API query for samples

EpiMed provides an API that allows programmatic access to available clinical data.

Query composition

http://epimed.univ-grenoble-alpes.fr/database/query/samples?key=value

Several "key-value" expressions can be chained with & symbol: 

http://epimed.univ-grenoble-alpes.fr/database/query/samples?key1=value1&key2=value2

Several values can be added with , symbol: 

http://epimed.univ-grenoble-alpes.fr/database/query/samples?key=value1,value2

Basic query parameters

Key Value
document
  • exp_group: download standard experimental grouping, DEFAULT
  • parameters: download original parameters
format
  • csv: create CSV file, DEFAULT
  • json: generate a result summary in JSON format
id_sample ID number(s) of samples, for example, id_sample=GSM748053,GSM748054
series a list of series, for example, series=GSE30219,GSE2109
id_platform a list of platforms, for example, id_platform=GPL96,GPL97
sex F, M
age_min minimal age
age_max maximal age
id_tissue_stage
  • 1: adult
  • 2: fetal
  • 3: not relevant
  • 4: embryonic
id_tissue_status
  • 1: Normal
  • 2: Pathological non tumoral
  • 3: Pathological tumoral
id_pathology ICD-10 pathology code
collection_method biopsy, cell line, isolated cells
id_topology ICD-O topology code
id_moprhology ICD-O morphology code
survival samples with survival only

Examples

Series

The following link generates the experimental grouping of GSE30219 series in CSV format:

http://epimed.univ-grenoble-alpes.fr/database/query/samples?series=GSE30219&document=exp_group&format=csv

"document=exp_group" and "format=csv" are optional as they are default values. The above query can be reduced to: 

http://epimed.univ-grenoble-alpes.fr/database/query/samples?series=GSE30219

Platforms

http://epimed.univ-grenoble-alpes.fr/database/query/samples?id_platform=GPL570,GPL96

Tissue status

Normal tissues:

http://epimed.univ-grenoble-alpes.fr/database/query/samples?id_tissue_status=1

Tissue stage

Adult tissues:

http://epimed.univ-grenoble-alpes.fr/database/query/samples?id_tissue_stage=1

Age

http://epimed.univ-grenoble-alpes.fr/database/query/samples?series=GSE30219&age_min=50&age_max=60

Survival

http://epimed.univ-grenoble-alpes.fr/database/query/samples?id_tissue_status=3&survival=true

or equivalent

http://epimed.univ-grenoble-alpes.fr/database/query/samples?id_tissue_status=3&survival