Programmatic data access

The full dataset that we provide for download can be found on the Downloadable data page. This section explain how to only download a subset of the data provided in XML, RDF, TSV or JSON format.

Individual entry

Data for an individual entry can be accessed in XML, RDF (trig), TSV or JSON format by adding the corresponding format extension to the ensembl gene ID as in the below URLs:

The XML format is the most comprehensive dataset of these. The TSV and JSON format contains the same data

Search queries

If you want to download a subset of the entries it is possible to do so by expressing it as a search query. To get the query use the search functionality to create the query, click search. You can then use the links at the top of search results to download the data in the specified format. The search supports the following query parameters for downloads:

Parameter Value Info
format xml,trig,tsv,json Format of the data. Required for downloads
compress yes,no Whether the result should be returned gz-compressed or not. The response may transparently be compressed even with compress=no if the client supports it.

The number of entries in the result set can be found in the response header X-Total-Results. It is possible to send a HEAD request to only get a count of the entries. The server may send the following status codes:

Status code Description
400 Bad request. There was a problem in the request or the query returns too many results.
500 Server side error in the processing of the request.

Customized TSV/JSON data

In addition to the above, it is possible to customize the retrieval of the data in TSV and JSON format. This is useful if you only need certain columns of the full dataset available in either TSV or JSON format. The URL to this api is: www.proteinatlas.org/api/search_download.php

Example:

Parameter Value Info
search <Search string> Search string for gene list. Required
format json,tsv Format of the data. Required
columns <comma separated list of specifiers> Columns for download. The specifiers for the columns can be found in the table below. Required
compress yes,no Whether the result should be returned gz-compressed or not. The response may transparently be compressed even with compress=no if the client supports it.

The table below shows the Column names in the data files with the corresponding name for use in the columns parameter in the API:

