kg_bacdive.transform_utils.mediadive package

Submodules

kg_bacdive.transform_utils.mediadive.mediadive module

MediaDive KG.

Example script to transform downloaded data into a graph format that KGX can ingest directly, in either TSV or JSON format: https://github.com/NCATS-Tangerine/kgx/blob/master/data-preparation.md

Input: any file in data/raw/ (that was downloaded by placing a URL in incoming.txt/yaml and running run.py download.

Output: transformed data in data/raw/MediaDive:

Output these two files: - nodes.tsv - edges.tsv

class kg_bacdive.transform_utils.mediadive.mediadive.MediaDiveTransform(input_dir=None, output_dir=None)

Bases: Transform

Template for how the transform class would be designed.

download_yaml_and_get_json(url, target_dir)

Download MetaDive data using a url.

Parameters:

url (str) – Path provided by MetaDive API.

Return type:

Dict[str, str]

get_compounds_of_solution(id)

Get ingredients of solutions via the MediaDive API>.

Parameters:

id (str) – ID of solution

Returns:

Dictionary of {compound_name: compound_id}

run(data_file=None)

Run the transformation.

standardize_compound_id(id)

Get IDs via Metadive API.

Parameters:

id (str) – Metadive compound ID

Returns:

Standardized ID

Module contents

BacDive transform.

class kg_bacdive.transform_utils.mediadive.MediaDiveTransform(input_dir=None, output_dir=None)

Bases: Transform

Template for how the transform class would be designed.

download_yaml_and_get_json(url, target_dir)

Download MetaDive data using a url.

Parameters:

url (str) – Path provided by MetaDive API.

Return type:

Dict[str, str]

get_compounds_of_solution(id)

Get ingredients of solutions via the MediaDive API>.

Parameters:

id (str) – ID of solution

Returns:

Dictionary of {compound_name: compound_id}

run(data_file=None)

Run the transformation.

standardize_compound_id(id)

Get IDs via Metadive API.

Parameters:

id (str) – Metadive compound ID

Returns:

Standardized ID