NRSP8 Aquaculture Project Update: A flexible platform for querying disparate oyster datasets (qDOD)



The goal of this project is to facilitate analysis, curation, and distribution of genomic data available for the Pacific oyster, Crassostrea gigas. The project merges experience developing genomic resources (Roberts, UW SAFS) with computing science expertise (Howe and Halperin, UW eScience Institute) to use SQLShare as a platform for aggregation and analysis of genomic data. SQLShare is a free, open to the public, web-based query-as-a-service platform designed to replace script-based scientific workflows with declarative queries. SQLShare provides a public data repository that accepts any tabular data  and allows the user to derive new datasets via standard database operations in the Structured Query Language (SQL). For the proposed project the objectives are to 1) Centralize datasets needed for effective analysis of oyster genomic data and 2) Provide a series of modules that provide examples of relevant queries. To this end, our team has worked together to improve features in SQLShare and provide a central resource that focuses on describing how the general public can use this platform to explore oyster datasets (https://github.com/sr320/qdod/wiki). This wiki includes a basic introduction to SQLShare as well as describing datasets and how to query and download data. The entire platform and documentation is completely open and can be easily used for any tabular data. We are continuing to add resources and are accepting feedback.