Difference between revisions of "MOD"

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m (Fixing ANISEED link)
m (Removed duplicated DB list)
 
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'''M'''odel '''O'''rganism '''D'''atabases are repositories for information on
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'''M'''odel '''O'''rganism '''D'''atabases are repositories for information on those organisms with a wealth of biological data that make them attractive to study as models of other species (including humans) that are more difficult to study directly [http://genome.wellcome.ac.uk/doc_WTD020803.html].
those organisms with a wealth of biological data that make them
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Historically, these model organism databases include the handful of species with extensive genomic research data, such as the [http://www.nih.gov/science/models/ NIH model organisms].
attractive to study as models of other
+
species including humans that are more difficult to study directly
+
[http://genome.wellcome.ac.uk/doc_WTD020803.html].
+
Historically, these model organism databases include the handful of species with
+
extensive genomic research data, such as the
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[http://www.nih.gov/science/models/ NIH model organisms].
+
  
The acronym has been extended to include '''Many''' organism and '''My''' organism databases,
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With the barriers to genome sequencing--particularly expense and time--rapidly coming down, collecting genetic and genomic data is no longer restricted to a small set of organisms. The acronym "GMOD" has been extended to include '''M'''ultiple organism and '''My''' organism databases, so that the MOD in GMOD can apply to any organism or genome database projects.
so that the MOD in GMOD applies to almost all organism/genome database
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projects.
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=GMOD Participating databases=
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A list of some of the databases and organizations using, contributing to, and developing GMOD components can be found on the [[GMOD Users]] page.
 
