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

Improving search interface software tools | Information retrieval

Software tools extending PubMed functionality by improving the search interface.

SBT
Desktop

SBT Sequence Bloom Tree

Allows to index a set of short-read sequencing experiments and then query them…

Allows to index a set of short-read sequencing experiments and then query them quickly for a given sequence. The SBT data structure facilitates searching short-read expression experiments for…

Pathguide
Dataset

Pathguide

Provides information on over 190 published online cellular pathway and network…

Provides information on over 190 published online cellular pathway and network databases. Pathguide is organised around approximate categories and a database can be stored in multiple categories if…

Missing…
Dataset

Missing ProteinPedia

Aims to collate any relevant data pertaining to any PE2-4 protein. Missing…

Aims to collate any relevant data pertaining to any PE2-4 protein. Missing ProteinPedia permits to define, summarize and discuss all available data for the so-called missing proteins, emphasizing why…

DIRECT
Dataset

DIRECT DNA-mutation Inventory to Refine and Enhance Cancer Treatment

Provides clinically relevant somatic mutations. DIRECT enables a genetically…

Provides clinically relevant somatic mutations. DIRECT enables a genetically informed approach to cancer medicine by providing clinicians access to tumor gene therapy-response information based on…

HMS
Web

HMS Hyperlink Management System

Updates and maintains hyperlinks among major public science databases.…

Updates and maintains hyperlinks among major public science databases. Hyperlink Management System automatically downloads the lists of data IDs for human genes and proteins and their relations from…

ScaleNet
Dataset

ScaleNet

Models biological diversity of scale insects through 300 years of published…

Models biological diversity of scale insects through 300 years of published research. ScaleNet is a manually-curated, web-accessible database that manages information about the systematics,…

MRS
Web
Desktop

MRS

Provides an in-house access to biological data banks. MRS give an access to…

Provides an in-house access to biological data banks. MRS give an access to more than 10 data banks. The software provides a configuration file that holds for each data bank all information about its…

GeNemo
Web

GeNemo

A web-based search engine for functional genomic data. GeNemo searches…

A web-based search engine for functional genomic data. GeNemo searches user-input data against online functional genomic datasets, including the entire collection of ENCODE and mouse ENCODE datasets.…

CellBase
Desktop

CellBase

Queries a centralized database containing the most relevant biological data…

Queries a centralized database containing the most relevant biological data sources. CellBase avoids problem coming from the increasing of data files, the different standards among repositories or…

EBI Search…
Web

EBI Search engine

A scalable text search engine that provides easy and uniform access to the…

A scalable text search engine that provides easy and uniform access to the biological data resources hosted at the European Bioinformatics Institute (EMBL-EBI). The data resources represented in EBI…

GExplore
Dataset

GExplore

Assists with large-scale data-mining related to gene function in Caenorhabditis…

Assists with large-scale data-mining related to gene function in Caenorhabditis elegans. GExplore contains information about the domain organization of the proteomes of 9 nematode species, can…

ICA
Desktop

ICA Insilicos Cloud Army

Adapts the popular X!Tandem peptide search engine to work with Hadoop MapReduce…

Adapts the popular X!Tandem peptide search engine to work with Hadoop MapReduce for reliable parallel execution of large searches. MR-Tandem is designed to drop in wherever X!Tandem is already in use…

CCT
Desktop

CCT Current Comparative Table

Enables to automate customized bioinformatics searches, typically of remote…

Enables to automate customized bioinformatics searches, typically of remote sequence or hidden Markov model (HMM) databases. CCT is useful to scientists who study large sets of molecules in today’s…

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…

Mantis
Desktop

Mantis

Allows users to query for the existence of sequences in large collections of…

Allows users to query for the existence of sequences in large collections of data sets. Mantis counts k-mer by using a counting quotient filter. It enables users to determine if the set of…

BioCarian
Dataset

BioCarian

Allows exploration of biological databases utilizing semantic web methods.…

Allows exploration of biological databases utilizing semantic web methods. BioCarian is a search engine that browses several selected public databases. The databases consist in a sample collection of…

