Bio-NLP resources database (BioNLPdb)

This page provides a compendium of Information Retrieval (IR), Information Extraction (IE), Text Mining and literature processing applications developed for providing access to information contained in life sciences and biomedical literature. Additionally links to some relevant scientific literature repositories and search engines are provided.

You can check out a page containing a list of ALL APPLICATIONS or search for specific tools using a basic keyword search.

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You can also check out a review article published in Genome Biology providing an overview of currently existing applications in biomedical text mining:

Krallinger M, Valencia A. and Hirschman L. Linking genes to literature: text mining, information extraction, and retrieval applications for biology Genome Biology 2008, 9(Suppl 2):S8

You can find below the list of latest tools added:
Date added Tool name Record
17th August 2009 PubNet
17th August 2009 STITCH
17th August 2009 MetaMap
17th August 2009 PMD2HD
14th August 2009 PLAN2L
12th August 2009 Figurome
11th August 2009 MedlineRanker
11th August 2009 SciMiner
10th August 2009 PPI Finder
10th August 2009 PAKORA
10th August 2009 GoGene
9th August 2009 BIGNER

You can contact us for:

Please send me through feedback through e-mail:

Tutorial/Teaching: Here you can find the link to a text mining tutorial/lecture I have prepared for bioinformatics and biology students. I gave this lecture at several summer schools and bioinformatics master courses held at different locations mostly within Spain. You can re-use these slides for your own presentation, but please be so kind and acknowledge where you took them from (i.e. by Krallinger,09).