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Web applications

Description
PubTator is a text-mining tool for annotating the entire PubMed articles with key biological entities (e.g. genes & diseases) and is available through both Web and API access.
Description
LitVar is a semantic search engine for linking genomic variant data in PubMed and PMC
Description
ezTag is a Web-based annotation system for tagging biomedical concepts via interactive learning.
Description
BioC viewer is a Web interface for displaying and merging annotations in BioC.
Description
Meshable helps search PubMed by utilizing MeSH and MeSH-derived topical terms.

Software

Description
TaggerOne is a general toolkit for biomedical named entity recognition and normalization. As a machine learning system it is not entity-specific but does require training data.
Description
tmChem is an open-source software tool for identifying chemical names. tmChem achieved the highest performance in BioCreative CHEMDNER task (over 87% F-measure)
Description
DNorm is the first technique to use machine learning to recognize and normalize disease names in biomedical text.
Description
GNormPlus is an end-to-end system that handles both gene/protein name and identifier detection in biomedical literature, including gene/protein mentions, family names and domain names.
Description
SR4GN is an open source tool for species recognition/disambiguation and is optimized for the Gene Normalization task.
Description
tmVar extracts a wide range of sequence variants in both protein and gene levels (e.g. substitution, deletion, etc) in HGVS formats.
Description
SimConcept uses patterns to identify individual mentions from a composite named entity (e.g. SMAD 1, 5, and 8).
Description
NegBio is a high-performance tool for negation and uncertainty detection in clinical text (e.g. radiology reports).