MARTIN KRALLINGER - BIOLOGY AND TEXT MINING RELATED LINKS

COLLECTION OF LINKS TO TOOLS, RESOURCES, GROUPS, EVALUATIONS, ETC. RELATED TO BIO-NLP

The aim of this "Links" page is to organize a collection of links of useful resources and tools for people interested in text mining, Bio-NLP, bioinformatics and molecular biology. The collection ranges from basic text repositories such as PubMed to very specific Bio-NLP applications and even lectures of text mining for bioinformatics and biology. Given this is an extremely interdisciplinary research field, involving people from statistics, mathematics, artificial intelligence, computational linguistics, bioinformatics, molecular biology and biomedicine it is hard to provide a comprehensive repository of links for each background and field of interest. Nevertheless, the usefulness of Bio-NLP applications for the people of the domain itself, namely life science researchers (and their feedback) should be a significant goal while developing Bio-NLP strategies.

GermOnline
Topic Description Example
Biomedical/Biochemistry Text databases and search engines Repositories of Biomedical, Molecular Biology and Biochemistry literature PubMed
BioNLP challenges Community-wide evaluations of BioNLP strategies BioCreative
Biomedicine text copora Corpora and training sets for NLP applied to Biology texts. GENIA
BioNLP tools Tools (online/downloadable) related to NLP in Molecular Biology iHOP
Commercial BioNLP tools Commercial text mining tools for the biomedical and molecular biology domain. BioAlma
Resources: Ontologies Ontologies in the biomedical domain GO
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.
Resources: Annotation databases Databases containing sequence and annotation data for genes and proteins. SwissProt
Resources: Protein structures Databases containing information releted to protein structural information SCOP
Bioinformatics groups Links to some of teh existing bioinformatics groups worldwide Helix Group
Computational linguistics groups Links to some groups working on computational linguistics. University of Sheffield
NLP / comp. linguistics dictionaries Dictionaries with basic NLP terminology. Glossary
NLP, IR, IE, ML tools NLP tools and useful resources. NLTK
Resources: 2d PAGE 2D polyacrylamide gel electrophoresis databases SWISS-2DPAGE
Biomedical text portals Text portals and engines for biomedical literature Scirus
Tutorials/presentations Links to presentations and tutorials related to NLP and BioNLP. Term Weighting
Lectures Bio-NLP/text mining Lectures and presentations - NLP and text mining in molecular biology. Master Bioinformatics, Barcelona 2005
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
BIO-NLP groups Research groups related to Bio-NLP or with publications and projects in this field. PDG
Mailing lists Links to mailing lists related to Bio-NLP, computational linguistics and bioinformatics. BioNLP.org
BioNLP projects Links to projects related to NLP and text mining in biology. BioMinT
Personal links Personal links to friends, colleagues, collaborators etc. Konstanze Krallinger Homepage




       

For comments and suggestions contact me: martink@cnb.uam.es.







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