Toward a Standardized Framework for Benthic Mapping Data and Metadata Integration in Florida

3.2.1 Standards for data collection

For acoustic bathymetry, experts recommended aligning with those of the Interagency Working Group on Ocean and Coastal Mapping (IWG-OCM), a working group of the National Science and Technology Council Subcommittee on Ocean Science and Technology. These recommendations are outlined in the Standard Ocean Mapping Protocol (SOMP; IWG-OCM, 2024). In short, the SOMP recommends using the International Hydrographic Organization’s (IHO) minimum bathymetry standards and feature detection requirements defined in Table 1 of IHO’s Publication S-44 Edition 6.1.0 (IHO, 2020), in tandem with the specification matrix in Chapter 7.6 of Publication S-44 for criteria ranges to enhance the minimum standards. Additional recommendations from the IWG-OCM include mapping to complete coverage, using set line spacing, data collection during transit, performing crosslines for validation, correcting for tides, and providing uncertainty.

For acoustic backscatter collected from multibeam echosounders, our group of experts recommended following the GeoHab Backscatter Working Group’s (BSWG) guidelines and recommendations for backscatter measurements by seafloor-mapping sonars, outlined in Rice et al. (2015) and also discussed in Lamarche and Lurton (2018).

For lidar bathymetry, the standards established by the United States Army Corps of Engineers (USACE) Engineering, Research and Development Center (ERDC) and their Joint Airborne Lidar Bathymetry Technical Center of Expertise (JALBTCX) are recommended. These Topo-Bathy Lidar Specifications are being developed by JALBTCX with the Naval Oceanographic Office (NAVOCEANO), the National Oceanic and Atmospheric Administration (NOAA), and the United States Geological Survey (USGS). The SOMP standards for lidar bathymetry are directly derived from these specifications.

3.2.2 Standards for data processing

For acoustic bathymetry, our expert group recommended using the CUBE (Combined Uncertainty and Bathymetry Estimator) algorithm (Calder and Wells, 2007) but recognized that developments in processing algorithms are common and that this recommendation is likely to change in the future.

For acoustic backscatter, the group recommended following the GeoHab Backscatter Working Group’s guidelines and recommendations for backscatter measurements by seafloor-mapping sonars, outlined in Schimel et al. (2015) and expanded upon in Schimel et al. (2018). However, they acknowledged that there are currently no standardized data processing approaches (Malik et al., 2019) and that these recommendations are subject to change.

For lidar data, the standards from the American Society for Photogrammetry and Remote Sensing (ASPRS) (ASPRS, 2024) associated with the open format LAS are recommended.

For satellite-derived bathymetry, they recommended following standards outlined in the IHO Publication B-13 (IHO, 2024).

3.2.3 Standards for data archiving and publication

Experts recommended that all data, including the raw (unprocessed) bathymetric and backscatter data, be shared with NOAA’s National Centers for Environmental Information (NCEI). For processed bathymetry and backscatter data, they recommended following the IHO’s S-102 Standard for Bathymetry, which includes the use of the “.bag” (bathymetric attributed grid) format for sharing bathymetry, a format that carries both bathymetry and uncertainty information. They also recommended that processed data be shared, regardless of data collection methods, with their uncertainty layer and at the highest achievable spatial resolution, with the Global Multi-Resolution Topography (GMRT) data synthesis, the Gulf Online Mapping Open Data Platform (GOMOD), and the IHO Data Center for Digital Bathymetry (IHO DCDB) (Table 1). They also noted that if the Florida Seafloor Mapping Initiative (FSMI) of the Florida Geographic Information Office starts offering data archiving in the future, it would be relevant to submit Florida data there.

3.2.4 Metadata standards

For bathymetric data, the subgroup of experts for bathymetric and backscatter data recommended that metadata standards align at minimum with Chapter 6 of the IHO’s Publication S-44 Edition 6.1.0 (IHO, 2020), but also recommended, when possible, adding all available information such as is outlined in Chapter 3 of IHO’s Publication B-12 for crowdsourced bathymetry (IHO, 2018a), Chapter 4 of Publication B-13 for satellite-derived bathymetry (IHO, 2024), and the S-100 Discovery Metadata Standard (IHO, 2018b), which were adapted by NOAA (see https://nauticalcharts.noaa.gov/learn/docs/precision-navigation/s-100_discovery_metadata_readme.pdf).

For backscatter data, standards have not yet been adopted internationally, but experts recommended following the suggestions made in Table 7.2 of the GeoHab Backscatter Working Group’s guidelines and recommendations (Lurton and Lamarche, 2015) and expanded upon in Schimel et al. (2018).

For lidar data, they recommended adopting the ASPRS LAS specifications and recommendations from Lück-Vogel et al. (2018). Metadata should be stored in an XML format.

