biolink-helper-pkg 1.0.0

Standalone BiolinkHelper module extracted from RTX

BiolinkHelper

BiolinkHelper is a lightweight Python utility class for working with a specific Biolink Model version. Its data source is the Biolink Model YAML file.

Overview

The BiolinkHelper class requires two mandatory inputs at initialization time:

• A Biolink Model version
• A local cache path where Biolink resources are stored (or will be stored)

No defaults are assumed.

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Installation

pip install biolink-helper-pkg

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Usage

Basic Example

from biolink_helper_pkg import BiolinkHelper

helper = BiolinkHelper(
    biolink_version="4.2.6",
    cached_path="/data/biolink_cache"
)

---

Class API

BiolinkHelper

class BiolinkHelper:

    def __init__(self, biolink_version, cached_path):
        ...

Parameters

Name	Type	Required	Description
biolink_version	str	Yes	The Biolink Model version to use (e.g. "4.2.6"). This value is mandatory and must be provided explicitly.
cached_path	str	Yes	Path to a directory used for caching Biolink YAML files and lookup maps. Must be readable and writable.

Both parameters are mandatory. Initialization will fail if either is missing or invalid.

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How to use

Examples of ways to get ancestors:

biolink_helper.get_ancestors("biolink:Drug")
biolink_helper.get_ancestors(["biolink:Drug", "biolink:Protein"])
biolink_helper.get_ancestors("biolink:Drug", include_mixins=False)
biolink_helper.get_ancestors("biolink:Protein", include_conflations=False)
biolink_helper.get_ancestors("biolink:treats")

Examples of ways to get descendants:

biolink_helper.get_descendants("biolink:ChemicalEntity")
biolink_helper.get_descendants(["biolink:ChemicalEntity", "biolink:Protein"])
biolink_helper.get_descendants("biolink:ChemicalEntity", include_mixins=False)
biolink_helper.get_descendants("biolink:Protein", include_conflations=False)
biolink_helper.get_descendants("biolink:related_to")

Ancestors/descendants are always returned in a list. Relevant mixins are included in the returned list by default, but you can turn that behavior off via the include_mixins parameter, as shown in some of the above examples. Inclusion of ARAX-defined conflations can be controlled via the include_conflations parameter (default is True).

Other available methods include getting canonical predicates:

biolink_helper.get_canonical_predicates("biolink:treated_by")
biolink_helper.get_canonical_predicates(["biolink:treated_by", "biolink:related_to"])

And filtering out mixins:

biolink_helper.filter_out_mixins(["biolink:ChemicalEntity", "biolink:PhysicalEssence"]])

Debugging

The JSON version saved in cached_path is just there for easier debugging/viewing.