Pipelining RDP Data to the 'Taxomatic'

摘要

This project was conceived to build on and enhance the results of previously funded research by integrating data and software that were used in building resources for the preparation of Bergeys Manual of Systematic Bacteriology, 2nd Edition (Volumes 1 & 2A-C) and the Ribosomal Database Project-II (RDP-II). Our objectives were to both enhance the value of the data and create a pipeline approach to keeping the data current. Earlier, we demonstrated the value of using exploratory data analysis (EDA) to visualize the relationships among large sets of SSU rRNA gene sequences that were used to construct a comprehensive phylogeny of prokaryotes. We developed Self-Organizing Self-Correcting Classification (SOSCC) algorithms that were computationally efficient and useful for unraveling problems within the underlying data (e.g., annotation errors, unresolved synonymies, taxonomic and nomenclatural errors). We deployed a web site, referred to as the Taxomatic, to make the results of our EDA analyses available and to enable comparisons of classifications. However, bottlenecks at the preprocessing stage limited deployment of our applications and data, making the web site essentially static and in need of frequent updates. This limited the usefulness of the web site to end users. To overcome the bottlenecks (which included hand alignment and computation of large matrices of pair-wise evolutionary distances), we proposed building a data pipeline between the Taxomatic applications and RDP-II web services.