3.2.5 Agreement with bathymetric and backscatter data and metadata standards

Overall, there was good agreement with the data standards proposed for this discipline (Table 2; Figure 2). In addition, respondents indicated that they were likely to adopt the standards (Table 2; Figure 2). Respondents provided no substantial comments or suggestions for the bathymetry and backscatter data standards, nor any additional comments.

3.3.1 Standards for data collection

The Ocean Best Practices System (OBPS; https://www.oceanbestpractices.org/) provides access to guidelines and training materials developed by the Ocean Biodiversity Information System (OBIS; https://obis.org/), the Marine Biodiversity Observation Network (MBON; https://marinebon.org/), and many other groups involved in the ocean observing and applications value chain. While there are many different data collection protocols, our experts recommended that the community use data collection protocols from OBPS if available. Furthermore, they recommended contributing to OBPS documentation on new practices for the benefit of a larger community. Practices archived with OBPS should be peer-reviewed and may be previously published, and practitioners may request that OBPS assist in having the practices ‘endorsed’ by a recognized group of experts, such as an expert panel of the Global Ocean Observing System or another group.

3.3.2. Standards for data processing

Experts recommended following the primer that the Earth Science Information Partnership (ESIP) Biological Data Standards Cluster (https://wiki.esipfed.org/Biological_Data_Standards_Cluster) has developed to help navigate different biological data standards and help format, curate, and enhance the interoperability of biological information. When biological data are being used to classify or characterize habitats, they noted that classification schemes are objective-dependent and that standards are difficult to apply. However, when appropriate, they recommended adopting the Coastal and Marine Ecological Classification Standard (CMECS) (FGDC, 2012), commonly applied nationally, or the International Union for Conservation of Nature (IUCN) Global Ecosystem Typology (https://global-ecosystems.org/) that is commonly applied internationally.

3.3.3 Standards for data archiving and publication

The team of experts on this type of data recommended depositing the data and metadata via repositories that are well-known and that explicitly seek to be interoperable and sustainable for the long term. At the global level, data should be published to the Ocean Biodiversity Information System (OBIS) and the Global Biodiversity Information Facility (GBIF) (Table 1) using the Integrated Publishing Toolkit (IPT; https://www.gbif.org/ipt). At the national level, they recommended NOAA’s Environmental Research Division’s Data Access Program (ERDDAP) and National Centers for Environmental Information (NCEI) (Table 1). In Florida, the Fish and Wildlife Conservation Commission’s Fish and Wildlife Research Institute (FWRI), the Florida Department of Environmental Protection (including the Florida Geological Survey), and the Florida Geospatial Open Data Portal of the Florida Geographic Information Office have relevant databases that should be consulted and used as repositories (Table 1).

3.3.4 Metadata standards

Experts in biology recommended following the primer that the Earth Science Information Partnership (ESIP; https://wiki.esipfed.org/Biological_Data_Standards_Cluster) has developed to help navigate different biological metadata standards and the Darwin Core (https://dwc.tdwg.org/) to format and publish biological metadata.

3.3.5 Agreement with biological data and metadata standards

For this discipline, there was good but slightly lower agreement and likelihood of adoption of the standards than for bathymetric data (Table 3; Figure 2). In addition, respondents indicated that they were likely to adopt the standards (Table 3; Figure 2).

We received additional comments from the respondents in our open-ended questions. One respondent found the metadata standards “difficult to interpret for implementation.” Another respondent recommended communication and education around standards. They have found that there is not enough education on standards, and they did not know of these standards before they took the survey.

3.4.1 Standards for data collection

Water column data is almost universally collected from Seabird CTDs (Conductivity, Temperature, and Depth sensors). Despite the constraints of the acronym, multiple other sensors, including O₂, transmissivity, fluorescence, and others that may be important to benthic chemistry, can make up the payload of these versatile instruments. Biogeochemists have also developed landers that can make measurements of chemical exchange at the seawater-sediment interface continuously for an amount of time determined by battery life with certain measurement payloads. The consulted experts recommended aligning data collection with the latest standards for data collection of discrete observations made aboard shipboard platforms, outlined in Jiang et al. (2022).

3.4.2 Standards for data processing

Generally, Seabird CTD data files need to be processed with Seabird software to produce files that are readable in most data analysis and visualization programs, such as Excel, Matlab, and Python, among others. Once processed, any of these platforms can be used to obtain metadata such as ship latitude and longitude, timestamps, and depths. Data from these deployments generally conform to the standards outlined in Jiang et al. (2022), which our team of experts recommended using. These standards include information about data header conventions as well as conventions for quality control flagging of data and missing values and encourage the use of the Exchange data file format.

