drugname-standardizer 1.2.5

A Python tool for standardizing drug names using the latest FDA's UNII Names list.

Drugname Standardizer

The Drugname Standardizer is a Python tool for standardizing drug names using the official FDA's UNII Names List archive. It notably supports both JSON and TSV/CSV input formats, making it easy to ensure consistent drug naming in datasets.

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Features

• A trusted source for drug synonyms : the package automatically downloads the latest version of the UNII Names file from the official FDA repository (montly check of an update). The UNII_Names.txt is saved to the package's data/ folder for use without redownload before next update. The user can also choose to indicate another local UNII Names file if a particular version is preferred.

• Parsing of the FDA's UNII Names List to map drug names (code / official / systematic / common / brand names) to a single preferred name (i.e. the Display Name of the UNII Names file).

• Input versatility:

  • a single drug name,
  • a list of drug names,
  • a JSON input file (a list of drugs to standardize)
  • a TSV input file (a dataframe containing a column of drugs to standardize)

• Provides both a Python package interface for scripting and a command-line interface (CLI) for direct use.

• Resolves naming ambiguities of the FDA's UNII Names file by selecting the shortest Display Names. Rare but exists: 55 / 986397 associations in UNII_Names_20Dec2024.txt. For example, for PRN1008 the ambiguity is solved by keeping RILZABRUTINIB whereas 2 associations exist:

  • PRN1008 ... ... RILZABRUTINIB, (.ALPHA.E,3S)-
  • PRN1008 ... ... RILZABRUTINIB

Warning:

There are code / official / systematic / common / brand names for drugs. Some are linked to different level of details about the compound. The standardization proposed here gathers information at the "upper" level (i.e. the less detailled one). I relied on the "Preferred Substance Name" (= the Display name field) indicated in the correspondence table provided by the FDA.
For instance : both 3'-((1R)-1-((6R)-5,6-DIHYDRO-4-HYDROXY-2-OXO-6-PHENETHYL-6-PROPYL-2H-PYRAN-3-YL)PROPYL)-5-(TRIFLUOROMETHYL)-2-PYRIDINESULFONANILIDE (systematic name) and Aptivus (brand name) become TIPRANAVIR.

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Usage

Python API

You can use the package programmatically in your Python scripts:

from drugname_standardizer import standardize

Examples:

- Get the preferred name for a specific drug:

drug_name = "GDC-0199"
preferred_name = standardize(drug_name)
print(preferred_name)  # Outputs: VENETOCLAX

- Standardize a list of drugs:

drug_names = ["GDC-0199", "Aptivus", "diodrast"]
preferred_names = standardize(drug_names)
print(preferred_names)  # Outputs: ["VENETOCLAX", "TIPRANAVIR", "IODOPYRACET"]

- Standardize a JSON file:

standardize(
    input_file = "drugs.json",
    file_type = "json",
    output_file = "standardized_drugs.json"
)
# Outputs: Standardized JSON file saved as standardized_drugs.json

- Standardize a TSV/CSV file:

standardize(
    input_file = "dataset.csv",
    file_type = "tsv",
    column_drug = 0,
    separator = ","
)
# Outputs: Standardized TSV file saved as dataset_drug_standardized.csv

Command-Line Interface

You can also use a CLI for standardizing a drug name, a JSON file or a TSV/CSV file.

• Required arguments:
  • --input, -i: A drug name or the path to a JSON/TSV file
• Optional arguments:
  • --file_type, -f: Type of the input file (json or tsv)
  • --output, -o: The output file name (relative path can be given). Defaults: the input file name with _drug_standardized added before the extension.
  • --column_drug, -c: Index of the column containing the drug names to standardize (required for TSV files). Starts at 0: 1st column = column 0.
  • --separator, -s: Field separator for TSV files. Defaults: \t.
  • --unii_file, -u: Path to a UNII Names List file. Defaults: automatic download of the latest version.

Examples:

- Get the preferred name for a specific drug:

drugname_standardizer -i DynaCirc

- Standardize a JSON file:

drugname_standardizer -i drugs.json -f json

- Standardize a TSV file: e.g., using a pipe as separator and a custom file name for the output:

drugname_standardizer -i dataset.tsv -f tsv -c 2 -s "|" -o standardized_dataset.tsv

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Installation

Using pip

python3 -m pip install drugname_standardizer

GitHub repository

git clone https://github.com/StephanieChevalier/drugname_standardizer.git
cd drugname_standardizer
pip install -r requirements.txt

Requirements:

• Python 3.7+
• Dependencies:
  • requests >= 2
  • tqdm >= 4

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How it works

1. Parse UNII File:

   • Reads the UNII Names List to create a mapping of drug names to the Display Name (i.e. the preferred name).
   • Resolves potential naming conflicts by selecting the shortest Display Name (55 / 986397 associations).

2. Standardize Names:

   • For a single drug name: return the preferred name.
   • For a list of drug names: maps drug names to their preferred names and return the updated list.
   • For JSON input: Maps drug names to their preferred names and saves the results to a JSON file.
   • For TSV input: Updates the specified column with standardized drug names and saves the modified DataFrame to a TSV file.

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Package structure

drugname_standardizer/
├── drugname_standardizer/
│   ├── __init__.py               # Package initialization
│   ├── standardizer.py           # Core logic for name standardization
│   └── data/
│       ├── UNII_Names.txt  # UNII Names List file (ensured to be no older than 1 month when available)
│       └── UNII_dict.pkl   # parsed UNII Names List
├── tests/
│   ├── __init__.py               
│   └── test_standardizer.py      # Unit tests for the package
├── LICENSE                       # MIT License
├── pyproject.toml                # Package configuration
├── README.md                     # Project documentation
└── requirements.txt              # Development dependencies

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License

This project is licensed under the MIT License - see the LICENSE file for details.