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Annotation software tools | Biomedical text mining

There exist a multitude of tools available for annotating biomedical corpora as an important resource in textmining.

tagtog
Web

tagtog

Helps in your workflow for text analysis and database curation. tagtog…

Helps in your workflow for text analysis and database curation. tagtog leverages manual user annotation in combination with automatic machine-learned annotation to provide accurate identification of…

BioCreative
Web

BioCreative Critical Assessment of Information Extraction systems in Biology

Promote the development of biomedical text mining applications. BioCreative…

Promote the development of biomedical text mining applications. BioCreative works closely with biocurators to understand the various curation workflows, the Text Mining (TM) tools that are being used…

Bio-SCoRes
Desktop

Bio-SCoRes

A modular framework for coreference resolution in biomedical text. Bio-SCoRes…

A modular framework for coreference resolution in biomedical text. Bio-SCoRes incorporates a variety of coreference types, their mentions and allows fine-grained specification of resolution…

NOBLE Coder
Desktop

NOBLE Coder

A recognition component for NLP (Natural Language Processing) pipelines. NOBLE…

A recognition component for NLP (Natural Language Processing) pipelines. NOBLE Coder implements a general algorithm for matching terms to concepts from an arbitrary vocabulary set. The system’s…

becas
Web

becas Biomedical Concept Annotation System

An API for biomedical concept identification and a web-based tool that…

An API for biomedical concept identification and a web-based tool that addresses these limitations. MEDLINE abstracts or free text can be annotated directly in the web interface, where identified…

Annotator
Web

Annotator

Get annotations for biomedical text with concepts from the ontologies. The…

Get annotations for biomedical text with concepts from the ontologies. The Annotator service has access to a large dictionary of biomedical terms derived from the United Medical Language System…

Markyt
Desktop

Markyt

A text-mining platform for the management of annotation projects. Markyt…

A text-mining platform for the management of annotation projects. Markyt provides an intuitive interface to visualize and edit annotated document sets, keeps track of multiples rounds of annotation…

CRAFT
Dataset

CRAFT Colorado Richly Annotated Full-Text

Collects full-text biomedical journal articles. CRAFT is a manually annotated…

Collects full-text biomedical journal articles. CRAFT is a manually annotated corpus with all coreferential phenomena of identity and apposition. It also identifies all mentions of nearly all…

iSimp
Desktop

iSimp A Sentence Simplification System for Biomedical Text

Provides simplified text to enhance the performance of Natural language…

Provides simplified text to enhance the performance of Natural language processing (NLP) systems and text mining (TM) applications. iSimp denotes simplified sentences in a corpus file, along with the…

PubTator
Web

PubTator

A Web-based tool for accelerating manual literature curation (e.g. annotating…

A Web-based tool for accelerating manual literature curation (e.g. annotating biological entities and their relationships) through the use of advanced text-mining techniques. As an all-in-one system,…

BioSWR
Web

BioSWR

Provides the bioinformatics community with annotated Web services descriptions…

Provides the bioinformatics community with annotated Web services descriptions in diverse formats. BioSWR is a web services registry that provides standard Resource Description Framework (RDF) based…

neXtA5
Dataset

neXtA5

Provides ranking service and interface embedded into a curation platform.…

Provides ranking service and interface embedded into a curation platform. NeXtA5 aims to supply an annotation workflow that will leverage automated methods for text analysis to speed up curation and…

BioQRator
Web

BioQRator

A web-based annotation tool for biomedical literature. BioQRator was designed…

A web-based annotation tool for biomedical literature. BioQRator was designed to support any task annotating entities and relationships. It is also one of the first web tools which support the BioC…

@Note
Web

@Note

A platform for Biomedical Text Mining (BioTM) that aims at the effective…

A platform for Biomedical Text Mining (BioTM) that aims at the effective translation of the advances between three distinct classes of users: biologists, text miners and software developers. Its main…

BioC Viewer
Dataset

BioC Viewer

A web-based tool for displaying and merging annotations in BioC. The BioC…

A web-based tool for displaying and merging annotations in BioC. The BioC Viewer assists BioGRID curators as a part of the BioCreative V BioC track (Collaborative Biocurator Assistant Task). For the…

USI
Desktop

USI User-oriented Semantic Indexer

A fast and intuitive method for indexing tasks. By only relying on neighbor…

A fast and intuitive method for indexing tasks. By only relying on neighbor documents, the User-oriented Semantic Indexer does not need a representative learning set. Yet, it provides better results…

