Using Model Organism Databases (MODs)

Stacia R. Engel1, Kevin A. MacPherson1

1 Stanford University School of Medicine, California
Publication Name:  Current Protocols Essential Laboratory Techniques
Unit Number:  Unit 11.4
DOI:  10.1002/cpet.4
Online Posting Date:  November, 2016
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Abstract

Model Organism Databases (MODs) represent the union of database technology and biology, and are essential to modern biological and medical research. Research communities are producing floods of new data, of increasingly different types and complexity. MODs assimilate this information from a wide variety of sources, organize it in a comprehensible manner, and make it freely available to the public via the Internet. MODs permit researchers to sort through massive amounts of data, providing access to key information that they might otherwise have overlooked. The protocols in this unit offer a general introduction to different types of data available in the growing number of MODs, and approaches for accessing, browsing, and querying these data. © 2016 by John Wiley & Sons, Inc.

Keywords: genome project; genetics; DNA sequence; gene model; protein function

     
 
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Table of Contents

  • Overview and Principles
  • Basic Protocol 1: General Guidelines for Using a Model Organism Database Using the Saccharomyces Genome Database as an Example
  • Basic Protocol 2: Obtaining a Sequence from JBrowse
  • Basic Protocol 3: Using Textpresso to Search Full‐Text Papers
  • Basic Protocol 4: Using InterMine to Perform Complex Data Queries
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

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Literature Cited

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Internet Resources
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  The Arabidopsis Information Resource (TAIR): Database of genetic and molecular biology data for the plant Arabidopsis thaliana.
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  Ashbya Genome Database (AGD): Database of gene annotation and microarray data for Ashbya gossypii and Saccharomyces cerevisiae.
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  Aspergillus Genome Database (AspGD): Resource for genomic sequence data and gene and protein information for Aspergilli.
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  Database that serves as a resource for genomic sequence data and gene and protein information for Candida albicans.
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  Resource for the biology and genomics of the social amoeba Dictyostelium discoideum.
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  Centralized resource linking various E. coli online information services, databases, and Web sites.
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  Database of Drosophila genes and genomes.
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  Generic Model Organism Database (GMOD) project: Collection of open‐source software tools for creating genome‐scale biological databases.
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  Data resource for comparative genome analysis in the grasses.
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  InterMine: Open‐source data warehouse system that enables the creation of biological databases that integrate multiple types of data from different sources.
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  Database of genomic sequence and genetic data for Paramecium tetraurelia.
  http://rgd.mcw.edu
  Rat Genome Database (RGD): Database of laboratory rat genetic and genomic data, including information for quantitative trait loci, mutations, and phenotypes.
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  Saccharomyces Genome Database (SGD): Scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae.
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  http://smedgd.neuro.utah.edu
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