SEARCH · Engineering Papers

Results for “metadata”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 739 records · Page 41

All sources NASA NTRS DOE OSTI

DOE OSTI2019

The future of legume genetic data resources: Challenges, opportunities, and priorities

Abstract Legumes, comprising one of the largest, most diverse, and most economically important plant families, are the subject of vibrant research and development worldwide. Continued improvement of legume crops will benefit from the recent proliferation of genetic (including genomic) resources; but the diversity, scale, and complexity of these resources presents challenges to those managing and using them. A workshop held in March of 2019 addressed questions of data resources and priorities for the legumes. The workshop identified various needs and recommendations: (a) Develop strategies to effectively store, integrate, and relate genetic resources collected in different projects. (b) Leverage information collected across many legume species by standardizing data formats and ontologies, improving the state of metadata about datasets, and increasing use of the FAIR data principles. (c) Advocate for the critical role that curators exercise in integrating complex datasets into databases and adding high value metadata that enable downstream analytics and facilitate practical applications. (d) Implement standardized software and database development practices to best leverage limited developer time and expertise gained from the various legume (and other) species. (e) Develop tools and databases that can manage genetic information for the world's plant genetic resources, enabling efficient incorporation of important traits into breeding programs. (f) Centralize information on databases, tools, and training materials and establish funding streams to support training and outreach.

Bauchet, Guillaume J.↗

DOE OSTI2018

Text-based Analytics for Biosurveillance

The ability to prevent, mitigate, or control a biological threat depends on how quickly the threat is identified and characterized. Ensuring the timely delivery of data and analytics is an essential aspect of providing adequate situational awareness in the face of a disease outbreak. This chapter outlines an analytic pipeline for supporting an advanced early warning system that can integrate multiple data sources and provide situational awareness of potential and occurring disease situations. The pipeline, includes real-time automated data analysis founded on natural language processing (NLP), semantic concept matching, and machine learning techniques, to enrich content with metadata related to biosurveillance. Online news articles are presented as an example use case for the pipeline, but the processes can be generalized to any textual data. In this chapter, the mechanics of a streaming pipeline are briefly discussed as well as the major steps required to provide targeted situational awareness. The text-based analytic pipeline includes various processing steps as well as identifying article relevance to biosurveillance (e.g., relevance algorithm) and article feature extraction (who, what, where, why, how, and when). The ability to prevent, mitigate, or control a biological threat depends on how quickly the threat is identified and characterized. Ensuring the timely delivery of data and analytics is an essential aspect of providing adequate situational awareness in the face of a disease outbreak. This chapter outlines an analytic pipeline for supporting an advanced early warning system that can integrate multiple data sources and provide situational awareness of potential and occurring disease situations. The pipeline, includes real-time automated data analysis founded on natural language processing (NLP), semantic concept matching, and machine learning techniques, to enrich content with metadata related to biosurveillance. Online news articles are presented as an example use case for the pipeline, but the processes can be generalized to any textual data. In this chapter, the mechanics of a streaming pipeline are briefly discussed as well as the major steps required to provide targeted situational awareness. The text-based analytic pipeline includes various processing steps as well as identifying article relevance to biosurveillance (e.g., relevance algorithm) and article feature extraction (who, what, where, why, how, and when).

