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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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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

INTERSECT Architecture Specification: System-of-systems Architecture (Version 0.5)

Oak Ridge National Laboratory (ORNL)’s Self-driven Experiments for Science / Interconnected ScienceEcosystem (INTERSECT) architecture project, titled “An Open Federated Architecture for the Laboratory of the Future”, creates an open federated hardware/software architecture for the laboratory of the future using a novel system of systems (SoS) and microservice architecture approach, connecting scientific instruments, robot-controlled laboratories and edge/center computing/data resources to enable autonomous experiments, “self-driving” laboratories, smart manufacturing, and artificial intelligence (AI)-driven design, discovery and evaluation. The architecture project is divided into three focus areas: design patterns; SoS architecture; and microservices architecture. The design patterns area focuses on describing science use cases as design patterns that identify and abstract the involved hardware/software components and their interactions interms of control, work and data flow. The SoS architecture area focuses on an open architecture specification for the federated ecosystem that clarifies terms, architectural elements, the interactions between them and compliance. The microservices architecture describes blueprints for loosely coupled microservices, standardized interfaces, and multi-programming language support. This document is the SoS Architecture specification only, and captures the system of systems architecture design for the INTERSECT Initiative and its components. It is intended to provide a deep analysis and specification of how the INTERSECT platform will be designed, and to link the scientific needs identified across disciplines with the technical needs involved in the support, development, and evolution of a science ecosystem. PLEASE NOTE: This is a working document and reflects current discussions and design activity among the authors. There may be inconsistencies within the document as different parts evolve at a different pace. We invite comments and thoughts from the public on this and following working drafts. The first finished version of this document is scheduled for release in September 2023.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

RECENT AMPX developments [Slides]

This presentation covers recent AMPX developments. Presentation highlights include the news of AMPX being openly available, link to source and configure options are included. The interconnections between AMPX and Generalized Nuclear Database Structure (GNDS) are additionally highlighted as well.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2017

Enhanced anti-counterfeiting measures for additive manufacturing: coupling lanthanide nanomaterial chemical signatures with blockchain technology

The significant rise of additive manufacturing (AM) in recent years is in part due to the open sourced nature of the printing processes and reduced cost and capital barriers relative to traditional manufacturing. However, this democratization of manufacturing spurs an increased demand for producers and end-users to verify the authenticity and quality of individual parts. To this end, we introduce an anti-counterfeiting method composed of first embedding engineered nanomaterials into features of a 3D-printed part followed by non-destructive interrogation of these features to quantify a chemical signature profile. The part specific chemical signature data is then linked to a securitized, distributed, and time-stamped blockchain ledger entry. To demonstrate the utility of this approach, lanthanide-aspartic acid nanoscale coordination polymers (Ln3+- Asp NCs) / poly(lactic) acid (PLA) composites were formulated and transformed into a filament feedstock for fused deposition modeling (FDM) 3D printing. In the present case, a quick-response (QR) code containing the doped Ln3+-Asp NCs was printed using a dual-extruder FDM printer into pure PLA parts. The QR code provides a searchable reference to an Ethereum-based blockchain entry. The QR code physical features also serve as defined areas to probe the signatures arising from the embedded Ln3+-Asp NCs. Visible fluorescence emission with UV-excitation was quantified in terms of color using a smartphone camera and incorporated into blockchain entries. Ultimately, linking unique chemical signature data to blockchain databases is anticipated to make the costs of counterfeiting AM materials significantly more prohibitive and transactions between those in the supply chain more trustworthy.

Additive Manufacturing↗
DOE OSTI2016

AN INVESTIGATION OF THE SOURCES OF EARTH-DIRECTED SOLAR WIND DURING CARRINGTON ROTATION 2053

In this work we analyze multiple sources of solar wind through a full Carrington Rotation (CR 2053) by analyzing the solar data through spectroscopic observations of the plasma upflow regions and the in situ data of the wind itself. Following earlier authors, we link solar and in situ observations by a combination of ballistic backmapping and potential-field source-surface modeling. We find three sources of fast solar wind that are low-latitude coronal holes. The coronal holes do not produce a steady fast wind, but rather a wind with rapid fluctuations. The coronal spectroscopic data from Hinode ’s Extreme Ultraviolet Imaging Spectrometer show a mixture of upflow and downflow regions highlighting the complexity of the coronal hole, with the upflows being dominant. There is a mix of open and multi-scale closed magnetic fields in this region whose (interchange) reconnections are consistent with the up- and downflows they generate being viewed through an optically thin corona, and with the strahl directions and freeze-in temperatures found in in situ data. At the boundary of slow and fast wind streams there are three short periods of enhanced-velocity solar wind, which we term intermediate based on their in situ characteristics. These are related to active regions that are located beside coronal holes. The active regions have different magnetic configurations, from bipolar through tripolar to quadrupolar, and we discuss the mechanisms to produce this intermediate wind, and the important role that the open field of coronal holes adjacent to closed-field active regions plays in the process.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

