A Schema for Digitized Surface Swab Site Metadata in Open-Source DNA Sequence Databases
Jingzhang Feng, Devin Daeschel, Damion Dooley, Emma Griffiths, Marc Allard, Ruth Timme, Yi Chen, Abigail B. Snyder
Abstract
The regular analysis of whole-genome sequence data in collections such as NCBI's Pathogen Detection Database is used by many public health organizations to detect outbreaks of infectious disease. However, isolate metadata in these databases are often incomplete and of poor quality. These complex, raw metadata must often be reorganized and manually formatted for use in aggregate analyses. These processes are inefficient and time-consuming, increasing the interpretative labor needed by public health groups to extract actionable information. The future use of open genomic epidemiology networks will be supported through the development of an internationally applicable vocabulary system with which swab site locations can be described.