Generic Model Organism Database

Model Organism Databases (MODs) describe genome and other information about important experimental organisms in the life sciences. Also called organism-specific databases, these databases capture the large volumes of data and information being generated by modern biology. Behind every MOD is a software system that is designed to help manage the data within the MOD, and to help users query and access those data. In the past, every MOD project developed its own software tools.

More recently, the Generic Model Organism Database (GMOD) Project began as an effort to create reusable software tools for developing 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 and the USDA Agricultural Research Service.

Additional recommended knowledge

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Software

The full list of GMOD software components is found on the GMOD home page. These components include:

• GMOD Core (Chado database and tools)
  • Chado : the Chado schema and tools to install it.
  • XORT  : a tool for loading and dumping chado-xml
  • GMODTools : extracts data from a Chado database into common genome bulk formats (GFF, Fasta, etc)
• MOD website
  • gmod-web/Turnkey  : a generic web front end for browsing database contents.
• Genome Editing and Visualization
  • Apollo  : a Java application for viewing and editing genome annotations
  • GBrowse  : a CGI application for displaying genome annotations
• Comparative Genomics
  • SynBrowse  : a GBrowse based synteny viewer
  • CMap  : a CGI application for displaying comparative maps
• Literature curation
  • PubSearch  : a Java servlet web application for annotating genes from literature
  • PubFetch  : a tool to facilitate literature collection for curators' use
  • Textpresso  : a text mining system for scientific literature
• Database querying tools
  • BioMart  : a query-oriented data management system
• Biological Pathways
  • 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 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

• Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. (2002). "The generic genome browser: a building block for a model organism system database.". Genome Res. 12: 1599-610.

• Colbourne JK, Singan VR, Gilbert DG. (2005). "wFleaBase: the Daphnia genome database.". BMC Bioinformatics. 6: 45.

• Chisholm RL, Gaudet P, Just EM, Pilcher KE, Fey P, Merchant SN, Kibbe WA. (2006). "dictyBase, the model organism database for Dictyostelium discoideum.". Nucleic Acids Res. 34(Database issue): D423-7..

• Wang L, Wang S, Li Y, Paradesi MS, Brown SJ. (2007). "BeetleBase: the model organism database for Tribolium castaneum.". Nucleic Acids Res. 35(Database issue): D476-9.

• Arnaiz O, Cain S, Cohen J, Sperling L. (2007). "ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data.". Nucleic Acids Res. 35(Database issue): D439-44.

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[1]
• DAS[2]
• The Genomics Unified Schema[3]
• Manatee: Manual Annotation Tool Etc, Etc...[4]
• Biocurator.org[5]
• Open Biomedical Ontologies
• The Sequence Ontology Project

See also

• Biological database
• Genome project
• Genomics
• Genome