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Unclassified software tools | Bio-entity identification

AnatomyTagger
Desktop

AnatomyTagger

Allows recognition of anatomical entity mentions in free text. AnatomyTagger is…

Allows recognition of anatomical entity mentions in free text. AnatomyTagger is a machine learning-based system that identifies molecular entities and whole organism mentions to facilitate…

AnatEM
Dataset

AnatEM Anatomical Entity Mention

Provides a corpus of documents that was used to train machine learning-based…

Provides a corpus of documents that was used to train machine learning-based taggers. AnatEM was built in parton the Anatomical Entity Mention (AnEM) and Multi-Level Event Extraction (MLEE) corpora.…

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…

BNER
Desktop

BNER Biomedical Named Entity Recognition

Allows users to recognize important biomedical entities (such as genes and…

Allows users to recognize important biomedical entities (such as genes and proteins) from text. BNER is a recurrent neural network (RNN) framework allowing capture of morphological and orthographic…

LiEtAl2017
Desktop

LiEtAl2017

Provides a convolutional neural network (CNN)-based ranking approach for…

Provides a convolutional neural network (CNN)-based ranking approach for biomedical entity normalization. The software takes advantages of semantic and morphological information of biomedical entity…

Glycan Reader
Web

Glycan Reader

Enables facile generation of the simulation systems of complex glycoconjugates…

Enables facile generation of the simulation systems of complex glycoconjugates with most sugar types and chemical modifications in the Protein Data Bank (PDB). Glycan Reader is a web application that…

AutoBind
Dataset

AutoBind

Provides about 14 000 protein-ligand complexes. AutoBind were constructed an…

Provides about 14 000 protein-ligand complexes. AutoBind were constructed an algorithm that automatically extracts information about protein- ligand-binding affinity. This tool is able to recognize…

LexEBI
Dataset

LexEBI Lexical Entities of Biological Interest

Provides a terminological resource that can serve as a hub for modern language…

Provides a terminological resource that can serve as a hub for modern language processing techniques and data integration solutions connecting literature with biomedical data. LexEBI is composed of…

GBIF’s…
Web
Desktop

GBIF’s name-parser

Divides scientific names into components and compares them against the…

Divides scientific names into components and compares them against the taxonomic backbone used by GBIF. GIBF’s name-parser can automate the curation of scientific names. It is based on regular…

NERChem
Dataset

NERChem

Assists in identification of chemical named entity mentions in chemical…

Assists in identification of chemical named entity mentions in chemical patents. NERChem is based on the conditional random fields model (CRF) and contains: (1) full-token word features; (2) BioNE…

Treetop
Desktop

Treetop

Permits to create parsers easily by describing them using a Parsing Expression…

Permits to create parsers easily by describing them using a Parsing Expression Grammar (PEG). Treetop allows to deal with languages that are much simpler than English. It transforms streams of…

Biodiversity
Desktop

Biodiversity

Parses taxonomic scientific name and breaks it into semantic elements.…

Parses taxonomic scientific name and breaks it into semantic elements. Biodiversity allows users to customize output parameters.

YASMEEN
Desktop

YASMEEN Yet Another Species Matching Execution Environment

Identifies species names matching between a set of input data and multiple…

Identifies species names matching between a set of input data and multiple reference data sets. YASMEEN is based on Concept Matching Engine and Tools (COMET) which models and supports generic data…

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