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.

Canto v840 – Community Literature Curation

Canto v840

:: 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, Cambridge Systems Biology Centre

:: 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.

PathBinder 1.0 – Explore Literature, Annotate Metabolic and Regulatory Interactions and Biomolecules

PathBinder 1.0

:: DESCRIPTION

PathBinder is a unique, plant-based tool to explore literature, and to annotate metabolic and regulatory interactions and biomolecules. PathBinder queries the MEDLINE database and retrieves sentences containing two terms of interest, and rank them based on their probability to describe interactions between the two given terms; each sentence is a clickable link pointing to the original online PubMed citation.

::DEVELOPER

Lifeng Zhang zlfpeak@iastate.edu

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 PathBinder

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S18.
PathBinder–text empirics and automatic extraction of biomolecular interactions.
Zhang L, Berleant D, Ding J, Cao T, Syrkin Wurtele E.

RANKER – PubMed-based Literature Mining software

RANKER

:: DESCRIPTION

RANKER is a PubMed-based literature mining software for ranking the importance of genes in a given context.

::DEVELOPER

Dr.Zhang’s Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • Orthomcl, BLAST (blastall and formatdb), and mcl.

:: DOWNLOAD

 RANKER

:: MORE INFORMATION

Citation

Yang L, Xu L, He L. 2009.
A CitationRank algorithm inheriting Google technology designed to highlight genes responsible for serious adverse drug reaction.
Bioinformatics. 25(17):2244-50.

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.

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