Package: biothings-client
Introbiothings_clientis an easy-to-use Python wrapper to access anyBiothings.api-based backend service. Currently, the following clients are available:gene - The client forMyGene.Info, which provides access to gene objects.variant - The clientMyVariant.Info, which provides access to genetic variant objects.chem - The client forMyChem.Info, which provides access to chemical/drug objects.disease - The client forMyDisease.Info, which provides access to disease objects.geneset - The client forMyGeneset.Info, which provides access to geneset/pathway objects.taxon - The client fort.biothings.io, which provides access to taxon objects.Requirementspython >=2.7 (including all python3 versions)(It may still work under python 2.6, but it’s not supported any more.)requests(install using “pip install requests”)Optional dependenciespandas(install using “pip install pandas”) is required for returning a list of variant objects asDataFrame.requests_cache(install using “pip install requests_cache”) is required for local caching of API requests.InstallationOption 1pip install biothings_clientOption 2download/extract the source code and run:python setup.py installOption 3install the latest code directly from the repository:pip install -e git+https://github.com/biothings/biothings_client.py#egg=biothings_clientVersion historyCHANGES.txtTutorialSee thequick start tutorialat thebiothings_client doc page.Documentationhttps://biothings-clientpy.readthedocs.ioUsageIn[1]:frombiothings_clientimportget_client# get a client for variant objectsIn[2]:mv=get_client("variant")In[3]:mv.getvariant("chr7:g.140453134T>C")Out[3]:#output below is collapsed{"_id":"chr7:g.140453134T>C","_version":1,"chrom":"7","cadd":{...},"clinvar":{...},"cosmic":{...},"dbnsfp":{...},"dbsnp":{...},"docm":{...},"hg19":{'end':140453134,'start':140453134},"mutdb":{...},"snpeff":{...},"vcf":{"alt":"C","position":"140453134","ref":"T"}}# get a client for gene objectsIn[7]:mg=get_client("gene")In[8]:mg.getgene(1017,'name,symbol,refseq')Out[8]:{'_id':'1017','_score':21.03413,'name':'cyclin dependent kinase 2','refseq':{'genomic':['NC_000012.12','NC_018923.2','NG_034014.1'],'protein':['NP_001277159.1','NP_001789.2','NP_439892.2','XP_011536034.1'],'rna':['NM_001290230.1','NM_001798.4','NM_052827.3','XM_011537732.1'],'translation':[{'protein':'NP_001789.2','rna':'NM_001798.4'},{'protein':'NP_439892.2','rna':'NM_052827.3'},{'protein':'NP_001277159.1','rna':'NM_001290230.1'},{'protein':'XP_011536034.1','rna':'XM_011537732.1'}]},'symbol':'CDK2'}# get a client for chems/drugsIn[9]:md=get_client("chem")In[10]:md.getchem("ATBDZSAENDYQDW-UHFFFAOYSA-N",fields="pubchem")Out[10]:{'_id':'ATBDZSAENDYQDW-UHFFFAOYSA-N','_version':1,'pubchem':{'chiral_atom_count':0,'chiral_bond_count':0,'cid':'CID4080429','complexity':250,'covalently-bonded_unit_count':1,'defined_atom_stereocenter_count':0,'defined_bond_stereocenter_count':0,'exact_mass':184.019415,'formal_charge':0,'heavy_atom_count':12,'hydrogen_bond_acceptor_count':3,'hydrogen_bond_donor_count':1,'inchi':'InChI=1S/C8H8O3S/c1-2-7-4-3-5-8(6-7)12(9,10)11/h2-6H,1H2,(H,9,10,11)','inchi_key':'ATBDZSAENDYQDW-UHFFFAOYSA-N','isotope_atom_count':0,'iupac':{'traditional':'3-vinylbesylic acid'},'molecular_formula':'C8H8O3S','molecular_weight':184.21232,'monoisotopic_weight':184.019415,'rotatable_bond_count':2,'smiles':{'isomeric':'C=CC1=CC(=CC=C1)S(=O)(=O)O'},'tautomers_count':1,'topological_polar_surface_area':62.8,'undefined_atom_stereocenter_count':0,'undefined_bond_stereocenter_count':0,'xlogp':1.4}}# get a client for taxaIn[11]:mt=get_client("taxon")In[12]:mt.gettaxon(9606)Out[12]:{'_id':'9606','_version':1,'authority':['homo sapiens linnaeus, 1758'],'common_name':'man','genbank_common_name':'human','has_gene':True,'lineage':[9606,9605,207598,9604,314295,9526,314293,376913,9443,314146,1437010,9347,32525,40674,32524,32523,1338369,8287,117571,117570,7776,7742,89593,7711,33511,33213,6072,33208,33154,2759,131567,1],'other_names':['humans'],'parent_taxid':9605,'rank':'species','scientific_name':'homo sapiens','taxid':9606,'uniprot_name':'homo sapiens'}ContactDrop us any feedback@biothingsapi