README.md

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 ;)