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Results for “Data, Open Access, Data Curation, Data Preservation”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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Nucleus: A pilot project

The proposal is to provide institutional infrastructure that facilitates management of research projects, research collaboration, and management, preservation, and discovery of data. Deploying such infrastructure will amplify the effectiveness, efficiency, and impact of research, as well as assist researchers in regards to compliance with both data management mandates and LANL security policy. This will facilitate discoverability of LANL research both within the lab and external to LANL.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Filling in Subsurface Storage Open Data Gaps - Updates to CCS Data Availability on EDX and EDX Spatial (FWP-1022465)

There is a need to preserve and efficiently access data resources to drive the next generation of research and development while ensuring compliance with DOE regulations. Over the last 10+ years, there has been ongoing efforts by the DOE Carbon Storage Program to ensure that there is effective data curation and preservation of DOE funded research leveraging the NETL-FECM data repository, the Energy Data eXchange (EDX). This talk presents updates about ongoing efforts to continue to support the mission of ensuring that carbon storage data is findable, accessible, interoperable, and reusable to the carbon storage stakeholder community through EDX and EDX Spatial. Presented at the NETL Carbon Management Review Meeting, Pittsburgh, 2024.

Morkner, Paige↗

Protein Data Bank (PDB): Fifty-three years young and having a transformative impact on science and society

This review article describes the co-evolution of structural biology as a discipline and the Protein Data Bank (PDB), established in 1971 as the first open-access data resource in biology by like-minded structural scientists. As the PDB archive grew in size and scope to encompass macromolecular crystallography, NMR spectroscopy, and cryo-electron microscopy, new technologies were developed to ingest, validate, curate, store, and distribute the information. Community engagement ensured that the needs of structural biologists (data depositors) and data consumers were met. Today, the archive houses more than 230,000 experimentally determined structures of proteins, nucleic acids, and macromolecular machines and their complexes with one another and small-molecule ligands. Aggregate costs of PDB data preservation are ~1% of the cost of structure determination. The enormous impact of PDB data on basic and applied research and education across the natural and medical sciences is presented and highlighted with illustrative examples. Enablement of de novo protein structure prediction (AlphaFold2, RoseTTAfold, OpenFold, etc.) is the most widely appreciated benefit of having a corpus of rigorously validated, expertly curated 3D biostructure data.

bioinformatics↗

Experimental Data Curation at Large Instrument Facilities with Open Source Software

The National Synchrotron Light Source II operating at Brookhaven National Laboratory since 2014 for the US Department of Energy is one of the newest and brightest storage-ring synchrotron facility in the world. NSLS-II, like other facilities, provides pre-processing of the raw data and some analysis capabilities to its users. We describe the research collaborations and open source infrastructure developed at large instrument facilities such as NSLS-II for the purpose of curating high value scientific data along the early stages of the data lifecycle. Data acquisition and curation tasks include storing experiment configuration, detector metadata, raw data acquisition with infrastructure that converts proprietary instrument formats to industry standards. In addition, we describe a specific effort for discovering sample information at NSLS-II and tracing the provenance of analysis performed on acquired images. We show that curation tasks must be embedded into software along the data life cycle for effectiveness and ease of use, and that loosely defined collaborations evolve around shared open source tools. Finally we discuss best practices for experimental metadata capture in such facilities, data access and the new challenges of scale and complexity posed by AI-based discovery for the synthesis of new materials.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Call to Action for Global Access to and Harmonization of Quality Information of Individual Earth Science Datasets

Knowledge about the quality of data and metadata is important to support informed decisions on the (re)use of individual datasets and is an essential part of the ecosystem that supports open science. Quality assessments reflect the reliability and usability of data. They need to be consistently curated, fully traceable, and adequately documented, as these are crucial for sound decision- and policy-making efforts that rely on data. Quality assessments also need to be consistently represented and readily integrated across systems and tools to allow for improved sharing of information on quality at the dataset level for individual quality attribute or dimension. Although the need for assessing the quality of data and associated information is well recognized, methodologies for an evaluation framework and presentation of resultant quality information to end users may not have been comprehensively addressed within and across disciplines. Global interdisciplinary domain experts have come together to systematically explore needs, challenges and impacts of consistently curating and representing quality information through the entire lifecycle of a dataset. This paper describes the findings of that effort, argues the importance of sharing dataset quality information, calls for community action to develop practical guidelines, and outlines community recommendations for developing such guidelines. Practical guidelines will allow for global access to and harmonization of quality information at the level of individual Earth science datasets, which in turn will support open science.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

GRDC. A Collaborative Framework for Radiological Background and Contextual Data Analysis

