Abstract

The constant improvement and falling prices of whole human genome Next Generation Sequencing (NGS) has resulted in rapid adoption of genomic information at both clinics and research institutions. Considered together, the complexity of genomics data, due to its large volume and diversity along with the need for genomic data sharing, has resulted in the creation of Application Programming Interface (API) for secure, modular, interoperable access to genomic data from different applications, platforms, and even organizations. The Genomics APIs are a set of special protocols that assist software developers in dealing with multiple genomic data sources for building seamless, interoperable applications leading to the advancement of both genomic and clinical research. These APIs help define a standard for retrieval of genomic data from multiple sources as well as to better package genomic information for integration with Electronic Health Records. This review covers three currently available Genomics APIs: a) Google Genomics, b) SMART Genomics, and c) 23andMe. The functionalities, reference implementations (if available) and authentication protocols of each API are reviewed. A comparative analysis of the different features across the three APIs is provided in the Discussion section. Though Genomics APIs are still under active development and have yet to reach widespread adoption, they hold the promise to make building of complicated genomics applications easier with downstream constructive effects on healthcare.

Highlights

  • As research is vital for the future of clinical genomics, the NIH on August 27, 2014, issued the Genomic Data Sharing (GDS) Policy that requires researchers to share any genomic data with the broader community [2]

  • Users benefit from Application Programming Interface (API) by having access to third-party applications created by the software developers, which provide data from multiple sources

  • This review focuses on one kind of API to be used with genomics related applications, termed Genomics APIs

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Summary

A Review on Genomics APIs

Rajeswari Swaminathan a,⁎, Yungui Huang a, Soheil Moosavinasab a, Ronald Buckley a, Christopher W. Beyond the great volume of data that researchers wish to share, there are many different formats, structures, and sources that make data integration a real bottleneck within data sharing protocols. To meet these rigorous and (somewhat) competing requirements, numerous groups have been working together to create Application Programming Interface (API). Some databases only contain raw read information whereas others can contain detailed information down to the variant level These data structure inconsistencies are growing along with the emergence of novel genomics technologies, making the process of data integration more cumbersome over time. We provide a comprehensive review to enable researchers and developers to use these API functions when designing similar applications

Genomics APIs
Google Genomics API
SMART Genomics API
Genomics API Authentication
Discussion
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