https://github.com/bio2bel/mesh

A Bio2BEL package for the Medical Subject Headings (MeSH; https://meshb.nlm.nih.gov)
https://github.com/bio2bel/mesh

biological-expression-language chemistry mesh phenotypes terminology

Last synced: 5 months ago
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A Bio2BEL package for the Medical Subject Headings (MeSH; https://meshb.nlm.nih.gov)

• Host: GitHub
• URL: https://github.com/bio2bel/mesh
• Owner: bio2bel
• License: mit
• Created: 2017-10-18T06:52:52.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2019-08-02T09:49:09.000Z (almost 7 years ago)
• Last Synced: 2025-10-02T04:26:58.349Z (9 months ago)
• Topics: biological-expression-language, chemistry, mesh, phenotypes, terminology
• Language: Python
• Homepage:
• Size: 74.2 KB
• Stars: 3
• Watchers: 2
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

Awesome Lists containing this project

README

          
Bio2BEL MeSH |build| |coverage| |documentation| |zenodo|

========================================================

Converts the MeSH hierarchy to BEL

Installation |pypi_version| |python_versions| |pypi_license|

------------------------------------------------------------

``bio2bel_mesh`` can be installed easily from `PyPI `_ with the

following code in your favorite terminal:

.. code-block:: sh

    $ python3 -m pip install bio2bel_mesh

or from the latest code on `GitHub `_ with:

.. code-block:: sh

    $ python3 -m pip install git+https://github.com/bio2bel/mesh.git@master

Setup

-----

MeSH can be downloaded and populated from either the Python REPL or the automatically installed command line utility.

Python REPL

~~~~~~~~~~~

.. code-block:: python

    >>> import bio2bel_mesh

    >>> mesh_manager = bio2bel_mesh.Manager()

    >>> mesh_manager.populate()

Command Line Utility

~~~~~~~~~~~~~~~~~~~~

.. code-block:: bash

    bio2bel_mesh populate

Links

-----

- `MeSH Tree Browser `_

- `SPARQL 1.1 Specification `_

- `MeSH Information `_

- `MeSH FTP `_

- `MeSH RDF Download `_

.. |build| image:: https://travis-ci.com/bio2bel/mesh.svg?branch=master

    :target: https://travis-ci.com/bio2bel/mesh

    :alt: Build Status

.. |coverage| image:: https://codecov.io/gh/bio2bel/mesh/coverage.svg?branch=master

    :target: https://codecov.io/gh/bio2bel/mesh?branch=master

    :alt: Coverage Status

.. |documentation| image:: https://readthedocs.org/projects/bio2bel-mesh/badge/?version=latest

    :target: https://bio2bel.readthedocs.io/projects/mesh/en/latest/?badge=latest

    :alt: Documentation Status

.. |climate| image:: https://codeclimate.com/github/bio2bel/mesh/badges/gpa.svg

    :target: https://codeclimate.com/github/bio2bel/mesh

    :alt: Code Climate

.. |python_versions| image:: https://img.shields.io/pypi/pyversions/bio2bel_mesh.svg

    :alt: Stable Supported Python Versions

.. |pypi_version| image:: https://img.shields.io/pypi/v/bio2bel_mesh.svg

    :alt: Current version on PyPI

.. |pypi_license| image:: https://img.shields.io/pypi/l/bio2bel_mesh.svg

    :alt: MIT License

.. |zenodo| image:: https://zenodo.org/badge/107369801.svg

    :target: https://zenodo.org/badge/latestdoi/107369801