SATORI
Server

SATORI Semantic AnnoTations and Ontological Relations Interface

Allows biomedical data management, analysis, and visualization. SATORI is a…

Allows biomedical data management, analysis, and visualization. SATORI is a web-based exploration system that combines search with visual browsing to provide an integrated exploration experience. The…

litDB
Desktop

litDB

Allows the maintenance of publication lists assigned to various topics. liDB…

Allows the maintenance of publication lists assigned to various topics. liDB allows researchers to store records of their own publications on a central server. It supports the calculation of impact…

FirebrowseR
Desktop

FirebrowseR

Automatically generates, testes and deploys such clients for rapid response to…

Automatically generates, testes and deploys such clients for rapid response to API changes. FirebrowseR provides a raw construct of an R function including all the comments, which will be rendered as…

LinkDB
Dataset

LinkDB

Supplies data concerning molecular biology. LinkDB is a collection of database…

Supplies data concerning molecular biology. LinkDB is a collection of database links. It contains the original links provided by each database and the indirect and reverse links that are computed.…

DBGET
Dataset

DBGET

Provides information about molecular biology topic. DBGET is a database…

Provides information about molecular biology topic. DBGET is a database allowing to search and extract entries from a diverse range of databases. In this resource, a database is considered as a…

DigSee
Web

DigSee Disease gene Search engine with evidence sentences

A search engine to find explicit association between genes and cancer through…

A search engine to find explicit association between genes and cancer through biological events. Although several Web-based text-mining systems are available to extract implicit relationship between…

GeneView
Web

GeneView

A semantic search engine for biomedical knowledge. GeneView is built upon a…

A semantic search engine for biomedical knowledge. GeneView is built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts. This semi-structured…

HubMed
Web

HubMed

An alternative search interface to the PubMed database of biomedical…

An alternative search interface to the PubMed database of biomedical literature, incorporating external web services and providing functions to improve the efficiency of literature search, browsing…

TogoDoc
Desktop
Mobile

TogoDoc

Helps researchers to isolate interesting papers from the ‘‘tsunami’’ of…

Helps researchers to isolate interesting papers from the ‘‘tsunami’’ of literature, in which, on average, more than one biomedical paper is added to MEDLINE every minute. The TogoDoc system…

sWM
Desktop

sWM Secure Wavelet Matrix

Searches a string in logarithmic time of |Σ|. sWM uses an additively…

Searches a string in logarithmic time of |Σ|. sWM uses an additively homomorphic encryption to build an efficient data structure called a wavelet matrix. In an experiment using a simulated string of…

PubData
Desktop

PubData

A user-friendly, cross-platform application that allows users to retrieve and…

A user-friendly, cross-platform application that allows users to retrieve and download data files from all bioinformatics databases. PubData uses keywords to search for specific biomedical data much…

rfishbase
Desktop

rfishbase

Provides interactive and programmatic access to the FishBase repository.…

Provides interactive and programmatic access to the FishBase repository. rfishbase allows interaction with data on over 30 000 fish species in the rich statistical computing environment. It enables…

OrChem
Desktop

OrChem

Adds registration and indexing of chemical structures to support fast…

Adds registration and indexing of chemical structures to support fast substructure and similarity searching. OrChem is an open source chemistry plugin / cartridge for the relational database system…

Native Health…
Dataset

Native Health Database

Contains bibliographic information and abstracts of health-related articles,…

Contains bibliographic information and abstracts of health-related articles, reports, surveys, and other resource documents pertaining to the health and health care of American Indians, Alaska…

Bioz, Inc
Dataset

Bioz, Inc

Mines hundreds of millions of pages of complex, dense and unstructured…

Mines hundreds of millions of pages of complex, dense and unstructured life-sciences papers, and then uses Natural Language Processing and Machine Learning to clean, tag and structure the data.…

esFragBag
Desktop

esFragBag entropy-scaling FragBag

Involves extending an existing codebase with new database generation and…

Involves extending an existing codebase with new database generation and similarity search functions. esFragBag is able to achieve an average factor of 10 speedup of the highly-optimized FragBag with…

