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At least 1,063 records · Page 59

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DOE OSTI2023

Ontologizing health systems data at scale: making translational discovery a reality

Common data models solve many challenges of standardizing electronic health record (EHR) data but are unable to semantically integrate all of the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68–99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2020

A Python Instrument Control and Data Acquisition Suite for Reproducible Research

Tools that standardize and automate experimental data collection are needed for greater confidence in research results. The National Synchrotron Light Source-II (NSLS-II) has generated an open-source Python data acquisition, management, and analysis software suite that automates X-ray experiments and collects an experimental record that facilitates complete reproducibility. Here, we show that the NSLS-II tools are not only useful for X-ray science at large-scale facilities by presenting an add-on package that adapts these tools for use in a small laboratory with common physics and electrical engineering instruments. The composite software suite eases and automates the execution of experiments, records extensive metadata, stores data in portable containers, and speeds up the analysis through tools for comprehensive searches. In total, this software suite increases the reproducibility of laboratory experiments. We demonstrate the software via the evaluation of two lock-in amplifiers-the miniature ADA2200 and the ubiquitous Stanford Research Systems (SRS) SR810. The frequency resolution, signal-to-noise ratio, and dynamic reserve of the lock-in amplifiers are measured and presented. The usage of the software suite is described throughout these measurements so that the reader can implement the tools in their lab.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2011

Adapting CALIPSO Climate Measurements for Near Real Time Analyses and Forecasting

The Cloud-Aerosol Lidar and Infrared Pathfinder satellite Observations (CALIPSO) mission was originally conceived and designed as a climate measurements mission, with considerable latency between data acquisition and the release of the level 1 and level 2 data products. However, the unique nature of the CALIPSO lidar backscatter profiles quickly led to the qualitative use of CALIPSO?s near real time (i.e., ? expedited?) lidar data imagery in several different forecasting applications. To enable quantitative use of their near real time analyses, the CALIPSO project recently expanded their expedited data catalog to include all of the standard level 1 and level 2 lidar data products. Also included is a new cloud cleared level 1.5 profile product developed for use by operational forecast centers for verification of aerosol predictions. This paper describes the architecture and content of the CALIPSO expedited data products. The fidelity and accuracy of the expedited products are assessed via comparisons to the standard CALIPSO data products.

Vaughan, Mark A.↗

DOE OSTI2026

The Linear Point Standard Ruler with DESI DR1 and DR2 Data

The linear point, a purely geometric feature in the monopole of the two-point correlation function, has been proposed as an alternative standard ruler. Compared to the peak in the correlation function, it is more robust to late-time nonlinear effects at the percent level. In light of improved simulations and high quality data, we revisit the robustness of the linear point and use it as an alternative to template-based fitting approaches typically used in BAO analyses. We present the linear point measurements on galaxy samples from the first and second data releases (DR1 and DR2) of the DESI survey. We convert the linear point into a dimensionless parameter $α_{iso,LP}$, defined as the ratio of the linear point in the fiducial cosmology and the observed value, analogous to the isotropic BAO scaling parameter $α_{iso}$ used in previous BAO measurements. Using the 2nd generation of AbacusSummit mock catalogs, we find that linear point measurements are more precise when calculated in the post-reconstruction regime with 15-60% smaller uncertainties than those pre-reconstruction. We find a systematic shift in the linear point measurements compared against the isotropic BAO measurements in mocks; we attribute this to the isotropic damping parameter responsible for smearing the linear point in the nonlinear regime. We propose a sample-dependent correction that mitigates the impact of late-time nonlinear effects. While this introduces a cosmology dependence in an otherwise model-independent measurement, this is necessary given the sub-percent precision dictated by current cosmological surveys. Comparing $α_{iso,LP}$ with isotropic BAO measurements made on the DESI DR1 and DR2 galaxy samples, we find excellent agreement after applying this correction, particularly post-reconstruction. We discuss future scope regarding cosmological inference with linear point measurements.

