Generic Model Organism Database

Model Organism Databases (MODs) describe genome and other information aboutimportant experimental organisms in the life sciences. Also calledorganism-specific databases, these databases capture the large volumesof data and information being generated by modern biology.Behind every MOD is a software system that is designed to helpmanage the data within the MOD, and to help users query and accessthose data. In the past, every MOD project developed its own softwaretools.

More recently, the [http://www.gmod.org Generic Model Organism Database (GMOD) Project] began as an effort to create reusable software tools fordeveloping MODs. GMOD is a loose federation of software applications (components) aimed at providing functionality that is needed by many or all model organism databases. Some of these software components are linked together by their use of a common database schema known as Chado. This project is funded by the US NIH, National Science Foundation and the USDA Agricultural Research Service.

oftware

The full list of GMOD software components is found on the [http://www.gmod.org GMOD home page] . These componentsinclude:

*GMOD Core (Chado database and tools)
** [http://www.gmod.org/Chado Chado] : the Chado schema and tools to install it.
** [http://www.gmod.org/XORT XORT ] : a tool for loading and dumping chado-xml
** [http://www.gmod.org/GMODTools GMODTools] : extracts data from a Chado database into common genome bulk formats (GFF, Fasta, etc)
*MOD website
** [http://turnkey.sf.net/ gmod-web/Turnkey ] : a generic web front end for browsing database contents.
*Genome Editing and Visualization
** [http://www.gmod.org/Apollo Apollo ] : a Java application for viewing and editing genome annotations
** [http://www.gmod.org/GBrowse GBrowse ] : a CGI application for displaying genome annotations
* Comparative Genomics
** [http://www.gmod.org/SynBrowse SynBrowse ] : a GBrowse based synteny viewer
** [http://www.gmod.org/CMap CMap ] : a CGI application for displaying comparative maps
*Literature curation
** [http://www.gmod.org/PubSearch PubSearch ] : a Java servlet web application for annotating genes from literature
** [http://www.gmod.org/PubFetch PubFetch ] : a tool to facilitate literature collection for curators' use
** [http://www.gmod.org/Textpresso Textpresso ] : a text mining system for scientific literature
*Database querying tools
** [http://www.gmod.org/BioMart BioMart ] : a query-oriented data management system
*Biological Pathways
** [http://bioinformatics.ai.sri.com/ptools/ Pathway Tools] : tools for metabolic pathway information, and analysis of high-throughput functional genomics data

Chado database schema

Chado makes extensive use of controlled vocabularies to type all entities in the database, so there is a feature table where gene, transcripts, exons, transposable elements, etc. are stored and their type is provided by the [http://sequenceontology.org/ Sequence Ontology] . When a new datatype comes along, the feature table requires no modification, only an update of the data in the database. The same is largely true of analysis data that can be stored in Chado as well.

The existing core modules of Chado are:
*sequence - for sequences/features
*cv - for controlled-vocabs/ontologies
*general - currently just dbxrefs
*organism - taxonomic data
*pub - publication and references
*companalysis - augments sequence module with computational analysis data
*map - non-sequence maps
*genetic - genetic and phenotypic data
*expression - gene expression

References

* cite journal
author= Christopher J. Mungall, David B. Emmert, The FlyBase Consortium
title= A Chado case study: an ontology-based modular schema for representing genome-associated biological information
journal=Bioinformatics
year= 2007
volume= 23
pages= i337-i346
url= http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i337
doi= 10.1093/bioinformatics/btm189
* cite journal
author= Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S.
title= The generic genome browser: a building block for a model organism system database.
journal=Genome Res.
year= 2002
volume= 12
pages= 1599–610
url= http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=12368253
doi= 10.1101/gr.403602

* cite journal
author= Colbourne JK, Singan VR, Gilbert DG.
title= wFleaBase: the Daphnia genome database.
journal=BMC Bioinformatics.
year= 2005
volume= 6
pages= 45
doi= 10.1186/1471-2105-6-45

* cite journal
author= Chisholm RL, Gaudet P, Just EM, Pilcher KE, Fey P, Merchant SN, Kibbe WA.
title= dictyBase, the model organism database for Dictyostelium discoideum.
journal=Nucleic Acids Res.
year= 2006
volume= 34(Database issue)
pages= D423–7.
url= http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=16381903
doi= 10.1093/nar/gkj090

* cite journal
author= Wang L, Wang S, Li Y, Paradesi MS, Brown SJ.
title= BeetleBase: the model organism database for Tribolium castaneum.
journal=Nucleic Acids Res.
year= 2007
volume= 35(Database issue)
pages= D476–9
url= http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=17090595
doi= 10.1093/nar/gkl776

* cite journal
author=Arnaiz O, Cain S, Cohen J, Sperling L.
title=ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data.
journal=Nucleic Acids Res.
year=2007
volume=35(Database issue)
pages=D439–44
doi=10.1093/nar/gkl777

Participating databases

The following organism databases are contributing to and/or adopting GMOD components for model organism databases.

Related projects

*Bioperl
*BioJava
*Ensembl
*Gene Ontology Software [http://www.godatabase.org/dev/doc/www-intro.html]
*DAS [http://biodas.org/]
*The Genomics Unified Schema [http://www.gusdb.org/]
*Manatee: Manual Annotation Tool Etc, Etc... [http://manatee.sourceforge.net/]
*Biocurator.org [http://biocurator.org/]
*Open Biomedical Ontologies
* [http://www.sequenceontology.org/ The Sequence Ontology Project]

ee also

*Biological database
*Genome project
*Genomics
*Genome