Column name Columns parameter value
Gene g
Gene synonym gs
Ensembl eg
Gene description gd
Uniprot up
Chromosome chr
Position chrp
Protein class pc
Evidence pe
HPA evidence evih
UniProt evidence eviu
NeXtProt evidence evin
MS evidence evim
RNA tissue specificity rnats
RNA tissue distribution rnatd
RNA tissue specificity score rnatss
RNA tissue specific NX rnatsm
RNA cell line specificity rnacls
RNA cell line distribution rnacld
RNA cell line specificity score rnaclss
RNA cell line specific NX rnaclsm
RNA cancer specificity rnacas
RNA cancer distribution rnacad
RNA cancer specificity score rnacass
RNA cancer specific FPKM rnacasm
RNA brain regional specificity rnabrs
RNA brain regional distribution rnabrd
RNA brain regional specificity score rnabrss
RNA brain regional specific NX rnabrsm
RNA blood cell specificity rnabcs
RNA blood cell distribution rnabcd
RNA blood cell specificity score rnabcss
RNA blood cell specific NX rnabcsm
RNA blood lineage specificity rnabls
RNA blood lineage distribution rnabld
RNA blood lineage specificity score rnablss
RNA blood lineage specific NX rnablsm
RNA mouse brain regional specificity rnambrs
RNA mouse brain regional distribution rnambrd
RNA mouse brain regional specificity score rnambrss
RNA mouse brain regional specific pTPM rnambrsm
RNA pig brain regional specificity rnapbrs
RNA pig brain regional distribution rnapbrd
RNA pig brain regional specificity score rnapbrss
RNA pig brain regional specific pTPM rnapbrsm
Antibody ab
Reliability (IH) relih
Reliability (Mouse Brain) relmb
Reliability (IF) relce
Subcellular location scl
Secretome location secl
Blood concentration - Conc. blood IM [pg/L] blconcia
Blood concentration - Conc. blood MS [pg/L] blconcms
Subcellular main location scml
Subcellular additional location scal
Antibody RRID abrr
Pathology prognostics - Breast cancer prognostic_breast_cancer
Pathology prognostics - Cervical cancer prognostic_cervical_cancer
Pathology prognostics - Colorectal cancer prognostic_colorectal_cancer
Pathology prognostics - Endometrial cancer prognostic_endometrial_cancer
Pathology prognostics - Glioma prognostic_glioma
Pathology prognostics - Head and neck cancer prognostic_head_and_neck_cancer
Pathology prognostics - Liver cancer prognostic_liver_cancer
Pathology prognostics - Lung cancer prognostic_lung_cancer
Pathology prognostics - Melanoma prognostic_melanoma
Pathology prognostics - Ovarian cancer prognostic_ovarian_cancer
Pathology prognostics - Pancreatic cancer prognostic_pancreatic_cancer
Pathology prognostics - Prostate cancer prognostic_prostate_cancer
Pathology prognostics - Renal cancer prognostic_renal_cancer
Pathology prognostics - Stomach cancer prognostic_stomach_cancer
Pathology prognostics - Testis cancer prognostic_testis_cancer
Pathology prognostics - Thyroid cancer prognostic_thyroid_cancer
Pathology prognostics - Urothelial cancer prognostic_urothelial_cancer
Tissue RNA - adipose tissue [NX] t_RNA_adipose_tissue
Tissue RNA - adrenal gland [NX] t_RNA_adrenal_gland
Tissue RNA - amygdala [NX] t_RNA_amygdala
Tissue RNA - appendix [NX] t_RNA_appendix
Tissue RNA - basal ganglia [NX] t_RNA_basal_ganglia
Tissue RNA - bone marrow [NX] t_RNA_bone_marrow
Tissue RNA - breast [NX] t_RNA_breast
Tissue RNA - cerebellum [NX] t_RNA_cerebellum
Tissue RNA - cerebral cortex [NX] t_RNA_cerebral_cortex
