In [51]:
import requests
import json
import pandas as pd
import seaborn as sns;
In [52]:
mytargets = ['DRD2', 'DRD4', 'PINK1', 'GRIN1', 'FUS', 'ANG', 'FRED', 'BERT']
disease = "EFO_0002508" # Parkinson's
#disease = "EFO_0000253" # ALS
maxresults = 100 # max 10,000
In [53]:
url = 'https://www.targetvalidation.org/api/latest/public/association/filter'
headers = {"Accept": "application/json"}
data = "{\"disease\":[\"" + disease + "\"], \"size\":" + str(maxresults) + "}"
response = requests.post(url, headers=headers, data=data)
output = response.json()
In [54]:
print json.dumps(output, indent=2)
{
"from": 0,
"facets": {},
"took": 98,
"therapeutic_areas": [],
"total": 1717,
"data": [
{
"target": {
"gene_info": {
"symbol": "ATP13A2",
"name": "ATPase 13A2"
},
"id": "ENSG00000159363"
},
"association_score": {
"datatypes": {
"literature": 0.06705213664546321,
"rna_expression": 0.0,
"genetic_association": 1.0,
"somatic_mutation": 0.0,
"known_drug": 0.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"overall": 1.0,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 1.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 0.9899124999999999,
"europepmc": 0.06705213664546321,
"gwas_catalog": 0.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 0.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"is_direct": true,
"disease": {
"efo_info": {
"therapeutic_area": {
"labels": [
"nervous system disease"
],
"codes": [
"EFO_0000618"
]
},
"path": [
[
"EFO_0000618",
"EFO_0002508"
],
[
"EFO_0000618",
"EFO_0005772",
"EFO_0002508"
]
],
"label": "Parkinson's disease"
},
"id": "EFO_0002508"
},
"evidence_count": {
"datatypes": {
"literature": 48.0,
"rna_expression": 0.0,
"genetic_association": 8.0,
"somatic_mutation": 0.0,
"known_drug": 0.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"total": 56.0,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 1.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 7.0,
"europepmc": 48.0,
"gwas_catalog": 0.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 0.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"id": "ENSG00000159363-EFO_0002508"
},
{
"target": {
"gene_info": {
"symbol": "DNAJC13",
"name": "DnaJ heat shock protein family (Hsp40) member C13"
},
"id": "ENSG00000138246"
},
"association_score": {
"datatypes": {
"literature": 0.05293821674225247,
"rna_expression": 0.0,
"genetic_association": 1.0,
"somatic_mutation": 0.0,
"known_drug": 0.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"overall": 1.0,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 0.0,
"uniprot_literature": 1.0,
"phenodigm": 0.0,
"eva": 0.0,
"europepmc": 0.05293821674225247,
"gwas_catalog": 0.0,
"intogen": 0.0,
"uniprot": 0.7,
"chembl": 0.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"is_direct": true,
"disease": {
"efo_info": {
"therapeutic_area": {
"labels": [
"nervous system disease"
],
"codes": [
"EFO_0000618"
]
},
"path": [
[
"EFO_0000618",
"EFO_0002508"
],
[
"EFO_0000618",
"EFO_0005772",
"EFO_0002508"
]
],
"label": "Parkinson's disease"
},
"id": "EFO_0002508"
},
"evidence_count": {
"datatypes": {
"literature": 10.0,
"rna_expression": 0.0,
"genetic_association": 2.0,
"somatic_mutation": 0.0,
"known_drug": 0.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"total": 12.0,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 0.0,
"uniprot_literature": 1.0,
"phenodigm": 0.0,
"eva": 0.0,
"europepmc": 10.0,
"gwas_catalog": 0.0,
"intogen": 0.0,
"uniprot": 1.0,
"chembl": 0.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"id": "ENSG00000138246-EFO_0002508"
},
{
"target": {
"gene_info": {
"symbol": "LRRK2",
"name": "leucine rich repeat kinase 2"
},
"id": "ENSG00000188906"
},
"association_score": {
"datatypes": {
"literature": 0.12505500113984228,
"rna_expression": 0.0,
"genetic_association": 1.0,
"somatic_mutation": 0.0,
"known_drug": 0.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"overall": 1.0,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 0.48999999999999994,
"europepmc": 0.12505500113984228,
"gwas_catalog": 1,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 0.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"is_direct": true,
"disease": {
"efo_info": {
"therapeutic_area": {
"labels": [
"nervous system disease"
],
"codes": [
"EFO_0000618"
]
},
"path": [
[
"EFO_0000618",
"EFO_0002508"
],
[
"EFO_0000618",
"EFO_0005772",
"EFO_0002508"
]
],
"label": "Parkinson's disease"
},
"id": "EFO_0002508"
},
"evidence_count": {
"datatypes": {
"literature": 925.0,
"rna_expression": 0.0,
"genetic_association": 6.0,
"somatic_mutation": 0.0,
