BioCreAtIvE resources

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.

Topic	Description	Example
BioCreAtIvE glossary	Glossary of terms, database names, concepts useful for BioCreAtIvE participants	BioCreAtIvE
Biomedical text copora	Corpora and training sets for NLP applied to Biology texts.	MedTag
BioNLP tools	Tools (online/downloadable) related to NLP in Molecular Biology	iHOP
Biomedical/Biochemistry Text databases and search engines	Repositories of Biomedical, Molecular Biology and Biochemistry literature	PubMed
Resources: Protein interactions	Protein interaction databases	MINT
Resources: Bio-ontologies	Ontologies in the biomedical domain	GO
Resources: Regulatory elements	Databases of regulatory elements, e.g. transcription factors.	(ORegAnno)
Resources: Annotation databases	Databases containing sequence and annotation data for genes and proteins.	SwissProt
Resources: Protein families	Databases related to protein families, domains, functional sites, etc	InterPro
Resources: Genomes	Databases of genomes of model organisms	WormBase
Resources: Microarrays	Databases of microarray expression data.	GermOnline
Resources: 2d PAGE	2D polyacrylamide gel electrophoresis databases	SWISS-2DPAGE
Resources: Protein structures	Databases containing information releted to protein structural information	SCOP
Commercial BioNLP tools	Commercial text mining tools for the biomedical and molecular biology domain.	BioAlma
NLP / comp. linguistics dictionaries	Dictionaries with basic NLP terminology.	Glossary
Genetics/biology glossary	Dictionaries and glossaries of genetics and molecular biology terms.	Hypermedia Glossary
NLP, IR, IE, ML tools	NLP tools and useful resources.	NLTK
Bioinformatics journals	Links to journals or publishers of bioinformatics and computational biology journals.	Bioinformatics
Bio-NLP reference repositories	Links to collections of article references relevant to the field of text mining and NLP in Biology.	BLIMP
Mailing lists	Links to mailing lists related to Bio-NLP, computational linguistics and bioinformatics.	BioNLP.org