OOI Biogeochemical Sensor Data: Best Practices and User Guide. Version 1.0.0.

The OOI Biogeochemical Sensor Data Best Practices and User Guide is intended to provide current and prospective users of data generated by biogeochemical sensors deployed on the Ocean Observatories Initiative (OOI) arrays with the information and guidance needed for them to ensure that the data is science-ready. This guide is aimed at researchers with an interest or some experience in ocean biogeochemical processes. We expect that users of this guide will have some background in oceanography, however we do not assume any prior experience working with biogeochemical sensors or their data. While initially envisioned as a “cookbook” for end users seeking to work with OOI biogeochemical (BGC) sensor data, our Working Group and Beta Testers realized that the processing required to meet the specific needs of all end users across a wide range of potential scientific applications and combinations of OOI BGC data from different sensors and platforms couldn’t be synthesized into a single “recipe”. We therefore provide here the background information and principles needed for the end user to successfully identify and understand all the available “ingredients” (data), the types of “cooking” (end user processing) that are recommended to prepare them, and a few sample “recipes” (worked examples) to support end users in developing their own “recipes” consistent with the best practices presented here. This is not intended to be an exhaustive guide to each of these sensors, but rather a synthesis of the key information to support OOI BGC sensor data users in preparing science-ready data products. In instances when more in-depth information might be helpful, references and links have been provided both within each chapter and in the Appendix

Exchange at the Estuary-Ocean Interface: Fluxes through the Golden Gate Channel

Residual flow and exchange along a channel connecting an embayment with the coastal ocean are examined experimentally, using direct observations of currents and scalar concentrations across the mouth of San Francisco Bay. The study encompasses separate experiments during each of three "seasons": winter/spring runoff (March 2002), summer upwelling (July 2003), and fall relaxation (October 2002). Within each experiment, transects across the channel were repeated approximately every 12 minutes for 25 hours during both sprilng and neap tides. Velocity was measured from a boat-mounted acoustic Doppler current profiler. Scalar concentrations were measured at the surface and from a tow-yoed SeaSciences Inc. Acrobat.Several sources of residual circulation were isolated: baroclinic flow, tidal pumping, and frictional phasing. We further isolated a portion of tidal pumping as tidal trapping of a headland eddy during flood tide. Density-driven flow is complicated by a dramatic growth in the cross-channel density gradient during the second half of ebb tide, whichdrives along-chmmel shear at the beginning flood tide, creating an asy1mnetry in frictional phasing.Velocity fields formed by residual circulation mechanisms combine with scalar concentration fiellds to defme scalar exchange processes. Net salinity exchange rates for each season are quantified with hmmonic analysis. Harmonic results m·e  then decomposed into flux mechanisms using temporal and spatial correlations. In tllis study, the temporal conelation of cross-sectionally averaged salinity and velocity (tidal pumping flux) is the largest component of the dispersive tlux of salinity into the bay. From the tidal pumping flux pmtion of the dispersive flux, it is shown that there is less exchange than was found in earlier studies. Furthernore, tidal pumping flux scales strongly with freshwater flow because of density-driven movement of a tidally trapped eddy and stratification-induced increases in ebb-flood frictional phasing. Complex bathymetry leads to salinity exchange that scales differently with flow than would be expected from simple tidal asymmetry and gravitational circulation models

Exchange at the Estuary-Ocean Interface: Fluxes through the Golden Gate Channel

Residual flow and exchange along a channel connecting an embayment with the coastal ocean are examined experimentally, using direct observations of currents and scalar concentrations across the mouth of San Francisco Bay. The study encompasses separate experiments during each of three "seasons": winter/spring runoff (March 2002), summer upwelling (July 2003), and fall relaxation (October 2002). Within each experiment, transects across the channel were repeated approximately every 12 minutes for 25 hours during both sprilng and neap tides. Velocity was measured from a boat-mounted acoustic Doppler current profiler. Scalar concentrations were measured at the surface and from a tow-yoed SeaSciences Inc. Acrobat.Several sources of residual circulation were isolated: baroclinic flow, tidal pumping, and frictional phasing. We further isolated a portion of tidal pumping as tidal trapping of a headland eddy during flood tide. Density-driven flow is complicated by a dramatic growth in the cross-channel density gradient during the second half of ebb tide, whichdrives along-chmmel shear at the beginning flood tide, creating an asy1mnetry in frictional phasing.Velocity fields formed by residual circulation mechanisms combine with scalar concentration fiellds to defme scalar exchange processes. Net salinity exchange rates for each season are quantified with hmmonic analysis. Harmonic results m·e  then decomposed into flux mechanisms using temporal and spatial correlations. In tllis study, the temporal conelation of cross-sectionally averaged salinity and velocity (tidal pumping flux) is the largest component of the dispersive tlux of salinity into the bay. From the tidal pumping flux pmtion of the dispersive flux, it is shown that there is less exchange than was found in earlier studies. Furthernore, tidal pumping flux scales strongly with freshwater flow because of density-driven movement of a tidally trapped eddy and stratification-induced increases in ebb-flood frictional phasing. Complex bathymetry leads to salinity exchange that scales differently with flow than would be expected from simple tidal asymmetry and gravitational circulation models

A model for community-driven development of best practices: the Ocean Observatories Initiative Biogeochemical Sensor Data Best Practices and User Guide

The field of oceanography is transitioning from data-poor to data-rich, thanks in part to increased deployment of in-situ platforms and sensors, such as those that instrument the US-funded Ocean Observatories Initiative (OOI). However, generating science-ready data products from these sensors, particularly those making biogeochemical measurements, often requires extensive end-user calibration and validation procedures, which can present a significant barrier. Openly available community-developed and -vetted Best Practices contribute to overcoming such barriers, but collaboratively developing user-friendly Best Practices can be challenging. Here we describe the process undertaken by the NSF-funded OOI Biogeochemical Sensor Data Working Group to develop Best Practices for creating science-ready biogeochemical data products from OOI data, culminating in the publication of the GOOS-endorsed OOI Biogeochemical Sensor Data Best Practices and User Guide. For Best Practices related to ocean observatories, engaging observatory staff is crucial, but having a “user-defined” process ensures the final product addresses user needs. Our process prioritized bringing together a diverse team and creating an inclusive environment where all participants could effectively contribute. Incorporating the perspectives of a wide range of experts and prospective end users through an iterative review process that included “Beta Testers’’ enabled us to produce a final product that combines technical information with a user-friendly structure that illustrates data analysis pipelines via flowcharts and worked examples accompanied by pseudo-code. Our process and its impact on improving the accessibility and utility of the end product provides a roadmap for other groups undertaking similar community-driven activities to develop and disseminate new Ocean Best Practices