Skip to main content

No project description provided

Project description

Python PyPI

Biolink Model Toolkit

Biolink Model Toolkit (BMT): A Python API for working with the Biolink Model.

BMT provides utility functions to look up Biolink Model for classes, relations, and properties based on Biolink CURIEs or external CURIEs that have been mapped to Biolink Model.

Note: Each release of BMT is pinned to a specific version of the Biolink Model to ensure consistency.

Installation

For users

BMT is available on PyPI and can be installed via pip:

pip install bmt

For developers

You can install BMT from GitHub as follows:

# clone the repo
git clone https://github.com/biolink/biolink-model-toolkit

# cd into the folder
cd biolink-model-toolkit

# install
python setup.py install

Documentation

The technical documentation for BMT can be found at bmt.readthedocs.io

Usage

BMT provides convenience methods to operate on the Biolink Model.

Using this toolkit you can,

  • Get Biolink Model elements corresponding to a given Biolink class or slot name
  • Get Biolink Model elements corresponding to a given external CURIE/IRI
  • Get ancestors for a given Biolink Model element
  • Get descendants for a given Biolink Model element
  • Get parent for a given Biolink Model element
  • Get children for a given Biolink Model element
  • Check whether a given Biolink Model element is part of a specified subset

Using the Toolkit class

The main entrypoint is the Toolkit class that provides various methods for accessing and working with the Biolink Model.

Getting a Biolink Model element based on its name

from bmt import Toolkit
t = Toolkit()
element = t.get_element('gene') # This returns the element for 'biolink:Gene'

Get a Biolink Model element based on its mappings

from bmt import Toolkit
t = Toolkit()
element_name = t.get_element_by_mapping('SEMMEDDB:CAUSES') # This returns 'causes'
element = t.get_element(element_name)

element_name = t.get_element_by_mapping('RO:0002410') # This returns 'causes'
element = t.get_element(element_name)

Get ancestors for a given Biolink Model element

from bmt import Toolkit
t = Toolkit()
ancestors = t.get_ancestors('gene')

The above returns a list of ancestors: ['gene', 'gene or gene product', 'macromolecular machine', 'genomic entity', 'molecular entity', 'biological entity', 'named thing']

Get descendants for a given Biolink Model element

from bmt import Toolkit
t = Toolkit()
descendants = t.get_descendants('gene or gene product')

The above returns a list of descendants: ['gene', 'gene product', 'gene product isoform', 'RNA product', 'noncoding RNA product', 'microRNA', 'RNA product isoform', 'transcript', 'protein', 'protein isoform']

Check whether a given string is a valid Biolink Model category

from bmt import Toolkit
t = Toolkit()
t.is_category('gene') # True
t.is_category('treats') # False

Check whether a given string is a valid Biolink Model predicate

from bmt import Toolkit
t = Toolkit()
t.is_predicate('related to') # True
t.is_predicate('interacts with') # True
t.is_predicate('disease') # False

Using the Toolkit class with different versions of Biolink Model

BMT is pinned to a specific version of Biolink Model at each release. This can be configured to use your custom version of Biolink Model YAML:

from bmt import Toolkit
t = Toolkit('/path/to/biolink-model.yaml')

The path can be a file path or a URL.

Project details


Download files

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

Source Distribution

bmt-0.7.8.tar.gz (12.4 kB view details)

Uploaded Source

Built Distribution

bmt-0.7.8-py3-none-any.whl (12.0 kB view details)

Uploaded Python 3

File details

Details for the file bmt-0.7.8.tar.gz.

File metadata

  • Download URL: bmt-0.7.8.tar.gz
  • Upload date:
  • Size: 12.4 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.6.0 importlib_metadata/4.2.0 pkginfo/1.8.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.3 CPython/3.7.4

File hashes

Hashes for bmt-0.7.8.tar.gz
Algorithm Hash digest
SHA256 17e4998569c0424d65c880935c018653eb3abb72be9efb3bafabe36d271f4050
MD5 ed276aeac7de41839d11651d7c1ec1ef
BLAKE2b-256 e2b2839bd94e34b6e2bcfef4644a2a4a6c3d4bcb013a6e919afb6f8f659ba372

See more details on using hashes here.

Provenance

File details

Details for the file bmt-0.7.8-py3-none-any.whl.

File metadata

  • Download URL: bmt-0.7.8-py3-none-any.whl
  • Upload date:
  • Size: 12.0 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.6.0 importlib_metadata/4.2.0 pkginfo/1.8.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.3 CPython/3.7.4

File hashes

Hashes for bmt-0.7.8-py3-none-any.whl
Algorithm Hash digest
SHA256 1665de3aa02e269d35d224325145d9d527d2f5e3184885f5c47ca70119add870
MD5 5c65a7fd24b4554970b85315a0c201e7
BLAKE2b-256 584fa567b03cfde9879c9b13cbe496325bc3a7c33d2795346c493a25b80056c4

See more details on using hashes here.

Provenance

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page