MSD CoP Webinar: Using Meta-Repositories To Facilitate Open Science in MSD Research

Context: This webinar was hosted by the MultiSector Dynamics Community of Practice (MSD CoP; https://multisectordynamics.org). Abstract: In this webinar, we will describe the use of a GitHub meta-repository, for documenting and disseminating the tools and data supporting MSD publications. The goal is to make it easier for others to understand the flow of data and code through your experiment and to be able to reproduce your results and figures with only the information you have provided for them. The webinar will cover the role of open science in the MSD community, the origins and purpose of meta-repositories, and step-by-step instructions and best practices for building a meta-repository starting from the GitHub template (https://github.com/IMMM-SFA/metarepo). We will also discuss how to leverage MSD-LIVE (https://msdlive.org/) in your meta-repository, provide links to numerous examples you can learn from, and discuss the role of meta-repositories in the IM3 project's open science mandates. Presenters : Chris R. Vernon, Casey D. Burleyson, Jennie Rice, and Mengqi Zhao Moderator: Pat M. Reed (MSD CoP Facilitation Team) This webinar was held on: February 22nd, 2024 from 2-3 PM ET

Open Science↗
DOE OSTI2014

Daymet: Daily Surface Weather Data on a 1-km Grid for North America, Version 2.

More information: http://daymet.ornl.gov Presenter: Ranjeet Devarakonda Environmental Sciences Division Oak Ridge National Laboratory (ORNL) Daymet: Daily Surface Weather Data and Climatological Summaries provides gridded estimates of daily weather parameters for North America, including daily continuous surfaces of minimum and maximum temperature, precipitation occurrence and amount, humidity, shortwave radiation, snow water equivalent, and day length. The current data product (Version 2) covers the period January 1, 1980 to December 31, 2013 [1]. The prior product (Version 1) only covered from 1980-2008. Data are available on a daily time step at a 1-km x 1-km spatial resolution in Lambert Conformal Conic projection with a spatial extent that covers the conterminous United States, Mexico, and Southern Canada as meteorological station density allows. Daymet data can be downloaded from 1) the ORNL Distributed Active Archive Center (DAAC) search and order tools (http://daac.ornl.gov/cgi-bin/cart/add2cart.pl?add=1219) or directly from the DAAC FTP site (http://daac.ornl.gov/cgi-bin/dsviewer.pl?ds_id=1219) and 2) the Single Pixel Tool [2] and THREDDS (Thematic Real-time Environmental Data Services) Data Server [3]. The Single Pixel Data Extraction Tool allows users to enter a single geographic point by latitude and longitude in decimal degrees. A routine is executed that translates the (lon, lat) coordinates into projected Daymet (x,y) coordinates. These coordinates are used to access the Daymet database of daily-interpolated surface weather variables. Daily data from the nearest 1 km x 1 km Daymet grid cell are extracted from the database and formatted as a table with one column for each Daymet variable and one row for each day. All daily data for selected years are returned as a single (long) table, formatted for display in the browser window. At the top of this table is a link to the same data in a simple comma-separated text format, suitable for import into a spreadsheet or other data analysis software. The Single Pixel Data Extraction Tool also provides the option to download multiple coordinates programmatically. A multiple extractor script is freely available to download at http://daymet.ornl.gov/files/daymet.zip. The ORNL DAAC s THREDDS data server (TDS) provides customized visualization and access to Daymet time series of North American mosaics. Users can subset and download Daymet data via a variety of community standards, including OPeNDAP, NetCDF Subset service, and Open Geospatial Consortium (OGC) Web Map/Coverage Service. The ORNL DAAC TDS also exposes Daymet metadata through its ncISO service to facilitate harvesting Daymet metadata records into 3rd party catalogs. References: [1] Thornton, P.E., M.M. Thornton, B.W. Mayer, N. Wilhelmi, Y. Wei, R. Devarakonda, and R.B. Cook. 2014. Daymet: Daily Surface Weather Data on a 1-km Grid for North America, Version 2. Data set. Available on-line [http://daac.ornl.gov] from Oak Ridge National Laboratory Distributed Active Archive Center, Oak Ridge, Tennessee, USA. [2] Devarakonda R., et al. 2012. Daymet: Single Pixel Data Extraction Tool. Available on-line [http://daymet.ornl.go/singlepixel.html]. [3] Wei Y., et al. 2014. Daymet: Thematic Real-time Environmental Data Services. Available on-line [http://daymet.ornl.gov/thredds_tiles.html].

