DGIpy

Python wrapper for querying a Drug-Gene Interaction Database (DGIdb) GraphQL API. DGIpy provides drug and gene records, drug-gene interactions, gene categories, source metadata, and FDA drug application information.

Installation

Install from PyPI:

python3 -m pip install dgipy

Usage

DGIpy is built around query functions that fetch data from the public DGIdb API. Results use a column-oriented dictionary: each key is a column name and each value is a list containing that column's values. The examples below show representative output; the contents of the live DGIdb database may change.

>>> from dgipy import get_genes
>>> results = get_genes(["BRAF"])
>>> results["gene_name"][0], results["gene_concept_id"][0], results["gene_aliases"][0][:5]
('BRAF', 'hgnc:1097', ['B-RAF PROTO-ONCOGENE, SERINE/THREONINE KINASE', 'BRAF1', 'BRAF-1', 'UCSC:UC003VWC.5', 'VEGA:OTTHUMG00000157457'])

This orientation enables easy use with the dataframe library of your choosing:

>>> import pandas as pd
>>> pd.DataFrame(results)[["gene_name", "gene_concept_id"]]
  gene_name gene_concept_id
0      BRAF        hgnc:1097
>>>
>>> import polars as pl  # not included in DGIpy dependencies
>>> pl.DataFrame(results).select("gene_name", "gene_concept_id")
shape: (1, 2)
┌───────────┬─────────────────┐
│ gene_name ┆ gene_concept_id │
│ ---       ┆ ---             │
│ str       ┆ str             │
╞═══════════╪═════════════════╡
│ BRAF      ┆ hgnc:1097       │
└───────────┴─────────────────┘

Available queries

Function	Description
get_drugs(terms, ...)	Look up drug records by name.
get_genes(terms, ...)	Look up gene records by name.
get_interactions(terms, ...)	Find drug-gene interactions by gene or drug name.
get_categories(terms, ...)	Find category annotations for genes.
get_sources(source_type=None, ...)	List DGIdb source metadata, optionally filtered by SourceType.
get_all_genes(...)	List all gene names and concept identifiers.
get_all_drugs(...)	List all drug names and concept identifiers. Import this function from dgipy.dgidb.
get_drug_applications(terms, ...)	Combine DGIdb application identifiers with Drugs@FDA product data.

The query functions accept an optional api_url argument when querying a DGIdb v5 instance other than the public endpoint:

from dgipy import get_genes

genes = get_genes(["BRAF"], api_url="https://example.org/api/graphql")

Development

Clone the repo and create a virtual environment:

git clone https://github.com/genomicmedlab/dgipy
cd dgipy
python3 -m virtualenv venv
source venv/bin/activate

Install development dependencies and pre-commit:

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

Check style with ruff:

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

Run tests with pytest:

pytest