Search NASA⌕ Search

SEARCH · Search NASA

Results for “Classification and taxonomy”

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.

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

At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Genomic Language model for Annotation of Repetitive Elements (GLARE) v1.0

GLARE (Genomic Language model for Annotation of Repetitive Elements) is a tool that classifies transposable elements (TEs)—the mobile, repetitive DNA sequences that make up large fractions of eukaryotic genomes. GLARE fine-tunes the NTv3-650M genomic language model on a harmonized collection of curated TE sequences from the PanTEon and Repbase reference databases, assigning each input sequence to one of 11 orders and 32 superfamilies in a Wicker-compatible taxonomy. Features. From nucleotide FASTA input, GLARE outputs per-sequence predictions, class summaries, composition figures, and an annotated FASTA. It provides calibrated confidence scores with optional abstention and runs on CPU or GPU. Uses. GLARE serves as a classification component in genome-annotation pipelines, downstream of TE discovery, supporting genome annotation and comparative and evolutionary genomics. Advantages. GLARE is the first repeat-element classifier to leverage a pretrained genomic language model. Combined with multi-database training, this approach outperformed all nine classifiers in the PanTEon benchmark, generalized better to unseen taxonomic clades, and remained robust to sequence orientation—a common failure mode of existing tools.

Bruna, Tomas [Lawrence Berkeley National Laborator↗
NASA NTRS2014

A Review of Current and Prospective Factors for Classification of Civil Unmanned Aircraft Systems

While progress is being made on integrating unmanned aircraft systems (UAS) into our national airspace on a broad scale, much work remains to establish appropriate certification standards and operational procedures, particularly with respect to routine commercial operations. This paper summarizes research to examine the extent to which today's civil aircraft taxonomy applies to UAS, and, if needed, how that taxonomy could be amended to better cover different UAS designs and operations. Factors that shape the current taxonomy, as defined in the Federal Aviation Regulations, were assessed for applicability to UAS, potential incompatibilities were identified, and additional factors were proposed that might be useful for an updated aircraft taxonomy intended to cover UAS. The results suggest the possibility of constructing new groups in the taxonomy for UAS under a restricted category that share common airworthiness standards. Establishing distinct groups for UAS and associated standards that enable low risk operations for compensation or hire could be a timely step toward full integration. Such a step would allow the civil aviation industry and regulators to gain valuable experience with UAS while carefully controlling access and potential harm to the aviation system as a whole.

Hayhurst, Kelly J.↗
DOE OSTI2022

Exploring New Ways to Classify Industries for Energy Analysis and Modeling

As the US moves closer to embracing a net zero greenhouse gas emissions position, combustion processes outside the power sector are becoming urgent concerns. Industry is an important end user of energy and relies on fossil fuels used directly for process heating and as feedstocks for a diverse range of applications. Fuel and energy use by industry is heterogeneous, meaning that even a single product group can vary broadly in its production routes and associated energy usage. In the US, the North American Industry Classification System (NAICS) serves as the basis for data collection and reporting. In turn, data based on NAICS is the foundation of most US energy modeling. Thus, the effectiveness of NAICS at representing energy use is a limiting condition for plans to improve energy efficiency and alternatives to fossil fuels in industry. Facility-level data to build more detail into heterogeneous sectors is scarce. This work explores alternative classification schemes for industry based on energy use characteristics, and provides a validation of an approach to make facility-level energy use estimates based on publicly available data from the greenhouse gas reporting program. First, several approaches to industrial taxonomies and their usefulness for industrial energy modeling are summarized. Data from Industrial Assessment Centers is analyzed using unsupervised machine learning techniques to detect clusters. Cladistics, an approach from biology, is adapted to energy and process characteristics of industries. A cladogram is presented for evolutionary directions in the iron and steel sector. Cladograms are a promising tool for constructing scenarios and summarizing directions of sectoral innovation. Finally, validation is performed for facility-level energy estimates from the US EPA Greenhouse Gas Reporting Program. This validation assists in making this data source available for use in energy modeling. Together, this work explores alternative approaches for categorizing industries in a way that aids understanding energy use, and presenting pathways for the future.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2022

Internal Reaction Mass Taxonomy and Narrow-Down Study

Internal reaction mass (IRM) wave energy converters (WEC) capture wave energy by reacting against a moving mass that is suspended within their hulls. Due to their hermetically sealed Power Take Off (PTO), compact form factor and relatively simple mooring requirements, the National Renewable Energy Laboratory has identified IRM WECs are good candidates for applications such as ocean observation. A literature review of existing IRM mechanisms lead to the classification of IRM WECs based on their principal method of energy capture and principal axes of operation. The IRM categories include sliding mass, pendular and gyroscopic devices. A narrow down study was conducted to ascertain the most promising mechanisms for further investigation; devices were evaluated based on a decision matrix of weighted criteria that included device power output, prototypability and power to mass ratio. The narrow down study identified the issue of achieving resonance with pendulum-based designs, as well as the poor response produced by reaction to long period waves. Chaotic pendula and methods to multiply agitation were identified as a means to increase power output. Alternative methods of power generation, such as triboelectric nanogenerators, were also identified as a technology that would benefit from multiplied agitation and chaotic motion. This work was funded under the U.S. Department of Energy's Water Power Technologies Office's Powering the Blue Economy portfolio.

