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Species name recognition software tools | Bio-entity identification

Species recognition has become increasingly important for the text mining community in recent years. In particular, it has been shown that accurately recognizing species and linking them to relevant genes or proteins is critical to the success of…
gnparser
Desktop

gnparser Global Names Parser

Parses scientific names of any complexity. gnparser identifies which…

Parses scientific names of any complexity. gnparser identifies which combinations of the most atomic parts of a name-string represent words or dates. It allows developers to define the rules that…

MicroPIE
Desktop

MicroPIE Microbial Phenomics Information Extractor

A natural language processing application for the rapid and efficient…

A natural language processing application for the rapid and efficient extraction of phenotypic character information from prokaryotic taxonomic descriptions. MicroPIE uses a robust supervised…

matK-QR
Desktop

matK-QR

Identifies a unique set of discriminating nucleotide patterns to generate a for…

Identifies a unique set of discriminating nucleotide patterns to generate a for plant species identification. matK-QR searches signatures in the query maturaseK (matK) gene sequences and predicts…

FindIT
Web

FindIT

Tries to index the taxonomic names using pattern-matching expressions and a…

Tries to index the taxonomic names using pattern-matching expressions and a lexicon of English words, providing a confidence score for resultant names. Rule-based, word frequency and regular…

OrganismTagger
Desktop

OrganismTagger

A hybrid rule-based/machine learning system to extract organism mentions from…

A hybrid rule-based/machine learning system to extract organism mentions from the literature. OrganismTagger includes tools for automatically generating lexical and ontological resources from a copy…

SR4GN
Desktop

SR4GN

An open source tool for species recognition and disambiguation in biomedical…

An open source tool for species recognition and disambiguation in biomedical text. In addition to the species detection function in existing tools, SR4GN is optimized for the gene normalization task.…

LINNAEUS
Desktop

LINNAEUS

An open source, stand-alone software system capable of recognizing and…

An open source, stand-alone software system capable of recognizing and normalizing species name mentions with speed and accuracy, and can therefore be integrated into a range of bioinformatics and…

taxonfinder
Web

taxonfinder

Detects scientific names in plain text. Given a string, taxonfinder will scan…

Detects scientific names in plain text. Given a string, taxonfinder will scan through the contents and use a dictionary-based approach to identifying which words and strings are latin scientific…

TaxonGrab
Desktop

TaxonGrab

An NLP (natural language processing) solution written in PHP, which leverages…

An NLP (natural language processing) solution written in PHP, which leverages systematic nomenclature rules that are used for taxonomic nomenclature in scientific publications. TaxonGrab may show…

uBioRSS
Dataset

uBioRSS

A 'taxonomically intelligent' service customized for the biological…

A 'taxonomically intelligent' service customized for the biological sciences. uBioRSS aggregates syndicated content from academic publishers and science news feeds, and then uses a…

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