Thornton, Peter E↗
DOE OSTI2017

The effect of support functions in a computerized procedure system on interface management tasks - 235

By adapting digital and computer technology, the design of main control rooms (MCR) in nuclear power plants has been changed. When operators operate a nuclear power plant, the tasks using soft controls in advanced MCRs include primary tasks and secondary tasks. Primary tasks are to control nuclear power plant devices and secondary tasks are to find appropriate screens or devices by screen navigations and selections before performing the primary task. The secondary task including interface management tasks is newly introduced in advanced MCRs. In this paper, the tasks are analyzed based on the simulation data of APR1400 which is one of the digitalized nuclear power plants. For analyzing tasks, the unit tasks are divided into three types: navigation, manipulation, and acknowledgement. The primary task represents the manipulation of devices and the secondary task indicates the navigating screens, opening control panels, closing control panels, and confirming the acknowledging alarms. To analyze the effect of support functions of a computerized procedure system (CPS), one of the functions which is expected to have a significant effect on the secondary tasks was considered, that is 'related screen link button.' Two factors, 'ratio of screen alteration' and 'ratio of using screen link button', were used to see the effect of 'related screen link button'. From the task analysis result, it was observed that the secondary tasks which is one of the unique features in advanced MCRs have a quite much portion than that of the primary tasks. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2023

Antarctic evidence for an abrupt northward shift of the Southern Hemisphere westerlies at 32 ka BP

High-resolution ice core records from coastal Antarctica are particularly useful to inform our understanding of environmental changes and their drivers. Here, we present a decadally resolved record of sea-salt sodium (a proxy for open-ocean area) and non-sea salt calcium (a proxy for continental dust) from the well-dated Roosevelt Island Climate Evolution (RICE) core, focusing on the time period between 40–26 ka BP. The RICE dust record exhibits an abrupt shift towards a higher mean dust concentration at 32 ka BP. Investigating existing ice-core records, we find this shift is a prominent feature across Antarctica. We propose that this shift is linked to an equatorward displacement of Southern Hemisphere westerly winds. Subsequent to the wind shift, data suggest a weakening of Southern Ocean upwelling and a decline of atmospheric CO 2 to lower glacial values, hence making this shift an important glacial climate event with potentially important insights for future projections.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

SUMMARY The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for “hot topic” research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei , T. atroviride , and T. virens , and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N -linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N -linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma , and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.

Schmoll, Monika↗
DOE OSTI2022

libwfa: Wavefunction analysis tools for excited and open‐shell electronic states

Abstract An open‐source software library for wavefunction analysis, libwfa, provides a comprehensive and flexible toolbox for post‐processing excited‐state calculations, featuring a hierarchy of interconnected visual and quantitative analysis methods. These tools afford compact graphical representations of various excited‐state processes, provide detailed insight into electronic structure, and are suitable for automated processing of large data sets. The analysis is based on reduced quantities, such as state and transition density matrices (DMs), and allows one to distill simple molecular orbital pictures of physical phenomena from intricate correlated wavefunctions. The implemented descriptors provide a rigorous link between many‐body wavefunctions and intuitive physical and chemical models, for example, exciton binding, double excitations, orbital relaxation, and polyradical character. A broad range of quantum‐chemical methods is interfaced with libwfa via a uniform interface layer in the form of DMs. This contribution reviews the structure of libwfa and highlights its capabilities by several representative use cases. This article is categorized under: Software > Quantum Chemistry Theoretical and Physical Chemistry > Spectroscopy

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET

To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Förster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor–acceptor pairs. Angle-dependent FRET measurements have proven challenging for nucleic acids due to the difficulties in incorporating fluorophores rigidly into local substructures in a biocompatible manner. Fluorescence turn-on RNA aptamers are genetically encodable tags that appear to rigidly confine their cognate fluorophores, and thus have the potential to report angular-resolved FRET. In this work, we use the fluorescent aptamers Broccoli and Mango-III as donor and acceptor, respectively, to measure the angular dependence of FRET. Joining the two fluorescent aptamers by a helix of variable length allowed systematic rotation of the acceptor fluorophore relative to the donor. FRET oscillated in a sinusoidal manner as a function of helix length, consistent with simulated data generated from models of oriented fluorophores separated by an inflexible helix. Analysis of the orientation dependence of FRET allowed us to demonstrate structural rigidification of the NiCo riboswitch upon transition metal-ion binding. This application of fluorescence turn-on aptamers opens the way to improved structural interpretation of ensemble and single-molecule FRET measurements of RNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Toward a Better Understanding of Species Interactions through Network Biology