Biomedical NLP↗

DOE OSTI2020

Generation and representation of synthetic smart meter data

Advanced energy algorithms running at big-data scale will be necessary to identify, realize, and verify energy savings to meet government and utility goals of building energy efficiency. Any algorithm must be well characterized and validated before it is trusted to run at these scales. Smart meter data from real buildings will ultimately be required for the development, testing, and validation of these energy algorithms and processes. However, for initial development and testing, smart meter data are difficult to work with due to privacy restrictions, noise from unknown sources, data accessibility, and other concerns which can complicate algorithm development and validation. This paper describes a new methodology to generate synthetic smart meter data of electricity use in buildings using detailed building energy modeling, which aims to capture the variability and stochastics of real energy use in buildings. The methodology can create datasets tailored to represent specific scenarios with known truth and controllable amounts of synthetic noise. Knowledge of ground truth also allows the development and validation of enhanced processes which leverage building metadata, such as building type or size (floor area), in addition to smart meter data. The methodology described in this paper includes the key influencing factors of real-world building energy use including weather data, occupant-driven loads, building operation and maintenance practices, and special events. Data formats to support workflows leveraging both synthetic meter data and associated metadata are proposed and discussed. Finally, example use cases of the synthetic meter data are described to illustrate potential applications.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2018

Correction to: Clinical Quantification of Myocardial Blood Flow Using PET: Joint Position Paper of the SNMMI Cardiovascular Council and the ASNC

The above position statement originally published containing errors in the author metadata; specifically, the Expert Content Reviewers—Andrew Einstein, Raymond Russell and James R. Corbett—were tagged as full authors of the paper. The article metadata has now been corrected to remove Drs. Einstein, Russell and Corbett from the author line, and the PubMed record has been updated accordingly.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2022

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future

Abstract As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.

Burley, Stephen K. (ORCID:0000000224879713)↗

DOE OSTI2017

EpiK: A Knowledge Base for Epidemiological Modeling and Analytics of Infectious Diseases

Computational epidemiology seeks to develop computational methods to study the distribution and determinants of health-related states or events (including disease), and the application of this study to the control of diseases and other health problems. Recent advances in computing and data sciences have led to the development of innovative modeling environments to support this important goal. The datasets used to drive the dynamic models as well as the data produced by these models presents unique challenges owing to their size, heterogeneity and diversity. These datasets form the basis of effective and easy to use decision support and analytical environments. As a result, it is important to develop scalable data management systems to store, manage and integrate these datasets. In this paper, we develop EpiK —a knowledge base that facilitates the development of decision support and analytical environments to support epidemic science. An important goal is to develop a framework that links the input as well as output datasets to facilitate effective spatio-temporal and social reasoning that is critical in planning and intervention analysis before and during an epidemic. The data management framework links modeling workflow data and its metadata using a controlled vocabulary. The metadata captures information about storage, the mapping between the linked model and the physical layout, and relationships to support services. EpiK is designed to support agent-based modeling and analytics frameworks—aggregate models can be seen as special cases and are thus supported. We use semantic web technologies to create a representation of the datasets that encapsulates both the location and the schema heterogeneity. The choice of RDF as a representation language is motivated by the diversity and growth of the datasets that need to be integrated. A query bank is developed—the queries capture a broad range of questions that can be posed and answered during a typical case study pertaining to disease outbreaks. The queries are constructed using SPARQL Protocol and RDF Query Language (SPARQL) over the EpiK. EpiK can hide schema and location heterogeneity while efficiently supporting queries that span the computational epidemiology modeling pipeline: from model construction to simulation output. As a result, we show that the performance of benchmark queries varies significantly with respect to the choice of hardware underlying the database and resource description framework (RDF) engine.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Unsupervised Azimuth Estimation of Solar Arrays in Low-Resolution Satellite Imagery through Semantic Segmentation and Hough Transform

This paper explains the use of a convolutional neural network (CNN) to segment solar panels in a satellite image containing solar arrays, and extract associated metadata from the arrays. A novel unsupervised technique is introduced to estimate the azimuth of each individual solar panel from the predicted mask of the convolutional neural network. This pipeline was developed with the aim of extracting necessary metadata for a solar installation, using only a set of latitude–longitude coordinates. Azimuth prediction results for 669 individual solar installations associated with 387 sites located across the United States are provided. A mean average error and median average error of 21.65 degrees and 1.0 degrees were obtained, respectively, when predicting the azimuth of the solar fleet data set, with about 80% of the results within an error of zero degrees of the ground truth azimuth value and about 85% within an error of 25 degrees. The predicted azimuth was then used to estimate the energy conversion of the solar arrays. Results show a 90.9 and 90.6 R-squared value for estimating alternating current (AC) and direct current (DC) energy, respectively, and a mean absolute percentage error (MAPE) of 1.70% in estimating the alternating current (AC) energy using the fully automated algorithm.

