interopdb

Python client and CLI for the Interop DB Registry API.

Interop DB is a federated registry that assigns unified identifiers to genes and strains across multiple biological databases, enabling cross-database queries with a single search. It integrates data from:

• ALEdb -- Adaptive Laboratory Evolution Database
• BiGGr -- Knowledgebase of genome-scale metabolic network reconstructions
• PanKB -- Pangenome Knowledge Base
• PMkbase -- Phenotype MicroArray Knowledge Base

Installation

pip install interopdb

Python API

from interopdb import InteropClient

client = InteropClient()

# Query a gene
result = client.get_gene("rpoB")
print(result["uid"], result["attributes"])

# Query a strain
result = client.get_strain("511145")

# Query a gene-strain pair
result = client.get_pair("rpoB", "511145")
for source in result["sources"]:
    print(source["source"], source["data"])

# Search entities by local ID, UID, or synonym
result = client.search_entities("dnaA")
for entity in result["entities"]:
    print(entity["local_id"], entity["source_db_name"])

# Search gene-strain relationships by a gene or strain
result = client.search_relationships("rpoB")
for rel in result["relationships"]:
    print(rel["gene_local_id"], rel["strain_local_id"])

# Save result to JSON
client.save_json(result, "output.json")

CLI

# Query entities
interopdb gene rpoB
interopdb strain 511145

# Query a gene-strain pair
interopdb pair rpoB 511145

# Search entities
interopdb search-entities dnaA

# Search relationships
interopdb search-relationships GCF_031662355.1

# Save to file
interopdb gene rpoB -o result.json