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 | |
| BioCreAtIvE MetaServer | Open text mining meta-server | 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 | |
| KDnuggets | General Analytics and Data Mining Resources | Apache Mahout |
