biolink-helper-pkg 1.0.1
Standalone BiolinkHelper module extracted from RTX
Requires Python: >=3.8

# BiolinkHelper

`BiolinkHelper` is a lightweight Python utility class for working with a specific **Biolink Model version**.
Its data source is the [Biolink Model YAML](https://github.com/biolink/biolink-model/blob/master/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.

---

## Installation


```bash
pip install biolink-helper-pkg
```

---

## Usage

### Basic Example

```python
from biolink_helper_pkg import BiolinkHelper

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

---

## Class API

### `BiolinkHelper`

```python
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.

---

#### 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.