"known_drug": 0.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"total": 931.0,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 1.0,
"europepmc": 925.0,
"gwas_catalog": 5.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 0.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"id": "ENSG00000188906-EFO_0002508"
},
{
"target": {
"gene_info": {
"symbol": "SNCA",
"name": "synuclein alpha"
},
"id": "ENSG00000145335"
},
"association_score": {
"datatypes": {
"literature": 0.1279404038724967,
"rna_expression": 0.00864837749664953,
"genetic_association": 1.0,
"somatic_mutation": 0.0,
"known_drug": 0.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"overall": 1.0,
"datasources": {
"expression_atlas": 0.00864837749664953,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 0.6975694444444444,
"europepmc": 0.1279404038724967,
"gwas_catalog": 0.9270529134794556,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 0.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"is_direct": true,
"disease": {
"efo_info": {
"therapeutic_area": {
"labels": [
"nervous system disease"
],
"codes": [
"EFO_0000618"
]
},
"path": [
[
"EFO_0000618",
"EFO_0002508"
],
[
"EFO_0000618",
"EFO_0005772",
"EFO_0002508"
]
],
"label": "Parkinson's disease"
},
"id": "EFO_0002508"
},
"evidence_count": {
"datatypes": {
"literature": 2032.0,
"rna_expression": 1.0,
"genetic_association": 17.0,
"somatic_mutation": 0.0,
"known_drug": 0.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"total": 2050.0,
"datasources": {
"expression_atlas": 1.0,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 4.0,
"europepmc": 2032.0,
"gwas_catalog": 13.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 0.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"id": "ENSG00000145335-EFO_0002508"
},
{
"target": {
"gene_info": {
"symbol": "DRD2",
"name": "dopamine receptor D2"
},
"id": "ENSG00000149295"
},
"association_score": {
"datatypes": {
"literature": 0.0746059308062336,
"rna_expression": 0.0,
"genetic_association": 0.0,
"somatic_mutation": 0.0,
"known_drug": 1.0,
"animal_model": 0.2347131290953496,
"affected_pathway": 0.0
},
"overall": 1.0,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.2347131290953496,
"eva": 0.0,
"europepmc": 0.0746059308062336,
"gwas_catalog": 0.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 1,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"is_direct": true,
"disease": {
"efo_info": {
"therapeutic_area": {
"labels": [
"nervous system disease"
],
"codes": [
"EFO_0000618"
]
},
"path": [
[
"EFO_0000618",
"EFO_0002508"
],
[
"EFO_0000618",
"EFO_0005772",
"EFO_0002508"
]
],
"label": "Parkinson's disease"
},
"id": "EFO_0002508"
},
"evidence_count": {
"datatypes": {
"literature": 137.0,
"rna_expression": 0.0,
"genetic_association": 0.0,
"somatic_mutation": 0.0,
"known_drug": 86.0,
"animal_model": 11.0,
"affected_pathway": 0.0
},
"total": 234.0,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 11.0,
"eva": 0.0,
"europepmc": 137.0,
"gwas_catalog": 0.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 86.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"id": "ENSG00000149295-EFO_0002508"
},
{
"target": {
"gene_info": {
"symbol": "MAOB",
"name": "monoamine oxidase B"
},
"id": "ENSG00000069535"
},
"association_score": {
"datatypes": {
"literature": 0.08655178316465198,
"rna_expression": 0.0,
"genetic_association": 0.0,
"somatic_mutation": 0.0,
"known_drug": 1.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"overall": 1.0,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 0.0,
"europepmc": 0.08655178316465198,
"gwas_catalog": 0.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 1,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"is_direct": true,
"disease": {
"efo_info": {
"therapeutic_area": {
"labels": [
"nervous system disease"
],
"codes": [
"EFO_0000618"
]
},
"path": [
[
"EFO_0000618",
"EFO_0002508"
],
[
"EFO_0000618",
"EFO_0005772",
"EFO_0002508"
]
],
"label": "Parkinson's disease"
},
"id": "EFO_0002508"
},
"evidence_count": {
"datatypes": {
"literature": 331.0,
"rna_expression": 0.0,
"genetic_association": 0.0,
"somatic_mutation": 0.0,
"known_drug": 30.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"total": 361.0,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 0.0,
"europepmc": 331.0,
"gwas_catalog": 0.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 30.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"id": "ENSG00000069535-EFO_0002508"
},
{
"target": {
"gene_info": {
"symbol": "SLC6A3",
"name": "solute carrier family 6 member 3"
},
"id": "ENSG00000142319"
},
"association_score": {
"datatypes": {
