biothings-client

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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.

.. _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

Support

python >=3.7

Optional dependencies

* `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>`_.

Installation

* 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

Version history

`CHANGES.txt <https://raw.githubusercontent.com/biothings/biothings_client.py/master/CHANGES.txt>`_

Tutorial

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>`_.

Documentation

https://biothings-clientpy.readthedocs.io

Usage

• 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)
  

Contact

Drop us any feedback @biothingsapi <https://twitter.com/biothingsapi>_