The Radiation Mobile Analysis Platform (RadMAP) is unique in its capability to collect both high quality radiological data from both gamma-ray detectors and fast neutron detectors and a broad array of contextual data that includes positioning and stance data, high-resolution 3D radiological data from weather sensors, LiDAR, and visual and hyperspectral cameras. The datasets obtained from RadMAP are both voluminous and complex and require analyses from highly diverse communities within both the national laboratory and academic communities. Maintaining a high level of transparency will enable analysis products to further enrich the RadMAP dataset. It is in this spirit of open and collaborative data that the RadMAP team proposed to collect, calibrate, and make available online data from the RadMAP system. The Berkeley Data Cloud (BDC) is a cloud-based data management framework that enables web-based data browsing visualization, and connects curated datasets to custom workflows such that analysis products can be managed and disseminated while maintaining user access rights. BDC enables cloud-based analyses of large datasets in a manner that simulates real-time data collection, such that BDC can be used to test algorithm performance on real and source-injected datasets. Using the BDC framework, a subset of the RadMAP datasets have been disseminated via the Gamma Ray Data Cloud (GRDC) that is hosted through the National Energy Research Science Computing (NERSC) Center, enabling data access to over 40 users at 10 institutions.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

The Materials Data Facility: Data Services to Advance Materials Science Research

With increasingly strict data management requirements from funding agencies and institutions, expanding focus on the challenges of research replicability, and growing data sizes and heterogeneity, new data needs are emerging in the materials community. The materials data facility (MDF) operates two cloudhosted services, data publication and data discovery, with features to promote open data sharing, self-service data publication and curation, and encourage data reuse, layered with powerful data discovery tools. The data publication service simplifies the process of copying data to a secure storage location, assigning data a citable persistent identifier, and recording custom (e.g., material, technique, or instrument specific)and automatically-extractedmetadata in a registrywhile the data discovery service will provide advanced search capabilities (e.g., faceting, free text range querying, and full text search) against the registered data and metadata. TheMDF services empower individual researchers, research projects, and institutions to (I) publish research datasets, regardless of size, from local storage, institutional data stores, or cloud storage, without involvement of thirdparty publishers; (II) build, share, and enforce extensible domain-specific custom metadata schemas; (III) interact with published data and metadata via representational state transfer (REST) application program interfaces (APIs) to facilitate automation, analysis, and feedback; and (IV) access a data discovery model that allows researchers to search, interrogate, and eventually build on existing published data. We describe MDF’s design, current status, and future plans.

data management↗

FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants

Abstract FatPlants, an open-access, web-based database, consolidates data, annotations, analysis results, and visualizations of lipid-related genes, proteins, and metabolic pathways in plants. Serving as a minable resource, FatPlants offers a user-friendly interface for facilitating studies into the regulation of plant lipid metabolism and supporting breeding efforts aimed at increasing crop oil content. This web resource, developed using data derived from our own research, curated from public resources, and gleaned from academic literature, comprises information on known fatty-acid-related proteins, genes, and pathways in multiple plants, with an emphasis on Glycine max, Arabidopsis thaliana, and Camelina sativa. Furthermore, the platform includes machine-learning based methods and navigation tools designed to aid in characterizing metabolic pathways and protein interactions. Comprehensive gene and protein information cards, a Basic Local Alignment Search Tool search function, similar structure search capacities from AphaFold, and ChatGPT-based query for protein information are additional features. Database URL: https://www.fatplants.net/

59 BASIC BIOLOGICAL SCIENCES↗

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies

Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies (OBO) Foundry was created to address this by facilitating the development, harmonization, application and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here, we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable, federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data Findable, Accessible, Interoperable, and Reusable (FAIR).

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

A Simple Standard for Sharing Ontological Mappings (SSSOM)

Abstract Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec. Database URL: http://w3id.org/sssom/spec

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Second Report of the Nuclear Data Subcommittee of the Nuclear Science Advisory Committee

