Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Relation extraction software tools | Biomedication text mining

CoPub
Web

CoPub

A text mining tool that detects co-occuring biomedical concepts in abstracts…

A text mining tool that detects co-occuring biomedical concepts in abstracts from the MedLine literature database. CoPub allows batch input of multiple human, mouse or rat genes and produces lists of…

GoPubMed
Web

GoPubMed

Allows users to explore PubMed search results with the Gene Ontology (GO), a…

Allows users to explore PubMed search results with the Gene Ontology (GO), a hierarchically structured vocabulary for molecular biology. GoPubMed provides the following benefits: first, it gives an…

DTMiner
Web

DTMiner

A framework for the automatic extraction of gene-disease relation from…

A framework for the automatic extraction of gene-disease relation from biomedical literature. DTMiner takes large biomedical literature repositories as inputs, identifies credible relationships…

EBIMed
Web

EBIMed

A web application that combines Information Retrieval and Extraction from…

A web application that combines Information Retrieval and Extraction from Medline. EBIMed finds Medline abstracts in the same way PubMed does. Then it goes a step beyond and analyses them to offer a…

AND-HCV
Desktop

AND-HCV Associative Network Discovery-HCV

A system for automated reconstruction of molecular genetic interaction…

A system for automated reconstruction of molecular genetic interaction networks. ANDSystem provides the reconstruction and analysis of semantic associative network, i.e., networks describing…

miRTex
Desktop

miRTex

Extracts microRNAs (miRNA)-target relations, miRNA-gene and gene-miRNA…

Extracts microRNAs (miRNA)-target relations, miRNA-gene and gene-miRNA regulation relations embedded in individual sentences. miRTex is a text mining system which can be integrated into…

FACTA+
Web

FACTA+ Finding Associated Concepts with Text Analysis

A real-time text-mining system for finding and visualizing indirect…

A real-time text-mining system for finding and visualizing indirect associations between biomedical concepts from MEDLINE abstracts. The system can be used as a text search engine like PubMed with…

CheTo
Desktop

CheTo ChemicalTopic

Identifies and retrieves chemical series from sets of molecules. CheTo permits…

Identifies and retrieves chemical series from sets of molecules. CheTo permits users to interactively visualize the chemical topic model. It can discover hidden structure in molecule sets and find…

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…

SCNN-DDI
Desktop

SCNN-DDI

A syntax convolutional neural network (SCNN) based drug-drug interaction (DDI)…

A syntax convolutional neural network (SCNN) based drug-drug interaction (DDI) extraction approach. In this approach, a novel word embedding (syntax word embedding) is proposed to exploit the…

@MInter
Desktop

@MInter Automated Text-mining of Microbial Interactions

A machine-learning-based text-mining system for automated identification and…

A machine-learning-based text-mining system for automated identification and extraction of microbial interaction data. @MInter complements manual annotation and curation through the identification of…

DeepDive
Desktop

DeepDive

An extractor for gene-gene interactions that identified candidate gene-gene…

An extractor for gene-gene interactions that identified candidate gene-gene relations within an input sentence. For each candidate relation, DeepDive computed a probability that the relation was a…

PIE the search
Web

PIE the search Protein Interaction information Extraction the search

Provides protein interaction information (PPI) articles for biologists,…

Provides protein interaction information (PPI) articles for biologists, baseline system performance for bio-text mining researchers and a compact PubMed-search environment for PubMed users. For easy…

GLAD4U
Web

GLAD4U Gene List Automatically Derived For You

Creates expert candidate gene lists. GLAD4U is a web-based gene retrieval and…

Creates expert candidate gene lists. GLAD4U is a web-based gene retrieval and prioritization tool. It uses NCBI eSearch API to find publications related to a user query and on the gene-to-publication…

ANDSystem
Desktop

ANDSystem Associative Network Discovery System

A tool developed for the reconstruction of molecular genetic networks.…

A tool developed for the reconstruction of molecular genetic networks. ANDSystem is based on an automated text- and data-mining techniques. It provides detailed description of the various types of…

DiMeX
Dataset

DiMeX eXtraction of Mutation association to Diseases

A text mining system for mutation-disease association extraction. DiMeX…

A text mining system for mutation-disease association extraction. DiMeX consists of a series of natural language processing modules that preprocess input text and apply syntactic and semantic…

TIN-X
Web

TIN-X

Visualizes the association between proteins and diseases, based on text mining…

Visualizes the association between proteins and diseases, based on text mining data processed from scientific literature. TIN-X provides an interactive visualization, ranking, and prioritization…

BELMiner
Web

BELMiner

Provides a rule-based semantic parser that extracts biological event…

Provides a rule-based semantic parser that extracts biological event relationship across sentences to translate the textual extractions to Biological Expression Language (BEL) statement as outlined…

Anni
Web

Anni

An online tool to aid the biomedical researcher with a broad range of…

An online tool to aid the biomedical researcher with a broad range of information needs. Anni provides an ontology-based interface to MEDLINE and retrieves documents and associations for several…