Smart Drug…
Web

Smart Drug Search

A search engine in assistance of antimicrobial research. Smart Drug Search is…

A search engine in assistance of antimicrobial research. Smart Drug Search is use for the screening of literature related to antimicrobial resistance, microbial virulence and topics alike. The search…

PubMed-EX
Desktop

PubMed-EX

A browser extension that marks up PubMed search results with additional…

A browser extension that marks up PubMed search results with additional text-mining information. PubMed-EX's page mark-up, which includes section categorization and gene/disease and relation…

iPubMed
Web
Mobile

iPubMed

A system for searching the MEDLINE database, implemented in a fully functional.…

A system for searching the MEDLINE database, implemented in a fully functional. Comparing with the most widely used PubMed system at NCBI, the iPubMed system contains two unique features: (i) being…

G-Bean
Web

G-Bean Graph based Biomedical search engine

A Web-based literature retrieval tool to query documents in MEDLINE database.…

A Web-based literature retrieval tool to query documents in MEDLINE database. The major contributions of G-Bean are three folds: 1) G-Bean uses a multithreaded parallel algorithm to automatically…

pubmed2ensembl
Web

pubmed2ensembl

An extension to the BioMart system that links over 2,000,000 articles in PubMed…

An extension to the BioMart system that links over 2,000,000 articles in PubMed to nearly 150,000 genes in Ensembl from 50 species. By allowing biologists to find the relevant literature on specific…

PubMatrix
Web

PubMatrix

Allows simple text based mining of the NCBI literature search service PubMed…

Allows simple text based mining of the NCBI literature search service PubMed using any two lists of keywords terms, resulting in a frequency matrix of term cooccurrence. PubMatrix is a web-based toll…

Researcher
Mobile

Researcher

Allows searchers to follow, filter and save papers from all journals relevant…

Allows searchers to follow, filter and save papers from all journals relevant to user’s research. Researcher is a mobile app that permits to (i) find and read academic journals by selecting from…

Taxadb
Desktop

Taxadb

Allows users to locally query the ncbi taxonomy.

Allows users to locally query the ncbi taxonomy.

Kopernio
Desktop

Kopernio

Permits users to get access to a large number of research papers. Kopernio…

Permits users to get access to a large number of research papers. Kopernio gives direct links to the full text articles without redirection or login step. It finds papers on university’s servers…

DESHCV
Dataset

DESHCV Dragon Exploratory System on Hepatitis C Virus

Provides a biomedical text-mining and relationship exploring knowledgebase.…

Provides a biomedical text-mining and relationship exploring knowledgebase. DESHCV is a comprehensive Hepatitis C Virus (HCV) online web resource. Users can retrieve information using specified…

SciVal
Web

SciVal

Gives access to research performance of about 8500 research institutions.…

Gives access to research performance of about 8500 research institutions. SciVal facilitates new discoveries, collaboration and access to knowledge in order to find funding. It is a support platform…

SciFeed
Web

SciFeed

Automates search query in literature database. SciFeed is based on SciLit which…

Automates search query in literature database. SciFeed is based on SciLit which contains more than 85 million of articles. It automatically sent a mail to user went a new article published correspond…

SJFinder
Web

SJFinder

Supports scientific community and connects members as a part of a global…

Supports scientific community and connects members as a part of a global research community. SJFinder offers a way to collect, extract and analyze data. It is able to suggest to user collaborators…

SciCurve
Web

SciCurve

Allows the exploration of life sciences from big data point of view. SciCurve…

Allows the exploration of life sciences from big data point of view. SciCurve permits users to explore a subject in great detail. It is a systematic literature review method and offers interactive…

ReadCube
Desktop
Mobile

ReadCube

Offers an intuitive way to read, manage and discover new literature. ReadCube…

Offers an intuitive way to read, manage and discover new literature. ReadCube offers features that permit to optimize PDF viewing, click on inline references, navigate to related articles, add inline…

PubNiche
Nontypeable

PubNiche

Offers a selection of scientific articles.

