SOSRA Data Quality and Coverage Evaluation (Deliverable 4.2.a)
Southeast Offshore Storage Resource Assessment (SOSRA): Data Quality and Coverage Evaluation (Deliverable 4.2.a)
Gray, Kimberly↗
SEARCH · Engineering Papers
Results for “resource data”
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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The medical science DMZ: a network design pattern for data-intensive medical science
Abstract Objective We describe a detailed solution for maintaining high-capacity, data-intensive network flows (eg, 10, 40, 100 Gbps+) in a scientific, medical context while still adhering to security and privacy laws and regulations. Materials and Methods High-end networking, packet-filter firewalls, network intrusion-detection systems. Results We describe a “Medical Science DMZ” concept as an option for secure, high-volume transport of large, sensitive datasets between research institutions over national research networks, and give 3 detailed descriptions of implemented Medical Science DMZs. Discussion The exponentially increasing amounts of “omics” data, high-quality imaging, and other rapidly growing clinical datasets have resulted in the rise of biomedical research “Big Data.” The storage, analysis, and network resources required to process these data and integrate them into patient diagnoses and treatments have grown to scales that strain the capabilities of academic health centers. Some data are not generated locally and cannot be sustained locally, and shared data repositories such as those provided by the National Library of Medicine, the National Cancer Institute, and international partners such as the European Bioinformatics Institute are rapidly growing. The ability to store and compute using these data must therefore be addressed by a combination of local, national, and industry resources that exchange large datasets. Maintaining data-intensive flows that comply with the Health Insurance Portability and Accountability Act (HIPAA) and other regulations presents a new challenge for biomedical research. We describe a strategy that marries performance and security by borrowing from and redefining the concept of a Science DMZ, a framework that is used in physical sciences and engineering research to manage high-capacity data flows. Conclusion By implementing a Medical Science DMZ architecture, biomedical researchers can leverage the scale provided by high-performance computer and cloud storage facilities and national high-speed research networks while preserving privacy and meeting regulatory requirements.
Peisert, Sean↗
Effective Tooling for Linked Data Publishing in Scientific Research
Challenges that make it difficult to find, share, and combine published data, such as data heterogeneity and resource discovery, have led to increased adoption of semantic data standards and data publishing technologies. To make data more accessible, interconnected and discoverable, some domains are being encouraged to publish their data as Linked Data. Consequently, this trend greatly increases the amount of data that semantic web tools are required to process, store, and interconnect. In attempting to process and manipulate large data sets, tools–ranging from simple text editors to modern triplestores– eventually breakdown upon reaching undefined thresholds. This paper offers a systematic approach that data publishers can use to categorize suitable tools to meet their data publishing needs. We present a real-world use case, the Resource Discovery for Extreme Scale Collaboration (RDESC), which features a scientific dataset(maximum size of 1.4 billion triples) used to evaluate a toolbox for data publishing in climate research. This paper also introduces a semantic data publishing software suite developed for the RDESC project.
Purohit, Sumit↗
Department of Energy WindSentinel Loan Program Description
The U.S. Department of Energy (DOE) currently owns two AXYS WindSentinel buoys that collect a comprehensive set of meteorological and oceanographic data to support resource characterization for wind energy offshore. The two buoys were delivered to DOE’s Pacific Northwest National Laboratory (PNNL) in September, 2014. After acceptance testing and initial performance testing and evaluation at PNNL’s Marine Sciences Laboratory in Sequim, Washington, the buoys have been deployed off the U.S. East Coast. One buoy was deployed approximately 42 km east of Virginia Beach, Virginia from December, 2014 through June, 2016. The second buoy was deployed approximately 5 km off Atlantic City, New Jersey in November, 2015. Data from the buoys are available to the public. Interested parties can create an account and log in to http://offshoreweb.pnnl.gov. In response to a number of inquiries and unsolicited proposals, DOE’s Wind Energy Technologies Office is implementing a program, to be managed by PNNL, to lend the buoys to qualified parties for the purpose of acquiring wind resource characterization data in areas of interest for offshore wind energy development. This document describes the buoys, the scope of the loans, the process of how borrowers will be selected, and the schedule for implementation of this program, including completing current deployments.
