biothings_client is an easy-to-use Python wrapper to access any Biothings.api -based backend service. Currently, the following clients are available:
- gene - The client for MyGene.Info, which provides access to gene objects.
- variant - The client MyVariant.Info, which provides access to genetic variant objects.
- chem - The client for MyChem.Info, which provides access to chemical/drug objects.
- disease - The client for MyDisease.Info, which provides access to disease objects.
- taxon - The client for t.biothings.io, which provides access to taxon objects.
python >=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")
- pandas (install using "pip install pandas") is required for returning a list of variant objects as DataFrame.
- requests_cache (install using "pip install requests_cache") is required for local caching of API requests.
- Option 1
pip install biothings_client- Option 2
download/extract the source code and run:
python setup.py install- Option 3
install the latest code directly from the repository:
pip install -e git+https://github.com/biothings/biothings_client.py
See the quick start tutorial at the biothings_client doc page.
In [1]: from biothings_client import get_client
# get a client for variant objects
In [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 objects
In [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/drugs
In [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 taxa
In [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'}Drop us any feedback @biothingsapi