3.4.3 Standards for data archiving and publication

Experts recommended archiving Florida benthic chemistry data in the Gulf of Mexico Research Initiative Information & Data Cooperative (GRIIDC) repository and the Biological and Chemical Oceanographic Data Management Office system (BCO-DMO) (Table 1).

3.4.4 Metadata standards

The experts indicated that to relate benthic chemistry to underlying geologic sampling, it is important to merge data types, such as hand-written deck logs for geologic data, with the depth-binned benthic chemistry data from the CTD and from discrete bottle samples taken near the boundary. Thus, it is important to populate deck logs for geological sampling with data that link geological and chemical data, like time of deployment (to calculate elapsed time between water column and sediment deployments), weather conditions (e.g., squalls delayed deployment after CTD casts), and other metadata that relate the geological samples to the water column measurements. Position, time, and local conditions are important metadata for benthic chemistry samples, but so are qualitative descriptions of the bottom. Once benthic samples are retrieved, it is important to link time-sensitive samples such as porewaters to water column data streams through sample labeling that makes indexing to deck logs and CTD casts possible. The standards outlined in Jiang et al. (2022) contain recommendations for sequential numbering of over-the-side deployments at each site or sequential numbering of unique sites for every over-the-side deployment. Our experts recommended adopting these simple recommendations, which, when adapted for geological as well as chemical data collection, can facilitate biogeochemical studies using observations of both types. Lander data should be referenced by the same over-the-side sequence as other deployments; however, the timestamp of the data recorded while deployed will be the most important metadata for the continuous data stream generated.

3.4.5 Agreement with chemistry data and metadata standards

Only three responses were received for the evaluation of recommendations for chemistry data, which is relatively low compared to other data types. The average level of agreement for the respondents was 5.45 on a 7-point scale (Table 4). They also were less likely to adopt these standards than respondents for other data types (Table 4). In addition to responding to the agreement questions in our survey, we received some open-form feedback on the chemistry recommendations. One of the respondents said that the scale of their program was smaller and did not require the specific data collection instruments considered for the proposed standards. In addition, respondents identified that they did not use Seabird equipment, and therefore their processing and data collection were different from what is recommended here.

3.5.1 Standards for data collection

For sediment collection methods (i.e., grab samplers, sediment cores, sediment traps, dredges), the consulted experts recommended using the standards established in the USGS East-Coast Sediment Analysis procedures, outlined in Poppe et al. (2014). For side-scan sonar data, they recommended following Chapter 6 of NOAA’s Hydrographic Survey Specifications and Deliverables (OCSHSD, 2022). For sub-bottom profilers and magnetometers, they recommended adopting the standards that are established by the IWG-OCM SOMP (IWG-OCM, 2024).

3.5.2 Standards for data processing

There is little consensus on the best ways to process most remotely-sensed data on geology and geomorphology (i.e., sidescan sonar data, sub-bottom seismic profiles, magnetometer data), as their processing requires the use of software packages that each have their own algorithms, workflows, and classification methods. The choice of these often depends on the project and its objectives; therefore, experts were reluctant to make specific recommendations, stating only that all choices must be justified. However, general recommendations for sidescan sonar data and sub-bottom seismic profile data included using computer-based supervised processing (e.g., filtering) and classification workflows (e.g., feature extraction procedures) to increase objectivity in the processing. Experts acknowledged that user contribution is often critical within these procedures, for example, to manually filter data or to tweak parameters to improve signal-to-noise ratio.

For sediment samples from grab samplers and sediment cores, they recommended processing and classifying them using the procedures listed in the USGS East-Coast Sediment Analysis (Poppe et al., 2014). The interpretation of general stratigraphic and formation names should be consistent with the North American Stratigraphic Code (NACSN, 2021), the standard applied by the USGS and the Florida Geological Survey.

3.5.3 Standards for data archiving and publication

It is the opinion of the consulted experts that formats of geospatial geological data should follow those applied by the USGS. Therefore, they recommended using GeoTIFF (.tif) as a raster data file format; for vector data, they recommended using the shapefile (.shp) format, despite its proprietary nature, because of its ubiquity and the open standard, machine-readable format GeoJSON that facilitates storage and exchange of geological geospatial data.

Geological data referencing the State of Florida should be archived at the Florida Geological Survey, which is housed in the Florida Department of Environmental Protection, and at the National Geologic Map Database (MGMDB) maintained by the USGS (Table 1).

3.5.4 Metadata standards

We recommend that metadata for geological data follow standards set by the Federal Geographic Data Committee (FGDC) Content Standard for Digital Geospatial Metadata (CSDGM; https://www.fgdc.gov/metadata/csdgm-standard), which are also applied by the USGS.