14 SOLAR ENERGY↗

DOE OSTI2017

Performance characterization of scientific workflows for the optimal use of Burst Buffers

Scientific discoveries are significantly rely on the analysis of large volumes of data from observations and simulations of complex phenomena. Scientists compose the complex analyses as workflows and execute them on large-scale HPC systems. The workflow structures are in contrast with monolithic single simulations that have often been the primary use case on HPC systems. At the same time, new storage paradigms such as Burst Buffers are becoming available on HPC platforms. In this paper, we analyze the performance characteristics of a Burst Buffer and two representative scientific workflows with the aim of optimizing the usage of a Burst Buffer, extending our previous analyses (Daley et al., 2016). Our key contributions are (a) developing a performance analysis methodology pertinent to Burst Buffers, (b) improving the use of a Burst Buffer in workflows with bandwidth-sensitive and metadata-sensitive I/O workloads, (c) highlighting the key data management challenges when incorporating a Burst Buffer in the studied scientific workflows.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations

This work is one of a series of articles by the Nanomaterial Data Curation Initiative. Other articles in this series discuss data curation workflows, data completeness and quality, curator responsibilities, and metadata. Many groups within the broad nanotechnology field are already developing data repositories and tools driven by their individual organizational goals. Integrating these data across disciplines, and with other non-nanotechnology resources, can support multiple objectives by reusing the same information, and can serve as the impetus for novel scientific discoveries through deeper data analyses. Based on the results of a community-based survey of organizations that maintain nanomaterial repositories, this article discusses current data integration practices in nanoinformatics and mature fields such as genomics, as well as nanotechnology-specific challenges impacting data integration. Recommendations for achieving integration of existing operational nanotechnology resources, as based on results from a community-wide survey, are presented herein. Nanotechnology-specific data integration challenges, if effectively resolved, can foster the application and validation of nanotechnology within and across disciplines.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2013

OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging

Mass spectrometry imaging (MSI) enables researchers to directly probe endogenous molecules directly within the architecture of the biological matrix. Unfortunately, efficient access, management, and analysis of the data generated by MSI approaches remain major challenges to this rapidly developing field. Despite the availability of numerous dedicated file formats and software packages, it is a widely held viewpoint that the biggest challenge is simply opening, sharing, and analyzing a file without loss of information. Here we present OpenMSI, a software framework and platform that addresses these challenges via an advanced, high-performance, extensible file format and Web API for remote data access (http://openmsi.nersc.gov). The OpenMSI file format supports storage of raw MSI data, metadata, and derived analyses in a single, self-describing format based on HDF5 and is supported by a large range of analysis software (e.g., Matlab and R) and programming languages (e.g., C++, Fortran, and Python). Careful optimization of the storage layout of MSI data sets using chunking, compression, and data replication accelerates common, selective data access operations while minimizing data storage requirements and are critical enablers of rapid data I/O. The OpenMSI file format has shown to provide >2000-fold improvement for image access operations, enabling spectrum and image retrieval in less than 0.3 s across the Internet even for 50 GB MSI data sets. To make remote high-performance compute resources accessible for analysis and to facilitate data sharing and collaboration, we describe an easy-to-use yet powerful Web API, enabling fast and convenient access to MSI data, metadata, and derived analysis results stored remotely to facilitate high-performance data analysis and enable implementation of Web based data sharing, visualization, and analysis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

A Guide to Using GitHub for Developing and Versioning Data Standards and Reporting Formats

