- Created by Javier Lopez, last modified by Julie Sullivan on Jun 02, 2020
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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) | CellBase v5 (Autumn 2020) | ||
Core | Ensembl Core | v79 | v82 | v99 |
Protein | UniProt | March 2015 | Release 2015_10 | Release 2020_02 |
InterPro | v50 | v54 | -- | |
Polyphen2/Sift | Ensembl 79 | Ensembl v82 | Ensembl v99 | |
Variation | Ensembl Variation | v79 | v82 | -- |
1000 genomes project | Phase 3 2016-05 | Phase 3 2016-05 | ||
ExAC | 0.3.1 | -- | ||
GoNL | Release 5 | -- | ||
UK10K | 2016-05 | 2016-05 | ||
ESP | 2016-05 | -- | ||
gnomAD Genomes | v3 | |||
TOPMed | 2020-04 | |||
DiscovEHR | 2020-04 | |||
GenomeAsia 100K | 2020-04 | |||
Regulatory | Ensembl Regulatory | v79 | v82 | v99 |
Ensembl Motif features | v99 | |||
mirBase | 22.1 | |||
mirTarBase | 7.0 | |||
Conservation | PhastCons | June 2016 | -- | |
PhyloP | June 2016 | -- | ||
GERP++ | June 2016 | -- | ||
Clinical | ClinVar | March 2015 | 2016-12 | 2020-02 |
COSMIC | v71 | v79 | v91 | |
HPO | 2015-11 | 2020-04 | ||
DisGeNET | Version 3.0 | 7.0 | ||
Disease ontology | 2020-05 | |||
Biological Networks | Reactome | v51 | June 2016 | -- |
IntAct | March 2015 | June 2016 | -- | |
Ontologies | Gene Annotation | 2020-05 | ||
Gene ontology (basic) | 2020-05 | |||
Others | DGIdb | 2.0 | v3.0.2 | |
Gene Expression Atlas | June 2016 | 2.0.14 | ||
CADD | v1.3 | -- | ||
gnomAD constraints | 2.1.1 |
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) | |||
hsapiens | Human | Homo sapiens | GRCh37.p13 | GRCh37.p13, GRCh37.p8 |
mmusculus | Mouse | Mus musculus | GRCm38.p2 | GRCm38.p5 |
rnorvegicus | Rat | Rattus norvegicus | Rnor_5.0 | Rnor_6.0 |
ptroglodytes | Chimp | Pan troglodytes | CHIMP2.1.4 | CHIMP2.1.4 |
agambiae | Anopheles | Gambiae | AgamP4 | AgamP4 |
athaliana | Arabidopsis | Thaliana | THAIR10 | THAIR10 |
btaurus | Bos | Taurus | UMD3.1 | UMD3.1 |
celegans | Caenorhabditis | Elegans | WBcel235 | WBcel235 |
cfamiliaris | Canis | Familiaris | CanFam3.1 | CanFam3.1 |
csabaeus | Chlorocebus | Sabaeus | ChlSab1.1 | ChlSab1.1 |
cintestinales | Ciona | Intestinalis | KH | KH |
drerio | Danio | Rerio | zv9 | GRCz10 |
dmelanogaster | Drosophila | Melanogaster | BDGP6 | BDGP6 |
ggallus | Gallus | Gallus | 4.0 | 5.0 |
gmax | Glycine | Max | V1.0 | V1.0 |
ggorilla | Gorilla | Gorilla | gorGor3.1 | gorGor3.1 |
lmajor | Leishmania | Major | ASM272v2 | ASM272v2 |
osativa | Oryza | Sativa | IRGSP-1.0 | IRGSP-1.0 |
olatipes | Oryzias | Latipes | HdrR | HdrR |
oaries | Ovis | Aries | Oar_v3.1 | Oar_v3.1 |
pfalciparum | Plasmodium | Falciparum | ASM276v1 | ASM276v1 |
scerevisiae | Saccharomyces | Cerevisiae | R64-1-1 | R64-1-1 |
slycopersicum | Solanum | Lycopersicum | SL2.40 | |
sscrofa | Sus | Scrofa | Sscrofa10.2 | Sscrofa10.2 |
