pharmacology, University of Colorado Health Sciences, USA MMAX2 General-purpose text annotation tool, EML Research gGmbH, Germany XConc SuiteXML based tools for corpus annotation, Tsujii Lab, Japan CALLISTO General-purpose text annotation tool, Mitre Corporation, USA Search ToolsPolySearch Extracts relations between two types of entities. University of Alberta, Canada. Entrez. Web application that finds information about biomedical entities in heterogeneous databases. NCBI, USA. CoPub. Detection of co-occurring biomedical concepts in abstracts. CDD, Center of Molecular and Biomolecular Informatics, Nijmegen, The Netherlands iHOP. Retrieving collections of co-mentioned proteins. CNB-CSIC, Madrid, Spain eUtils. Tools that provide access to Entrez data. NCBI, USA MiMIr2. Search of protein interactions. NIH Natioanl Center for Integrative Biomedical Informatics, USA GIN. System for browsing articles and molecule interaction information. CLAIR Group, University of Michigan, USA MedEvi Search engine for biomedical concepts. EMBL-EBI, Cambridge, UK GoPubMed. Shows the most qualifying concepts in GO and MeSH for a search. Technische Universitaet Dresden, Germany EBIMed. Web application that finds associations between biomedical entities. EMBL-European Bioinformatics Institute, UK. MedGene. Web application that retrieves biomedical relationships based on the co-citations of all Medline records. Harvard University, USA. LitMiner. Literature mining tool based on co-citations. Helmholtz Zentrum, Munich, Germany. Ali Baba. Tool that visualizes the result of searching biomedical relations in abstracts. Humboldt University, Germany. BioText. Search engine. University of California, Berkeley, USA. MedstractPlus. Mines relations from Medline. Brandeis University, Waltham, USA. Knowledge discoveryBitola. Biomedical discovery support system. Abbreviation - acronym findersARGH Biomedical Acronym Resolver provided by the eTBLAST team, UT Southwestern, USA JACRO JULIE Lab Acronym Annotator CorporaCorpora linked in the Biocreative web page Becorpus Biocaster Event Corpus and Tools by Nigel Collier Links by Martin Krallinger, Universidad Autónoma de Mdrid, Spain ART Corpus Aberystwyth University, UK PennBioIE CYP LDC BioScope University of Szeged, Hungary GENIA University of Tokyo, Japan GENIA EVENT University of Tokyo, Japan DEP GENIA Institute of Computational Linguistics at the University of Zurich, Switzerland. The GENIA corpus parsed with the Pro3Gres parser GENIA TreeBank 1.0 University of Tokyo, Japan GREC corpus, NaCTeM. BioInfer Bio Information Extraction Resource, University of Turku, Finland PPI corpora, University of Turku, Finland PASBio, predicate-argument structures, National Institute of Informatics, Tokyo, Japan Parsed MEDLINE developed by the Tsujii Laboratory of the University of Tokyo, Japan Hedge classification dataset , by B. Medlock, NLIP Group, University of Cambridge, UK AIMED PPI corpus , by R. Bunescu et al. 2005, Department of Computer Science, University of Texas, USA Yapex Training and test data for the protein tagger Yapex. Linnaeus corpus of species names. Corpora for NLPby Jörg Hakenberg. Meta-knowledge GENIA corpusby NACTEM DatabasesOMIM Compendium of human genes and genetic phenotypes, Johns Hopkins University School of Medicine Links to biomedical databases from the Health Sciences Library, University of Buffalo Links to biomedical databases from Israel Science and Technology Links to Molecular Biology Databases from the Introduction to Bioinformatics Course by L. Hunter UMLS Unified Medical Language System MeSH Medical Subject Headings, U.S. National Library of Medicine MeSH HUGO Gene Nomenclature Committee Research groups/centers - projectsHITRL, Sydney, Australia NICTA, Melbourne, Australia CLAIR, Department of Electrial Engineering and Computer Science, University of Michigan, USA Tsujii Laboratory, Graduate School of Information Science and Technology, The