"literature": 0.07529074250150272,
"rna_expression": 0.022124178395501022,
"genetic_association": 0.0,
"somatic_mutation": 0.0,
"known_drug": 1.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"overall": 1.0,
"datasources": {
"expression_atlas": 0.022124178395501022,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 0.0,
"europepmc": 0.07529074250150272,
"gwas_catalog": 0.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 1,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"is_direct": true,
"disease": {
"efo_info": {
"therapeutic_area": {
"labels": [
"nervous system disease"
],
"codes": [
"EFO_0000618"
]
},
"path": [
[
"EFO_0000618",
"EFO_0002508"
],
[
"EFO_0000618",
"EFO_0005772",
"EFO_0002508"
]
],
"label": "Parkinson's disease"
},
"id": "EFO_0002508"
},
"evidence_count": {
"datatypes": {
"literature": 20.0,
"rna_expression": 1.0,
"genetic_association": 0.0,
"somatic_mutation": 0.0,
"known_drug": 2.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"total": 23.0,
"datasources": {
"expression_atlas": 1.0,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 0.0,
"europepmc": 20.0,
"gwas_catalog": 0.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 2.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"id": "ENSG00000142319-EFO_0002508"
},
{
"target": {
"gene_info": {
"symbol": "COMT",
"name": "catechol-O-methyltransferase"
},
"id": "ENSG00000093010"
},
"association_score": {
"datatypes": {
"literature": 0.08462014828981981,
"rna_expression": 0.0,
"genetic_association": 0.0,
"somatic_mutation": 0.0,
"known_drug": 1.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"overall": 1.0,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 0.0,
"europepmc": 0.08462014828981981,
"gwas_catalog": 0.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 1,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"is_direct": true,
"disease": {
"efo_info": {
"therapeutic_area": {
"labels": [
"nervous system disease"
],
"codes": [
"EFO_0000618"
]
},
"path": [
[
"EFO_0000618",
"EFO_0002508"
],
[
"EFO_0000618",
"EFO_0005772",
"EFO_0002508"
]
],
"label": "Parkinson's disease"
},
"id": "EFO_0002508"
},
"evidence_count": {
"datatypes": {
"literature": 305.0,
"rna_expression": 0.0,
"genetic_association": 0.0,
"somatic_mutation": 0.0,
"known_drug": 21.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"total": 326.0,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 0.0,
"europepmc": 305.0,
"gwas_catalog": 0.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 21.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"id": "ENSG00000093010-EFO_0002508"
},
{
"target": {
"gene_info": {
"symbol": "BCHE",
"name": "butyrylcholinesterase"
},
"id": "ENSG00000114200"
},
"association_score": {
"datatypes": {
"literature": 0.07833431427755484,
"rna_expression": 0.0,
"genetic_association": 0.0,
"somatic_mutation": 0.0,
"known_drug": 1.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"overall": 1.0,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 0.0,
"europepmc": 0.07833431427755484,
"gwas_catalog": 0.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 1,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"is_direct": true,
"disease": {
"efo_info": {
"therapeutic_area": {
"labels": [
"nervous system disease"
],
"codes": [
"EFO_0000618"
]
},
"path": [
[
"EFO_0000618",
"EFO_0002508"
],
[
"EFO_0000618",
"EFO_0005772",
"EFO_0002508"
]
],
"label": "Parkinson's disease"
},
"id": "EFO_0002508"
},
"evidence_count": {
"datatypes": {
"literature": 71.0,
"rna_expression": 0.0,
"genetic_association": 0.0,
"somatic_mutation": 0.0,
"known_drug": 5.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"total": 76.0,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 0.0,
"europepmc": 71.0,
"gwas_catalog": 0.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 5.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"id": "ENSG00000114200-EFO_0002508"
},
{
"target": {
"gene_info": {
"symbol": "DDC",
"name": "dopa decarboxylase"
},
"id": "ENSG00000132437"
},
"association_score": {
"datatypes": {
"literature": 0.06658972964758132,
"rna_expression": 0.020344180017235106,
"genetic_association": 0.0,
"somatic_mutation": 0.0,
"known_drug": 1.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"overall": 1.0,
"datasources": {
"expression_atlas": 0.020344180017235106,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 0.0,
"europepmc": 0.06658972964758132,
"gwas_catalog": 0.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 1,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
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"rna_expression": 0.0,
