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A Community Convention for Ecological Forecasting: Output Files and Metadata Version 1.0

This paper summarizes the open community conventions developed by the Ecological Forecasting Initiative (EFI) for the common formatting and archiving of ecological forecasts and the metadata associated with these forecasts. Such open standards are intended to promote interoperability and facilitate forecast communication, distribution, validation, and synthesis. For output files, we first describe the convention conceptually in terms of global attributes, forecast dimensions, forecasted variables, and ancillary indicator variables. We then illustrate the application of this convention to the two file formats that are currently preferred by the EFI, netCDF (network common data form), and comma-separated values (CSV), but note that the convention is extensible to future formats. For metadata, EFI's convention identifies a subset of conventional metadata variables that are required (e.g., temporal resolution and output variables) but focuses on developing a framework for storing information about forecast uncertainty propagation, data assimilation, and model complexity, which aims to facilitate cross-forecast synthesis. The initial application of this convention expands upon the Ecological Metadata Language (EML), a commonly used metadata standard in ecology. To facilitate community adoption, we also provide a Github repository containing a metadata validator tool and several vignettes in R and Python on how to both write and read in the EFI standard. Lastly, we provide guidance on forecast archiving, making an important distinction between short-term dissemination and long-term forecast archiving, while also touching on the archiving of code and workflows. Overall, the EFI convention is a living document that can continue to evolve over time through an open community process.

Michael C. Dietze↗

A Standard Reference Model for Data Archives

An implementable Data Archive Architecture is being developed for trusted digital repositories based on the Reference Model for an Open Archival Information System (OAIS) – ISO 14721. A set of interoperable protocols and interface specifications are planned that will offer capabilities for accessing, merging, and re-using data, both within and across the operational boundaries of trustworthy digital repositories. The model will also provide support for the fundamental scientific need to verify the reproducibility of results. This standards development task is being performed by the Data Archive Interoperability (DAI) working group within the Consultative Committee for Space Data Systems (CCSDS). The architecture integrates concepts from the OAIS Reference Model, the ISO/IEC 11179 Metadata Registry (MDR) standard, the CCSDS Reference Architecture for Space Information Management (RASIM), the proposed draft recommended practice document, Information Preparation to Enable Long Term Use (IPELTU), and three decades of digital repository development for science research.

Ambacher, Bruce↗

Design and Construction of a NASA Airborne and Field Investigation Inventory

NASA conducts airborne and field investigations that produce a wealth of valuable research data. Unfortunately, this data is often scattered across individual scientist hard drives or NASA Distributed Active Archive Centers and it can be difficult to locate and retrieve. Although satellite data has been successfully consolidated by tools such as EarthData Search, airborne and field investigation data present unique challenges stemming from the variability of temporal, spatial, platform, and instrument metadata. To address these difficulties with data retrieval and metadata variability, the Interagency Implementation and Concepts Team established an Airborne Data Management Group to improve airborne data search, understanding, access, and use. Surveys have been conducted of end users in order to build query lists that will drive the augmentation and standardization of existing metadata. Detailed metadata was then laboriously compiled from present and historic airborne and field investigations to build a database that will enable intelligent data search and retrieval. The inventory structure and function will be described and demonstrated. The purpose of this presentation is to bring awareness to this effort, to highlight and describe the issues and complications in development, and to increase user interest prior to public release in 2020.

Davis, Carson↗

GHRSST-14 DAS-TAG Report

The DAS-TAG provides the informatics and data management expertise in emerging information technologies for the GHRSST community. It provides expertise in data and metadata formats and standards, fosters improvements for GHRSST data curation, experiments with new data processing paradigms, and evaluates services and tools for data usage. It provides a forum for producer and distributor data management issues and coordination.

data processing↗

Exploring NASA GES DISC Data with Interoperable Services

Overview of NASA GES DISC (NASA Goddard Earth Science Data and Information Services Center) data with interoperable services: Open-standard and Interoperable Services Improve data discoverability, accessibility, and usability with metadata, catalogue and portal standards Achieve data, information and knowledge sharing across applications with standardized interfaces and protocols Open Geospatial Consortium (OGC) Data Services and Specifications Web Coverage Service (WCS) -- data Web Map Service (WMS) -- pictures of data Web Map Tile Service (WMTS) --- pictures of data tiles Styled Layer Descriptors (SLD) --- rendered styles.

