Context-MMIA – miRNA-mRNA Target Prediction system combining Expression data and Literature data.

Context-MMIA

:: DESCRIPTION

Context-MMIA is miRNA-mRNA target prediction system combining expression data and literature data.

::DEVELOPER

Bio & Health Informatics Lab , Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Oh M, Rhee S, Moon JH, Chae H, Lee S, Kang J, Kim S.
Literature-based condition-specific miRNA-mRNA target prediction.
PLoS One. 2017 Mar 31;12(3):e0174999. doi: 10.1371/journal.pone.0174999. PMID: 28362846; PMCID: PMC5376335.

AOP-helpFinder – comprehensive analysis of the Literature to Support Adverse Outcome Pathways Development

AOP-helpFinder

:: DESCRIPTION

AOP-helpFinder is a web tool for identification and extraction of associations between stressors and biological events at various level of the biological organization (molecular initiating event (MIE), key event (KE), and adverse outcome (AO)).

::DEVELOPER

AOP-helpFinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Jornod F, Jaylet T, Blaha L, Sarigiannis D, Tamisier L, Audouze K.
AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development.
Bioinformatics. 2021 Oct 30:btab750. doi: 10.1093/bioinformatics/btab750. Epub ahead of print. PMID: 34718414.

MetDisease 1.1.0 – Connecting Metabolites to Diseases via Literature

MetDisease 1.1.0

:: DESCRIPTION

MetDisease is an app for Cytoscape, the bioinformatics network visualization tool. The app is used to annotate a metabolic network with MeSH disease terms, explore related diseases within a network, and link to PubMed references corresponding to any network node and selection of MeSH terms. MeSH terms are controlled vocabulary terms used by the National Library of Medicine to describe the content of the articles indexed in PubMed.

::DEVELOPER

MetDisease team

:: SCREENSHOTS

MetDisease

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 MetDisease

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 23. [Epub ahead of print]
MetDisease–connecting metabolites to diseases via literature.
Duren W1, Weymouth T, Hull T, Omenn GS, Athey B, Burant C, Karnovsky A.

RIscoper – RNA Interaction Extraction from Literatures

RIscoper

:: DESCRIPTION

RIscoper (RNA Interactome Scoper) represents the first tool for full-scale RNA interactome scanning and was developed for extracting RRIs from the literature based on the N-gram model.

::DEVELOPER

WD Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

RIscoper

:: MORE INFORMATION

Citation

Zhang Y, Liu T, Chen L, Yang J, Yin J, Zhang Y, Yun Z, Xu H, Ning L, Guo F, Jiang Y, Lin H, Wang D, Huang Y, Huang J.
RIscoper: a tool for RNA-RNA interaction extraction from the literature.
Bioinformatics. 2019 Sep 1;35(17):3199-3202. doi: 10.1093/bioinformatics/btz044. PMID: 30668649.

Canto v1651 – Community Literature Curation

Canto v1651

:: DESCRIPTION

Canto is an online annotation tool which has been developed to allow researchers to curate the genetic and molecular data from their publications for inclusion in public biological databases.

::DEVELOPER

Val Wood

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • GCC
  • CLucene

:: DOWNLOAD

 Canto

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 12.
Canto: an online tool for community literature curation.
Rutherford KM1, Harris MA, Lock A, Oliver SG, Wood V.

DISEASES – Disease-gene Associations Mined from Literature

DISEASES

:: DESCRIPTION

DISEASES is a frequently updated web resource that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies.

::DEVELOPER

JensenLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DISEASES

:: MORE INFORMATION

Citation

DISEASES: text mining and data integration of disease-gene associations.
Pletscher-Frankild S, Pallejà A, Tsafou K, Binder JX, Jensen LJ.
Methods. 2015 Mar;74:83-9. doi: 10.1016/j.ymeth.2014.11.020.

PubSearch 0.8.1 – Literature Curation Management System

PubSearch 0.8.1

:: DESCRIPTION

PubSearch is a literature curation management system designed to store and manage the available literature for an organism or system of interest. It provides database curators with a powerful literature search capability, stores relevant biological information, creates automatic associations between the biological information and the literature, and provides a user-friendly web interface for manual validation and curation.

::DEVELOPER

PubSearch Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 PubSearch

:: MORE INFORMATION

Citation

Yoo, D, Xu, I, Berardini, T, Rhee, S, Narayanasamy, V, Twigger, S (2006)
PubSearch and PubFetch: a simple management system for semiautomated retrieval and annotation of biological information from the literature..
Curr Protoc Bioinformatics. 2006 Mar;Chapter 9:Unit9.7.

Pubcrawl – Networks of Literature-based Semantic Distances with Protein Domain Interactions

Pubcrawl

:: DESCRIPTION

Pubcrawl is an interactive web application that generates normalized medline distances for terms, and then returns a network topology based on the term distances and protein domain interactions.

Pubcrawl Online Version

::DEVELOPER

Shmulevich Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Pubcrawl

:: MORE INFORMATION