DISEASES
Dataset

DISEASES

A resource which aims to be the most comprehensive freely available database of…

A resource which aims to be the most comprehensive freely available database of disease–gene associations. DISEASES is based on an open-source text-mining software that recognizes diseases and…

E3Miner
Web

E3Miner

A web-based text mining tool that extracts and incorporates comprehensive…

A web-based text mining tool that extracts and incorporates comprehensive knowledge about E3s with their underlying mechanisms. E3Miner integrates available E3 data not only from the published…

BWS
Web

BWS BIOSMILE Web Search

A web-based NCBI-PubMed search application, which can analyze articles for…

A web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object, location, manner, time, etc. After…

ToxReporter
Desktop

ToxReporter

Compiles information from a broad selection of resources and limits display of…

Compiles information from a broad selection of resources and limits display of the information to user-selected areas of interest. ToxReporter is a PERL-based web-application which utilizes a MySQL…

silverCID
Dataset

silverCID silver for Chemical Induced Diseases

A silver standard corpus for chemical-induced diseases (CID) relation…

A silver standard corpus for chemical-induced diseases (CID) relation extraction. Two novel aspects that makes othe SilverCID corpus different from other resources are (i) it was built automatically…

BRONCO
Dataset

BRONCO Biomedical entity Relation ONcology COrpus

A corpus that contains more than 400 variants and their relations with genes,…

A corpus that contains more than 400 variants and their relations with genes, diseases, drugs, and cell lines in the context of cancer and anti-tumor drug screening research. BRONCO can be utilized…

crowd cid relex
Desktop

crowd cid relex

A crowdsourcing approach to extracting chemical-disease relations (CDRs) from…

A crowdsourcing approach to extracting chemical-disease relations (CDRs) from PubMed abstracts in the context of the BioCreative V community-wide biomedical text mining challenge. Five non-expert…

CD-REST
Web

CD-REST Chemical Disease Relation Extraction SysTem

An end-to-end system for extracting chemical-induced disease relations in…

An end-to-end system for extracting chemical-induced disease relations in biomedical literature. CD-REST consists of two main components: (1) a chemical and disease named entity recognition and…

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…

PPI finder
Web

PPI finder

A web-based tool to mine human PPIs from PubMed abstracts based on their…

A web-based tool to mine human PPIs from PubMed abstracts based on their co-occurrences and interaction words, followed by evidences in human PPI databases and shared terms in GO database. PPI Finder…

eFIP
Web

eFIP extracting Functional Impact of Phosphorylation

A tool to support article selection and information extraction of functional…

A tool to support article selection and information extraction of functional impact of phosphorylated proteins. The current version focuses on protein-protein interactions (PPIs) as functional…

PPLook
Desktop

PPLook

A PPI search system which automatically extracts and visualizes protein-protein…

A PPI search system which automatically extracts and visualizes protein-protein interaction (PPI) from text. Given a query protein name, PPLook can search a dataset for other proteins interacting…

eGIFT
Web

eGIFT extracting Gene Information From Text

Identifies terms and documents that are relevant to a gene and its products.…

Identifies terms and documents that are relevant to a gene and its products. Additional functionalities of eGIFT include finding terms in documents for a group of genes, finding genes sharing a…

BioLabeler
Web

BioLabeler

Extracts UMLS concepts from biomedical texts such as scientific paper…

Extracts UMLS concepts from biomedical texts such as scientific paper abstracts, experiments descriptions or medical notes and can be used to automatically curate and annotate BioMedical Literature…

PPInterFinder
Web

PPInterFinder

A web-based text mining tool to extract human PPIs from biomedical literature.…

A web-based text mining tool to extract human PPIs from biomedical literature. PPInterFinder uses relation keyword co-occurrences with protein names to extract information on PPIs from MEDLINE…

Coremine…
Web

Coremine Medical

A product of the PubGene Company designed to be used by anyone seeking…

A product of the PubGene Company designed to be used by anyone seeking information on health, medicine and biology. It is ideal for those seeking an overview of a complex subject while allowing the…

Biblio-MetReS
Desktop

Biblio-MetReS

Analyzes scientific documents to find the interactions between genes/proteins…

Analyzes scientific documents to find the interactions between genes/proteins in order to reconstruct molecular networks. Biblio-MetReS relies on a central database with the genomes and gene…

CPNM
Web

CPNM Context-specific Protein Network Miner

Derives context-specific protein interactions networks (PINs) in real-time from…

Derives context-specific protein interactions networks (PINs) in real-time from the PubMed database based on a set of user-input keywords and enhanced PubMed query system. CPNM provides a tool for…

Nermal
Web

Nermal

A protein prioritizer that helps to find those proteins that have a strong…

A protein prioritizer that helps to find those proteins that have a strong relationship with the protein that you enter in the search field. The relationship between two proteins is based on the…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.