Giovanni↗

A Survey of Complex Object Technologies for Digital Libraries

Many early web-based digital libraries (DLs) had implicit assumptions reflected in their architecture that the unit of focus in the DL (frequently "reports" or "e-prints") would only be manifested in a single, or at most a few, common file formats such as PDF or PostScript. DLs have now matured to the point where their contents are commonly no longer simple files. Complex objects in DLs have emerged from in response to various requirements, including: simple aggregation of formats and supporting files, bundling additional information to aid digital preservation, creating opaque digital objects for e-commerce applications, and the incorporation of dynamic services with the traditional data files. We examine a representative (but not necessarily exhaustive) number of current and recent historical web-based complex object technologies and projects that are applicable to DLs: Aurora, Buckets, ComMentor, Cryptolopes, Digibox, Document Management Alliance, FEDORA, Kahn-Wilensky Framework Digital Objects, Metadata Encoding & Transmission Standard, Multivalent Documents, Open eBooks, VERS Encapsulated Objects, and the Warwick Framework.

Nelson, Michael L.↗

Value-added Data Services at the Goddard Earth Sciences Data and Information Services Center

The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC), in addition to serving the Earth Science community as one of the major Distributed Active Archives Centers (DAACs), provides much more than just data. Among the value-added services available to general users are subsetting data spatially and/or by parameter, online analysis (to avoid downloading unnecessarily all the data), and assistance in obtaining data from other centers. Services available to data producers and high-volume users include consulting on building new products with standard formats and metadata and construction of data management systems. A particularly useful service is data processing at the DISC (i.e., close to the input data) with the users algorithm. This can take a number of different forms: as a configuration-managed algorithm within the main processing stream; as a stand-alone program next to the on-line data storage; as build-it-yourself code within the Near-Archive Data Mining (NADM) system; or as an on-the-fly analysis with simple algorithms embedded into the web-based tools. Partnerships between the GES DISC and scientists, both producers and users, allow the scientists to concentrate on science, while the GES DISC handles the data management, e.g., formats, integration, and data processing. The existing data management infrastructure at the GES DISC supports a wide spectrum of options: from simple data support to sophisticated on-line analysis tools, producing economies of scale and rapid time-to-deploy. At the same time, such partnerships allow the GES DISC to serve the user community more efficiently and to better prioritize on-line holdings. Several examples of successful partnerships are described in the presentation.

Leptoukh, Gregory G.↗

Organizing Diverse, Distributed Project Information

SemanticOrganizer is a software application designed to organize and integrate information generated within a distributed organization or as part of a project that involves multiple, geographically dispersed collaborators. SemanticOrganizer incorporates the capabilities of database storage, document sharing, hypermedia navigation, and semantic-interlinking into a system that can be customized to satisfy the specific information-management needs of different user communities. The program provides a centralized repository of information that is both secure and accessible to project collaborators via the World Wide Web. SemanticOrganizer's repository can be used to collect diverse information (including forms, documents, notes, data, spreadsheets, images, and sounds) from computers at collaborators work sites. The program organizes the information using a unique network-structured conceptual framework, wherein each node represents a data record that contains not only the original information but also metadata (in effect, standardized data that characterize the information). Links among nodes express semantic relationships among the data records. The program features a Web interface through which users enter, interlink, and/or search for information in the repository. By use of this repository, the collaborators have immediate access to the most recent project information, as well as to archived information. A key advantage to SemanticOrganizer is its ability to interlink information together in a natural fashion using customized terminology and concepts that are familiar to a user community.