17 WIND ENERGY↗
Population structure limits the use of genomic data for predicting phenotypes and managing genetic resources in forest trees
There is overwhelming evidence that forest trees are locally adapted to climate. Thus, genecological models based on population phenotypes have been used to measure local adaptation, infer genetic maladaptation to climate, and guide assisted migration. However, instead of phenotypes, there is increasing interest in using genomic data for gene resource management. We used whole-genome resequencing and common-garden experiments to understand the genetic architecture of adaptive traits in black cottonwood. We studied the potential of using genome-wide association studies (GWAS) and genomic prediction to detect causal loci, identify climate-adapted phenotypes, and inform gene resource management. We analyzed population structure by partitioning phenotypic and genomic (single-nucleotide polymorphism) variation among 840 genotypes collected from 91 stands along 16 rivers. Most phenotypic variation (60 to 81%) occurred among populations and was strongly associated with climate. Population phenotypes were predicted well using genomic data (e.g., predictive abilityr> 0.9) but almost as well using climate or geography (r> 0.8). In contrast, genomic prediction within populations was poor (r< 0.2). We identified many GWAS associations among populations, but most appeared to be spurious based on pooled within-population analyses. Hierarchical partitioning of linkage disequilibrium and haplotype sharing suggested that within-population genomic prediction and GWAS were poor because allele frequencies of causal loci and linked markers differed among populations. Given the urgent need to conserve natural populations and ecosystems, our results suggest that climate variables alone can be used to predict population phenotypes, delineate seed zones and deployment zones, and guide assisted migration.
Science & Technology - Other Topics↗
Geothermal direct heat use: Market potential/penetration analysis for Federal Region 9
A preliminary study was made of the potential for geothermal direct heat use in Arizona, California, Hawaii, and Nevada (Federal Region 9). An analysis was made of each state to: (1) define the resource, based on the latest available data; (2) assess the potential market growth for geothermal energy; and (3) estimate the market penetration, projected to 2020. Findings of the study include the following: (1) Potentially economical hydrothermal resources exist in all four states of the Region: however, the resource data base is largely incomplete, particularly for low to moderate temperature resources. (2) In terms of beneficial heat, the total hydrothermal resource identified so far for the four states is on the order of 43 Quads, including an estimated 34 Quads of high temperature resources which are suitable for direct as well as electrical applications. (3) In California, Hawaii, and Nevada, the industrial market sector has somewhat greater potential for penetration than the residential/commercial sector. In Arizona, however, the situation is reversed, due to the collocation of two major metropolitan areas (Phoenix and Tucson) with potential geothermal resources.
Powell, W.↗
National Geothermal Data System (NGDS) Geothermal Data: Community Requirements and Information Engineering
To satisfy the critical need for geothermal data to advance geothermal energy as a viable renewable energy contender, the U.S. Department of Energy is investing in the development of the National Geothermal Data System (NGDS). This paper outlines efforts among geothermal data providers nationwide to supply cutting edge geo-informatics. NGDS geothermal data acquisition, delivery, and methodology are discussed. In particular, this paper addresses the various types of data required to effectively assess geothermal energy potential and why simple links to existing data are insufficient. To create a platform for ready access by all geothermal stakeholders, the NGDS includes a work plan that addresses data assets and resources of interest to users, a survey of data providers, data content models, and how data will be exchanged and promoted, as well as lessons learned within the geothermal community.
15 GEOTHERMAL ENERGY↗
Resource management implications of ERTS-1 data to Ohio
Initial experimental analysis of ERTS-1 imagery has demonstrated that remote sensing from space is a means of delineating and inventorying Ohio's strip-mined areas, detecting power plant smoke plumes, and proving the data necessary for periodically compiling land use maps for the entire state. The nature and extent of these problems throughout Ohio, how ERTS data can contribute to their solution, and estimates of the long term significance of these initial findings to overall resource management interests in Ohio are summarized.
