Genomics API allowing for seamless sharing of genetic data

The Global Alliance for Genomics and Health (GA4GH) - an international coalition of over 200 organisations formed to enable the sharing of genomic and clinical data - has announced a new application programming interface (API) which will allow DNA data providers and consumers to better share information and work together on a global scale.

The open-source Genomics API, referred to as Version 0.5, is a standard, open tool promoting data interoperability, and will be part of a suite of Genomics APIs being developed by the Global Alliance. The API enables the interoperable exchange of information contained in DNA sequence reads across multiple organisations and on multiple platforms.

“This new Genomics API is an exciting step toward interoperability in genomic data,” said David Haussler, co-chair of the Data Working Group, which developed the API. “It advances the Global Alliance’s mission of enabling the sharing of genomic and clinical data to improve human health. Because this new API lets researchers work consistently with genomic data across institutions and platforms, it will help realise the benefits that come from large-scale genomic data sharing, allowing us to find the needle in the haystack for patients with rare diseases.”

The Genomics API Version 0.5 uses an open development process to allow the wider bioinformatics community to participate. While the Data Working Group has a core team of active developers, all interested developers from any institution can further engage with the platform by exploring sample apps, building implementations from scratch or from existing samples, or by providing feedback on the API and its documentation.

The API will allow the interoperable exchange of genomic information across multiple organisations and on multiple platforms. Image credit: Global Alliance for Genomics and Health.

The Genomics API Version 0.5 builds off Version 0.1, which was also developed by members of the Data Working Group and is in use by organisations including the European Bioinformatics Institute (EMBL-EBI), the US National Center for Biotechnology Information (NCBI), Google, Genome Savant and Harvard Medical School’s Biomedical Cybernetics Laboratory. As analysis tools adopt the new API, researchers will be able to extend their own infrastructure to utilise cloud resources, such as those available from Amazon Web Services, Google Cloud Platform and Microsoft Azure.

“We are using the Global Alliance’s work to enable apps for the TBResist initiative that bridge from raw sequence data to clinically useful phenotypes,” said Professor Gil Alterovitz, director of the Biomedical Cybernetics Laboratory. “Also, the Substitutable Medical Applications and Reusable Technology (SMART) Genomics platform is using the Global Alliance interface to enable interoperability between electronic medical record information (HL7) and raw genetic sequence information.”

The API is built on file formats developed over the last five years for large-scale genomic sequencing projects, but features cleaner models, with a modern, easy-to-use data description schema and a web-enabled interface. According to Dr Richard Durbin, acting head of computational genomics at the Wellcome Trust Sanger Institute and leader of the genome informatics group, it will “enable genomic data processing to move beyond research file formats into modern computing and data architectures, facilitating controlled data sharing and the effective use of these new technologies for both clinical and research benefit”.

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