Keller, Richard M.↗

Greenland Geothermal Heat Flow Database and Map (Version 1)

We compile and analyze all available geothermal heat flow measurements collected in and around Greenland into a new database of 419 sites and generate an accompanying spatial map. This database includes 290 sites previously reported by the International Heat Flow Commission (IHFC), for which we now standardize measurement and metadata quality. This database also includes 129 new sites, which have not been previously reported by the IHFC. These new sites consist of 88 offshore measurements and 41 onshore measurements, of which 24 are subglacial. We employ machine learning to synthesize these in situ measurements into a gridded geothermal heat flow model that is consistent across both continental and marine areas in and around Greenland. This model has a native horizontal resolution of 55 km. In comparison to five existing Greenland geothermal heat flow models, our model has the lowest mean geothermal heat flow for Greenland onshore areas. Our modeled heat flow in central North Greenland is highly sensitive to whether the NGRIP (North GReenland Ice core Project) elevated heat flow anomaly is included in the training dataset. Our model's most distinctive spatial feature is pronounced low geothermal heat flow (< 40 mW m−2) across the North Atlantic Craton of southern Greenland. Crucially, our model does not show an area of elevated heat flow that might be interpreted as remnant from the Icelandic plume track. Finally, we discuss the substantial influence of paleoclimatic and other corrections on geothermal heat flow measurements in Greenland. The in situ measurement database and gridded heat flow model, as well as other supporting materials, are freely available from the GEUS Dataverse (https://doi.org/10.22008/FK2/F9P03L; Colgan and Wansing, 2021).

William Colgan↗

Interoperability and Other Aspects of Guiding Data Producers for the Benefit of End Users

The purpose of this paper is to discuss how the Climate and Forecast (CF) Metadata Conventions and netCDF standard have influenced the recommendations and guidance provided to producers of data products based on NASA’s Earth observations. It has been long-recognized that interoperable datasets and use of standards and conventions are beneficial to the users of these datasets, especially those who make use of multiple datasets for their research and applications. The Dataset Interoperability Working Group (DIWG), one of NASA’s Earth Science Data System Working Groups (ESDSWGs), was established in 2013, and has developed and published many recommendations. The Data Product Development Guide (DPDG) Working Group, established in 2018 as another of the ESDSWGs, has published a DPDG for Data Producers and a Quick Start Guide, incorporating guidance from many sources, including the recommendations from the DIWG. The DPDG includes recommendations regarding data formats (prominently netCDF-4) and metadata based primarily on the CF Metadata Conventions and the Attribute Convention for Data Discovery (ACDD). In early 2023, it was decided that the Resource Center for Data Producers (RCDP) Working Group be established as another ESDSWG, with the goals of providing all the information relevant and helpful for data producers via an easily accessible website, and of recommending how the DPDG and QSG could be maintained as living documents, given the rapidly changing technologies, and the need for incorporating the experience and feedback from the users of these documents.

Data product development↗

Enabling Model Organism and Commercial Astronaut Data Access Through the NASA Open Science Data Repository

NASA’s Open Science Data Repository (OSDR) brings together omics data from NASA’s GeneLab project and non-omics data, including physiological, phenotypic, imaging, and behavioral data from NASA’s Ames Life Sciences Data Archive (ALSDA) collected from decades of space biology research, providing open and FAIR (findable, accessible, interoperable, and reusable) access of these precious data to scientists world-wide. This rich source of meticulously curated metadata and data from spaceflight and analog studies has been mined by the scientific community resulting in dozens of high impact scientific publications that reveals a complex network of molecular and physiological effects of spaceflight across living systems, from microbes to plants, to mammals. Understanding how these effects translate to the human condition is critical as we move deeper into the era of commercial space travel. However, the integration of data, specifically omics data, from astronauts is particularly challenging due to their sensitive nature. OSDR has risen to this challenge by developing a mechanism to control access to identifiable levels of omics data, such as raw sequence data, while enabling public access to processed, unidentifiable, data and associated metadata that will allow the scientific community to interrogate human astronaut data alongside data from model organisms to begin answering these critical questions. The 2021 SpaceX Inspiration4 (I4) mission collected a comprehensive atlas of biological measurements from four civilian astronauts, providing a wealth of data to characterize the effects of spaceflight on the human body. These data include both non-omics and omics assays such as direct RNA sequencing (RNA-seq), single nuclei ATAC-seq and RNA-seq, metagenomics, proteomics, and comprehensive metabolic and cytokine panels, all of which have been integrated into the OSDR system across no less than 9 studies. Each study has been carefully curated using community-backed OSDR standards for sample and assay level metadata ensuring these data are findable and accessible. In addition to hosting both raw and processed data from the principal investigator team for each assay type, the GeneLab team plans to re-process the I4 omics data using GeneLab’s standard processing pipelines. The GeneLab processed data outputs will allow for comparisons across studies on OSDR and enable visualization of these data through the OSDR data visualization platform thereby enabling data reusability and interoperability. Here we describe the robust privacy and security protocols implemented by OSDR to safeguard sensitive health data from astronauts while facilitating metadata and processed data sharing for research purposes. We further provide a road map for navigating the vast amount of data provided for each I4 study on the OSDR, including experimental design, associated experiments, payloads, and missions, data generation and analysis protocols, and associated scientific articles. Additionally, we illustrate how to interrogate the standardized metadata provided in the sample and assay tables as well as various means to download and access the data including programmatically through the GeneLab Open API (GLOpenAPI). The open access of datasets in NASA’s OSDR provides a unique opportunity for the scientific community, as well as citizen scientists and students, to continue using OSDR resources to further unlock profound insights into the consequences of space travel on the human body. Through implementation of security measures to protect sensitive human data, the OSDR seeks to strengthen the science exchange between the Biological and Physical Sciences Program and the Human Research Program, per recommendation 4-1 of the 2023-2032 Decadal Survey, and encourage further sharing and dissemination of astronaut data to provide the scientific community with the resources needed to lay the groundwork for developing targeted mitigation strategies to help withstand the rigors of long-duration spaceflight.

