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What is opy_Targets?

Opentargets.org uses GraphQL API to explore it's content via coding. This ensemble of functions aim is to make it easy to use the API via our beloved coding language - python <3

Python dependencies

(requires Python 3)

  • pandas
  • requests
  • json

Usage

Example:

Lets say you want to get SNPS of gene you think is related to a disease

import opy_targets as opy

ENDOMETRIOSIS_EFO_ID = 'EFO_0001065'
GENE_ESNG_ID = ENSG00000196208

opy.get_snp_data(GENE_ESNG_ID,ENDOMETRIOSIS_ID).head(4)

output:

variantRsId variantId studyId studySampleSize publicationFirstAuthor label chr location disease_ID gene_related
0 rs11674184 2_11581409_T_G GCST004549 208903 Sapkota Y intron_variant 2 11581409 EFO_0001065 ENSG00000196208
1 rs11674184 2_11581409_T_G GCST004549_2 208903 Sapkota Y intron_variant 2 11581409 EFO_0001065 ENSG00000196208
2 rs13394619 2_11587381_G_A GCST001720 13997 Nyholt DR intron_variant 2 11587381 EFO_0001065 ENSG00000196208
3 rs77294520 2_11520829_G_C GCST004549_2 208903 Sapkota Y intergenic_variant 2 11520829 EFO_0001065 ENSG00000196208

Most of the chances you don't know the genes related to the disease. NO PROBLEM!

Lets say you want to know which SNP associate with a disease you study

import opy_targets as opy

#

ENDOMETRIOSIS_EFO_ID = 'EFO_0001065'

opy.get_SNP_df(ENDOMETRIOSIS_ID).head()

output:

variantRsId variantId studyId studySampleSize publicationFirstAuthor label chr location disease_ID gene_related
0 rs11674184 2_11581409_T_G GCST004549 208903 Sapkota Y intron_variant 2 11581409 EFO_0001065 ENSG00000196208
1 rs13394619 2_11587381_G_A GCST001720 13997 Nyholt DR intron_variant 2 11587381 EFO_0001065 ENSG00000196208
2 rs77294520 2_11520829_G_C GCST004549_2 208903 Sapkota Y intergenic_variant 2 11520829 EFO_0001065 ENSG00000196208
3 rs58502716 2_11592421_G_GAATCAC FINNGEN_R5_N14_ENDOMETRIOSIS 77257 FINNGEN_R5 intron_variant 2 11592421 EFO_0001065 ENSG00000196208

You can change parameters such as the amount of genes retrived for each disease (25 default) and the sorting method of them (genetic association). check the functions docstring.

Enjoy ;)