Offers a selection of scientific articles.

PubPeer
Dataset

PubPeer

Enables innovative approaches for community interaction. PubPeer is an online…

Enables innovative approaches for community interaction. PubPeer is an online journal club. It is searchable thank DOI, PMID, arXiv ID, keyword or author name.

PubChase
Web
Mobile

PubChase

Permits to stay connected with biomedical research on fields of interest.…

Permits to stay connected with biomedical research on fields of interest. PubChase allows users to create their own library to store, organize and access articles through different platforms. It is…

Paperscape
Dataset

Paperscape

Displays an interactive map that represents the arXiv repository for scientific…

Displays an interactive map that represents the arXiv repository for scientific research papers. Paperscape represents each paper by a circle, with the size of a circle related to how often that…

Paperity
Dataset

Paperity

Regroups open access journals and articles. Paperity is multi-disciplinary and…

Regroups open access journals and articles. Paperity is multi-disciplinary and aims to facilitate access to literature. The goal of the platforms is to regroup integrality of open access literature.…

Nowomics
Web

Nowomics

Permits to follow news about life science. Nowomics allows users to construct…

Permits to follow news about life science. Nowomics allows users to construct personalized feeds that returns new life science papers. It is based on text mining methods and is able to identify…

Scizzle
Web

Scizzle

Allows to automatically discover new papers in users’ field. Scizzle…

Allows to automatically discover new papers in users’ field. Scizzle facilitates the researchers work by avoiding making search on PubMed and permits to earn time. It offers an easy to use…

Biovista Vizit
Web

Biovista Vizit

Helps biomedical scientists with their research and discovery work. Biovista…

Helps biomedical scientists with their research and discovery work. Biovista Vizit is a visual bibliography search tool based on PubMed that permits to collaborate and helps to share information.…

Bio-In
Dataset

Bio-In

Offers the capability to integrate, aggregate, analyze and visualize biomedical…

Offers the capability to integrate, aggregate, analyze and visualize biomedical data from a wide variety of structured and unstructured information repositories. Bio-In combines its extensive…

XTractor
Dataset

XTractor

Allows semantic searching from the public literature sources. XTractor provides…

Allows semantic searching from the public literature sources. XTractor provides association information with reference to various biomedical entities. The metadata is linked to more than 20 external…

PubCrawler
Dataset

PubCrawler

Scans daily updates of medical databases. PubCrawler offers a database that…

Scans daily updates of medical databases. PubCrawler offers a database that helps keeping scientists informed of the current contents of Medline and GenBank, by listing new database entries that…

drfinddata
Desktop

drfinddata

Finds public databases by data type. drfinddata searches the Data Resource…

Finds public databases by data type. drfinddata searches the Data Resource Catalogue to find entries with EDAM data terms matching a query string. The first search is of the EDAM ontology data…

Stssearch
Desktop

Stssearch

Searches a DNA database for matches with a set of sequence-tagged sites (STS)…

Searches a DNA database for matches with a set of sequence-tagged sites (STS) primers. stssearch reports expected matches. For each pair of primers, it looks for matches between the primers and the…

MethodBox
Desktop

MethodBox

Finds the variables needed to support a particular research question. MethodBox…

Finds the variables needed to support a particular research question. MethodBox gets to the variables faster and lets download only the data needed. It enables to browse and download data files,…

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…

Genes2WordCloud
Web

Genes2WordCloud

A web application that enables users to quickly identify biological themes from…

A web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. Genes2WordCloud provides users with…

BOSS
Web

BOSS Biomedical Object Search System

Fills the gap between either ends of the spectrum by allowing users to pose…

Fills the gap between either ends of the spectrum by allowing users to pose context-free queries and by returning a structured set of results. Furthermore, BOSS exhibits the characteristic of good…

