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 discovery software tools and databases | Biomedical text mining

ExpressionBlast
Dataset

ExpressionBlast

Uses automated text analysis to identify and merge replicates and to determine…

Uses automated text analysis to identify and merge replicates and to determine the type of each array in the series. ExpressionBlast processes expression data sets in Gene Expression Omnibus (GEO)…

MatchMiner
Web

MatchMiner

Navigates the complex world of gene and gene product identifiers. MatchMiner…

Navigates the complex world of gene and gene product identifiers. MatchMiner provides two primary functions: (i) LookUp, that translates an input list of gene identifiers into a matching output list…

PolySearch
Web

PolySearch

An online text-mining system for identifying relationships between human…

An online text-mining system for identifying relationships between human diseases, genes, proteins, drugs, metabolites, toxins, metabolic pathways, organs, tissues, subcellular organelles, positive…

e!DAL
Web

e!DAL electronic data archive library

Publishes and shares research data. e!DAL’s main features are version…

Publishes and shares research data. e!DAL’s main features are version tracking, metadata management, information retrieval, registration of persistent identifiers (DOI), an embedded HTTP(S) server…

LitInspector
Desktop

LitInspector

Performs large scale text mining on more than 20 million PubMed entries.…

Performs large scale text mining on more than 20 million PubMed entries. LitInspector's sophisticated gene recognition and intuitive color coding increase the readability of abstracts and lets…

Chilibot
Web

Chilibot

Searches PubMed literature database (abstracts) about specific relationships…

Searches PubMed literature database (abstracts) about specific relationships between proteins, genes, or keywords. The results are returned as a graph. Chilibot distills scientific relationships from…

COLO-tuple
Desktop

COLO-tuple

Compares metagenomic samples using long k-tuple features. COLO-tuple can (i)…

Compares metagenomic samples using long k-tuple features. COLO-tuple can (i) detect the relationship between species with high similarity and separate them well; (ii) reveal major groups among…

HiPub
Web
Desktop

HiPub

Recognizes, annotates and translates biomedical entities (e.g., genes,…

Recognizes, annotates and translates biomedical entities (e.g., genes, proteins, drugs and diseases) from texts into networks for knowledge discovery. HiPub visualizes texts as interactive biomedical…

MELODI
Web

MELODI Mining Enriched Literature Objects to Derive Intermediates

Identifies mechanistic pathways between any two biomedical concepts. MELODI can…

Identifies mechanistic pathways between any two biomedical concepts. MELODI can generate hypotheses for further investigation. It identifies enriched overlapping objects which have been assigned to…

libFLASM
Desktop

libFLASM

A software library for solving fixed-length approximate string matching (FLASM)…

A software library for solving fixed-length approximate string matching (FLASM) under both the edit and the Hamming distance models. libFLASM exposes two functions: one to solve FLASM under the edit…

PubNet
Web

PubNet

A web-based tool that extracts several types of relationships returned by…

A web-based tool that extracts several types of relationships returned by PubMed queries and maps them into networks, allowing for graphical visualization, textual navigation, and topological…

MuGeX
Web

MuGeX Mutation Gene eXtractor

Automatically extracts mutation-gene pairs from MEDLINE abstracts for a given…

Automatically extracts mutation-gene pairs from MEDLINE abstracts for a given disease. With automatic extraction techniques, MuGeX overcomes the problems of information retrieval from public…

BC5CIDTask
Desktop

BC5CIDTask

Utilizes simple yet effective linguistic features to extract relations with…

Utilizes simple yet effective linguistic features to extract relations with maximum entropy models. This chemical-induced disease (CID) relation extraction tool consisted of two specific subtasks:…

BioSimplify
Desktop

BioSimplify

Introduces and facilitates the use of a novel model for sentence simplification…

Introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction. BioSimplify is an open source sentence…

