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At least 19 records

Metadata for a systematic description of signal data

This chapter aims to provide a comprehensive overview of metadata types that may be useful during system design, optimization, and automation. Metadata are grouped into three main categories: (a) metadata describing signal generation, (b) metadata describing signal quality, and (c) contextual information in the form of annotations. Each of these categories is introduced and explained in three separate sections. Importantly, this chapter mainly answers what is considered metadata. To a lesser degree, recommendations are made regarding the selection of metadata for long-term storage. Chapter 4 will explain where and how to store metadata. Chapters 5 and 6 explain how to collect certain metadata through dedicated sensor validation tests (Chapter 5) or algorithmic analysis (Chapter 6).

Alferes, Janelcy↗

The need for standardization and improved open (meta)data practices in metaproteomics

Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization across experimental and bioinformatics stages hinder reproducibility and comparability, limiting integration with other omics data. We here present a community-developed reporting checklist tailored to the specific needs of metaproteomics. We also outline current efforts to enable structured and interoperable metadata capture, drawing on standards from proteomics and microbiome research wherever possible. By promoting transparent reporting and advancing metadata practices, our recommendations aim to align metaproteomics more closely with FAIR principles and support reproducible and interoperable research practices.

Armengaud, Jean [Universite Paris-Saclay, France]↗

Performance and Reliability Assessment of the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) Data Advisor (ADA)

The Atmospheric Radiation Measurement (ARM) User Facility provides one of the world's largest openly accessible repositories of atmospheric observations through the ARM Data Discovery platform. Although the repository contains more than three decades of measurements collected from permanent observatories, mobile facilities, aircraft campaigns, and field experiments, identifying appropriate datasets can be challenging, particularly for new users unfamiliar with ARM instrumentation and datastream organization. To improve data accessibility, the ARM Data Center developed the ARM Data Advisor (ADA), an artificial intelligence-powered assistant designed to facilitate scientific data discovery, dataset interpretation, and user guidance. This report evaluates ADA's performance as a domain-specific scientific assistant using realistic atmospheric science workflows. The evaluation examines five key capabilities: data retrieval and curation efficiency, hallucination resistance, scientific reasoning, response to ambiguous queries, and content retention and session continuity. Representative prompts were developed to simulate typical interactions between researchers and the ARM Data Discovery platform, and ADA's responses were assessed for retrieval completeness, scientific accuracy, consistency, and practical usefulness. In these representative tests, ADA reduced the complexity of discovering and accessing ARM datasets by recommending appropriate datastreams, explaining instrumentation, interpreting metadata, and assisting with data processing workflows. ADA also exhibits strong domain knowledge of atmospheric science terminology and generally resists hallucination by acknowledging unavailable datasets and requesting clarification when appropriate. Overall, the results indicate that ADA represents a promising advancement in scientific data discovery within the ARM User Facility and has considerable potential to improve researcher productivity, particularly for new users and interdisciplinary scientists seeking efficient access to ARM observations.

Salvador, Christian [ORNL] (ORCID:0000000283287777↗

NEPATEC2.0: NEPA Text Corpus v2.0

The National Environmental Policy Act of 1969, as amended (NEPA), is a major environmental law in the United States, requiring Federal agencies to consider and document potential environmental impacts before deciding on a proposed action. Modernization of NEPA and permitting processes faces significant challenges due to the lack of standardized formats and interoperable systems for organizing and sharing NEPA-related information across agencies. Much of the information gathered during NEPA reviews is written into documents such as categorical exclusions, environmental assessments, and environmental impact statements, then filed in predominately independent agency file stores that may or may not be publicly accessible. The application of metadata and data standards, such as those recommended by the Council on Environmental Quality (CEQ), to NEPA documents offers a shared vocabulary and structure for key entities like projects, processes, and documents that can streamline information exchange and enhance collaboration across systems. In this work, we publicly release NEPATEC2.0, an expanded corpus of NEPA documents with associated metadata. NEPATEC2.0 encompasses approximately 120,000 documents from 60,000 projects prepared by more than 60 different agencies. Modeled to align with CEQ metadata standards, NEPATEC2.0 promotes consistency in environmental reviews and supports the ongoing effort to modernize permitting technologies by facilitating more transparent, efficient, and data-driven decision-making. Importantly, NEPATEC2.0 demonstrates the possibilities and limitations of large language model-based prompting to extract information from NEPA documents at scale.

