VICC normalization routine for therapies


Keywords
bioinformatics, bioinformatics-data, precision-medicine
License
MIT
Install
pip install thera-py==0.3.5

Documentation

Therapy Normalization

Services and guidelines for normalizing drug (and non-drug therapy) terms

Developer instructions

The following sections include instructions specifically for developers.

Installation

For a development install, we recommend using Pipenv. See the pipenv docs for direction on installing pipenv in your compute environment.

Once installed, from the project root dir, just run:

pipenv sync

Deploying DynamoDB Locally

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

Initialize development environment

Code style is managed by flake8 and checked prior to commit.

We use pre-commit to run conformance tests.

This ensures:

  • Style correctness
  • No large files
  • AWS credentials are present
  • Private key is present

Pre-commit must be installed before your first commit. Use the following command:

pre-commit install

Running tests

Unit tests are provided via 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.

Updating the database

Before you use the CLI to update the database, run the following in a separate terminal to start DynamoDB on port 8000:

java -Djava.library.path=./DynamoDBLocal_lib -jar DynamoDBLocal.jar -sharedDb

To change the port, simply add -port value.

Setting Environment Variables

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

export RXNORM_API_KEY={rxnorm_api_key}

HemOnc.org data requires a Harvard Dataverse API key. After creating a user account on the Harvard Dataverse website, you can follow these instructions to generate a key. Once you have a key, set the following environment variable:

export DATAVERSE_API_KEY={your api key}

Update source(s)

The Therapy Normalizer currently aggregates therapy data from:

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

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

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

python3 -m therapy.cli --update_all

The data/ subdirectory within the package source should house all desired input data. Files for all sources should follow the naming convention demonstrated below (with version numbers/dates changed where applicable).

therapy/data
├── 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
│   ├── drug_forms.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 SourceFormatException 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.