Amanda Marie Saravia-butler↗

Enabling Model Organism and Commercial Astronaut Data Access Through the NASA Open Science Data Repository

NASA’s Open Science Data Repository (OSDR) brings together omics data from NASA’s GeneLab project and non-omics data, including physiological, phenotypic, imaging, and behavioral data from NASA’s Ames Life Sciences Data Archive (ALSDA) collected from decades of space biology research, providing open and FAIR (findable, accessible, interoperable, and reusable) access of these precious data to scientists world-wide. This rich source of meticulously curated metadata and data from spaceflight and analog studies has been mined by the scientific community resulting in dozens of high impact scientific publications that reveals a complex network of molecular and physiological effects of spaceflight across living systems, from microbes to plants, to mammals. Understanding how these effects translate to the human condition is critical as we move deeper into the era of commercial space travel. However, the integration of data, specifically omics data, from astronauts is particularly challenging due to their sensitive nature. OSDR has risen to this challenge by developing a mechanism to control access to identifiable levels of omics data, such as raw sequence data, while enabling public access to processed, unidentifiable, data and associated metadata that will allow the scientific community to interrogate human astronaut data alongside data from model organisms to begin answering these critical questions. The 2021 SpaceX Inspiration4 (I4) mission collected a comprehensive atlas of biological measurements from four civilian astronauts, providing a wealth of data to characterize the effects of spaceflight on the human body. These data include both non-omics and omics assays such as direct RNA sequencing (RNA-seq), single nuclei ATAC-seq and RNA-seq, metagenomics, proteomics, and comprehensive metabolic and cytokine panels, all of which have been integrated into the OSDR system across no less than 9 studies. Each study has been carefully curated using community-backed OSDR standards for sample and assay level metadata ensuring these data are findable and accessible. In addition to hosting both raw and processed data from the principal investigator team for each assay type, the GeneLab team plans to re-process the I4 omics data using GeneLab’s standard processing pipelines. The GeneLab processed data outputs will allow for comparisons across studies on OSDR and enable visualization of these data through the OSDR data visualization platform thereby enabling data reusability and interoperability. Here we describe the robust privacy and security protocols implemented by OSDR to safeguard sensitive health data from astronauts while facilitating metadata and processed data sharing for research purposes. We further provide a road map for navigating the vast amount of data provided for each I4 study on the OSDR, including experimental design, associated experiments, payloads, and missions, data generation and analysis protocols, and associated scientific articles. Additionally, we illustrate how to interrogate the standardized metadata provided in the sample and assay tables as well as instructions for how to download and access the data. The I4 datasets described here re present the first ever comprehensive collection of commercial astronaut data.