environmental review↗

NEPATEC v2.0: Standardized Metadata and Text Corpus of National Environmental Policy Act Documents

The National Environmental Policy Act of 1969, as amended (NEPA), is a major environmental law in the United States, requiring Federal agencies to consider and document potential environmental impacts before deciding on a proposed action. Modernization of NEPA and permitting processes faces significant challenges due to the lack of standardized formats and interoperable systems for organizing and sharing NEPA-related information across agencies. Much of the information gathered during NEPA reviews is written into documents such as categorical exclusions, environmental assessments, and environmental impact statements, then filed in predominately independent agency file stores that may or may not be publicly accessible. The application of metadata and data standards, such as those recommended by the Council on Environmental Quality (CEQ), to NEPA documents offers a shared vocabulary and structure for key entities like projects, processes, and documents that can streamline information exchange and enhance collaboration across systems. In this work, we publicly release NEPATEC2.0, an expanded corpus of NEPA documents with associated metadata. NEPATEC2.0 encompasses approximately 120,000 documents from 60,000 projects prepared by more than 60 different agencies. Modeled to align with CEQ metadata standards, NEPATEC2.0 promotes consistency in environmental reviews and supports the ongoing effort to modernize permitting technologies by facilitating more transparent, efficient, and data-driven decision-making. Importantly, NEPATEC2.0 demonstrates the possibilities and limitations of large language model-based prompting to extract information from NEPA documents at scale.

54 ENVIRONMENTAL SCIENCES↗

MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment

DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields—isotope, isotopolog, isotopolog label, labeling approach, and gradient position—and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.

Simpson, Abigayle↗

Do we have globally representative data to understand soil processes?

Understanding and modeling soils and soil organic matter (SOM) are central to a variety of human needs, from food production to ecosystem management. Soil data have been collected for over a century, but the global spatial and process representativeness of soil data remains unclear. We assessed the representativeness of currently available soil data that could be used to understand a variety of SOM processes. We used 16 open-source soil databases and data from over 281,000 unique locations globally, categorizing the databases into three main data types necessary to understand SOM processes: soil carbon stocks and fluxes, mechanistic drivers of these stocks and fluxes, and soil carbon gain or loss potential. We found that stock and driver data have extensive global coverage. However, data on soil carbon gain or loss potential, particularly data describing change in soils over time such as time series data, are severely limited in their global coverage. We conclude that while significant strides have been made in measuring soil carbon stocks and fluxes, and their drivers, we are limited in global data related to changes in soils over time. Our recommendations for soil data generators are to ensure precise metadata reporting and prioritizing sampling in underrepresented areas like tropical, arctic, mountainous, wetland and arid regions. We also encourage designing revisit schemes that explicitly support change detection and reporting multi-modal datasets that can aid in model development. Targeted measurement of low coverage soil data types and regions is necessary for a range of applications including current and future biogeochemical predictions, and their management and policy implications.

carbon fluxes↗

Shaping the Future of Self-Driving Autonomous Laboratories Workshop

The "Shaping the Future of Self-Driving Autonomous Laboratories" workshop, held in Denver on November 7-8, 2024, brought together leading experts from materials science and computing to address the growing need to revolutionize scientific research through AI-driven autonomous laboratories. The workshop identified critical challenges, including the integration of heterogeneous data, development of AI systems that understand fundamental physical principles, and comprehensive safety protocols. Key recommendations emerged around developing universal laboratory equipment interfaces, implementing automated metadata collection systems, and creating hybrid AI approaches that combine data-driven learning with scientific principles. The workshop emphasized maintaining human oversight while leveraging automation, transforming scientific education to prepare the next generation of researchers, and establishing a national consortium leveraging DOE facilities as anchors for broader collaboration with academia and industry. Participants stressed the urgency of addressing the growing disconnect between human decision-making timescales and modern instrumentation capabilities, highlighting the need for strategic automation while preserving essential human insight and oversight in the research process.