PubReMiner
Web

PubReMiner

A front-end for the popular PubMed literature database at the NCBI. When you…

A front-end for the popular PubMed literature database at the NCBI. When you submit your query (which can be any query that can be processed by PubMed), PubReMiner will process the result of that…

BabelMeSH
Web
Mobile

BabelMeSH

A cross-language tool for searching MEDLINE/PubMed. Queries can be submitted as…

A cross-language tool for searching MEDLINE/PubMed. Queries can be submitted as single terms or complex phrases in French, Spanish and Portuguese. Citations will be sent to the user in English.…

Pubget
Web

Pubget

Permits to conduct searches of the medical literature and retrieving full-text…

Permits to conduct searches of the medical literature and retrieving full-text PDFs. Pubget’s search functionality and add-on features are evaluated to determine potential for library instruction…

askMEDLINE
Web
Mobile

askMEDLINE

A useful search tool for clinicians, researchers, and other information seekers…

A useful search tool for clinicians, researchers, and other information seekers interested in finding current evidence in MEDLINE/PubMed. The text-only format could be convenient for users with…

BioWAP
Web

BioWAP Bioinformatics Wireless Application Protocol

Permits to access to biological databases and bioinformatics applications on…

Permits to access to biological databases and bioinformatics applications on the web. BioWAP includes major biological databases and applications demonstrating a simple method of implementing…

Knowledge.bio
Dataset

Knowledge.bio

An online tool to explore established and potential gene-disease associations…

An online tool to explore established and potential gene-disease associations in the context of other biomedical relations. Knowledge.bio provides access to a network of interconnected concepts mined…

DB-PABP
Dataset

DB-PABP

Documents publicly available and experimentally determined polyanion-binding…

Documents publicly available and experimentally determined polyanion-binding proteins (PABPs). DB-PABP is a database that provides information collected from original literature reports of…

SyStemCell
Dataset

SyStemCell

Gathers information about stem cell research. SyStemCell is a manually-curated…

Gathers information about stem cell research. SyStemCell is a manually-curated database which contains data extracted of more than 280 PubMed’ publications. It aims to provide a basic platform to…

Gene2EST
Web

Gene2EST

Searches expressed sequence tag (EST) databases with eukaryotic gene-sized…

Searches expressed sequence tag (EST) databases with eukaryotic gene-sized queries. Gene2EST brings together a set of tools enabling efficient retrieval of ESTs matching large DNA queries and their…

DSEARCH
Desktop

DSEARCH

Allows the user to utilize the idle clock cycles of machines to perform large…

Allows the user to utilize the idle clock cycles of machines to perform large searches using the most sensitive algorithms. DSEARCH is a fully cross-platform parallel database search program that…

SALSA
Web

SALSA Searching with Assembly of Local Sequence Alignments

Computes a gapped alignment of two sequences. SALSA uses dynamic programming to…

Computes a gapped alignment of two sequences. SALSA uses dynamic programming to build an accurate alignment based on the fragments initially identified. It produces a good estimate of the optimal…

PATIKAweb
Desktop

PATIKAweb

Provides a web interface for retrieving and analyzing biological pathways in…

Provides a web interface for retrieving and analyzing biological pathways in the PATIKA database, which contains data integrated from various prominent public pathway databases. PATIKAweb features a…

SciMiner
Desktop
Web

SciMiner

A web-based literature mining and functional analysis tool that identifies…

A web-based literature mining and functional analysis tool that identifies genes and proteins using a context specific analysis of MEDLINE abstracts and full texts. SciMiner scans biomedical…

GoWeb
Web

GoWeb

A semantic search engine to answer questions in the biomedical domain. GoWeb…

A semantic search engine to answer questions in the biomedical domain. GoWeb combines classical keyword-based web search with text-mining and ontologies to navigate large results sets and facilitate…

Information

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