Amanda M Saravia-Butler↗

Additional Metadata Guidelines to Improve the Structure and Usability of HDF and NetCDF Files

The Hierarchical Data Format (HDF) and Network Common Data Form (NetCDF) are data file formats created to aid users in the creation or use of scientific data. These file formats are useful for handling large data volumes and hosting extensive metadata as global attributes or variables and are popular with the modeling community. HDF and NetCDF files are largely used with remote sensing data and have been used to support measurements from numerous campaigns, from satellite to aircraft or ground and mobile based measurements. The files from airborne field studies, however, vary greatly in terms of the file structure and the amount and content of metadata. Information relevant to the file that can be useful to the user such as the data producer, location where data was taken, variable descriptions, or information about the instrument might not be included in the file. This metadata might be present in another file in the dataset containing the same data using the International Consortium for Atmospheric Research on Transport and Transformation (ICARTT) format. Recently, the Aerosols, Clouds, and their Interactions for Earth System Models (MACIE) group started a grassroots effort to develop a set of requirements for the HDF and NetCDF files for field studies, aiming to make the data products more interoperable and usable. Particularly, these requirements seek to make the files more compliant to Climate and Forecast (CF) metadata conventions and to standardize the file structure and the global and variable attributes. These requirements would help to ensure that HDF and NetCDF files contain adequate metadata to better support their use for research, e.g., the modeling community, and to enhance the usability and interoperability of data for research communities at large. To be presented are the details of the MACIE requirements as well as examples of the implementation of these requirements for merge files and lidar observation data files.

Sean Leavor↗

Extending CF Conventions to Enhance Data FAIRness for Atmospheric Composition Observations

The Hierarchical Data Format (HDF) and Network Common Data Form (NetCDF) are data file formats created to aid users in the creation or use of scientific data. These file formats are useful for handling large data volumes and hosting extensive metadata as global, group, or variable attributes and are popular with the modeling community. HDF and NetCDF files are widely used with atmospheric remote sensing data and have been used to support measurements from numerous field campaigns, from satellite to aircraft or ground and mobile based measurements. The files from airborne field studies, however, vary greatly in terms of the file structure and the amount and content of their metadata. Information relevant to the file that can be useful to the user such as the data producer, location where data was taken, variable descriptions, or information about the instrument might not be included in the file. Recently, the Measurements of Aerosols, Clouds, and their Interactions for Earth System Models (MACIE) group started a grassroots effort to develop a CF-based template for the HDF and NetCDF files for field studies, with the aim of making the data products more interoperable and usable. This template seeks to make the files more compliant to Climate and Forecast (CF) metadata conventions and to standardize the file structure and the global and variable attributes. The template would help to ensure that HDF and NetCDF files contain adequate metadata to better support their use for research, e.g., the modeling community, and to enhance the usability and interoperability of data for research communities at large. The draft template has been applied to recent field studies for various instruments and their merge files in support of the Atmosphere Observing System (AOS) project. The details of the revised template are to be presented, as well as examples of the implementation of these requirements for merge files and lidar observation data files and issues revealed during the implementation process.

Sean Leavor↗

Transformation of the NASA Life Sciences Portal to a FAIR Data Point

The FAIR principles emphasize optimizing metadata, the vast majority of which are textual in nature, and often organized into attribute name-value pairs. This uniformity has led to the development of guidelines and best practices for providing programmatic access to scientific data through their metadata, yielding the first iteration of the FAIR Data Point Specifications (FDPS). A key feature of the FDPS is its support for automated agents seeking and fetching data without first needing to learn a plethora of different application programming interfaces. These software agents can interrogate metadata catalogs that adhere to FDPS in a uniform manner because each catalog describes itself and its metadata schema consistently. This approach enhances the sustainability of data retrieval support, allowing systems to refine and update their metadata schemas as needed and without requiring data-seeking software agents to change how they interrogate FDPS catalogs. An essential aspect of the FDPS is the standardization of data catalog semantics, which formalizes concepts such as “metadata” and “metadata service” and links them to other concepts specifications including the Data Catalog Vocabulary (DCAT), a W3C standard that is also the basis of NASA-STD-2831 “Metadata Standard for Data Discoverability,” authored by NASA’s Office of the Chief Information Officer. The FDPS references DCAT (version 2) elements which focus on the distribution of datasets and support the goal of stream-lined catalog integration across repositories for improved data discovery. Additionally, the FDPS also prescribe the use of Linked Data Platform elements for data catalog-metadata record containment descriptions, allowing users to ascertain which data and metadata belong to which catalogs. NASA’s Life Sciences Portal is implementing the FDPS while formalizing its metadata schema to support the accelerated synthesis of knowledge from space life sciences investigations.