The central importance of the nuclear data curated by the US Nuclear Data Program (USNDP) for clean energy generation, national security, nonproliferation, medical applications, and space exploration as well as basic science was described in a prior report issued by the DOE/NSF Nuclear Science Advisory Committee subcommittee on Nuclear Data (NSAC-ND) in September 2022. In this report, we present a set of fourteen (14) recommendations that will enhance and advance DOE-NP's stewardship of nuclear data. The first three recommendations focus on the existing core USNDP capabilities, namely: 1) Support the nuclear structure evaluation workforce to improve the currency, consistency, and accessibility of the Evaluated Nuclear Structure Data File (ENSDF); 2) Enhance nuclear reaction evaluation within the USNDP in support of the Evaluated Nuclear Data File (ENDF) through expansion of the workforce and integration of high-performance computing, automation, and machine learning and; 3) Continue atomic mass evaluation in support AME and NUBASE databases. This is followed by eight (8) recommendations representing new cross-cutting initiatives involving both measurement and evaluation to address outstanding nuclear data needs. These new initiatives require a highly trained, diverse workforce that includes personnel with expertise from both inside and outside the nuclear physics community from which evaluators have traditionally been recruited. As such, many of these initiatives are accomplished via a Topical Nuclear Data Collaborations (TNDC). A TNDC is made up of domestic and international stakeholders, subject matter and nuclear data experts, and nuclear data evaluators and features a workforce development plan to ensure that nuclear data evaluators maintain currency in the relevant applications and are seen as equity partners in the endeavor. These include: 1) Establish a coordinated effort to improve evaluation and modeling in nuclear astrophysics for stellar dynamics, multi-messenger astronomy and nucleosynthesis; 2) Initiate a TNDC to develop and maintain nuclear structure evaluation beyond discrete states, including nuclear level densities, photon strength functions and photonuclear data for improved reaction modeling, and exploring nuclear structure at finite temperature; 3) Create a TNDC to perform correlated fission data evaluation, including cross sections, fragment yields, v(A), v(E n ) for nuclear energy, national security, nonproliferation and basic science; 4) From a panel of subject matter experts to establish and annually update a roster of key decay data to nurture its accelerated dissemination including both measurement and evaluation for targeted high-value nuclides for national security, nonproliferation and medical applications; 5) Comprehensive, consistent neutron-induced structure and reaction data for nuclear energy, national security, nonproliferation and planetary nuclear spectroscopy; 6) Charged-particle stopping powers for detector design, space effects and ion beam therapy; 7) High-energy reactions for space exploration and medical nuclide production, and; 8) The creation of an infrastructure for open data and data preservation for use by the entire nuclear physics community. All told, these initiatives require approximately $6.5M increase in NP support of the USNDP in fiscal year 2023 dollars and would require at least 3-5 years to carry out due to the length of time needed to recruit and train new nuclear data researchers. This relatively modest investment would help ensure that the fruits of the nuclear data research carried out by DOE-NP and its collaborators would be brought to bear to address some of the most important needs of our nation and the world. To ensure effective execution of this plan, we present an overview of recruitment, training, and retention goals for the USNDP, the centerpiece of which is a mutually agreed upon code of conduct. Finally, we identify the facility and instrumentation needed to perform the recommended experimental activities. This includes a short review of target fabrication capabilities, reactors, neutron beam, light- and heavy-stable ion, gamma-ray, high-energy and radioactive ion beam facilities. Lastly, a more complete appendix of experimental facilities previously compiled is included with new input provided for 6 facilities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE Repository Metadata Profile (DRMP): A Metadata Framework for Advancing Interoperability and AI Readiness Across Scientific Repositories

The Department of Energy (DOE) funds a diverse and distributed ecosystem of repositories that steward scientific data, publications, and software across its research programs, user facilities, and national laboratories. While significant progress has been made in standardizing dataset-level metadata, the metadata describing repositories themselves (their identity, governance, access interfaces, policies, and technical capabilities) remains inconsistent and fragmented across DOE-funded systems. This variability limits discoverability, interoperability, automated validation, and AI-driven analysis, all of which are increasingly essential for modern scientific workflows. To address this gap, the DOE Data Curation Working Group (DCWG) developed the DOE Repository Metadata Profile (DRMP). The DRMP is a practical, community-driven framework that defines how repositories can describe themselves in a consistent, machine-actionable, and scalable manner. The DRMP is not a new metadata schema. Instead, it is a mapping profile and structured element set capturing the essential characteristics of DOE repositories. It harmonizes repository-level metadata across six widely adopted community schemas: RE3Data; DCAT-US v3; Schema.org; Dublin Core; DataCite 4.6; and PREMIS 3.0. This harmonization eliminates reinvention and enables interoperability within DOE and across the broader scientific ecosystem. A core objective of the DRMP is to reduce burden on repositories by allowing them to reuse their existing metadata through a Rosetta-style crosswalk rather than redesigning local implementations. The profile introduces a three-level conformance model that supports incremental adoption: • Level 1 – Minimum Viable Record (MVR): foundational identification elements required for workflows, project registration, and basic repository presence. • Level 2 – Interoperable: structured metadata enabling alignment with national and international discovery systems. • Level 3 – AI-Ready: enhanced provenance, policy transparency, fixity, semantic context, and capabilities that support automated reasoning, model training governance, and machine-assisted curation. To support implementation, the DRMP includes JSON Schema definitions, OpenAPI patterns, and MCP templates that allow repositories to publish machine-readable metadata directly within existing platforms. These resources are modular and lightweight, enabling adoption without major architectural change. Adopting the DRMP enables repositories to: • Enhance discoverability and interoperability by aligning identifiers, classifications, and descriptive elements across widely used schema standards. • Support federated discovery and cross-registration across DOE systems, Data.gov, and international catalogs. • Enable AI agents and workflow orchestration systems to interpret repository-level metadata within the American Science Cloud (AmSC) through Model Context Protocol (MCP)-based context publication. • Demonstrate alignment with DOE’s open science, stewardship, and FAIR data priorities. This guidance represents a community-driven step forward. Through voluntary adoption and continued feedback, the DRMP advances a cohesive, machine-actionable description of DOE repositories that supports FAIR data practices, preparing the infrastructure for AI-enabled research, and strengthening the discoverability and reuse of DOE’s scientific outputs.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