3.5.5 Agreement with geological data and metadata standards

Respondents who had an expertise in or experience with geological data provided a range of responses to the agreement and likelihood of adoption questions. The mean of agreement for all standards was 5.50 on a 7-point scale (Table 5; Figure 2), and respondents indicated that they were likely to adopt the standards (Table 5; Figure 2).

Reflecting these lower scores (Table 3), respondents had a few comments on our open-ended survey questions. One theme that came up is that the USGS protocols are overly complicated and not useful for every type of geological data collection. One respondent found that wet sieving was not a standard practice and that the ASTM standards are more applicable. One theme in the comments was that there are a plethora of various sampling and geological techniques that are used in benthic geological methods. These approaches have different goals and achievable spatial resolutions that make standard guidelines, particularly about data collection, difficult. Some respondents recommended open-source data processing with protocols defined by end users, as many projects require the flexibility to meet their needs. For data archiving, one respondent found that proprietary formats should not be recommended. In addition, it is necessary to consider other users (such as those who do not use Geographic Information Systems (GIS)) for these standards (i.e., inclusions of .kmz files make standards more accessible). Respondents also indicated that in their experience, FGS would not store offshore or coastal data, despite the fact that it aligns with their mission as a state agency.

3.6.1 Standards for data collection

The group of experts on oceanographic data recommended using the Ocean Best Practices System (https://www.oceanbestpractices.org) for finding examples of data collection protocols and best practices for all physical oceanography survey instruments. They also noted that methods for maintaining and controlling fleets of gliders are under development (see Ma et al., 2023). The Underwater Glider User Group, ‘UG2’, hosts a webpage on glider best practices (https://underwatergliders.org/) that includes a “Data Management & Tools” section. The experts also recommended protocols from NOAA’s Integrated Ocean Observing System (IOOS; https://ioos.noaa.gov/), which provides guidance on instrument calibration and data handling through its Quality Assurance/Quality Control of Real Time Oceanographic Data (QARTOD; IOOS, 2020) project.

3.6.2 Standards for data processing

Experts recommended the IOOS QARTOD project guidelines for data processing, outlined in IOOS (2020). The principles of QARTOD were developed for real-time systems but are adaptable and usable for non-real-time measurements. These seven main principles are 1) every observation must have a quality descriptor; 2) use automated QA; 3) quality flags must be described in metadata; 4) observers should independently calibrate the instrument; 5) describe the calibration method in metadata; 6) describe calibration accuracy and data error bounds; 7) utilize manual checks on real-time data feed.

3.6.3 Standards for data archiving and publication

Scientific data collected by research institutions and served on their dedicated data web servers, such as the Coastal Ocean Monitoring and Prediction System (COMPS; https://comps.marine.usf.edu), should be archived and publicly distributed by two Integrated Ocean Observing System (IOOS) regional associations, the Gulf of America Coastal Ocean Observing (GCOOS) and the Southeast Coastal Ocean Observing System (SECOORA) (Table 1). Both GCOOS and SECOORA data portals serve large multivariate databases with established guidelines and provide good search engines using both map-based and text-based searching. Experts also recommended archiving profiles of currents from operational Acoustic Doppler Current Profilers (ADCP) in the NOAA-developed platform Currents Measurement Interface for the Study of Tides (C-MIST) (Table 1). They also note that the National Buoy Data Center (NDBC), a federal provider of meteorological and oceanographic data, is a relevant option but does not have a public submission center; thus, contributing to NDBC requires first contacting them directly.

3.6.4 Metadata standards

The group of experts consulted recommended the Integrated Ocean Observing System (IOOS) and Climate and Forecast (CF) metadata standards for documenting, organizing, and distributing data and metadata. IOOS provides online verification of data fitness for use (i.e., IOOS Compliance Checker). The CF data model (https://cfconventions.org/) provides guidance on data management such as data naming, formatting, and metadata standards optimized for geophysical variables, as well as software to manage and verify conformance of data to CF standards.

Newly developed ocean data and metadata standards are described by the S-100 system (IHO, 2018b) for inclusion in electronic charting and information systems. The IHO Universal Hydrographic Data Model supports a wide variety of hydrographic-related digital data sources and focuses on the inclusion of data in digital navigation charts. The S-100 is fully aligned with mainstream international geospatial standards, particularly the ISO 19100 series of geographic standards, thereby enabling the easier integration of hydrographic data and applications into geospatial solutions, especially electronic navigation charts. S-100 standards are optional but should be considered by anyone deploying long-term operational oceanographic instrumentation.

3.6.5 Agreement with physical oceanography data and metadata standards

Only two respondents evaluated the physical oceanography proposed standards, so results must be interpreted with caution. Their level of agreement and likelihood of adoption are listed in Table 6.