Uberoi, N. [Yale U.] (ORCID:0000000275179629)↗

DOE OSTI2026

HPC ODA Commons [SWR-26-003]

HPC ODA Commons is a community-driven platform for standardizing HPC operational data analytics. HPC sites generate enormous volumes of operational data - scheduler logs, accounting records, monitoring streams - but turning that data into actionable insight is needlessly hard. Each site builds bespoke parsers, schemas, and evaluation pipelines. Results can't be compared across institutions. Promising analytics ideas stay siloed because there's no shared language for describing the data, the experiments, or the outcomes. HPC ODA Commons fixes this by establishing community-governed contracts - versioned schemas, canonical artifacts, and benchmark recipes - that make ODA workflows discoverable, reproducible, and comparable. It pairs these standards with a practical, CLI-first toolkit that lets operators and researchers go from raw logs to standardized results without sending data off-cluster.

Menear, Kevin [National Laboratory of the Rockies ↗

DOE OSTI2025

Instrumentation and methods for efficient time-resolved X-ray crystallography of biomolecular systems with sub-10 ms time resolution

Time-resolved X-ray crystallography has great promise to illuminate structure–function relations and key steps of enzymatic reactions with atomic resolution. The dominant methods for chemically-initiated reactions require complex instrumentation at the X-ray beamline, significant effort to operate and maintain this instrumentation, and enormous numbers (∼10 5 –10 9 ) of crystals per time point. We describe instrumentation and methods that enable high-throughput time-resolved study of biomolecular systems using standard crystallography sample supports and mail-in X-ray data collection at standard high-throughput cryocrystallography synchrotron beamlines. The instrumentation allows rapid reaction initiation by mixing of crystals and substrate/ligand solution, rapid capture of structural states via thermal quenching with no pre-cooling perturbations, and yields time resolutions in the single-millisecond range, comparable to the best achieved by any non-photo-initiated method in both crystallography and cryo-electron microscopy. Our approach to reaction initiation has the advantages of simplicity, robustness, low cost, adaptability to diverse ligand solutions and small minimum volume requirements, making it well suited to routine laboratory use and to high-throughput screening. We report the detailed characterization of instrument performance, present structures of binding of N -acetylglucosamine to lysozyme at time points from 8 ms to 2 s determined using only one crystal per time point, and discuss additional improvements that will push time resolution toward 1 ms.

Indergaard, John A. (ORCID:000000022367699X)↗

DOE OSTI2022

labquake_future_prediction

The labquake_future_prediction code is a collection of python modules and scripts that serves as supporting information for the article “Predicting future laboratory fault friction through deep learning” for publication in the journal of “Geophysical Research Letters”. It is designed to predict laboratory fault slips in the immediate future by scanning continuous acoustic emission (AE) waveforms recorded in laboratory biaxial shear experiments. The predictions are made with a deep learning model based on convolutional encoder-decoder (CED) models and the Transformer model primarily developed for Natural Language Processing (NLP). The deep learning model is trained with the tensorflow package using publicly available laboratory data sets in standard binary file format in numpy. The utility functions for reading data files, configuring model hyperparameters, constructing the CED and Transformer models, training and testing of the models are defined in python module files. The workflow of training the models for labquake future predictions and the multiple GPU’s rapid model hyperparameter optimization as described in the journal article, are demonstrated in accompanying python script files and Jupyter notebooks.

Wang, Kun↗

NASA NTRS1984

A review and analysis of boundary layer transition data for turbine application

A symposium on transition in turbines was held at the NASA Lewis Research Center. One recommendation of the working groups was the collection of existing transition data to provide standard cases against which models could be tested. A number of data sets from the open literature that include heat transfer data in apparently transitional boundary layers, with particular application to the turbine environment, were reviewed and analyzed to extract transition information from the heat transfer data. The data sets reviewed cover a wide range of flow conditions, from low speed, flat plate tests to full scale turbine airfoils operating at simulated turbine engine conditions. The results indicate that free stream turbulence and pressure gradient have strong, and opposite, effects on the location of the start of transition and on the length of the transition zone.

