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Critical Assessment of Information Extraction in Biology - data sets are available from Resources/Corpora and require registration.


BioNLP repositories [2004-01-02]

Among useful resources are many of the existing NLP tools, data contained in biological databases, some text mining and IE tools developed for the biological domain, as well as references to articles which outline existing strategies in this domain. Some links to existing collections, databases as well as repositories are provided in this page. We will try to add new links to additional useful resources.

BioCreAtIvE glossaryGlossary of terms, database names, concepts useful for BioCreAtIvE participantsBioCreAtIvE
BioCreAtIvE MetaServerOpen text mining meta-serverBioCreAtIvE
Biomedical text coporaCorpora and training sets for NLP applied to Biology texts.MedTag
BioNLP toolsTools (online/downloadable) related to NLP in Molecular BiologyiHOP
Biomedical/Biochemistry Text databases and search enginesRepositories of Biomedical, Molecular Biology and Biochemistry literaturePubMed
Resources: Protein interactionsProtein interaction databasesMINT
Resources: Bio-ontologiesOntologies in the biomedical domainGO
Resources: Regulatory elementsDatabases of regulatory elements, e.g. transcription factors.(ORegAnno)
Resources: Annotation databasesDatabases containing sequence and annotation data for genes and proteins.SwissProt
Resources: Protein familiesDatabases related to protein families, domains, functional sites, etcInterPro
Resources: GenomesDatabases of genomes of model organismsWormBase
Resources: MicroarraysDatabases of microarray expression data.GermOnline
Resources: 2d PAGE2D polyacrylamide gel electrophoresis databasesSWISS-2DPAGE
Resources: Protein structuresDatabases containing information releted to protein structural informationSCOP
Commercial BioNLP toolsCommercial text mining tools for the biomedical and molecular biology domain.BioAlma
NLP / comp. linguistics dictionariesDictionaries with basic NLP terminology.Glossary
Genetics/biology glossaryDictionaries and glossaries of genetics and molecular biology terms.Hypermedia Glossary
NLP, IR, IE, ML toolsNLP tools and useful resources.NLTK
Bioinformatics journalsLinks to journals or publishers of bioinformatics and computational biology journals.Bioinformatics
Bio-NLP reference repositoriesLinks to collections of article references relevant to the field of text mining and NLP in Biology.BLIMP
Mailing listsLinks to mailing lists related to Bio-NLP, computational linguistics and
KDnuggetsGeneral Analytics and Data Mining ResourcesApache Mahout