Abstract Data standardization combined with descriptive metadata facilitate data reuse, which is the ultimate goal of the Findable, Accessible, Interoperable, and Reusable (FAIR) principles. Community data or metadata standards are increasingly created through an approach that emphasizes collaboration between various stakeholders. Such an approach requires platforms for collaboration on the development process that centers on sharing information and receiving feedback. Our objective in this study was to conduct a systematic review to identify data standards and reporting formats that use version control for developing data standards and to summarize common practices, particularly in earth and environmental sciences. Out of 108 data standards and reporting formats identified in our review, 32 used GitHub as the version control platform, and no other platforms were used. We found no universally accepted methodology for developing and publishing data standards. Many GitHub repositories did not use key features that could help developers to gather user feedback, or to create and revise standards that build on previous work. We provide guidance for community‐driven standard development and associated documentation on GitHub based on a systematic review of existing practices.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

Tracking materials science data lineage to manage millions of materials experiments and analyses

Abstract In an era of rapid advancement of algorithms that extract knowledge from data, data and metadata management are increasingly critical to research success. In materials science, there are few examples of experimental databases that contain many different types of information, and compared with other disciplines, the database sizes are relatively small. Underlying these issues are the challenges in managing and linking data across disparate synthesis and characterization experiments, which we address with the development of a lightweight data management framework that is generally applicable for experimental science and beyond. Five years of managing experiments with this system has yielded the Materials Experiment and Analysis Database (MEAD) that contains raw data and metadata from millions of materials synthesis and characterization experiments, as well as the analysis and distillation of that data into property and performance metrics via software in an accompanying open source repository. The unprecedented quantity and diversity of experimental data are searchable by experiment and analysis attributes generated by both researchers and data processing software. The search web interface allows users to visualize their search results and download zipped packages of data with full annotations of their lineage. The enormity of the data provides substantial challenges and opportunities for incorporating data science in the physical sciences, and MEAD’s data and algorithm management framework will foster increased incorporation of automation and autonomous discovery in materials and chemistry research.

Soedarmadji, Edwin↗

DOE OSTI2019

Linking in silico MS/MS spectra with chemistry data to improve identification of unknowns

Confident identification of unknown chemicals in high resolution mass spectrometry (HRMS) screening studies requires cohesive workflows and complementary data, tools, and software. Chemistry databases, screening libraries, and chemical metadata have become fixtures in identification workflows. To increase confidence in compound identifications, the use of structural fragmentation data collected via tandem mass spectrometry (MS/MS or MS2) is vital. However, the availability of empirically collected MS/MS data for identification of unknowns is limited. Researchers have therefore turned to in silico generation of MS/MS data for use in HRMS-based screening studies. This paper describes the generation en masse of predicted MS/MS spectra for the entirety of the US EPA’s DSSTox database using competitive fragmentation modelling and a freely available open source tool, CFM-ID. The generated dataset comprises predicted MS/MS spectra for ~700,000 structures, and mappings between predicted spectra, structures, associated substances, and chemical metadata. Together, these resources facilitate improved compound identifications in HRMS screening studies. These data are accessible via an SQL database, a comma-separated export file (.csv), and EPA’s CompTox Chemicals Dashboard.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2021

A synthetic building operation dataset

Abstract This paper presents a synthetic building operation dataset which includes HVAC, lighting, miscellaneous electric loads (MELs) system operating conditions, occupant counts, environmental parameters, end-use and whole-building energy consumptions at 10-minute intervals. The data is created with 1395 annual simulations using the U.S. DOE detailed medium-sized reference office building, and 30 years’ historical weather data in three typical climates including Miami, San Francisco, and Chicago. Three energy efficiency levels of the building and systems are considered. Assumptions regarding occupant movements, occupants’ diverse temperature preferences, lighting, and MELs are adopted to reflect realistic building operations. A semantic building metadata schema - BRICK, is used to store the building metadata. The dataset is saved in a 1.2 TB of compressed HDF5 file. This dataset can be used in various applications, including building energy and load shape benchmarking, energy model calibration, evaluation of occupant and weather variability and their influences on building performance, algorithm development and testing for thermal and energy load prediction, model predictive control, policy development for reinforcement learning based building controls.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

