BioThings SDK

Introduction

What’s BioThings?

We use “BioThings” to refer to objects of any biomedical entity-type represented in the biological knowledge space, such as genes, genetic variants, drugs, chemicals, diseases, etc.

BioThings SDK

SDK represents “Software Development Kit”. BioThings SDK provides a Python-based toolkit to build high-performance data APIs (or web services) from a single data source or multiple data sources. It has the particular focus on building data APIs for biomedical-related entities, a.k.a “BioThings”, though it’s not necessarily limited to the biomedical scope. For any given “BioThings” type, BioThings SDK helps developers to aggregate annotations from multiple data sources, and expose them as a clean and high-performance web API.

The BioThings SDK can be roughly divided into two main components: data hub (or just “hub”) component and web component. The hub component allows developers to automate the process of monitoring, parsing and uploading your data source to an Elasticsearch backend. From here, the web component, built on the high-concurrency Tornado Web Server , allows you to easily setup a live high-performance API. The API endpoints expose simple-to-use yet powerful query features using Elasticsearch’s full-text query capabilities and query language.

BioThings API

We also use “BioThings API” (or BioThings APIs) to refer to an API (or a collection of APIs) built with BioThings SDK. For example, both our popular MyGene.Info and MyVariant.Info APIs are built and maintained using this BioThings SDK.

Installing BioThings SDK

You can install the latest stable BioThings SDK release with pip from PyPI, like:

pip install biothings

You can install the latest development version of BioThings SDK directly from our github repository like:

pip install git+https://github.com/biothings/biothings.api.git#egg=biothings

Alternatively, you can download the source code, or clone the BioThings SDK repository and run:

python setup.py install