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| Chado database schema | |
| 2>
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
[edit] Tags: | |
| Software | |
| 2>
The full list of GMOD software components is found on the GMOD Components 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
Tripal : a web front end based on Drupal.
Genome Editing and Visualization
Apollo : a Java application for viewing and editing genome annotations
GBrowse : a CGI application for displaying genome annotations
JBrowse : a JavaScript application for displaying genome annotations
Pathway Tools : a genome browser with a comparative mode
Comparative Genomics
GBrowse_syn : a GBrowse based synteny viewer
CMap : a CGI application for displaying comparative maps
Literature curation
Textpresso : a text mining system for scientific literature
Database querying tools
BioMart : a query-oriented data management system
InterMine : open source data warehouse system
Biological Pathways
Pathway Tools : tools for metabolic pathway information, and analysis of high-throughput functional genomics data
Regulatory Networks
Pathway Tools : supports definition of regulatory interactions and browsing of regulatory networks
Analysis
Galaxy
MAKER
[edit] Tags:Software,Genome,Genomics, | |
| References | |
| 2>
Christopher J. Mungall, David B. Emmert, The FlyBase Consortium (2007). "A Chado case study: an ontology-based modular schema for representing genome-associated biological information". Bioinformatics 23 (13): i337-i346. doi:10.1093/bioinformatics/btm189. PMID 17646315. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i337.
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 (10): 1599–610. doi:10.1101/gr.403602. PMC 187535. PMID 12368253.
Colbourne JK, Singan VR, Gilbert DG. (2005). "wFleaBase: the Daphnia genome database.". BMC Bioinformatics. 6: 45. doi:10.1186/1471-2105-6-45. PMC 555599. PMID 15752432.
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) (Database issue): D423–7.. doi:10.1093/nar/gkj090. PMC 1347453. PMID 16381903.
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) (Database issue): D476–9. doi:10.1093/nar/gkl776. PMC 1669707. PMID 17090595.
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) (Database issue): D439–44. doi:10.1093/nar/gkl777. PMC 1669747. PMID 17142227.
[edit] Tags:Model Organism, | |
| Participating databases | |
| 2>
The following organism databases are contributing to and/or adopting GMOD components for model organism databases.
ANISEED
AntonosporaDB
ATIDB
Arabidopsis
BeeBase
BeetleBase
Bovine Genome Database (BGD)
BioHealthBase
Bovine QTL Viewer
Cattle EST Gene Family Database
CGD
CGL
ChromDB
Chromosome 7 Annotation Project
CSHLmpd
Database of Genomic Variants
DictyBase
DroSpeGe
EcoCyc
FlyBase
Fungal Comparative Genomics
Fungal Telomere Browser
Gallus Genome Browser
GeneDB
GrainGenes
Gramene
HapMap
Human 2q33
Human Genome Segmental Duplication Database
IVDB
MAGI
Marine Biological Lab Organism Databases
MGI
Non-Human Segmental Duplication Database
OMAP
OryGenesDB
Oryza Chromosome 8
Pathway Tools
ParameciumDB
PeanutMap
PlantsDB
PlasmoDB
PseudoCAP
PossumBase
PUMAdb
RGD
SGD
SGD Lite
SmedDB
Sol Genomics Network
Soybase
Soybean Gbrowse Database
T1DBase
TAIR
TGD
TGI
TIGR
TIGR Rice Genome Browser
ToxoDB
TriAnnot BAC Viewer
VectorBase
wFleaBase
WormBase
XanthusBase
Xenbase
[edit] Tags:Databases,Model Organism Databases, | |
| Related projects | |
| 2>
Bioperl, BioJava, Biopython, BioRuby, etc.
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
[edit] Tags:Bioperl,Biojava,Biopython,Bioruby,Ensembl, | |
| See also | |
| 2>
Biological database
Genome project
Genomics
Genome
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