Within the last decade, there has been an explosion of multi-omics data generated for several microbial systems. At the same time, new methods of analysis have emerged that are based on inferring networks that link features both within and between species based on correlation in abundance. These developments prompt two important questions. What can be done with network approaches to better understand microbial species interactions? What challenges remain in applying network approaches to query the more complex systems of natural settings? Here, I briefly describe what has been done and what questions still need to be answered. Over the next 5 to 10 years, we will be in a strong position to infer networks that contain multiple kinds of omic data and describe systems with multiple species. These applications will open the door for a better understanding and use of microbiomes across a variety of fields.

Microbiology↗
DOE OSTI2014

US Woody Crop Yield Potential Database Documentation with Referenced Yield Summary Tables

A woody crop yield potential (WCYP) database was created containing yield results with as much associated information as was available concerning the sites, soils, and experimental treatments. The database summarizes a very broad set of old and new standing biomass data from plantation-grown hardwoods and softwoods established under a wide range of conditions across the United States and Canada. The WCYP database, together with this document, is being published to disseminate information on what is available in the literature with respect to yield evaluations and to inform people that not all yield data in the open literature are suitable for evaluation of “potential” regional yields. It has also been presented with the hope that much more information will be collected and added to the WCYP database. The current set of data in the WCYP database is derived from 41 unique reference sources describing 79 experiments in the United States or southern Canada with a total of 473 different treatments. The database contains several worksheets. The worksheet that reports the complete yield curves contains roughly 1,660 rows of data and 81 columns of parameters reporting yields and associated treatment factors. Separate worksheets, linked by the source publication author and year, describe the sites and soils associated with each experiment; another separate worksheet assembles only the final yields deemed appropriate for yield potential analysis. There are additional worksheets with conversion factors relevant to the database and notes pertaining to decisions made regarding organization of the data. This technical manuscript describes how the information was assembled to create the WCYP database that is simultaneously being published on the US Department of Energy (DOE) Bioenergy Knowledge Discovery Framework website maintained by Oak Ridge National Laboratory (ORNL). A summary table with links to all worksheets in the database can be found at the web address https://www.bioenergykdf.net/WCYP .

09 BIOMASS FUELS↗
DOE OSTI2019

2019 Wireless Test Bed Range Manual

Idaho National Laboratory (INL), Next Generation Wireless Test Bed (NGWTB) program, is part of the Critical Infrastructure Protection (CIP) initiative. Our nation’s reliance on wireless and Internet technology is rapidly evolving as more corporations and government agencies, employees, and handheld devices include mobile connectivity for both voice and data. The competitive advantage offered by a mobile workforce is leading many corporations to make wireless integration and convergence a top business priority. Similarly, military systems worldwide are rapidly embracing next-generation commercial technologies to accelerate network-centric capabilities and provide enhanced situational awareness. While handheld devices such as laptops, BlackBerrys, and cell phones once had limited mobility and range, they are rapidly incorporating new and multiple protocols such as Bluetooth, Wi-Fi, Satellite, and broadband cellular (3G/4G) on a single platform to increase their effectiveness and agility. Worldwide there is exponential growth in public Wi-Fi and/or Satellite connectivity access nodes, and 3G/4G cellular continues to evolve and expand the range and speed of these devices. Additionally, critical infrastructure networks, previously isolated or connected with dedicated wireline circuits, are incorporating Zigbee for wireless sensor networks, wireless LANs for maintenance functions, and cellular or Internet based backhaul to manage control centers. Yet with all the build-up surrounding wireless technology, few understand the complexities surrounding wireless protocols and security, the risks of converged network infrastructures, need for interoperability of communication systems, or mitigation measures to safely use and improve new technologies in both commercial and military environments. With no single vendor source for all the telecommunications equipment needed for wireless infrastructure upgrades, and no one entity providing end-to-end testing or independent validation, the INL's NGWTB program fulfills a niche for facilitating integrated testing of multiple technologies, across multiple wireless domains, of next generation wireless telecommunications systems. NGWTB engineers and technicians have constructed and operate domain infrastructure in the Wireless Personal Area Network (WPAN), Wireless Local Area Network (WLAN), Wireless Metropolitan Area Networks (WMAN), and Wireless Wide Area Networks (WWAN). Advantages that make the INL's NGWTB the place to conduct project and programmatic testing include: • NTIA Experimental Station authority • Geographically isolated and low-noise radio frequency (RF) test areas located on a 890 sm DOE reservation • Access to isolated high-speed LAN and FOT networks The rollout of next-generation networks will involve deploying new technologies at every level including new: handsets, frequencies, antenna arrays, cell configurations that are optimized for both data and voice, massive upgrade of cell controllers’ “land-line” phone links from low bandwidth connections to higher capacity fiber or wireless backhaul, and integration of voice switching and Internet/data network protocols (Voice-Over-IP, Web phones). These systems are expected to greatly transform our nation's communications infrastructure and the types of services it provides.

