stringx 0.6.0

STRING DB API Client

STRINGX

STRINGX is an API client for the STRING database, built on top of HTTPX.

Features

Inspired on the well-established usability of httpx, stringx provides a clean and easy to use interface to the STRING API while following usage recommendations and best practices:

• Requires client identification;
• Uses POST requests;
• Allows linking to a specific STRING version;
• When applicable, enforces specifying the species parameter.

A customizable client allows targeting any API version and provides support for all output formats available: TSV, JSON, XML, etc...

Installation

STRINGX requires Python 3.9+ and is available on PyPI.

$ pip install stringx

Usage

The stringx module provides a direct interface to the current API version. JSON is the default response format and can be easily integrated with pandas for further processing.

import pandas as pd
import stringx

stringx.identity = ""  # please identify yourself

df = pd.Dataframe(
    stringx.network(identifiers=["7227.FBpp0074940", "7227.FBpp0082908"], species=7227)
)

[!TIP] STRING understands a variety of identifiers and does its best to disambiguate your input. Nevertheless, it is recommended to map your identifiers first. Querying the API with a disambiguated identifier (for example 9606.ENSP00000269305 for human TP53) will guarantee much faster server response.

Client Identification

The STRING API requires its callers to identify themselves. To address this, STRINGX enforces that the identity value is set. If done at the module level all subsequent requests will carry this information.

import stringx

stringx.identity = "my_project_name"

You can also identify your clients independently.

import stringx

with stringx.Client(identity="my_project_name") as client:
    ...

with stringx.Client(
    address="https://version-10-5.string-db.org",
    identity="[e-mail]"
) as client:
    ...

Regardless of how you choose to do it, STRINGX always appends its own information to your identity.

Using one of the clients instantiated above as example, the caller_identity parameters passed to the STRING API would be my_project_name (python-stringx/x.y.z).

Documentation

🚧🚧🚧

Refer to the official API documentation for details.

License

STRING data is freely available under a CC-BY-4.0 license. Please provide appropriate credit when using the data. No changes or additions are made to the data by STRINGX.