Tissue RNA - cervix, uterine [NX] t_RNA_cervix,_uterine
Tissue RNA - colon [NX] t_RNA_colon
Tissue RNA - corpus callosum [NX] t_RNA_corpus_callosum
Tissue RNA - ductus deferens [NX] t_RNA_ductus_deferens
Tissue RNA - duodenum [NX] t_RNA_duodenum
Tissue RNA - endometrium 1 [NX] t_RNA_endometrium_1
Tissue RNA - epididymis [NX] t_RNA_epididymis
Tissue RNA - esophagus [NX] t_RNA_esophagus
Tissue RNA - fallopian tube [NX] t_RNA_fallopian_tube
Tissue RNA - gallbladder [NX] t_RNA_gallbladder
Tissue RNA - heart muscle [NX] t_RNA_heart_muscle
Tissue RNA - hippocampal formation [NX] t_RNA_hippocampal_formation
Tissue RNA - hypothalamus [NX] t_RNA_hypothalamus
Tissue RNA - kidney [NX] t_RNA_kidney
Tissue RNA - liver [NX] t_RNA_liver
Tissue RNA - lung [NX] t_RNA_lung
Tissue RNA - lymph node [NX] t_RNA_lymph_node
Tissue RNA - midbrain [NX] t_RNA_midbrain
Tissue RNA - olfactory region [NX] t_RNA_olfactory_region
Tissue RNA - ovary [NX] t_RNA_ovary
Tissue RNA - pancreas [NX] t_RNA_pancreas
Tissue RNA - parathyroid gland [NX] t_RNA_parathyroid_gland
Tissue RNA - pituitary gland [NX] t_RNA_pituitary_gland
Tissue RNA - placenta [NX] t_RNA_placenta
Tissue RNA - pons and medulla [NX] t_RNA_pons_and_medulla
Tissue RNA - prostate [NX] t_RNA_prostate
Tissue RNA - rectum [NX] t_RNA_rectum
Tissue RNA - retina [NX] t_RNA_retina
Tissue RNA - salivary gland [NX] t_RNA_salivary_gland
Tissue RNA - seminal vesicle [NX] t_RNA_seminal_vesicle
Tissue RNA - skeletal muscle [NX] t_RNA_skeletal_muscle
Tissue RNA - skin 1 [NX] t_RNA_skin_1
Tissue RNA - small intestine [NX] t_RNA_small_intestine
Tissue RNA - smooth muscle [NX] t_RNA_smooth_muscle
Tissue RNA - spinal cord [NX] t_RNA_spinal_cord
Tissue RNA - spleen [NX] t_RNA_spleen
Tissue RNA - stomach 1 [NX] t_RNA_stomach_1
Tissue RNA - testis [NX] t_RNA_testis
Tissue RNA - thalamus [NX] t_RNA_thalamus
Tissue RNA - thymus [NX] t_RNA_thymus
Tissue RNA - thyroid gland [NX] t_RNA_thyroid_gland
Tissue RNA - tongue [NX] t_RNA_tongue
Tissue RNA - tonsil [NX] t_RNA_tonsil
Tissue RNA - urinary bladder [NX] t_RNA_urinary_bladder
Tissue RNA - vagina [NX] t_RNA_vagina
Tissue RNA - B-cells [NX] t_RNA_B-cells
Tissue RNA - dendritic cells [NX] t_RNA_dendritic_cells
Tissue RNA - granulocytes [NX] t_RNA_granulocytes
Tissue RNA - monocytes [NX] t_RNA_monocytes
Tissue RNA - NK-cells [NX] t_RNA_NK-cells
Tissue RNA - T-cells [NX] t_RNA_T-cells
Tissue RNA - total PBMC [NX] t_RNA_total_PBMC
Cell RNA - A-431 [NX] cell_RNA_A-431
Cell RNA - A549 [NX] cell_RNA_A549
Cell RNA - AF22 [NX] cell_RNA_AF22
Cell RNA - AN3-CA [NX] cell_RNA_AN3-CA
Cell RNA - ASC diff [NX] cell_RNA_ASC_diff
Cell RNA - ASC TERT1 [NX] cell_RNA_ASC_TERT1
Cell RNA - BEWO [NX] cell_RNA_BEWO
Cell RNA - BJ [NX] cell_RNA_BJ
Cell RNA - BJ hTERT+ [NX] cell_RNA_BJ_hTERT+
Cell RNA - BJ hTERT+ SV40 Large T+ [NX] cell_RNA_BJ_hTERT+_SV40_Large_T+
Cell RNA - BJ hTERT+ SV40 Large T+ RasG12V [NX] cell_RNA_BJ_hTERT+_SV40_Large_T+_RasG12V
Cell RNA - CACO-2 [NX] cell_RNA_CACO-2
Cell RNA - CAPAN-2 [NX] cell_RNA_CAPAN-2
Cell RNA - Daudi [NX] cell_RNA_Daudi
Cell RNA - EFO-21 [NX] cell_RNA_EFO-21
Cell RNA - fHDF/TERT166 [NX] cell_RNA_fHDF/TERT166
Cell RNA - HaCaT [NX] cell_RNA_HaCaT
Cell RNA - HAP1 [NX] cell_RNA_HAP1
Cell RNA - HBEC3-KT [NX] cell_RNA_HBEC3-KT
Cell RNA - HBF TERT88 [NX] cell_RNA_HBF_TERT88
