Example script to retrieve phenotype data for a C. elegans gene using the WormBase REST API

retrieve_phenotypeinfo_from_wormbase.py

# script to retrieve the phenotype info for a particular gene from WormBase 

import requests, sys
 
server = "http://rest.wormbase.org"
ext = "/rest/field/gene/WBGene00000079/phenotype"

r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})

if not r.ok:
    r.raise_for_status()
    sys.exit()

decoded = r.json()
# print(decoded)

# based on looking at the example http://rest.wormbase.org/rest/field/gene/WBGene00000079/phenotype
phenotypes = decoded["phenotype"]
phenotypes = phenotypes["data"]
for phenotype in phenotypes:
    phenotype = phenotype["phenotype"]
    phenotype_id = phenotype["id"]
    label = phenotype["label"] 
    print("id=",phenotype_id,"label=",label)

print("FINISHED\n")