36 MATERIALS SCIENCE↗

Best Practices for Nuclear Experiment Data Preservation at Idaho National Laboratory: A Guide for Researchers and Reactor Operators

Preserving experimental data is essential for supporting advancements in nuclear science and ensuring the longevity of Idaho National Laboratory's contributions to reactor technology and safety. This report provides a comprehensive guide to best practices for experimental data management and preservation, focusing on standardized data formats, redundancy in storage, metadata documentation, and alignment with international standards. By following these recommendations, experimentalists and reactor operators can enhance the accessibility, reproducibility, and utility of critical datasets for regulatory review, validation computational methods, and future research.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

PNNL INFRARED REFRACTIVE INDEX (n/k) DATASET FOR SEVEN PAH SOLIDS AT ROOM TEMPERATURE

This dataset is an open-source repository of spectral data measured at Pacific Northwest National Laboratory (PNNL). This database provides quantitative values for the complex index of refraction for seven polycyclic aromatic hydrocarbon (PAH) solids. A list of the chemicals is available in the readme file. These spectra consist of the optical constants, i.e., the real, n(ν), and imaginary, k(ν), refractive indices, over the spectral range from 7,800 to 400 cm-1 (1.28 – 25 μm). The conditions under which the individual data were acquired are described in the associated metadata files, and the user is strongly encouraged to read and understand this information to ensure the data are used appropriately for your application. Recommended Citation for Dataset Jessica M Salcido, Jeremy D. Erickson, Ashley M. Bradley, Russell G. Tonkyn, Timothy J. Johnson and Tanya L. Myers. 2026. PNNL INFRARED REFRACTIVE INDEX (n/k) DATASET FOR SEVEN PAH SOLIDS AT ROOM TEMPERATURE. [Data Set] PNNL DataHub. INSERT DOI License Information This work is marked with CC0 1.0: https://creativecommons.org/publicdomain/zero/1.0/. The authors do request that you appropriately cite the dataset when referencing or using the dataset.

Salcido, Jessica Marie Ortola↗

Explainable discrepancy checker and diagnosis for digital Twin-based supervisory control system

By virtually representing a physical object and process, a digital twin (DT) enables optimal autonomous operations by combining classical and novel frameworks in sensors, state predictions, and multi-input/multi-output systems. A DT’s values depend on how well models estimate quantities of interest and on how uncertainty is handled. Moreover, DTs often combine physics-based and data-driven models with mixed fidelities, where classical uncertainty quantification (UQ) struggles with many sources of uncertainty and real-time constraints. Here, this work presents a UQ-based discrepancy checking and diagnosis tool for a DT-based supervisory control system. The tool is developed using metadata from an automated DT development process to learn correlations between sources of uncertainties and outcomes. During operation, it compares predictions with measurements, attributes discrepancies to dominant sources, and recommends parameter and configuration updates. We verify the workflow on a synthetic temperature-control problem and deploy it on a virtual Thermal Energy Delivery System, reducing mismatch and improving control robustness.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

Challenges of open data in aquatic sciences: issues faced by data users and data providers