2G↗
DOE OSTI2024

GeoBridge: Connecting Communities to Geothermal Information and Opportunities: Preprint

The geothermal community is well established with long-standing events, organizations, and tools that are known across the geothermal community. But many of these tools and resources are located behind pay walls, require memberships, or are otherwise difficult to find, especially for people looking to join the geothermal community. These barriers to access can prevent outsiders from discovering valuable geothermal resources, limiting the geothermal community's potential for collaboration with other communities, such as clean energy entrepreneurs looking to expand into geothermal energy. The Department of Energy's (DOE) GeoBridge serves to bring these communities together by acting as a single, publicly accessible, searchable portal that facilitates easy access to available geothermal knowledge and information. It works to expand and diversify the pool of geothermal stakeholders by providing in-roads to geothermal information and community resources. It helps build a stronger geothermal community; one inclusive of individuals and groups from a variety of different backgrounds, including potential investors and start-up companies looking to accelerate innovation in geothermal technologies. By linking communities to geothermal information, analysis and expertise, GeoBridge serves as a launch point, directing interested parties to existing data and tools, events, educational resources, STEM programs, permitting and regulatory information, and other resources that can be used to evaluate, promote, and discover geothermal opportunities.

access↗
DOE OSTI2016

Dynamic analysis environment for nuclear forensic analyses

We report a Dynamic Analysis Environment (DAE) software package is introduced to facilitate group inclusion/exclusion method testing, evaluation and comparison for pre-detonation nuclear forensics applications. Employing DAE, the multivariate signatures of a questioned material can be compared to the signatures for different, known groups, enabling the linking of the questioned material to its potential process, location, or fabrication facility. Advantages of using DAE for group inclusion/exclusion include built-in query tools for retrieving data of interest from a database, the recording and documentation of all analysis steps, a clear visualization of the analysis steps intelligible to a non-expert, and the ability to integrate analysis tools developed in different programming languages. Two group inclusion/exclusion methods are implemented in DAE: principal component analysis, a parametric feature extraction method, and k nearest neighbors, a nonparametric pattern recognition method. Spent Fuel Isotopic Composition (SFCOMPO), an open source international database of isotopic compositions for spent nuclear fuels (SNF) from 14 reactors, is used to construct PCA and KNN models for known reactor groups, and 20 simulated SNF samples are utilized in evaluating the performance of these group inclusion/exclusion models. For all 20 simulated samples, PCA in conjunction with the Q statistic correctly excludes a large percentage of reactor groups and correctly includes the true reactor of origination. As a result, employing KNN, 14 of the 20 simulated samples are classified to their true reactor of origination.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

TIME-DEPENDENT NONEXTENSIVITY ARISING FROM THE ROTATIONAL EVOLUTION OF SOLAR-TYPE STARS

Nonextensive formalism is a generalization of the Boltzmann-Gibbs statistics. In this formalism, the entropic index q is a quantity characterizing the degree of nonextensivity and is interpreted as a parameter of long-memory or long-range interactions between the components of the system. Since its proposition in 1988, this formalism has been applied to investigate a wide variety of natural phenomena. In stellar astrophysics, a theoretical distribution function based on nonextensive formalism (q distributions) has been successfully applied to reproduce the distribution of stellar radial and rotational velocity data. In this paper, we investigate the time variation of the entropic index q obtained from the distribution of rotation, Vsin i, for a sample of 254 rotational data for solar-type stars from 11 open clusters aged between 35.5 Myr and 2.6 Gyr. As a result, we have found an anti-correlation between the entropic index q and the age of clusters, and that the distribution of rotation Vsin i for these stars becomes extensive for an age greater than about 170 Myr. Assuming that the parameter q is associated with long-memory effects, we suggest that the memory of the initial angular momentum of solar-type stars can be scaled by the entropic index q. We also propose a physical link between the parameter q and the magnetic braking of stellar rotation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

KG-Hub—building and exchanging biological knowledge graphs

Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of KGs is lacking. Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of KGs. Features include a simple, modular extract–transform–load pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial–environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate KGs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph ML, including node embeddings and training of models for link prediction and node classification.

59 BASIC BIOLOGICAL SCIENCES↗