Gaugler, R. E.↗

NASA NTRS1985

A review and analysis of boundary layer transition data for turbine application

Gaugler, R. E.↗

NASA NTRS1990

The EOS data and information system

The Earth Observing System (EOS) is proposed as a 1991 new initiative by NASA as part of the Mission to Planet Earth. One of the key components of the EOS program is the EOS Data and Information System (EOSDIS). Two independent Phase B studies of EOSDIS were conducted from January 1989 through April 1990. Some of the key challenges faced by EOSDIS are: satisfying the data and information needs of a diverse multidisciplinary scientific community integrating product generation algorithms for over two dozen instruments, keeping up with an orbital average data rate of over 50 Mb/sec and assuring prompt generation of standard products, reprocessing data as product generation algorithms change, and storing, and managing information about tens of Petabytes of data over the 15-year life of the mission.

Ramapriyan, H. K.↗

DOE OSTI2020

Measurement Uncertainty in One-Of-A-Kind Event Data Analysis

A golden standard in science is to repeat an experiment a statistically significant number of times, recording data using the same set of detectors and the same data analysis methodology. In such case experimental error includes both the range of true values generated by repetitions of the experiment, and measurement uncertainty caused by the detector. They are independent. It is a huge and too frequently used simplification, to assume that one can measure multiple repetitions of an identical experiment, resulting in identical true experimental value. Repetitions, as similar is it is experimentally achievable, have unavoidable built-in differences resulting in a range of the true values rather than in a single value. When modern, very sensitive and well calibrated measurement systems are used, this range is not negligible, and sometimes dominates over the measurement uncertainty. Range of true values depends on built-in differences in physics of the experiment. Stochastic physical processes result typically in a broader range of true values than non-stochastic processes do. Measurement uncertainty depends on a measurement method (properties of the detector not of the experiment). Modern measurement methods, including digital ones, frequently make the measurement uncertainty very small. When data from one–of –a kind experiment are analyzed, only the measurement uncertainty is reported. It provides no information about the range of true experimental values, neither about reliability of a reported data point. Reliability of a data point is in general independent from its measurement uncertainty. However, in practice reliable measurement methods frequently have high measurement uncertainty, while low reliability methods are applied to limit measurement uncertainty. Comparison of reliable data with high measurement uncertainty to not so reliable data measured with low uncertainty is discussed – in different scenarios different data analysis methods are applicable. Methods for data analysis from an experiment repeated statistically significant number of times are very well developed. They do not require a detailed expertise in physics of an experiment, nor in the properties of the measurement system used, and meaning of the reported uncertainty is well understood in any scientific community. It all changes when data from one-of-a-kind experiment is analyzed. Analyst’s expertise is required both in the physics of the experiment and in all aspects of the measurement system, all possible malfunctions. Data users must remember that only measurement uncertainty is reported from any one-of-a-kind experiment. Theory with simulations may provide estimation of expected built-in differences in the experiment, and by this of expected range of true values for a given experiment; yet measurement uncertainty can never be used in place of the range of true experimental values.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS2010

CCSDS - Advancing Spaceflight Technology for International Collaboration

The Consultative Committee for Space Data Systems (CCSDS) has been developing data and communications standards since 1982, with the objective of providing interoperability for enabling international collaboration for spaceflight missions. As data and communications technology has advanced, CCSDS has progressed to capitalize on existing products when available and suitable for spaceflight, and to develop innovative new approaches when available products fail. The current scope of the CCSDS architecture spans the end-to-end data architecture of a spaceflight mission, with ongoing efforts to develop and standardize cutting-edge technology. This manuscript describes the overall architecture, the position of CCSDS in the standards and international mission community, and some CCSDS processes. It then highlights in detail several of the most interesting and critical technical areas in work right now, and how they support collaborative missions. Special topics include: Delay/Disruption Tolerant Networking (DTN), Asynchronous Message Service (AMS), Multispectral/Hyperspectral Data Compression (MHDC), Coding and Synchronization, Onboard Wireless, Spacecraft Monitor and Control, Navigation, Security, and Time Synchronization/Correlation. Broad international participation in development of CCSDS standards is encouraged.