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The following databases/organizations are contributing to and/or adopting GMOD components, as of early 2007.  See [[GMOD Users]] for a more detailed list.
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{|
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|-
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|[http://www.aniseed.cnrs.fr/fgb2/gbrowse/ciona_intestinalis_v3/ ANISEED]
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|[http://gmod.mbl.edu/perl/site/antonospora01 AntonosporaDB]
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|[http://atidb.org ATIDB]
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|-
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|[http://racerx00.tamu.edu/bee_resources.html BeeBase]
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|[http://www.bioinformatics.ksu.edu/BeetleBase/ BeetleBase]
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|[http://bovinegenome.org/ BGD]
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|-
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|[http://www.biohealthbase.org/GSearch/ BioHealthBase]
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|[http://bovineqtl.tamu.edu Bovine QTL Viewer]
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|[http://racerx00.tamu.edu/cgi-test/searchCattleDatabase.html Cattle EST Gene Family Database]
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|-
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|[http://www.candidagenome.org/ CGD]
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|[http://www.yandell-lab.org/cgl/ CGL]
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|[http://www.chromdb.org/ ChromDB ]
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|-
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|[http://www.chr7.org/cgi-bin/gbrowse/gbrowse/chr7_v2 Chromosome 7 Annotation Project]
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|[http://rulai.cshl.edu/cshlmpd/credit.html CSHLmpd]
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|[http://projects.tcag.ca/variation/cgi-bin/gbrowse/hg17 Database of Genomic Variants]
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|-
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|[http://www.dictybase.org DictyBase] (see [[:Category:DictyBase|also]])
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|[http://insects.eugenes.org/DroSpeGe/ DroSpeGe]
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|[http://ecocyc.org/ EcoCyc] (see [[Pathway Tools|also]])
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|-
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|[http://ecoliwiki.net EcoliWiki]
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|[http://www.flybase.org FlyBase] (see [[:Category:FlyBase|also]])
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|[http://fungalgenomes.org/ Fungal Comparative Genomics]
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|-
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|[http://genome.kbrin.uky.edu/fungi_tel/browser.html Fungal Telomere Browser]
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|[http://genome.ucsc.edu/cgi-bin/hgGateway?org=Chicken Gallus Genome Browser]
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|[http://www.genedb.org/ GeneDB]
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|-
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|[http://www.generationcp.org/ Generation Challenge Programme]
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|[http://wheat.pw.usda.gov/ GrainGenes]
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|[http://www.gramene.org Gramene]
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|-
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|[http://www.hapmap.org/cgi-perl/gbrowse/ HapMap]
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|[http://t1dbase.cimr.cam.ac.uk/cgi-bin/gbrowse/2q33/ Human 2q33]
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|[http://projects.tcag.ca/cgi-bin/duplication/dupbrowse/human_b36 Human Genome Segmental Duplication Database]
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|-
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|[http://influenza.genomics.org.cn/ IVDB]
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|[http://magi.plantgenomics.iastate.edu/ MAGI]
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|[http://gmod.mbl.edu/  Marine Biological Lab Organism Databases]
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|-
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|[http://www.informatics.jax.org/ MGI] (see [[:Category:MGI|also]])
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|[http://projects.tcag.ca/xenodup/gbrowse.php Non-Human Segmental Duplication Database]
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|[http://www.omap.org/ OMAP]
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|-
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|[http://orygenesdb.cirad.fr/ OryGenesDB]
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|[http://map.lab.nig.ac.jp/cgi-bin/gbrowse/Oryza_chr8/ Oryza Chromosome 8]
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|[http://bioinformatics.ai.sri.com/ptools/ Pathway Tools] (see [[Pathway Tools|also]])
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|-
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|[http://paramecium.cgm.cnrs-gif.fr/ ParameciumDB] (see [[ParameciumDB|also]])
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|[http://peanutgenetics.tamu.edu/cmap/ PeanutMap]
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|[http://mips.gsf.de/cgi-bin/proj/plant/gbrowse/synbrowse PlantsDB]
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|-
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|[http://www.plasmodb.org/ PlasmoDB]
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|[http://v2.pseudomonas.com/whats_new.jsp PseudoCAP]
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|[http://www.possumbase.org.nz/cgi-bin/gbrowse/mondom4/ PossumBase]
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|-
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|[http://puma.princeton.edu/ PUMAdb]
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|[http://rgd.mcw.edu RGD] (see [[:Category:RGD|also]])
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|[http://www.yeastgenome.org SGD] (see [[:Category:SGD|also]])
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|-
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|[http://sgdlite.princeton.edu/ SGD Lite]
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|[http://smedgd.neuro.utah.edu/ SmedGD]
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|[http://www.sgn.cornell.edu/ Sol Genomics Network] (see [[:Category:SGN|also]])
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|-
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|[http://soybase.agron.iastate.edu/ Soybase]
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|[http://soybeangenome.siu.edu/ Soybean Gbrowse Database]
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|[http://t1dbase.org/cgi-bin/dispatcher.cgi/Welcome/display T1DBase]
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|-
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|[http://www.arabidopsis.org TAIR] (see [[:Category:TAIR|also]])
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|[http://www.ciliate.org/help/Locus.shtml TGD]
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|[http://biocomp.dfci.harvard.edu/tgi/ TGI]
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|-
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|[http://www.tigr.org TIGR]
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|[http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice MSU Rice Genome Browser]
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|[http://v3-0.toxodb.org/ ToxoDB]
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|-
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|[http://urgi.versailles.inra.fr/projects/TriAnnot/GBrowse.php TriAnnot BAC Viewer]
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|[http://www.vectorbase.org VectorBase]
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|[http://wfleabase.org/ wFleaBase]
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|-
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|[http://www.wormbase.org WormBase] (see [[:Category:WormBase|also]])
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|[http://www.xanthusbase.org/ XanthusBase]
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|[http://www.xenbase.org/ Xenbase]
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|-
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|}
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= See also =
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* [[GMOD Users]]
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* [[Standard URL]]
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* [http://en.wikipedia.org/wiki/Generic_Model_Organism_Database Wikipedia GMOD]
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[[Category:FAQ]]
 
[[Category:FAQ]]
 
[[Category:GMOD Community]]
 
[[Category:GMOD Community]]

Latest revision as of 20:21, 6 March 2013

Model Organism Databases are repositories for information on those organisms with a wealth of biological data that make them attractive to study as models of other species (including humans) that are more difficult to study directly [1]. Historically, these model organism databases include the handful of species with extensive genomic research data, such as the NIH model organisms.

With the barriers to genome sequencing--particularly expense and time--rapidly coming down, collecting genetic and genomic data is no longer restricted to a small set of organisms. The acronym "GMOD" has been extended to include Multiple organism and My organism databases, so that the MOD in GMOD can apply to any organism or genome database projects.

A list of some of the databases and organizations using, contributing to, and developing GMOD components can be found on the GMOD Users page.