platform↗

TOLNet’s FAIR Journey: Yesterday, Today, and Tomorrow

The Tropospheric Ozone Lidar Network (TOLNet) has generated over a decade of ozone vertical profile data products over North America and contributed to several air quality focused field studies. The science value of the TOLNet data has been demonstrated in numerous peer-reviewed publications on air quality and ozone relevant research. As the broad scientific community has moved towards adopting FAIR Principles to make data more findable, accessible, interoperable, and (re)usable, the TOLNet team has been consistently making data more FAIR. This effort has many challenges, partially reflecting on the FAIR principles being domain agnostic while the implementation needs to be domain specific. The FAIR principles declare the dependence on the community standards, domain-relevant metadata, and rich metadata. This presentation uses the TOLNet data and data system as an example to explore the best practices to implement FAIR principle. Particularly, we will examine the metadata and the “richness” to support findability and usability as well as machine-to-machine actionability via API. Last year, as part of our FAIR journey, we launched the TOLNet website (https://tolnet.larc.nasa.gov/) and the API (https://tolnet.larc.nasa.gov/api/). Part of this process included extracting and cataloging metadata across the entire TOLNet mission timeframe. This enabled users to search through the mission by various metadata criteria, improving the findability and accessibility. And computers could connect directly to the TOLNet API to extract both metadata and data, providing a level of interoperability never present before for TOLNet data. On top of that, all new TOLNet data is now automatically validated using the API to ensure it complies with GEOMS standards, aiding in reusability. It takes both technology and scientists working together to make progress. The next step is to evaluate the current TOLNet offerings against NASA’s Practical Guide for Open, Free & FAIR NASA Earth Science Data Products (https://doi.org/10.5067/DOC/ESCO/ESDSWG-0002V1).

TOLNet↗

Community Coordinated Modeling Center Support of Science Needs for Integrated Data Environment

Space science models are essential component of integrated data environment. Space science models are indispensable tools to facilitate effective use of wide variety of distributed scientific sources and to place multi-point local measurements into global context. The Community Coordinated Modeling Center (CCMC) hosts a set of state-of-the- art space science models ranging from the solar atmosphere to the Earth's upper atmosphere. The majority of models residing at CCMC are comprehensive computationally intensive physics-based models. To allow the models to be driven by data relevant to particular events, the CCMC developed an online data file generation tool that automatically downloads data from data providers and transforms them to required format. CCMC provides a tailored web-based visualization interface for the model output, as well as the capability to download simulations output in portable standard format with comprehensive metadata and user-friendly model output analysis library of routines that can be called from any C supporting language. CCMC is developing data interpolation tools that enable to present model output in the same format as observations. CCMC invite community comments and suggestions to better address science needs for the integrated data environment.

Kuznetsova, M. M.↗

Architectures Toward Reusable Science Data Systems

Science Data Systems (SDS) comprise an important class of data processing systems that support product generation from remote sensors and in-situ observations. These systems enable research into new science data products, replication of experiments and verification of results. NASA has been building systems for satellite data processing since the first Earth observing satellites launched and is continuing development of systems to support NASA science research and NOAAs Earth observing satellite operations. The basic data processing workflows and scenarios continue to be valid for remote sensor observations research as well as for the complex multi-instrument operational satellite data systems being built today. System functions such as ingest, product generation and distribution need to be configured and performed in a consistent and repeatable way with an emphasis on scalability. This paper will examine the key architectural elements of several NASA satellite data processing systems currently in operation and under development that make them suitable for scaling and reuse. Examples of architectural elements that have become attractive include virtual machine environments, standard data product formats, metadata content and file naming, workflow and job management frameworks, data acquisition, search, and distribution protocols. By highlighting key elements and implementation experience we expect to find architectures that will outlast their original application and be readily adaptable for new applications. Concepts and principles are explored that lead to sound guidance for SDS developers and strategists.

Data Processing↗