A three-year dataset supporting research on building energy management and occupancy analytics

Abstract This paper presents the curation of a monitored dataset from an office building constructed in 2015 in Berkeley, California. The dataset includes whole-building and end-use energy consumption, HVAC system operating conditions, indoor and outdoor environmental parameters, as well as occupant counts. The data were collected during a period of three years from more than 300 sensors and meters on two office floors (each 2,325 m 2 ) of the building. A three-step data curation strategy is applied to transform the raw data into research-grade data: (1) cleaning the raw data to detect and adjust the outlier values and fill the data gaps; (2) creating the metadata model of the building systems and data points using the Brick schema; and (3) representing the metadata of the dataset using a semantic JSON schema. This dataset can be used in various applications—building energy benchmarking, load shape analysis, energy prediction, occupancy prediction and analytics, and HVAC controls—to improve the understanding and efficiency of building operations for reducing energy use, energy costs, and carbon emissions.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

A compendium of multi-omics data illuminating host responses to lethal human virus infections

Human infections caused by viral pathogens trigger a complex gamut of host responses that limit disease, resolve infection, generate immunity, and contribute to severe disease or death. Here, we present experimental methods and multi-omics data capture approaches representing the global host response to infection generated from 45 individual experiments involving human viruses from the Orthomyxoviridae, Filoviridae, Flaviviridae, and Coronaviridae families. Analogous experimental designs were implemented across human or mouse host model systems, longitudinal samples were collected over defined time courses, and global multi-omics data (transcriptomics, proteomics, metabolomics, and lipidomics) were acquired by microarray, RNA sequencing, or mass spectrometry analyses. For comparison, we have included transcriptomics datasets from cells treated with type I and type II human interferon. Raw multi-omics data and metadata were deposited in public repositories, and we provide a central location linking the raw data with experimental metadata and ready-to-use, quality-controlled, statistically processed multi-omics datasets not previously available in any public repository. This compendium of infection-induced host response data for reuse will be useful for those endeavouring to understand viral disease pathophysiology and network biology.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2019

Qresp, a tool for curating, discovering and exploring reproducible scientific papers

We propose a strategy and present a simple tool to facilitate scientific data reproducibility by making available, in a distributed manner, all data and procedures presented in scientific papers, together with metadata to render them searchable and discoverable. In particular, we describe a graphical user interface (GUI), Qresp, to curate papers (i.e. generate metadata) and to explore curated papers and automatically access the data presented in scientific publications.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2016

Antimicrobial resistance prediction in PATRIC and RAST

The emergence and spread of antimicrobial resistance (AMR) mechanisms in bacterial pathogens, coupled with the dwindling number of effective antibiotics, has created a global health crisis. Being able to identify the genetic mechanisms of AMR and predict the resistance phenotypes of bacterial pathogens prior to culturing could inform clinical decision-making and improve reaction time. At PATRIC (http://patricbrc.org/), we have been collecting bacterial genomes with AMR metadata for several years. In order to advance phenotype prediction and the identification of genomic regions relating to AMR, we have updated the PATRIC FTP server to enable access to genomes that are binned by their AMR phenotypes, as well as metadata including minimum inhibitory concentrations. Using this infrastructure, we custom built AdaBoost (adaptive boosting) machine learning classifiers for identifying carbapenem resistance in Acinetobacter baumannii , methicillin resistance in Staphylococcus aureus , and beta-lactam and co-trimoxazole resistance in Streptococcus pneumoniae with accuracies ranging from 88–99%. We also did this for isoniazid, kanamycin, ofloxacin, rifampicin, and streptomycin resistance in Mycobacterium tuberculosis , achieving accuracies ranging from 71–88%. Lastly, this set of classifiers has been used to provide an initial framework for species-specific AMR phenotype and genomic feature prediction in the RAST and PATRIC annotation services.

59 BASIC BIOLOGICAL SCIENCES↗