University of Tokyo, Japan GRIB, Research Unit on Biomedical Informatics, Barcelona, Spain Bioinformatics Laboratory, Turku Center for Computer Science, University of Turku, Finland Biomedical Text Mining Group, Center for Computational Pharmacology University of Colorado Health Sciences Center, USA BioText University of Berkeley, USA NaCTeM National Centre for Text Mining, School of Computer Science, University of Manchester, UK Biomine Department of Computer Science, University of Helsinki, Finland Mining the Bibliome Based at the IRCS, University of Pennsylvania, USA Lexical Systems Group located within the Cognitive Science Branch of the Lister Hill Center for Biomedical Communications, USA BioSemantics Based at the Center for Human and Clinical Genetics of the Leiden University Medical Center, The Netherlands ProjectsOntoGene Institute of Computational Linguistics, University of Zurich, Switzerland LiteratureSelected Bibliography for Text Mining for Biomedicine by Sophia Ananiadou BLIMP Biomedical LIterature (and text) Mining Publications, Queen's University, Canada Researchers |
BioCreAtIvE Critical Assessment for Information Extraction in Biology BIONLP Natural language processing of biology text, founded by Bob Futrelle Conferences and workshopsDecember 18-21, 2011. Special Session ICMLA 2011, Special Session on Machine Learning for Biomedical Literature Analysis and Text Retrieval, Honolulu, Hawaii, USA. October 24, 2011. DTMBIO 2011, 5th International Workshop on Data and Text Mining in Biomedical Informatics. Glasgow, Scotland. October 25-26, 2010. SMBM 2010 2010, 4th International Symposium on Semantic Mining in Biomedicine. Hinxton, Cambridgeshire, UK. September 2-4, 2010. Cancer Bioinformatics Workshop. Cambridge, UK. July 2010. BioNLP 2010. ACL Workshop. Uppsala, Sweden. July 9-13, 2010. ISBM 2010. The 18th Annual International Conference on Intelligent Systems for Molecular Biology. Boston, USA June 5 or 6, 2010. Louhi 2010 Second Louhi one-day workshop on Text and Data Mining of Health Documents. LA, USA May 18, 2010. BioTxtM 2010 LREC Workshop on Building and Evaluating Resources for Biomedical Text Mining. Malta. May 10-11, 2010. BioTM 2010 Workshop Advances in Bio Text Mining. Ghent, Belgium. June 28-29, 2009. BioLINK 2009. The Ninth Annual Meeting of the ISMB BioLINK Special Interest Group: Text Mining, Image Analysis, and the future of Scientific Publishing. Stockholm, Sweden June 11-13, 2009. iCBBE2009. The 3rd International Conference on Bioinformatics and Biomedical Engineering, Beijing, China June 4-5, 2009. BioNLP 2009. In cojunction with NAACL-HLT 2009, Boulder, Colorado. This year's meeting will host a shared task run by the GENIA group at the University of Tokyo November 30, 2008. BioSearch 2008. HCSNet Next-Generation Search Workshop on Search in Biomedical Information, Queensland University of Technology, Brisbane September 4-6, 2008. Louhi 2008. First Louhi Conference on Text Mining and Data Mining of Clinical Documents, University of Turku, Findland September 1-3, 2008. SMBM 2008. Third International Symposium on Semantic Mining in Biomedicine, University of Turku, Findland July 19-23, 2008. ISMB 2008. 16th Annual International Conference Intelligent Systems for Molecular Biology, Toronto, Canada June 19, 2008. BioNLP 2008. A workshop of ACL 2008 Columbus, OH May 27, 2008. DRMed 2008 1st International Workshop on Describing Medical Web Resources, Göteborg, Sweden May 26, 2008. Building and evaluating resources for biomedical text mining A workshop of LREC, Marrakech Slides available. February 21-22, 2008. Finding the Hidden Knowledge: Text mining for biology and medicine. Glasgow, Scotland January 4-8, 2008. PSB 2008, Pacific Symposium on Biocomputing 2008 Proceedings of Session on NLP. April 23-25, 2007. BioCreAtIvE 2, Second Biocreative Workshop, CNIO, Madrid 2007 Proceedings. |
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