Kearney, Mike↗

DOE OSTI2023

A Data Deposition Platform for Sharing Nuclear Magnetic Resonance Data

Nuclear magnetic resonance (NMR) data are rarely deposited in open databases, leading to loss of critical scientific knowledge. Existing data reporting methods (images, tables, lists of values) contain less information than raw data, and are poorly standardized. Together, these issues limit FAIR (findable, accessible, interoperable, reusable) access to these data, which in turn creates barriers for compound dereplication and the development of new data-driven discovery tools. Existing NMR databases are either not designed for natural products data, or employ complex deposition interfaces that disincentivize deposition. Journals, including the Journal of Natural Products (JNP), are now requiring data submission as part of the publication process, creating the need for a streamlined, user-friendly mechanism to deposit and distribute NMR data. Recently, our team reported the development of the Natural Products Magnetic Resonance Database (NP-MRD; www.np-mrd.org). Here in this paper we present a new data deposition platform for the NP-MRD project that is designed to enable users to deposit NMR data for published or submitted manuscripts in under five minutes. This platform includes a suite of automated data extraction and standardization tools, together with a simple-to-use web-based interface and detailed error reporting to simplify the data deposition process and is available at www.np-mrd.org/submissions.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2022

A System for Standardizing and Combining U.S. Environmental Protection Agency Emissions and Waste Inventory Data

The U.S. Environmental Protection Agency (USEPA) provides databases that agglomerate data provided by companies or states reporting emissions, releases, wastes generated, and other activities to meet statutory requirements. These databases, often referred to as inventories, can be used for a wide variety of environmental reporting and modeling purposes to characterize conditions in the United States. Yet, users are often challenged to find, retrieve, and interpret these data due to the unique schemes employed for data management, which could result in erroneous estimations or double-counting of emissions. To address these challenges, a system called Standardized Emission and Waste Inventories (StEWI) has been created. The system consists of four python modules that provide rapid access to USEPA inventory data in standard formats and permit filtering and combination of these inventory data. When accessed through StEWI, reported emissions of carbon dioxide to air and ammonia to water are reduced approximately two- and four-fold, respectively, to avoid duplicate reporting. StEWI will greatly facilitate the use of USEPA inventory data in chemical release and exposure modeling and life cycle assessment tools, among other things. To date, StEWI has been used to build the recent USEEIO model and the baseline electricity life cycle inventory database for the Federal LCA Commons.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Soft costs and EVSE – Knowledge gaps as a barrier to successful projects

There has been a recent push to increase access to electric vehicle (EV) charging infrastructure. The National Electric Vehicle Infrastructure (NEVI) program, part of the Bipartisan Infrastructure Law (BIL) has made significant funding available for major charging infrastructure projects along state thruways, and many state and local incentives exist for EV owners to install chargers in their homes. However, deployment of these chargers has not kept up with demand, primarily due to issues in project planning, permitting processes, and unforeseen delays. This paper serves as a review of the current understanding of these and other non-hardware costs in EV charging infrastructure projects (collectively known as “soft costs”). We found that soft costs in EV charging infrastructure projects are not well understood. Specifically, there is little agreement on how soft costs should be categorized and tracked, and less agreement still on best practices for controlling these costs and lowering barriers to infrastructure deployment. A broader review of EV charging infrastructure cost analyses shows that these costs can have significant impacts on project outcomes. EV charging infrastructure projects may be able to examine the success of the solar industry in lowering soft costs, and a similar effort may lower project costs significantly. Further work on standardizing and collecting data on EV charging infrastructure costs is required to begin addressing and controlling these costs.

