Skip to main content

A simple pythonic interface to biomart.

Project description

A simple and pythonic biomart interface for Python.

The intent of pybiomart is to provide a simple interface to biomart, which can be used to easily query biomart databases from Python. In this sense, pybiomart aims to provide functionality similar to packages such as biomaRt (which provides access to biomart from R).


Documentation is available at:


Retrieving and querying a dataset using the server interface:

from pybiomart import Server

server = Server(host='')

dataset = (server.marts['ENSEMBL_MART_ENSEMBL']

dataset.query(attributes=['ensembl_gene_id', 'external_gene_name'],
              filters={'chromosome_name': ['1','2']})

Retrieving a dataset directly with known dataset name:

from pybiomart import Dataset

dataset = Dataset(name='hsapiens_gene_ensembl',

dataset.query(attributes=['ensembl_gene_id', 'external_gene_name'],
              filters={'chromosome_name': ['1','2']})


Released under the MIT license.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for pybiomart, version 0.2.0
Filename, size File type Python version Upload date Hashes
Filename, size pybiomart-0.2.0-py2-none-any.whl (10.6 kB) File type Wheel Python version py2 Upload date Hashes View
Filename, size pybiomart-0.2.0-py3-none-any.whl (10.6 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size pybiomart-0.2.0.tar.gz (195.8 kB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page