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Biodiversity and Ecological Data Integration and Interoperability
Session Time January 9th; 1:30 pm to 5:00 pm
Location Forest Glen
Description Today’s most pressing ecological and biodiversity questions-- such as how climate change will affect species distributions and ecosystem processes or how to manage fisheries or protecting biodiversity—depend on integration of data from many sources. This session will bring together biodiversity and ecological data managers and scientists from diverse set of federal organizations and academia who focus on data integration and interoperability to discuss progress made and opportunities and challenges in data integration. Talks will follow three main themes: 1) progress made on data integration and challenges reconciling data and metadata standards, 2) tools for finding, managing, sharing, and visualizing ecological data, and 3) research using integrated data to address today’s current challenges such as climate change and Ocean Acidification. The goal of this session is to find opportunities to collaborate on informatics in biodiversity and ecology between federal agencies and academia.
Chair Hassan Moustahfid
Presentations and Notes Click Here!

Talk Length (min) Title Presenter
3D.1 15 Biological and Ecological Data Management Operations in the Foundation for IOOS Success Jennifer Bosch
3D.2 15 Integrating marine species observations and making them accessible to the world through OBIS Abigail Benson
3D.3 15 Developing a Biodiversity Data Management Toolkit through the Marine Biodiversity Observation Network Rob Bochenek
3D.4 15 EML, KNB, and ERDDAP Bob Simons
3D.5 15 Beginning a comparison of new animal telemetry data exchange standards to existing database architecture in NOAA OR&R’s DIVER Explorer – applying animal telemetry lessons learned from Deepwater Horizon Troy L. Baker
3D.6 15 The benefits and challenges of data integration and visualization for the NCEI Water Column Sonar Data Archive Carrie Wall
3D.7 15 Managing Deep-Sea Coral and Sponge Biodiversity Data Matt Dornback
3D.8 75 Open Discussion

3D.1 Biological and Ecological Data Management Operations in the Foundation for IOOS Success

Jennifer Bosch (NOS/US IOOS)

Hassan Moustahfid

Data accessibility and effective data management operations are the foundation for success for any observing system. United States Integrated Ocean Observing System (IOOS) Data Management and Communications (DMAC) subsystem have taken a strong lead in formalizing data standards and encouraging the use of interoperable web standards for sharing data and metadata. For almost a decade, IOOS has rolled out regional applications of biological and ecological data science related to fish species absence and abundance. Additional biological data capabilities have expanded with growing levels of participation, evolving infrastructure, and new advances in global standards adoption such as those emerging from Global Biodiversity Information Facility (GBIF) and Ocean Biogeography Information System (OBIS). The foundation of IOOS accomplishments to date relies on adoption and careful compliance with global standards such as Ratified Darwin Core (DwC) and Climate & Forecast Conventions (CF). These standards do not simply assure that biological data content, quality, and data flow are effective, they are also fundamentally involved in assuring biological data integration with other oceanographic data types to enable modeling and synthesis.

Building on this foundation, and leveraging the technical and organizational infrastructure of IOOS regional participants, IOOS and OBIS are developing more application capabilities for standard biological web services, such as animal telemetry. We have begun technical investigation of developing mechanisms that will address more IOOS biological variables, and GOOS Essential Biological Variables (EBVs) and offer solutions to local, regional and global efforts such as Convention of Biological Diversity Biodiversity Assessment. These data integrations can drive transformative research and enable the implementation of US IOOS.

Keywords: biology, ecology, ocean observing, data management, standards, IOOS, OBIS, GBIF, GOOS, EBVs, Darwin Core, Climate forecasts, bioinformatics.

3D.2 Integrating marine species observations and making them accessible to the world through OBIS

Abigail Benson (USGS/USGS)

The Ocean Biogeographic Information System (OBIS) which is part of the International Oceanographic Data and Information Exchange (IODE) of the Intergovernmental Oceanographic Commission (IOC), works to integrate and make accessible observations of marine life. Through recent developments, OBIS has implemented a new API and library for R (rOBIS) as well as a new website. These developments increase accessibility and usability for the Darwin Core aligned data managed by OBIS. In addition to these recent improvements, OBIS has been working with the Global Ocean Observing System (GOOS) through the Biology and Ecosystems Panel to help draft the Essential Ocean Variables as well as the Marine Biodiversity Observation Network (MBON) of the Group on Earth Observations Biodiversity Observation Network (GEOBON) to advance the goals for all three groups toward a better understanding of marine ecosystems.

