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Databases Providing SO Compliant Annotations

Below is a list of databases which we have found provide SO compliant data for download in either GFF3, ChaosXML or Chado database dumps (GBrowse links were included if they provide GFF dumps from the browser). We have not verified that these data sources validate to the appropriate data formats. Please send us a link if you would like to be included in (or removed from) this list.

Database Description Organism Data Types
WormBase Genome database of nematode worms Caenorhabditis species
FlyBase Genome database of fruitflies Drosophila species
Saccharomycese Genome Database Genome database of Saccharomycese yeast Saccharomycese cerivisiae and related species
DictyBase Genome database of the slime mold Dictyostelium discoideum
ParameciumDB Genome database of the unicellular cilliate Paramecium Paramecium tetraurelia
VectorBase Genome database for a variety of mosquito, tick, louse human disease vectors Anopheles species, Culex quinquefasciatus, Ixodes scapularis, and Pediculus humanus
Schizosaccharomyces pombe Genome database for the fission yeast Schizosaccharomyces pombe Schizosaccharomyces pombe
wFleaBase Genome database for the water flea Daphnia pulex
Tair Genome database for water cress Arabidopsis thaliana
SmedGD Genome database for the planarian Schmidtea mediterranea Schmidtea mediterranea
FishMap Zebrafish genomics knowledgebase Danio rerio
AntonosporaDB A microsporidia species used as a biological control agent for grasshoppers Antonospora locustae
Aniseed Genome database for the sea squirt Ciano intestinalis
ApiDB/EuPathDB Database of Eukaryotic Pathogens Crytosporidium, Giardia, Plasmodium, Theileria, Toxoplasma, Trichomonas
BeetleBase Genome database for the flour beetle Tribolium castaneum
BGD Genome database for the cow Bos tarus
BioHealthBase Genome database for five organism groups that pose a threat to public health Influenza virus, Mycobacterium tuberculosis, Franscisella tularensis, Microsporidia, Ricinus communis
Brachionus plicatilis A Genome database for the rotifer Brachionus plicatilis Brachionus plicatilis
Emiliania huxleyi Informatics support for the Emiliania huxleyi serial analysis of gene expression project Emiliania huxleyi
Fungal Comparitive Genomics A large collection of genome data from a wide variety of fungi Many fungi from Ascomycota, Basidiomycota, and Zygomycota
GrainGenes Genome database for the grains Triticea and Avena Triticea (wheat, barley rye) and Avena (oats)
Gramene Genome databases for cereals as well as grape and poplar Oryza species, Zea maize, Sorguhm bicolor, Vitis vinifera, Populus trichocarpa
HapMap International HapMap project Homo sapiens
MSU Rice Genome Browser Rice Genome Annotation Project Oryza species
OryGenesDB A database for rice reverse genetics Oryza satvia
OryzaSNP Consortium A database for rice genetic variation Oryza satvia
PlantsDB A synteny browser for plants Brachypodium distachyon, Arabidopsis thaliana, Medicago truncatula, Lotus japonicus, Oryza sativa, Zea mays, Sorghum bicolor
PseudoCAP Pseudomonas genome database Pseudomonas species
RGD Rat genome database Rattus norvegicus
SGD Lite Yeast SNP Browser Saccharomyces cerevisiae
SOL Genomics Network Genome database for a variety of ethnobotanically important species Species from the Solanaceae, Rubiaceae, and Plantaginaceae families
Soybase Genome database for soybean Glycine max
SpBase Sea urchin genome database Strongylocentrotus purpuratus
TGD Tetrahymena genome database Tetrahymena thermophila
Trypanosoma brucei brucei RNA editing database Trypanosoma brucei brucei RNA editing database Trypanosoma brucei brucei
Vicogenta Viewer for comparing genomes to Arabidopsis Arabidopsis thaliana

* Some databases serve multiple genomes and may not provide all resources for all genomes.