biothings-client 0.3.1

Python Client for BioThings API services.

Intro

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.

Requirements

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”)

Optional dependencies

• 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.

Installation

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#egg=biothings_client

Version history

CHANGES.txt

Tutorial

See the quick start tutorial at the biothings_client doc page.

Documentation

https://biothings-clientpy.readthedocs.io

Usage

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'}

Contact

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