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Information extraction software tools and databases | Biomedical text mining

Information extraction steps

MetaMap
Web
Desktop

MetaMap

Maps biomedical text to the Unified Medical Language System (UMLS)…

Maps biomedical text to the Unified Medical Language System (UMLS) Metathesaurus or, equivalently, to discover Metathesaurus concepts referred to in text. MetaMap breaks the text into phrases and…

NegEx
Desktop

NegEx

Identifies negation in textual medical records. NegEx implements several…

Identifies negation in textual medical records. NegEx implements several phrases indicating negation, filters out sentences containing phrases that falsely appear to be negation phrases, and limits…

KDBI
Dataset

KDBI Kinetic Data of Bio-molecular Interaction database

Provides experimentally determined kinetic data of protein–protein,…

Provides experimentally determined kinetic data of protein–protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligand binding or reaction events described in the literature. KDBI…

Genome…
Dataset

Genome Properties

Provides a collection of definitions for the higher-level attributes. Genome…

Provides a collection of definitions for the higher-level attributes. Genome Properties ascribes higher-level attributes to a species when a sufficient set of molecular markers are detected in its…

HITEx
Desktop

HITEx Health Information Text Extraction

Manipulates text reports to extract specific terms and knowledge from them.…

Manipulates text reports to extract specific terms and knowledge from them. HITEx is an open-source natural language processing (NLP) software application. The software is built on top of Gate…

ChemDataExtract…
Desktop

ChemDataExtractor

Consists of a modular document processing pipeline with extensible components…

Consists of a modular document processing pipeline with extensible components for natural language processing that achieve state-of-the-art performance for POS tagging and chemical named entity…

PubMedPortable
Desktop

PubMedPortable

Provides the infrastructure to combine standalone applications by exporting…

Provides the infrastructure to combine standalone applications by exporting different data formats. PubMedPortable automatically builds a PostgreSQL relational database schema and a Xapian full text…

ConText
Desktop

ConText

Determines whether clinical conditions mentioned in clinical reports are…

Determines whether clinical conditions mentioned in clinical reports are negated, hypothetical, historical, or experienced by someone other than the patient. ConText obtains reasonable to good…

Vigi4Med…
Desktop

Vigi4Med Scraper

Extracts structured data from web forums. Vigi4Med Scraper is part of the…

Extracts structured data from web forums. Vigi4Med Scraper is part of the Vigi4Med project for detecting adverse drug reactions in social networks. It is highly configurable; using a configuration…

DataMed
Dataset

DataMed

Helps researchers to find data of interest in a broad spectrum of high quality…

Helps researchers to find data of interest in a broad spectrum of high quality repositories. DataMed is designed to be, for data, what PubMed has been for the scientific literature. DataMed stores…

Multi-Label…
Desktop

Multi-Label Representation

Recognizes not only disorder mentions in the form of contiguous or…

Recognizes not only disorder mentions in the form of contiguous or discontiguous words but also mentions whose spans overlap with each other. Multi-Label Representation is an approach to recognize…

MPTM
Web
Desktop

MPTM Mining Protein Post-Translational Modifications

Extracts and organizes comprehensive post-translational modifications (PTMs)…

Extracts and organizes comprehensive post-translational modifications (PTMs) information from literature in PubMed. MPTM provides literature mining service for hydroxylation, myristoylation. It…

Elsevier…
Dataset

Elsevier DataSearch

Permits users to search several types of information. Elsevier DataSearch is a…

Permits users to search several types of information. Elsevier DataSearch is a platform that works with a search engine. Results of a query send back toward dataset such as ScienceDirect or arXiv.…

T-GOWler
Desktop

T-GOWler Generalized Ontology-based WorkfLow minER within Texts

Provides a pipeline to extract abstract patterns within texts. T-GOWler is a…

Provides a pipeline to extract abstract patterns within texts. T-GOWler is a system that contains two main engines: (i) WfExtractor extracts workflows from texts and builds a workflow database, and…

WfMiner
Desktop

WfMiner

Generates generalized subgraphs of workflows out of concrete ones. WfMiner…

Generates generalized subgraphs of workflows out of concrete ones. WfMiner creates frequent patterns using a level-wise pattern generation on the top of the ontology and a specific…