Cell RNA - HDLM-2 [NX] cell_RNA_HDLM-2
Cell RNA - HEK 293 [NX] cell_RNA_HEK_293
Cell RNA - HEL [NX] cell_RNA_HEL
Cell RNA - HeLa [NX] cell_RNA_HeLa
Cell RNA - Hep G2 [NX] cell_RNA_Hep_G2
Cell RNA - HHSteC [NX] cell_RNA_HHSteC
Cell RNA - HL-60 [NX] cell_RNA_HL-60
Cell RNA - HMC-1 [NX] cell_RNA_HMC-1
Cell RNA - HSkMC [NX] cell_RNA_HSkMC
Cell RNA - hTCEpi [NX] cell_RNA_hTCEpi
Cell RNA - hTEC/SVTERT24-B [NX] cell_RNA_hTEC/SVTERT24-B
Cell RNA - hTERT-HME1 [NX] cell_RNA_hTERT-HME1
Cell RNA - HUVEC TERT2 [NX] cell_RNA_HUVEC_TERT2
Cell RNA - K-562 [NX] cell_RNA_K-562
Cell RNA - Karpas-707 [NX] cell_RNA_Karpas-707
Cell RNA - LHCN-M2 [NX] cell_RNA_LHCN-M2
Cell RNA - MCF7 [NX] cell_RNA_MCF7
Cell RNA - MOLT-4 [NX] cell_RNA_MOLT-4
Cell RNA - NB-4 [NX] cell_RNA_NB-4
Cell RNA - NTERA-2 [NX] cell_RNA_NTERA-2
Cell RNA - PC-3 [NX] cell_RNA_PC-3
Cell RNA - REH [NX] cell_RNA_REH
Cell RNA - RH-30 [NX] cell_RNA_RH-30
Cell RNA - RPMI-8226 [NX] cell_RNA_RPMI-8226
Cell RNA - RPTEC TERT1 [NX] cell_RNA_RPTEC_TERT1
Cell RNA - RT4 [NX] cell_RNA_RT4
Cell RNA - SCLC-21H [NX] cell_RNA_SCLC-21H
Cell RNA - SH-SY5Y [NX] cell_RNA_SH-SY5Y
Cell RNA - SiHa [NX] cell_RNA_SiHa
Cell RNA - SK-BR-3 [NX] cell_RNA_SK-BR-3
Cell RNA - SK-MEL-30 [NX] cell_RNA_SK-MEL-30
Cell RNA - T-47d [NX] cell_RNA_T-47d
Cell RNA - THP-1 [NX] cell_RNA_THP-1
Cell RNA - TIME [NX] cell_RNA_TIME
Cell RNA - U-138 MG [NX] cell_RNA_U-138_MG
Cell RNA - U-2 OS [NX] cell_RNA_U-2_OS
Cell RNA - U-2197 [NX] cell_RNA_U-2197
Cell RNA - U-251 MG [NX] cell_RNA_U-251_MG
Cell RNA - U-266/70 [NX] cell_RNA_U-266/70
Cell RNA - U-266/84 [NX] cell_RNA_U-266/84
Cell RNA - U-698 [NX] cell_RNA_U-698
Cell RNA - U-87 MG [NX] cell_RNA_U-87_MG
Cell RNA - U-937 [NX] cell_RNA_U-937
Cell RNA - WM-115 [NX] cell_RNA_WM-115
Blood RNA - basophil [NX] blood_RNA_basophil
Blood RNA - classical monocyte [NX] blood_RNA_classical_monocyte
Blood RNA - eosinophil [NX] blood_RNA_eosinophil
Blood RNA - gdTCR [NX] blood_RNA_gdTCR
Blood RNA - intermediate monocyte [NX] blood_RNA_intermediate_monocyte
Blood RNA - MAIT T-cell [NX] blood_RNA_MAIT_T-cell
Blood RNA - memory B-cell [NX] blood_RNA_memory_B-cell
Blood RNA - memory CD4 T-cell [NX] blood_RNA_memory_CD4_T-cell
Blood RNA - memory CD8 T-cell [NX] blood_RNA_memory_CD8_T-cell
Blood RNA - myeloid DC [NX] blood_RNA_myeloid_DC
Blood RNA - naive B-cell [NX] blood_RNA_naive_B-cell
Blood RNA - naive CD4 T-cell [NX] blood_RNA_naive_CD4_T-cell
Blood RNA - naive CD8 T-cell [NX] blood_RNA_naive_CD8_T-cell
Blood RNA - neutrophil [NX] blood_RNA_neutrophil
Blood RNA - NK-cell [NX] blood_RNA_NK-cell
Blood RNA - non-classical monocyte [NX] blood_RNA_non-classical_monocyte
Blood RNA - plasmacytoid DC [NX] blood_RNA_plasmacytoid_DC
Blood RNA - T-reg [NX] blood_RNA_T-reg
Blood RNA - total PBMC [NX] blood_RNA_total_PBMC
Brain RNA - amygdala [NX] brain_RNA_amygdala
Brain RNA - basal ganglia [NX] brain_RNA_basal_ganglia
Brain RNA - cerebellum [NX] brain_RNA_cerebellum
Brain RNA - cerebral cortex [NX] brain_RNA_cerebral_cortex
Brain RNA - hippocampal formation [NX] brain_RNA_hippocampal_formation
Brain RNA - hypothalamus [NX] brain_RNA_hypothalamus
Brain RNA - midbrain [NX] brain_RNA_midbrain
Brain RNA - olfactory region [NX] brain_RNA_olfactory_region
Brain RNA - pons and medulla [NX] brain_RNA_pons_and_medulla
Brain RNA - thalamus [NX] brain_RNA_thalamus