Free use and redistribution of data (i.e., Open Data) increases the reproducibility, transparency, and pace of aquatic sciences research. However, barriers to both data users and data providers may limit the adoption of Open Data practices. Here, we describe common Open Data challenges faced by data users and data providers within the aquatic sciences community (i.e., oceanography, limnology, hydrology, and others). These challenges were synthesized from literature, authors’ experiences, and a broad survey of 174 data users and data providers across academia, government agencies, industry, and other sectors. Through this work, we identified seven main challenges: 1) metadata shortcomings, 2) variable data quality and reusability, 3) open data inaccessibility, 4) lack of standardization, 5) authorship and acknowledgement issues 6) lack of funding, and 7) unequal barriers around the globe. Our key recommendation is to improve resources to advance Open Data practices. This includes dedicated funds for capacity building, hiring and maintaining of skilled personnel, and robust digital infrastructures for preparation, storage, and long-term maintenance of Open Data. Further, to incentivize data sharing we reinforce the need for standardized best practices to handle data acknowledgement and citations for both data users and data providers. We also highlight and discuss regional disparities in resources and research practices within a global perspective.

54 ENVIRONMENTAL SCIENCES↗

A cost and community perspective on the barriers to microbiome data reuse

Microbiome research is becoming a mature field with a wealth of data amassed from diverse ecosystems, yet the ability to fully leverage multi-omics data for reuse remains challenging. To provide a view into researchers’ behavior and attitudes towards data reuse, we surveyed over 700 microbiome researchers to evaluate data sharing and reuse challenges. We found that many researchers are impeded by difficulties with metadata records, challenges with processing and bioinformatics, and problems with data repository submissions. We also explored the cost constraints of data reuse at each step of the data reuse process to better understand “pain points” and to provide a more quantitative perspective from sixteen active researchers. The bioinformatics and data processing step was estimated to be the most time consuming, which aligns with some of the most frequently reported challenges from the community survey. From these two approaches, we present evidence-based recommendations for how to address data sharing and reuse challenges with concrete actions for future work.

59 BASIC BIOLOGICAL SCIENCES↗

Hybrid-BPR (Bayesian Personalized Ranking with Feature Embeddings and Explicit Negative Sampling) [SWR-26-039]

Hybrid-BPR is a Python library for Bayesian Personalized Ranking (BPR) with two key capabilities that go beyond standard BPR implementations: 1. User and item feature embeddings - incorporate content-based signals (genres, tags, metadata) alongside collaborative filtering. 2. Implicit negative interactions - use observed non-interactions (e.g. viewed-but-not-clicked) as negative training signal instead of random sampling from the full item space. The software is built for recommender systems research with MLflow experiment tracking, parallel hyperparameter sweeps, and standard ranking metrics.

Sandhu, Rimple [National Laboratory of the Rockies↗

Metadata Standards for the NSE: Extended Field Standards

This standard presents a set of optional metadata fields for managed digital objects within the Nuclear Security Enterprise (NSE) and provides a deeper look at data representation in metadata by looking at the representation of 1) Records Management required metadata, and 2) common representations of technical/scientific data. Metadata standardization is a critical enabler for effectively sharing data, documents, and other digital objects between NSE sites, and for tracing the digital thread at the object level. Standardization is necessary for both schemas and vocabularies, meaning that both field standards and value standards must be specified. This document serves as a complementary field standard, recommending an optional set of fields that should be uniformly built for all managed digital objects within the NSE. This document specifically focuses on extending the shared discovery layer defined in the first white paper by introducing additional descriptive and data representation fields that improve cross-site search and interpretation.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Challenges and Vision for Standardization of Biopolymer Data Sets for Machine Learning

Machine learning (ML) is transforming materials research, yet potential for biopolymer discovery remains constrained by fragmented data and nonstandardized reporting. Biopolymers differ significantly from synthetic polymers, requiring specialized approaches to represent their biosynthetic origins, hierarchical structures, and application-specific metrics. In this Perspective, we identify three core challenges limiting biopolymer representation: information encoding, data quality, and data sharing. We describe the most pressing issues and propose commensurate approaches to address each key challenge. Recommendations include the design and adoption of biopolymer-specific fingerprinting and representation frameworks, development of hybrid human-large language model (LLM) data extraction strategies, and expanding Findable, Accessible, Interoperable, Reusable (FAIR)-compliant repositories. We propose a robust foundation to define interoperable, high-quality data sets that capture the full context of biopolymer materials. Standardized metadata, shared ontologies, and community-driven infrastructure would enable scalable, reproducible workflows and accelerate the ML-driven development of biopolymers.

