biothings-client 0.5.1

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 MyTaxon.Info, which provides access to taxon objects.

Support

Python >=3.7

Optional dependencies

• dataframe support (install using pip install biothings_client[dataframe])

  pandas is required for returning query results as a DataFrame.

• caching support (install using pip install biothings_client[caching], requires Python >=3.8)

  Allows local caching of client queries to a SQLite database. Requires:

  • hishel

  • anysqlite

Installation

• Option 1. Install from pypi repository using pip:

  pip install biothings_client

• Option 2. Install the latest commit from the github repository using pip:

  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

• Synchronous client.

  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.

  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)

Contact

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