32 - ENERGY CONSERVATION, CONSUMPTION, AND UTILIZA↗

DOE OSTI2024

Schema Elements for Granta Annual Report: FY2024

Granta: Materials Intelligence (Granta: MI) is a commercial database software distributed by Ansys, Inc. that is utilized by the Nuclear Security Enterprise (NSE) to organize and store relevant materials data. Lack of standard and well-documented database schema is the primary obstacle to an NSE materials data management solution, so the objective of this project is to create and document such a schema. In FY21, an approach for designing, documenting, and managing a standard database schema was described based on the creation of schema elements (collections of attributes used to describe particular aspects of the data) to be used as building blocks for creating various database tables without duplication. In FY22, these methods were applied through a multi-site collaboration to create and document the schema elements necessary to build a thermogravimetric analysis (TGA) testing table. In FY23 the schema was expanded to include elements for a differential scanning calorimetry (DSC) table, along with schema for supporting metadata tables including Instruments, Projects, Documents, and Testing Series. In FY24 the following progress was made, again through multi-site collaboration: • The existing schema elements were modified to accommodate thermomechanical analysis (TMA) data, and a table, Test Data: TMA, was created for managing TMA data. • The elements necessary for the following additive manufacturing (AM) data tables (directed at data specific to selective laser sintering AM technology) were created: • AM Builds • AM Processes • AM Part Designs • Built AM Parts • AM Feedstock Materials • AM Feedstock Material Batches • The elements necessary for creating a Calibrated Material Models table were created, and the Calibrated Material Models table was created. In FY25 the existing schema will be deployed on the production enterprise Granta instance on the enterprise secure network. Schema elements will be appended, and new elements created as necessary, to allow the creation of tables specifically to support materials testing, AM process development, and design and analysis for modernization programs.

36 MATERIALS SCIENCE↗

NASA NTRS2004

The NASA Micro-Pulse Lidar Network (MPLNET): Co-location of Lidars with AERONET

We present the formation of a global-ground based eye-safe lidar network, the NASA Micro-Pulse Lidar Network (MPLNET). The aim of MPLNET is to acquire long-term observations of aerosol and cloud vertical profiles at unique geographic sites within the NASA Aerosol Robotic Network (AERONET). Network growth follows a federated approach, pioneered by AERONET, wherein independent research groups may join MPLNET with their own instrument and site. MPLNET utilizes standard instrumentation and data processing algorithms for efficient network operations and direct comparison of data between each site. The micro-pulse lidar is eye-safe, compact, and commercially available, and most easily allows growth of the network without sacrificing standardized instrumentation gods. Red-time data products (next-day) are available, and include Level 1 daily lidar signal images from the surface to -2Okm, and Level 1.5 aerosol extinction provides at times co-incident with AERONET observations. Testing of our quality assured aerosol extinction products, Level 2, is near completion and data will soon be available. Level 3 products, continuous daylight aerosol extinction profiles, are under development and testing has begun. An overview of h4PL" will be presented. Successful methods of merging standardized lidar operations with AERONET will also be discussed, with the first 4 years of MPLNET results serving as an example.

Welton, Ellsworth J.↗

NASA NTRS1993

The advanced orbiting systems testbed program: Results to date

The Consultative Committee for Space Data Systems Recommendations for Packet Telemetry and Advanced Orbiting Systems (AOS) propose standard solutions to data handling problems common to many types of space missions. The Recommendations address only space/ground and space/space data handling systems. Goddard Space Flight Center's AOS Testbed (AOST) Program was initiated to better understand the Recommendations and their impact on real-world systems, and to examine the extended domain of ground/ground data handling systems. Central to the AOST Program are the development of an end-to-end Testbed and its use in a comprehensive testing program. Other Program activities include flight-qualifiable component development, supporting studies, and knowledge dissemination. The results and products of the Program will reduce the uncertainties associated with the development of operational space and ground systems that implement the Recommendations. The results presented in this paper include architectural issues, a draft proposed standardized test suite and flight-qualifiable components.

Newsome, Penny A.↗