Generic Model Organism Database

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 [ 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.


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

*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


* 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
year= 2007
volume= 23
pages= i337-i346
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
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.
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
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.
volume=35(Database issue)

Participating databases

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

Related projects

*Gene Ontology Software []
*DAS []
*The Genomics Unified Schema []
*Manatee: Manual Annotation Tool Etc, Etc... []
* []
*Open Biomedical Ontologies
* [ The Sequence Ontology Project]

ee also

*Biological database
*Genome project

Wikimedia Foundation. 2010.

Игры ⚽ Нужен реферат?

Look at other dictionaries:

  • Model organism — Escherichia coli is a gram negative prokaryotic model organism …   Wikipedia

  • Открытые биомедицинские онтологии — (OБO, англ. Open Biomedical Ontologies. ранее использовался термин англ. Open Biological Ontologies  Открытые Биологические Онтологии)  инициатива научного сообщества по выработке единого понятийного аппарата в различных… …   Википедия

  • FlyBase — is an online bioinformatics database of the biology and genome of the model organism Drosophila melanogaster and related Drosophilid dipterans. The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists… …   Wikipedia

  • Substitution model — A substitution model describes the process from which a sequence of characters of a fixed size from some alphabet changes into another set of traits. For example, in cladistics, each position in the sequence might correspond to a property of a… …   Wikipedia

  • Gmod — may refer to:*The Generic Model Organism Database (GMOD) an open source software project for model organism databases. *Garry s Mod (GMod) a sandbox mod for the first person shooter computer game Half Life 2 …   Wikipedia

  • Beebase — [ resources.html BeeBase] is an online bioinformatics database that displays data related to Apis mellifera , the European honey bee. It was developed in collaboration with the Honey Bee Genome Sequencing Consortium.In …   Wikipedia

  • National Evolutionary Synthesis Center — The US National Evolutionary Synthesis Center (NESCent) is a scientific research center located in Durham, North Carolina. Known by its acronym NESCent (which rhymes with “crescent”), the center’s goal is to promote collaborative, cross… …   Wikipedia

  • Plant ontology — (PO) is a set of controlled vocabularies (ontologies), developed by the Plant Ontology Consortium. These ontologies describe plant structures and growth and developmental stages, providing a semantic framework for cross species queries across… …   Wikipedia

  • Open Biomedical Ontologies — (abbreviated OBO; formerly Open Biological Ontologies) is an effort to create controlled vocabularies for shared use across different biological and medical domains. As of 2006, OBO forms part of the resources of the U.S. National Center for… …   Wikipedia

  • Ontology engineering — Example of a constructed MBED Top Level Ontology based on the Nominal set of views.[1] Ontology engineering in computer science and information science is a new field, which studies the methods and methodologies for building ontologies: formal… …   Wikipedia

Share the article and excerpts

Direct link
Do a right-click on the link above
and select “Copy Link”