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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.
* geneset - The client for MyGeneset.Info_, which provides access to geneset/pathway objects.
* taxon - The client for t.biothings.io_, which provides access to taxon objects.
.. _t.biothings.io: https://t.biothings.io .. _Biothings.api: https://biothings.io .. _MyGene.Info: https://mygene.info .. _MyVariant.Info: https://myvariant.info .. _MyChem.Info: https://mychem.info .. _MyDisease.Info: https://mydisease.info .. _MyGeneset.Info: https://mygeneset.info
python >=3.7
* `pandas <http://pandas.pydata.org>`_ (install using "pip install pandas") is required for returning a list of variant objects as `DataFrame <http://pandas.pydata.org/pandas-docs/stable/dsintro.html#dataframe>`_.
* Option 1. Install from pypi repository using pip:
.. code-block:: bash
pip install biothings_client
* Option 2. Install the latest commit from the github repository using pip:
.. code-block:: bash
pip install -e git+https://github.com/biothings/biothings_client.py#egg=biothings_client
`CHANGES.txt <https://raw.githubusercontent.com/biothings/biothings_client.py/master/CHANGES.txt>`_
See the `quick start tutorial <https://biothings-clientpy.readthedocs.io/en/latest/doc/Quick-Start.html>`_ at the `biothings_client doc page <https://biothings-clientpy.readthedocs.io/en/latest/index.html>`_.
https://biothings-clientpy.readthedocs.io
Synchronous client.
.. code-block:: python
from biothings_client import get_client
# get a client for variant objects
mv = get_client("variant")
mv.getvariant("chr7:g.140453134T>C")
# 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
mg = get_client("gene")
mg.getgene(1017, 'name,symbol,refseq')
{'_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
md = get_client("chem")
md.getchem("ATBDZSAENDYQDW-UHFFFAOYSA-N", fields="pubchem")
{'_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
mt = get_client("taxon")
mt.gettaxon(9606)
{'_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'}
Asynchronous client.
.. code-block:: python
from biothings_client import get_async_client
# get a client for variant objects
mv = get_async_client("variant")
await mv.getvariant("chr7:g.140453134T>C")
# get a client for gene objects
mg = get_async_client("gene")
await mg.getgene(1017, 'name,symbol,refseq')
# get a client for chems/drugs
md = get_async_client("chem")
await md.getchem("ATBDZSAENDYQDW-UHFFFAOYSA-N", fields="pubchem")
# get a client for taxa
mt = get_async_client("taxon")
await mt.gettaxon(9606)
Drop us any feedback @biothingsapi <https://twitter.com/biothingsapi>_
FAQs
Python Client for BioThings API services.
We found that biothings-client demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 2 open source maintainers collaborating on the project.
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