36 MATERIALS SCIENCE↗

Metadata Standards for the NSE: Core Fields

This standard presents a core set of metadata fields required for each managed digital object within the Nuclear Security Enterprise (NSE). Metadata standardization is a critical enabler for two primary objectives: 1) effectively sharing data, documents, and other digital objects between NSE sites; and 2) supporting digital engineering through the digital thread at the object level. Standardization is necessary for both schemas and vocabularies, meaning that both field standards and value standards must be specified. This document serves as a foundational field standard, recommending a core set of fields that should be uniformly required for all managed digital objects within the NSE.

99 GENERAL AND MISCELLANEOUS↗

Videos, photos, and AI-derived grain size data associated with “High-throughput AI Video Surveys Enable Reproducible Multiscale Sediment Size Mapping, with Implications for Hydrobiogeochemical Parameterization”

NOTE: The manuscript associated with this data package is currently in review. The data may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final dataset and additional metadata. This data package is associated with the manuscript “High-throughput AI Video Surveys Enable Reproducible Multiscale Sediment Size Mapping, with Implications for Hydrobiogeochemical Parameterization” under review. This data package includes five data types: 1) raw photos and videos from drone survey and walking smartphone surveys; 2) images derived from raw videos; 3) manual labeling of reference scales; 4) metadata for all images and photo resolution derived from artificial intelligence (AI) models or manual labels, 5) grain size data obtained from AI models for all photos, 6) metadata and grain size data after quality control, 7) summaries of sample efficiency for all data, and 8) computational fluid dynamics (CFD) data used to support hydro-biogeochemical (HBGC) parameter estimation. Such data is used to 1) demonstrate significant improvements in accuracy, efficiency, and quality control for grain size data collection with the help of AI models, 2) study the spatial heterogeneity of grain size and observation reproducibility based on tens of thousands of data points generated by the AI models, and 3) evaluate the impacts of grain size heterogeneity on key HBGC parameters across sediment-to-reach and hourly-to-yearly scales. In particular, the data package contains 116 folders and 179696 files. The files include 41 videos in .mov format, 64047 photos in .jpg format, 13541 video-derived photos in .png format, 12747 segmentation mask data in .tif format, 12747 segmentation data in .json format, 24771 .csv files that with metadata and grain size for each individual photo as well as water depth and velocity data from CFD and observation, 51791 .txt files of raw AI predicted labels, and 11 flight record data in .srt format. The summary for all metadata and grain size statistics information is included in “Scales_V3_NG.csv” and “Statistics_V3_NG.csv”. The summary for data that pass data quality control (QC) level 0-2 is included in “QCStatistics_V3_NG.csv”. The QC level 0 represents photos whose photo resolution is positive, excluding photos that miss reference scale. The QC level 1 means reference scale circularity uncertainty is less than 5% for smartphone images while representing photo resolution is larger than 0.44 mm/pixel for drone images. The QC level 2 means excluding photos whose grain number is less than 100, a minimum number of grains recommended by classic literature. The summary for each video’s name, length, frame rates, survey area, grain number, survey efficiency, etc. can be found in “QCSummary_V3_NG.csv”. The summary for site name, GPS coordinates, and number of images at each site can be found in “SitesSummary_V3_*.csv” files. Overall computational efficiency summary is reported in Table 4 of accompanying manuscript. Additionally, the nitrate concentration data used in this work was downloaded from an existing dataset published on ESS-DIVE (Boat-Dragged Sensor Hanford Reach.csv; Conner A. et al., 2020). We thank the United States Forest Service, Washington Department of Fish and Wildlife, Washington Department of Natural Resources, Cowiche Canyon Conservatory, Port of Benton, and the Confederated Tribes and Bands of the Yakama Nation for access to field locations where the data were collected. We also thank the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate data collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