Thera-Py

Thera-Py normalizes free-text names and references for drugs and other biomedical therapeutics to stable, unambiguous concept identifiers to support genomic knowledge harmonization.

Live OpenAPI service

Installation

Install from PyPI:

python3 -m pip install thera-py

Usage

Deploying DynamoDB Locally

We use Amazon DynamoDB for data storage. To deploy locally, follow these instructions.

Setting Environment Variables

RxNorm requires a UMLS license, which you can register for one here. You must set the UMLS_API_KEY environment variable to your API key. This can be found in the UTS 'My Profile' area after singing in.

export UMLS_API_KEY=12345-6789-abcdefg-hijklmnop  # make sure to replace with your key!

HemOnc.org data requires a Harvard Dataverse API token. You must create a user account on the Harvard Dataverse website, you can follow these instructions to create an account and generate an API token. Once you have an API token, set the following environment variable:

export HARVARD_DATAVERSE_API_KEY=12345-6789-abcdefgh-hijklmnop  # make sure to replace with your key!

Update source(s)

The Therapy Normalizer currently aggregates therapy data from:

To update source(s), simply set --sources to the source(s) you wish to update separated by spaces. For example, the following command updates ChEMBL and Wikidata:

python3 -m therapy.cli --sources="chembl wikidata"

You can update all sources at once with the --update_all flag:

python3 -m therapy.cli --update_all

Thera-Py can retrieve all required data itself, using the wags-tails library. By default, data will be housed under ~/.local/share/wags_tails/ in a format like the following:

~/.local/share/wags_tails
├── chembl
│   └── chembl_27.db
├── chemidplus
│   └── chemidplus_20200327.xml
├── drugbank
│   └── drugbank_5.1.8.csv
├── guidetopharmacology
│   ├── guidetopharmacology_ligand_id_mapping_2021.3.tsv
│   └── guidetopharmacology_ligands_2021.3.tsv
├── hemonc
│   ├── hemonc_concepts_20210225.csv
│   ├── hemonc_rels_20210225.csv
│   └── hemonc_synonyms_20210225.csv
├── ncit
│   └── ncit_20.09d.owl
├── rxnorm
│   ├── rxnorm_drug_forms_20210104.yaml
│   └── rxnorm_20210104.RRF
└── wikidata
    └── wikidata_20210425.json

Updates to the HemOnc source depend on the Disease Normalizer service. If the Disease Normalizer database appears to be empty or incomplete, updates to HemOnc will also trigger a refresh of the Disease Normalizer database. See its README for additional data requirements.

Create Merged Concept Groups

The /normalize endpoint relies on merged concept groups. The --update_merged flag generates these groups:

python3 -m therapy.cli --update_merged

Specifying the database URL endpoint

The default URL endpoint is http://localhost:8000. There are two different ways to specify the database URL endpoint.

The first way is to set the --db_url flag to the URL endpoint.

python3 -m therapy.cli --update_all --db_url="http://localhost:8001"

The second way is to set the environment variable THERAPY_NORM_DB_URL to the URL endpoint.

export THERAPY_NORM_DB_URL="http://localhost:8001"
python3 -m therapy.cli --update_all

Starting the therapy normalization service

From the project root, run the following:

uvicorn therapy.main:app --reload

Next, view the OpenAPI docs on your local machine:

http://127.0.0.1:8000/therapy

FAQ

A data import method raised a SourceFormatError instance. How do I proceed?

TheraPy will automatically try to acquire the latest version of data for each source, but sometimes, sources alter the structure of their data (e.g. adding or removing CSV columns). If you encounter a SourceFormatException while importing data, please notify us by creating a new issue if one doesn't already exist, and we will attempt to resolve it.

In the meantime, you can force TheraPy to use an older data release by removing the incompatible version from the source data folder, manually downloading and replacing it with an older version of the data per the structure described above, and calling the CLI with the --use_existing argument.

Citation

If you use Thera-Py in scientific works, please cite the following article:

Matthew Cannon, James Stevenson, Kori Kuzma, Susanna Kiwala, Jeremy L Warner, Obi L Griffith, Malachi Griffith, Alex H Wagner, Normalization of drug and therapeutic concepts with Thera-Py, JAMIA Open, Volume 6, Issue 4, December 2023, ooad093, https://doi.org/10.1093/jamiaopen/ooad093

Development

Clone the repo and create a virtual environment:

git clone https://github.com/cancervariants/therapy-normalization
cd therapy-normalization
python3 -m virtualenv venv
source venv/bin/activate

Install development dependencies and pre-commit:

python3 -m pip install -e '.[dev,test]'
pre-commit install

Check style with ruff:

python3 -m ruff format . && python3 -m ruff check --fix .

Run tests with pytest:

pipenv run pytest

By default, tests will employ an existing DynamoDB database. For test environments where this is unavailable (e.g. in CI), the THERAPY_TEST environment variable can be set to initialize a local DynamoDB instance with miniature versions of input data files before tests are executed.

export THERAPY_TEST=true

Sometimes, sources will update their data, and our test fixtures and data will become incorrect. The tests/scripts/ subdirectory includes scripts to rebuild data files, although most fixtures will need to be updated manually.