MalaCards: A Comprehensive Automatically‐Mined Database of Human Diseases

Noa Rappaport1, Michal Twik1, Noam Nativ1, Gil Stelzer1, Iris Bahir1, Tsippi Iny Stein1, Marilyn Safran2, Doron Lancet1

1 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel, 2 Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.24
DOI:  10.1002/0471250953.bi0124s47
Online Posting Date:  September, 2014
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Abstract

Systems medicine provides insights into mechanisms of human diseases, and expedites the development of better diagnostics and drugs. To facilitate such strategies, we initiated MalaCards, a compendium of human diseases and their annotations, integrating and often remodeling information from 64 data sources. MalaCards employs, among others, the proven automatic data‐mining strategies established in the construction of GeneCards, our widely used compendium of human genes. The development of MalaCards poses many algorithmic challenges, such as disease name unification, integrated classification, gene‐disease association, and disease‐targeted expression analysis. MalaCards displays a Web card for each of >19,000 human diseases, with 17 sections, including textual summaries, related diseases, related genes, genetic variations and tests, and relevant publications. Also included are a powerful search engine and a variety of categorized disease lists. This unit describes two basic protocols to search and browse MalaCards effectively. Curr. Protoc. Bioinform. 47:1.24.1‐1.24.19. © 2014 by John Wiley & Sons, Inc.

Keywords: biological database; network medicine; disease database; symptoms; bioinformatics; medical database; integrated information retrieval; GeneCards

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Searching and Browsing MalaCards
  • Basic Protocol 2: Exploring a MalaCard
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

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   Safran, M. , Dalah, I. , Alexander, J. , Rosen, N. , Iny Stein, T. , Shmoish, M. , Nativ, N. , Bahir, I. , Doniger, T. , Krug, H. , Sirota‐Madi, A. , Olender, T. , Golan, Y. , Stelzer, G. , Harel, A. , and Lancet, D. 2010. GeneCards version 3: The human gene integrator. Database (Oxford) 2010:baq020.
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   Stelzer, G. , Dalah, I. , Stein, T.I. , Satanower, Y. , Rosen, N. , Nativ, N. , Oz‐Levi, D. , Olender, T. , Belinky, F. , Bahir, I. , Krug, H. , Perco, P. , Mayer, B. , Kolker, E. , Safran, M. , and Lancet, D. 2011. In‐silico human genomics with GeneCards. Hum. Genomics 5:709‐717.
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Internet Resources
   http://www.genecards.org/
  GeneCards (http://www.genecards.org/) is a compendium of human genes that provides genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes. It is being developed and maintained by the Crown Human Genome Center at the Weizmann Institute of Science.
   http://www.genecards.org/index.php?path=Gene
  GeneDecks is a novel analysis tool which provides a similarity metric by highlighting shared descriptors between genes, based on the rich annotation within the GeneCards compendium of human genes. GeneDecks features Partner Hunter and Set Distiller.
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