WfExtractor
Desktop

WfExtractor

Extracts workflows from texts and builds a workflow database. WfExtractor…

Extracts workflows from texts and builds a workflow database. WfExtractor processes in three steps: (1) named entity extraction, (2) link extraction, and (3) workflow reconstruction from the…

Gene-cocite
Web

Gene-cocite

Accepts a list of genes and returns a list of the papers which cocite any two…

Accepts a list of genes and returns a list of the papers which cocite any two or more of the genes. Gene-cocite is a web app designed to be an easy to use first step for biological researchers…

MedXN
Desktop

MedXN Medication Extraction and Normalization

Extracts comprehensive medication information and normalizes it to the most…

Extracts comprehensive medication information and normalizes it to the most appropriate RxNorm concept unique identifier (RxCUI) as specifically as possible. MedXN focuses on medication normalization…

Minorthird
Desktop

Minorthird

Uses as an SDK/API for machine learning and information extraction, primarily…

Uses as an SDK/API for machine learning and information extraction, primarily on text data. Minorthird's toolkit of learning methods is integrated tightly with the tools for manually and…

cTakes
Desktop

cTakes

Allows to extract information from electronic medical record clinical…

Allows to extract information from electronic medical record clinical free-text. cTakes is a natural language processing system.

CLAMP
Desktop

CLAMP Clinical Language Annotation Modeling and Processing Toolkit

Enables recognition and automatic encoding of clinical information in narrative…

Enables recognition and automatic encoding of clinical information in narrative patient reports. CLAMP is based on proven methods in many clinical Natural Language Processing (NLP) challenges. It is…

GENE-E
Desktop

GENE-E

Supports visual data exploration. GENE-E is a matrix visualization and analysis…

Supports visual data exploration. GENE-E is a matrix visualization and analysis platform that includes heat map, clustering, filtering, charting, marker selection, and many other tools. In addition…

EnsemblDb3
Desktop

EnsemblDb3

A package of capabilities for querying Ensembl MySQL databases and for…

A package of capabilities for querying Ensembl MySQL databases and for "administering" them. EnsembDb3 permits querying genomes, variation and comparas into Ensembl databases.

ContextD
Web

ContextD

In order to extract meaningful information from electronic medical records,…

In order to extract meaningful information from electronic medical records, such as signs and symptoms, diagnoses, and treatments, it is important to take into account the contextual properties of…

Target Text…
Web

Target Text Extractor

Discovers and extracts target text patterns. Target Text Extractor can work…

Discovers and extracts target text patterns. Target Text Extractor can work from complex annotations and withdraw gene symbols.

Java MIAPE API
Desktop

Java MIAPE API Java Minimal Information About a Proteomics Experiment API

Permits extraction and management of MIAPE information from commonly used…

Permits extraction and management of MIAPE information from commonly used proteomics data files. Java MIAPE API is an open source Java application programming interface (API) designed in modules that…

RAZOR
Web

RAZOR

Allows text mining and creation of molecular simulations. RAZOR is a web…

Allows text mining and creation of molecular simulations. RAZOR is a web platform that helps the understanding of disease mechanisms and discovering of Parkinson’s Disease’s therapeutics.

G3data
Desktop

G3data

Permits to extract data from a graph. G3data can be applied on all graphs…

Permits to extract data from a graph. G3data can be applied on all graphs published in literature where data are not given.

MC Miner
Desktop

MC Miner Molecular Connections Miner

Allows users to mine information from a range of unstructured data sources to…

Allows users to mine information from a range of unstructured data sources to create structured outputs. MC Miner is a state-of-the-art text mining engine that provides data usable to develop custom…

EDirect
Desktop

EDirect Entrez Direct

Permits to give access to the NCBI's interconnected databases. EDirect…

Permits to give access to the NCBI's interconnected databases. EDirect permits to describe separately individual operations. It allows the utilization of Boolean operators and parentheses in…

CLAMP-Cancer
Desktop
TinySVM
Desktop

TinySVM

Implements Support Vector Machines (SVMs) for the problem of pattern…

Implements Support Vector Machines (SVMs) for the problem of pattern recognition. TinySVM is a new generation learning algorithms based on recent advances in statistical learning theory, and applied…

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