Disimweb
Dataset

Disimweb Disimweb: The disease similarity browser

Enables the user to obtain the similarity measure between over 28.5 million…

Enables the user to obtain the similarity measure between over 28.5 million pairs of diseases. Disimweb is a full interactive browser. This software is a method able to summarise the information…

MedEvi
Web

MedEvi

A search engine that imposes positional restriction on occurrences matching…

A search engine that imposes positional restriction on occurrences matching multi-term queries, based on the observation that terms with semantic relations which are explicitly stated in text are not…

PathTex
Desktop

PathTex

A system designed to integrate a pathway visualizer, text mining systems and…

A system designed to integrate a pathway visualizer, text mining systems and annotation tools into a seamless environment. This will enable biologists to freely move between parts of a pathway and…

EventMine
Web

EventMine

A machine learning-based pipeline system, which extracts events from documents…

A machine learning-based pipeline system, which extracts events from documents that already contain named entity annotations (e.g., genes/proteins, etc.). Given appropriate training data, EventMine…

GCAT
Web

GCAT

Determines the functional coherence of gene sets by performing latent semantic…

Determines the functional coherence of gene sets by performing latent semantic analysis of Medline abstracts. A Latent Semantic Indexing (LSI) model was built using over 1 million Medline abstracts…

FAUN
Web

FAUN Feature Annotation Using Nonnegative matrix factorization

A Web-based bioinformatics software environment to facilitate both the…

A Web-based bioinformatics software environment to facilitate both the discovery and classification of functional relationships among genes. FAUN not only assists researchers to use biomedical…

LAITOR
Desktop
Gene-disease…
Dataset

Gene-disease Networking

Employs a range of in silico methodologies using internally developed text…

Employs a range of in silico methodologies using internally developed text mining engine to identify, analyze and visualize gene-disease associations. GeneNet has Customized workflows for comparing…

Arrowsmith
Web

Arrowsmith

Identify meaningful links between two sets of Medline articles. Arrowsmith…

Identify meaningful links between two sets of Medline articles. Arrowsmith allows users to identify biologically meaningful links between any two sets of articles A and C in PubMed, even when these…

PCorral
Web

PCorral Protein Corral

A web application that combines information retrieval and extraction from…

A web application that combines information retrieval and extraction from Medline. PCorral retrieves the Medline abstracts that match your search criteria in the same way PubMed does. Then it…

MEDIE
Web

MEDIE

An intelligent search engine to retrieve biomedical correlations from MEDLINE,…

An intelligent search engine to retrieve biomedical correlations from MEDLINE, based on indexing by natural language processing and text mining techniques. You can find abstracts/sentences in MEDLINE…

CRONOS
Web

CRONOS

Maps identifiers, gene names and protein names from various resources like…

Maps identifiers, gene names and protein names from various resources like UniProt, RefSeq and Ensembl. CRONOS is a versatile tool that contains entries from five mammalian organisms. Beside gene and…

PubDNA Finder
Dataset

PubDNA Finder

Allows user to realize advanced researches about sequences of nucleic acids.…

Allows user to realize advanced researches about sequences of nucleic acids. PubDNA Finder is an online repository linking PubMed Central manuscripts to the different genetic sequences appearing in…

GeneRanker
Web

GeneRanker

Permits to obtain a ranked list of genes related to a specific disease or…

Permits to obtain a ranked list of genes related to a specific disease or biological process. GeneRanker combines gene-disease associations with protein-protein interactions (ppi) in order to rank…

OnTheFly!
Web

OnTheFly!

A web-based application that applies biological named entity recognition to…

A web-based application that applies biological named entity recognition to enrich Microsoft Office, PDF and plain text documents. OnTheFly is also able to extract the bioentities mentioned in a set…

sigterms
Desktop

sigterms

A desktop software application which retrieves all microRNA:mRNA functional…

A desktop software application which retrieves all microRNA:mRNA functional pairs represented by an experimentally derived set of genes. Sigterms computes, for each microRNA, an enrichment statistic…

Information

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