vvinifera | Vitis | Vinifera | IGGP_12x | IGGP_12x |
zmays | Zea | Mays | AGPv3 | AGPv3 |
afumigatus | Aspergillus | Fumigatus | A1163 | |
anidulans | Aspergillus | Nidulans | ASM1142v1 | |
ecoli | Esherichia | Coli | HUSEC2011CHR1 | |
fcatus | Felis | Catus | ||
mpneumoniae | Mycoplasma | Pneumoniae | M129 (ASM2734v1) | |
sbicolor | Sorghum | Bicolor | Sorbi1 |
[DEPRECATED] Release v3
Data sources and versions
Core features
- Ensembl Release 79 (March 2015): Core data for all species are built from Ensembl v79, so **_Homo sapiens_** uses now assembly GRCh38.p2 and GENCODE 22, you can query the rest of assemblies at [**Ensembl table of assemblies**](http://www.ensembl.org/info/website/archives/assembly.html). These includes genome sequence, gene sets, variation and regulation. Ensembl Release 75 (Feb 2014) is used only for keeping old **_Homo sapiens_ GRCh37** assembly.
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
- Gene Expression Atlas
- Gene disease association: DisGeNET
- DGIdb: http://dgidb.genome.wustl.edu/
Available species
`species` | Name | Scientific name | Assembly |
hsapiens | human | Homo sapiens | GRCh37.p13 |
mmusculus | mouse | Mus musculus | GRCm38.p2 |
rnorvegicus | rat | Rattus norvegicus | Rnor_5.0 |
ptroglodytes | chimp | Pan troglodytes | CHIMP2.1.4 |
ggorilla | gorilla | Gorilla gorilla | gorGor3.1 |
pabelii | orangutan | Pongo abelii | PPYG2 |
mmulatta | macaque | Macaca mulatta | MMUL 1.0 |
sscrofa | pig | Sus scrofa | Sscrofa10.2 |
cfamiliaris | dog | Canis familiaris | CanFam 3.1 |
ecaballus | horse | Equus caballus | Equ Cab 2 |
ocuniculus | rabbit | Oryctolagus cuniculus | OryCun2.0 |
ggallus | chicken | Gallus gallus | Galgal4 |
btaurus | cow | Bos taurus | UMD3.1 |
fcatus | cat | Felis catus | Felis_catus_6.2 |
drerio | zebrafish | Danio rerio | Zv9 |
cintestinalis | Ciona intestinalis | KH | |
dmelanogaster | fruitfly | Drosophila melanogaster | BDGP 5 |
dsimulans | Drosophila simulans | dsim_caf1 | |
dyakuba | Drosophila yakuba | dyak_caf1 | |
agambiae | mosquito | Anopheles gambiae | AgamP4 |
celegans | worm | Caenorhabditis elegans | WS235 |
scerevisiae | yeast | Saccharomyces cerevisiae | R64-1-1 |
spombe | Schizosaccharomyces pombe | ASM294v2 | |
afumigatus | Aspergillus fumigatus | TIGR | |
aniger | Aspergillus niger | DSM | |
anidulans | Aspergillus nidulans | ASM1142v1 | |
aoryzae | Aspergillus oryzae | NITE | |
pfalciparum | malaria parasite | Plasmodium falciparum | 3D7 |
lmajor | Plasmodium falciparum | ASM276v1 | |
athaliana | Arabidopsis thaliana | TAIR10 | |
alyrata | Arabidopsis lyrata | v.1.0 | |
bdistachyon | Brachypodium distachyon | v1.0 | |
osativa | Oryza sativa Indica | ASM465v1 | |
gmax | Glycine max | V1.0 | |
vvinifera | Vitis vinifera | IGGP_12x | |
zmays | Zea mays | AGPv3 |
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