Preprint Communication Version 1 Preserved in Portico This version is not peer-reviewed

Optimizing Open Data to Support One Health: Best Practices to Ensure Interoperability of Genomic Data from Microbial Pathogens

Ruth E. Timme
* ORCID logo ,
William J. Wolfgang
,
Maria Balkey
,
Sai Laxmi Gubbala Venkata
,
Robyn Randolph
,
Marc Allard
,
Errol Strain
Version 1 : Received: 14 April 2020 / Approved: 16 April 2020 / Online: 16 April 2020 (05:26:42 CEST)

A peer-reviewed article of this Preprint also exists.

Timme, R.E., Wolfgang, W.J., Balkey, M. et al. Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens. One Health Outlook 2, 20 (2020). https://doi.org/10.1186/s42522-020-00026-3 Timme, R.E., Wolfgang, W.J., Balkey, M. et al. Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens. One Health Outlook 2, 20 (2020). https://doi.org/10.1186/s42522-020-00026-3

Abstract

The holistic approach of One Health, which sees human, animal, plant, and environmental health as a unit, rather than discrete parts, requires not only interdisciplinary cooperation, but standardized methods for communicating and archiving data, enabling participants to easily share what they have learned and allow others to build upon their findings.Ongoing work by NCBI and the GenomeTrakr project illustrates how open data platforms can help meet the needs of federal and state regulators, public health laboratories, departments of agriculture, and universities. Here we describe how microbial pathogen surveillance can be transformed by having an open access database along with Best Practices for contributors to follow. First, we describe the open pathogen surveillance framework, hosted on the NCBI platform. We cover the current community standards for WGS quality, provide an SOP for assessing your own sequence quality and recommend QC thresholds for all submitters to follow. We then provide an overview of NCBI data submission along with step by step details. And finally, we provide curation guidance and an SOP for keeping your public data current within the database. These Best Practices can be models for other open data projects, thereby advancing the One Health goals of Findable, Accessible, Interoperable and Re-usable (FAIR) data.

Keywords

Genomic Epidemiology; GenomeTrakr; microbial pathogen surveillance, NCBI submission; whole genome sequencing; QA/QC; One Health

Subject

Biology and Life Sciences, Virology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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