3D.3 Developing a Biodiversity Data Management Toolkit through the Marine Biodiversity Observation Network

Rob Bochenek (Axiom Data Science, LLC/NOS/IOOS)

The Marine Biodiversity Observation Network (MBON) is part of a series of three regional efforts to aiming to distribute knowledge and understanding of the patterns and drivers of change in marine biodiversity. These regions provide a wide range of ecosystems including deep sea, reefs, estuaries, and the continental shelf and bring together remote sensing, genomics, ecology, biogeochemistry, and physical data which are essential for studying ecosystem, biodiversity, and oceanographic conditions over time. The MBON demonstration projects are working together to collaboratively refine best practices for increased interoperability (metadata, data sharing, services, and discovery) of the diverse, distributed and often times massive datasets. An integrated MBON demonstration data portal enables visualization of biodiversity data sets in concert with the host of physical, environmental, and biological data housed at the regional and national data centers. This dedicated demonstration portal includes biological data sets and products from the Monterey Bay, Florida Keys, and Arctic regions and provides a centralized and easy to use interface to discover, visualize, analyze, and download data. Axiom Data Science and a team of Monterey Bay and Florida scientists are working on the development of a generalized biodiversity indices tool that allow researchers and managers to perform data analyses online. MBON data management and product development efforts, such as the real-time biodiversity indices tool, demonstrate both large-scale interoperability and enhanced performance and effectiveness in scientific data analysis work flows.



ERDDAP is a free, open source, data server that gives users a simple, consistent way to download subsets of gridded and tabular scientific datasets in common file formats and make graphs and maps. ERDDAP is well suited to working with ecological data. ERDDAP administrators can now quickly and easily add datasets to ERDDAP based on the information in Ecological Metadata Language (EML) files, which are widely used in the ecological community. This opens up the possibility of quickly and easily setting up an ERDDAP which has both environmental data (from NOAA, NASA, and the USGS) and ecological data (from the Knowledge Network for Biocomplexity, KNB, and other groups) and which would serve as a bridge between the two communities.

3D.5 Beginning a comparison of new animal telemetry data exchange standards to existing database architecture

Troy L. Baker (NOS/OR&R/Assessment & Restoration Division)

Benjamin Shorr (NOS/OR&R), Nicolas Eckardt (NOS/OR&R), Dr. Hassan Moustahfid (NOS/ASTADM), Dr. Matthew Howard (NWS)

Multiple animal telemetry studies in the Gulf of Mexico began after the Deepwater Horizon oil spill during the Natural Resource Damage Assessment (NRDA). These field investigations started in 2010 and continued in 2015, and until recently data were embargoed because of an agency litigation hold. A new data exchange standard for acoustic, archival, and satellite tags is an opportunity for GCOOS/OR&R to evaluate how existing and future telemetry data collected for NRDAs is more easily shared with the Animal Telemetry Network. The authors have begun an extensive side-by-side evaluation of data fields in the data exchange standard and OR&R’s DIVER Explorer system. Although the schema evaluation and data transfer is not fully completed, results will be presented with implications for how OR&R’s architecture may be modified to aid data transfer with GCOOS Data Management and Communications (DMAC) services, or other entities. OR&R also is beginning to explore the concept of a more formal data specification package to give to Principal Investigators working on future NRDA studies involving telemetry, similar to the approach OR&R uses for other data types in NRDAs, such as Electronic Data Deliverable specifications given to analytical laboratories. Project goals related to sharing specific animal datasets will be discussed.

3D.6 The benefits and challenges of data integration and visualization for the NCEI Water Column Sonar Data

Carrie Wall (NESDIS/NCEI/CCOG and University of Colorado at Boulder)

Charles Anderson (NESDIS)

Scientific echosounders aboard NOAA fishery survey vessels are used to estimate biomass, measure fish school morphology, and characterize habitat. These surveys produce large volumes of data that are costly and difficult to maintain due to their size, complexity, and proprietary format that requires specific software and extensive knowledge. However, through proper management they can deliver valuable information beyond their original collection purpose. In order to maximize the benefit to the public, the data must be easily discoverable and accessible. Access to ancillary data is also essential for complete environmental context and ecosystem assessment. NOAA’s National Centers for Environmental Information, in partnership with the National Marine Fisheries Service and the University of Colorado, created a national archive for the stewardship and distribution of water column sonar data. A data access web page allows users to query the metadata and access the raw sonar data. Visualization products allow researchers and the public to understand the quality and content of large volumes of archived data. Such products transform the complex raw data into a digestible image and are highly valuable for a broad audience of varying backgrounds. Links to concurrently collected oceanographic and bathymetric data are being integrated into the data access page to provide an ecosystem-wide understanding of the area surveyed. The need and benefit of having associated oceanographic data readily available for each cruise along with visual imagery for the raw acoustic data is apparent. Efficiently finding and linking to disparately-archived data, and processing large volumes of acoustic data remain a challenge.

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