OnASSIs
Desktop

OnASSIs Ontology Annotation and Semantic SImilarity software

Permits annotation thank to ontology terms. OnASSIs is able to compute semantic…

Permits annotation thank to ontology terms. OnASSIs is able to compute semantic similarity measures based on the structure of the ontology between different annotated samples. It allows users to…

Utopia…
Desktop

Utopia Documents

Connects the static content of scientific articles to the dynamic world of…

Connects the static content of scientific articles to the dynamic world of online content. Utopia Documents brings up-to-date information directly to the desktop with a brand new look and feel that…

Argo
Web

Argo

A workbench for building text-mining solutions with the use of a rich graphical…

A workbench for building text-mining solutions with the use of a rich graphical user interface, for the process of biocuration. Central to Argo are customizable workflows that users compose by…

MyMiner
Web

MyMiner

A free and user-friendly text annotation tool aimed to assist in carrying out…

A free and user-friendly text annotation tool aimed to assist in carrying out the main biocuration tasks and to provide labelled data for the development of text mining systems. MyMiner allows easy…

Bionotate
Web

Bionotate

A collaborative annotation tool for relation extraction in biomedical text.…

A collaborative annotation tool for relation extraction in biomedical text. BioNotate is a text annotation tool written in Javascript that allows collaborative annotation of relationships between…

Semantator
Desktop
Web

Semantator Semantic Annotator

A semantic-web-based environment for annotating data of interest in biomedical…

A semantic-web-based environment for annotating data of interest in biomedical documents, browsing and querying the annotated data, and interactively refining annotation results if needed. Through…

TIES
Web

TIES Text Information Extraction System

Identifies, annotates, and indexes clinical documents. TIES is a natural…

Identifies, annotates, and indexes clinical documents. TIES is a natural language processing (NLP) pipeline and clinical document search engine. It supports tissue ordering and acquisition, building…

RightField
Desktop

RightField

Adds ontology term selection to Excel spreadsheets. RightField can specify a…

Adds ontology term selection to Excel spreadsheets. RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet…

Djeen
Desktop

Djeen Database for Joomla's Extensible Engine

Allows managing project associated with heterogeneous data types while…

Allows managing project associated with heterogeneous data types while enforcing annotation integrity and minimum information. Djeen is a new Research Information Management System (RIMS) for…

Medical…
Desktop

Medical Treebank

A handbook of domain-customized syntactic parsing guidelines based on iterative…

A handbook of domain-customized syntactic parsing guidelines based on iterative annotation and adjudication between two institutions (Kaiser Permanente and Vanderbilt University). Special…

Knowtator
Desktop

Knowtator

A general-purpose text annotation tool that is integrated with the Protégé…

A general-purpose text annotation tool that is integrated with the Protégé knowledge representation system. Knowtator facilitates the manual creation of training and evaluation corpora for a…

MMAX2
Desktop

MMAX2

A GUI-based text annotation tool for creating and visualizing annotations.…

A GUI-based text annotation tool for creating and visualizing annotations. MMAX2 uses a flexible stand-off XML data format, and has advanced and customizable methods for information and relation…

BRAT
Web

BRAT Brat Rapid Annotation Tool

A web-based tool for text annotation; that is, for adding notes to existing…

A web-based tool for text annotation; that is, for adding notes to existing text documents. BRAT is designed in particular for structured annotation, where the notes are not freeform text but have a…

GATE Teamware
Web

GATE Teamware

A web-based management platform for collaborative annotation & curation.…

A web-based management platform for collaborative annotation & curation. GATE Teamware is a cost-effective environment for annotation and curation projects, enabling you to harness a broadly…

BioC
Desktop

BioC

A simple format to share text data and annotations. BioC allows a large number…

A simple format to share text data and annotations. BioC allows a large number of different annotations to be represented including sentences, tokens, parts of speech, named entities such as genes or…

GoGene
Web

GoGene

Helps to quickly find interpretations of results from high-throughput…

Helps to quickly find interpretations of results from high-throughput experiments together with relevant literature or to simply scan the literature for discussed genes. GoGene provides the most…

MILANO
Web

MILANO Microarray Literature-based Annotation

Allows annotation of lists of genes derived from microarray results by user…

Allows annotation of lists of genes derived from microarray results by user defined terms. MILANO expands the gene names to include all their informative synonyms while filtering out gene symbols…

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