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Python Client for BioThings Explorer

Project description

BioThings Explorer

Test BioThings Explorer Python Package Codacy Badge Codacy Badge Documentation Status PyPI

Introduction

This is the development repo for the python client of BioThings Explorer. This tool aims at helping users querying and linking results from a variety of biomedical relevant APIs through one interface. The project is funded by the NCATS Translator project.

P.S. — Documentation is Available at //biothings-explorer.readthedocs.io.

Revelant Concepts

  1. BioLink Model

    The BioLink Model defines a high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations. BioThings Explorer restructures outputs from different APIs into the data model defined by BioLink, so that they can be easily connected and queried.

  2. SmartAPI

    SmartAPI aims to maximize the FAIRness (Findability, Accessibility, Interoperability, and Reusability) of web-based Application Programming Interfaces (APIs). Rich metadata is essential to properly describe your API so that it becomes discoverable, connected, and reusable. BioThings Explorer takes advantage of the rich metadata information described in SmartAPI and create a meta knowledge graph, allowing BioThings Explorer to autonomously query a distributed knowledge graph. The distributed knowledge graph is made up of biomedical APIs that have been annotated with semantically-precise descriptions of their inputs and outputs.

Current Integrated APIs

How to use the package

Official Documentation is Available at //biothings-explorer.readthedocs.io

Jupyter notebook demo is located at this folder.

Some real world use cases of BioThings Explorer.

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