"genetic_association": 0.6181925756315331,
"somatic_mutation": 0.0,
"known_drug": 0.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"overall": 0.6315113473309536,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 0.0,
"europepmc": 0.05327508679768204,
"gwas_catalog": 0.6181925756315331,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 0.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"is_direct": true,
"disease": {
"efo_info": {
"therapeutic_area": {
"labels": [
"nervous system disease"
],
"codes": [
"EFO_0000618"
]
},
"path": [
[
"EFO_0000618",
"EFO_0002508"
],
[
"EFO_0000618",
"EFO_0005772",
"EFO_0002508"
]
],
"label": "Parkinson's disease"
},
"id": "EFO_0002508"
},
"evidence_count": {
"datatypes": {
"literature": 10.0,
"rna_expression": 0.0,
"genetic_association": 3.0,
"somatic_mutation": 0.0,
"known_drug": 0.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"total": 13.0,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 0.0,
"europepmc": 10.0,
"gwas_catalog": 3.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 0.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"id": "ENSG00000152214-EFO_0002508"
},
{
"target": {
"gene_info": {
"symbol": "SPPL2C",
"name": "signal peptide peptidase like 2C"
},
"id": "ENSG00000185294"
},
"association_score": {
"datatypes": {
"literature": 0.0,
"rna_expression": 0.0,
"genetic_association": 0.631067674779749,
"somatic_mutation": 0.0,
"known_drug": 0.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"overall": 0.631067674779749,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 0.0,
"europepmc": 0.0,
"gwas_catalog": 0.631067674779749,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 0.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"is_direct": true,
"disease": {
"efo_info": {
"therapeutic_area": {
"labels": [
"nervous system disease"
],
"codes": [
"EFO_0000618"
]
},
"path": [
[
"EFO_0000618",
"EFO_0002508"
],
[
"EFO_0000618",
"EFO_0005772",
"EFO_0002508"
]
],
"label": "Parkinson's disease"
},
"id": "EFO_0002508"
},
"evidence_count": {
"datatypes": {
"literature": 0.0,
"rna_expression": 0.0,
"genetic_association": 1.0,
"somatic_mutation": 0.0,
"known_drug": 0.0,
"animal_model": 0.0,
"affected_pathway": 0.0
},
"total": 1.0,
"datasources": {
"expression_atlas": 0.0,
"gene2phenotype": 0.0,
"uniprot_literature": 0.0,
"phenodigm": 0.0,
"eva": 0.0,
"europepmc": 0.0,
"gwas_catalog": 1.0,
"intogen": 0.0,
"uniprot": 0.0,
"chembl": 0.0,
"cancer_gene_census": 0.0,
"reactome": 0.0,
"eva_somatic": 0.0,
"disgenet": 0.0
}
},
"id": "ENSG00000185294-EFO_0002508"
}
],
"size": 100
}
In [55]:
df = pd.DataFrame()
for target in output['data']:
# If the target is in our list then add it to the DataFrame
if target['target']['gene_info']['symbol'] in mytargets:
# Add all the association scores in one hit
s = pd.Series(target['association_score']['datatypes'])
# Append the overall score
s['overall'] = target['association_score']['overall']
# Use the target as the series name
s.name = str(target['target']['gene_info']['symbol'])
# Append the series to our DataFrame
df = df.append(s, ignore_index=False)
# Reorder and rename columns to match OpenTargets viz
df = df.reindex(columns=['overall','genetic_association','somatic_mutation','known_drug','affected_pathway','rna_expression','literature','animal_model'])
df.columns = ['Association score', 'Genetic associations', 'Somatic mutations', 'Drugs', 'Affected pathways', 'RNA expression', 'Text mining', 'Animal models']
In [56]:
print "Targets that have an association to " + disease + ":"
print df.index.tolist()
print
print "Targets that had no recorded association in the top " + str(maxresults) + " results returned for disease " + disease + ":"
print list(set(mytargets)-set(df.index))
Targets that have an association to EFO_0002508:
['DRD2', 'DRD4', 'GRIN1', 'PINK1']
Targets that had no recorded association in the top 100 results returned for disease EFO_0002508:
['BERT', 'ANG', 'FUS', 'FRED']
In [57]:
print df
Association score Genetic associations Somatic mutations Drugs \
DRD2 1.000000 0.000000 0.0 1.0
DRD4 1.000000 0.000000 0.0 1.0
GRIN1 1.000000 0.000000 0.0 1.0
PINK1 0.885694 0.885694 0.0 0.0
Affected pathways RNA expression Text mining Animal models
DRD2 0.0 0.0 0.074606 0.234713
DRD4 0.0 0.0 0.051901 0.000000
GRIN1 0.0 0.0 0.023233 0.000000
PINK1 0.0 0.0 0.000000 0.000000
In [58]:
%matplotlib inline
sns.set()
ax = sns.heatmap(df, cmap="Blues", annot=True, linewidths=2)
sns.plt.show()
In [ ]:
Content source: theoplatt/jupyter
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