Sweet, D. C.↗
The Water Cycle from Space: Use of Satellite Data in Land Surface Hydrology and Water Resource Management
This slide presentation reviews how our understanding of the water cycle is enhanced by our use of satellite data, and how this informs land surface hydrology and water resource management. It reviews how NASA's current and future satellite missions will provide Earth system data of unprecedented breadth, accuracy and utility for hydrologic analysis.
Laymon, Charles↗
Proceedings of the National Conference on Energy Resource Management. Volume 1: Techniques, Procedures and Data Bases
Topics dealing with the integration of remotely sensed data with geographic information system for application in energy resources management are discussed. Associated remote sensing and image analysis techniques are also addressed.
Brumfield, J. O.↗
Low-Income Energy Affordability Data (LEAD) Tool
This resource summary covers the Low-Income Energy Affordability Data (LEAD) Tool, which helps stakeholders make data-driven decisions on energy goals and program planning by improving their understanding of low-income and moderate-income household energy characteristics.
Low-Income Energy Affordability Data Tool, LEAD To↗
RCSB Protein Data Bank 1D tools and services
Abstract Motivation Interoperability between polymer sequences and structural data is essential for providing a complete picture of protein and gene features and helping to understand biomolecular function. Results Herein, we present two resources designed to improve interoperability between the RCSB Protein Data Bank, the NCBI and the UniProtKB data resources and visualize integrated data therefrom. The underlying tools provide a flexible means of mapping between the different coordinate spaces and an interactive tool allows convenient visualization of the 1-dimensional data over the web. Availabilityand implementation https://1d-coordinates.rcsb.org and https://rcsb.github.io/rcsb-saguaro. Supplementary information Supplementary data are available at Bioinformatics online.
59 BASIC BIOLOGICAL SCIENCES↗
Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research
Introduction The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped. Methods To bridge this gap, we leveraged recent advancements in human genomics infrastructure, such as the integration of the Human Cell Atlas Data Portal with Terra, a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools, and collaborate. In parallel, the Single Cell Expression Atlas at EMBL-EBI offers a comprehensive data ingestion portal for high-throughput sequencing datasets, including plants, protists, and animals (including humans). Developing data tools connecting these resources would offer significant advantages to the agricultural genomics community. The FAANG data portal at EMBL-EBI emphasizes delivering rich metadata and highly accurate and reliable annotation of farmed animals but is not computationally linked to either of these resources. Results Herein, we describe a pilot-scale project that determines whether the current FAANG metadata standards for livestock can be used to ingest scRNA-seq datasets into Terra in a manner consistent with HCA Data Portal standards. Importantly, rich scRNA-seq metadata can now be brokered through the FAANG data portal using a semi-automated process, thereby avoiding the need for substantial expert curation. We have further extended the functionality of this tool so that validated and ingested SC files within the HCA Data Portal are transferred to Terra for further analysis. In addition, we verified data ingestion into Terra, hosted on Azure, and demonstrated the use of a workflow to analyze the first ingested porcine scRNA-seq dataset. Additionally, we have also developed prototype tools to visualize the output of scRNA-seq analyses on genome browsers to compare gene expression patterns across tissues and cell populations. This JBrowse tool now features distinct tracks, showcasing PBMC scRNA-seq alongside two bulk RNA-seq experiments. Discussion We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem based on Findable, Accessible, Interoperable, and Reusable (FAIR) SC principles to facilitate SC-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species.
