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Data sources

A Web Service is available to query currently available data sources:

http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/#!/Meta/getVersion

Please, find below a summary of all data sources information:


Category


Data source

Version/Date
CellBase v3 (March 2015)CellBase v4 (June 2016)
CoreEnsembl Corev79v82
ProteinUniProtMarch 2015Release 2015_10
InterProv50v54
Polyphen2/SiftEnsembl 79Ensembl v82
VariationEnsembl Variationv79v82
1000 genomes project
Phase 3 2016-05
ExAC
0.3.1
GoNL
Release 5
UK10K
2016-05
ESP
2016-05
RegulatoryEnsembl Regulatoryv79v82
ConservationPhastCons
June 2016
PhyloP
June 2016
GERP++
June 2016
Clinical

ClinVarMarch 20152016-12
COSMICv71v79
HPO
2015-11
DisGeNET
Version 3.0
Biological NetworksReactomev51June 2016
IntActMarch 2015June 2016
OthersDGIdb
2.0

Gene Expression Atlas
June 2016

CADD
v1.3


Species

A Web Service is available to query all available species and assemblies:

http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/meta/species

Please, find below a summary of available species data:


Id


Common Name


Scientific Name

Assembly
CellBase v3 (March 2015)CellBase v4 (June 2016)
hsapiensHumanHomo sapiensGRCh37.p13GRCh37.p13, GRCh37.p8
mmusculusMouseMus musculusGRCm38.p2GRCm38.p5
rnorvegicusRatRattus norvegicusRnor_5.0 Rnor_6.0
ptroglodytesChimpPan troglodytesCHIMP2.1.4CHIMP2.1.4
agambiaeAnophelesGambiaeAgamP4AgamP4
athalianaArabidopsisThalianaTHAIR10THAIR10
btaurusBosTaurusUMD3.1UMD3.1
celegansCaenorhabditisElegansWBcel235WBcel235
cfamiliarisCanisFamiliarisCanFam3.1CanFam3.1
csabaeusChlorocebusSabaeusChlSab1.1ChlSab1.1
cintestinalesCionaIntestinalisKHKH
drerioDanioReriozv9GRCz10
dmelanogasterDrosophilaMelanogasterBDGP6BDGP6
ggallusGallusGallus4.05.0
gmaxGlycineMaxV1.0V1.0
ggorillaGorillaGorillagorGor3.1gorGor3.1
lmajorLeishmaniaMajorASM272v2ASM272v2
osativaOryzaSativaIRGSP-1.0IRGSP-1.0
olatipesOryziasLatipesHdrRHdrR
oariesOvisAriesOar_v3.1Oar_v3.1
pfalciparumPlasmodiumFalciparumASM276v1ASM276v1
scerevisiaeSaccharomycesCerevisiaeR64-1-1R64-1-1
slycopersicumSolanumLycopersicumSL2.40
sscrofaSusScrofaSscrofa10.2Sscrofa10.2
vviniferaVitisViniferaIGGP_12xIGGP_12x
zmaysZeaMaysAGPv3AGPv3
afumigatusAspergillusFumigatus
A1163
anidulansAspergillusNidulans
ASM1142v1
ecoliEsherichiaColi
HUSEC2011CHR1
fcatusFelisCatus

mpneumoniaeMycoplasmaPneumoniae
M129 (ASM2734v1)
sbicolorSorghumBicolor
Sorbi1


[DEPRECATED] Release v3

Data sources and versions

Core features

Protein

  • UniProt (Release March 2015)
  • InterPro v50 v50 (Release Feb 2015)
  • Polyphen2/Sift from Ensembl v79

Variation

  • Ensembl v79 Variation (dbSNP 142)
  • Population frequencies: 1000 genomes project, ESP (ExAC in preparation).

Regulatory

  • Ensembl v79 Regulatory
  • miRNAs:
  • miRBase (Release 21)
  • miRTarBase (Release 4.5)
  • TargetScan (Release 6.0)

Clinical association

  • ClinVar (Release March 2015)
  • GWAS Catalog
  • COSMIC v71 (Release March 2015)

Conservation scores

  • PhastCons
  • PhyloP
  • (GERP++ in preparation)

Systems biology

  • IntAct (Release March 2015)
  • (Reactome 51 in preparation)

Others

Available species

`species`NameScientific nameAssembly
hsapienshumanHomo sapiensGRCh37.p13
mmusculusmouseMus musculusGRCm38.p2
rnorvegicusratRattus norvegicusRnor_5.0
ptroglodyteschimpPan troglodytesCHIMP2.1.4
ggorillagorillaGorilla gorillagorGor3.1
pabeliiorangutanPongo abeliiPPYG2
mmulattamacaqueMacaca mulattaMMUL 1.0
sscrofapigSus scrofaSscrofa10.2
cfamiliarisdogCanis familiarisCanFam 3.1
ecaballushorseEquus caballusEqu Cab 2
ocuniculusrabbitOryctolagus cuniculusOryCun2.0
ggalluschickenGallus gallusGalgal4
btauruscowBos taurusUMD3.1
fcatuscatFelis catusFelis_catus_6.2
dreriozebrafishDanio rerioZv9
cintestinalis
Ciona intestinalisKH
dmelanogasterfruitflyDrosophila melanogasterBDGP 5
dsimulans
Drosophila simulansdsim_caf1
dyakuba
Drosophila yakubadyak_caf1
agambiaemosquitoAnopheles gambiaeAgamP4
celeganswormCaenorhabditis elegansWS235
scerevisiaeyeastSaccharomyces cerevisiaeR64-1-1
spombe
Schizosaccharomyces pombeASM294v2
afumigatus
Aspergillus fumigatusTIGR
aniger
Aspergillus nigerDSM
anidulans
Aspergillus nidulansASM1142v1
aoryzae
Aspergillus oryzaeNITE
pfalciparummalaria parasitePlasmodium falciparum3D7
lmajor
Plasmodium falciparumASM276v1
athaliana
Arabidopsis thalianaTAIR10
alyrata
Arabidopsis lyratav.1.0
bdistachyon
Brachypodium distachyonv1.0
osativa
Oryza sativa IndicaASM465v1
gmax
Glycine maxV1.0
vvinifera
Vitis viniferaIGGP_12x
zmays
Zea maysAGPv3

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