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GNAT recognizes gene names in text and maps them to NCBI Entrez Gene
GNAT is a BioNLP/textmining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID.
March 2017: We started to upload GNAT output on Medline.
Framework for textmining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java.
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Contextor is a light-weight simple-to-use Java based library to help developers and researchers working with the general concept of a resource; as examples, resources can be text resources, web resources, images and videos.
Moara is a biological textmining tool and consists of a Java library and some auxiliary MySQL databases for gene/protein training and extraction of mentions and its further normalization and disambiguation.
OpenDMAP (Open Source Direct Memory Access Parser) is a natural language processing (textmining) application: a semantic parser for information extraction.
LAITOR is a textmining software developed to find co-occurrence of biological entities (gene/protein terms) together with biointeractions and concepts term from customized dictionaries.
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@Note2 is now available in www.anote-project.org
@Note is a Biomedical TextMining workbench that integrates current Biomedical TextMining (BioTM) methods and provides biologists with intuitive tools capable of supporting their bibliographic searches and further literature curation.
GraphSpider is a pattern matcher which searches parsed text in phrase-structure tree or dependency graph format for syntactic structures matching a set of patterns in MPL, a regexp-like pattern language. Applications: information extraction, textmining.