Genetics & Heredity↗
Building an Integrated Ecosystem of Computational and Observational Facilities to Accelerate Scientific Discovery
Future scientific discoveries will rely on flexible ecosystems that incorporate modern scientific instruments, high performance computing resources, parallel distributed data storage, and performant networks across multiple, independent facilities. In addition to connecting physical resources, such an ecosystem presents many challenges in logistics and accessibility, especially in orchestrating computations and experiments that span across leadership computing systems and experimental instruments. Past efforts have typically been application-specific or limited to interfaces for computing resources. This paper proposes a general framework for integrating computation resources and instrument operations, addressing challenges in code development/execution, data staging and collection, software stack, control mechanisms, resource authorization and governance, and hardware integration. We also describe a demonstration use case wherein a Bayesian optimization algorithm running on an edge computing resource guides a scanning probe microscope to autonomously and intelligently characterize a material sample. This science edge ecosystem framework will provide a blueprint for federating multi-institutional, disparate resources and orchestrating scientific workflows across them to enable next-generation discoveries.
Somnath, Suhas↗
Harmonizing model organism data in the Alliance of Genome Resources
The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein–protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.
59 BASIC BIOLOGICAL SCIENCES↗
UMLS users and uses: a current overview
Abstract The US National Library of Medicine regularly collects summary data on direct use of Unified Medical Language System (UMLS) resources. The summary data sources include UMLS user registration data, required annual reports submitted by registered users, and statistics on downloads and application programming interface calls. In 2019, the National Library of Medicine analyzed the summary data on 2018 UMLS use. The library also conducted a scoping review of the literature to provide additional intelligence about the research uses of UMLS as input to a planned 2020 review of UMLS production methods and priorities. 5043 direct users of UMLS data and tools downloaded 4402 copies of the UMLS resources and issued 66 130 951 UMLS application programming interface requests in 2018. The annual reports and the scoping review results agree that the primary UMLS uses are to process and interpret text and facilitate mapping or linking between terminologies. These uses align with the original stated purpose of the UMLS.
Amos, Liz↗
Centralized Interactive Phenomics Resource: an integrated online phenomics knowledgebase for health data users
Development of clinical phenotypes from electronic health records (EHRs) can be resource intensive. Several phenotype libraries have been created to facilitate reuse of definitions. However, these platforms vary in target audience and utility. Here, we describe the development of the Centralized Interactive Phenomics Resource (CIPHER) knowledgebase, a comprehensive public-facing phenotype library, which aims to facilitate clinical and health services research. The platform was designed to collect and catalog EHR-based computable phenotype algorithms from any healthcare system, scale metadata management, facilitate phenotype discovery, and allow for integration of tools and user workflows. Phenomics experts were engaged in the development and testing of the site. The knowledgebase stores phenotype metadata using the CIPHER standard, and definitions are accessible through complex searching. Phenotypes are contributed to the knowledgebase via webform, allowing metadata validation. Data visualization tools linking to the knowledgebase enhance user interaction with content and accelerate phenotype development. The CIPHER knowledgebase was developed in the largest healthcare system in the United States and piloted with external partners. The design of the CIPHER website supports a variety of front-end tools and features to facilitate phenotype development and reuse. Health data users are encouraged to contribute their algorithms to the knowledgebase for wider dissemination to the research community, and to use the platform as a springboard for phenotyping. CIPHER is a public resource for all health data users available at https://phenomics.va.ornl.gov/ which facilitates phenotype reuse, development, and dissemination of phenotyping knowledge.
60 APPLIED LIFE SCIENCES↗
Advanced aerospace remote sensing systems for global resource applications
The Landsat program, which was concerned with testing the use of satellite data for global resource observations, has been an unqualified success, and users of Landsat data demand now that repetitive global multispectral data be provided on a routine basis for a wide variety of applications. A review is provided of the current status of NASA's land observation program, new developments in advanced aerospace remote sensing techniques, and issues related to the development and testing of new prototype systems by the U.S. The current Landsat program is considered along with developments in solid-state imaging technology, short wave infrared research using the Space Shuttle, the Shuttle Orbiter camera payload system large format camera, and advanced research in thermal remote sensing. Attention is also given to the potential of imaging radar for global resource observations, and research related to geopotential field mapping.
Taranik, J. V.↗