ENGINEERING,TIDAL AND WAVE POWER↗
DOE OSTI2023

Updated Virophage Taxonomy and Distinction from Polinton-like Viruses

Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of “hyperparasitism” in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection and replication strategy, ability to integrate into protist and giant virus genomes and potential role in antiviral defense have made virophages a topic of broad interest. However, one limitation for further studies is the lack of clarity regarding the nomenclature and taxonomy of this group of viruses. Specifically, virophages have been linked in the literature to other “virophage-like” mobile genetic elements and viruses, including polinton-like viruses (PLVs), but there are no formal demarcation criteria and proper nomenclature for either group, i.e., virophage or PLVs. Here, as part of the ICTV Virophage Study Group, we leverage a large set of genomes gathered from published datasets as well as newly generated protist genomes to propose delineation criteria and classification methods at multiple taxonomic ranks for virophages ‘sensu stricto’, i.e., genomes related to the prototype isolates Sputnik and mavirus. Based on a combination of comparative genomics and phylogenetic analyses, we show that this group of virophages forms a cohesive taxon that we propose to establish at the class level and suggest a subdivision into four orders and seven families with distinctive ecogenomic features. Finally, to illustrate how the proposed delineation criteria and classification method would be used, we apply these to two recently published datasets, which we show include both virophages and other virophage-related elements. Overall, we see this proposed classification as a necessary first step to provide a robust taxonomic framework in this area of the virosphere, which will need to be expanded in the future to cover other virophage-related viruses such as PLVs.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2016

Taxonomies and Albedos of Near-Earth Asteroids

Characterizing near-Earth asteroids (NEAs) can help to assess the risk of possible impactors. Over many decades, asteroids have been spectrally classified into numerous taxonomic systems, most notably those of Tholen, Bus, and Bus-DeMeo. By mapping these various taxonomic systems to broader categories called complexes, it is easier to study the relationship between classifications and other physical parameters. There has recently been an increase in the number of objects with measured albedos which is advantageous for characterization because the albedo and absolute magnitude can be used to determine diameter. Knowing an asteroids diameter helps us better understand dangers they may pose.

Napier, Kate↗
NASA NTRS2004

The Tropical Convective Spectrum: Archetypal Vertical Structures - 1

A taxonomy of tropical convective vertical structures is constructed through cluster analysis of three years of Tropical Rainfall Measuring Mission [TRMM] Precipitation Radar [PR] vertical profiles, their surface rainfall and associated radar-based classifiers (convective/stratiform and bright band existence). archetypal profile types are identified. These include nine convective types, divided into warm, "just cold", midlevel, deep and deep/wet-growth categories, seven stratiform types, divided into warm, "just cold", midlevel and deep categories, three "mixed" types (deep profiles with low reflectivity aloft), and six fragment types (non-precipitating anvils and sheared deep convective profiles). The taxonomy allows for description of any storm or local Convective spectrum by the nine primary convective and stratiform types, a significant reduction over full three-dimensional radar data which nonetheless retains vertical structure information. The analysis provides a quasi-independent corroboration of the TRMM 2A23 convective/stratiform classification. The global frequency of occurrence and contribution to rainfall for the profile types is presented, demonstrating primary rainfall contribution by midlevel glaciated convection and similar depth decaying/stratiform stages. Close correspondence is found between deep convective profile frequency and annualized lightning production. Passive microwave and lightning properties associated with the profiles are reported, and cases presented illustrating known nonuniqueness problems with 85 and 37 GHz brightness temperature pairs (the same pairs corresponding to both convective and stratiform profiles), and how supplementary lightning information might be used to mitigate these problems.

Boccippio, Dennis J.↗
NASA NTRS2003

Spectroscopy and Photometry of Mars Trojans

Mars is the only terrestrial planet known to have co-orbiting "Trojan" asteroids. We have obtained visible and near-IR reflectance spectra of three of these objects: 5261 Eureka and 1998 VF31 in the L5 region and 1999 UJ7 in the L4 region. We also obtained JHK spectrophotometry and a visible lightcurve for 5261 Eureka. The asteroid 5261 Eureka has a visible spectrum that is classified as Sr in the Bus taxonomy, and has infrared colors consistent with the A-class asteroids. The data for 1998 VF31 have a restricted wavelength range, but are most consistent with the Sr or Sa class, though we note a marginal consistency with the D class. We can rule out a C-class classification. 1999 UJ7 has an X-class or T-class spectrum, which is unlike that of the other two Mars Trojans. The photometric data for Eureka are limited, but we can constrain the period to longer than 5 hours (likely 5.556 hours) and lightcurve amplitude of at least 0.15 magnitude at this viewing geometry. The spectral differences among the Mars Trojans suggests that either they did not all form at their present solar distances or that they have not always been at their present sizes. 0 2003 Elsevier Inc. All rights reserved. Keywords: Asteroids; Asteroids, composition; Spectroscopy; Satellites of Mars

Rivkin, A. S.↗
NASA NTRS2003

Spectroscopy and Photometry of Mars Trojans

Mars is the only terrestrial planet known to have co-orbiting Trojan asteroids. We have obtained visible and near-IR reflectance spectra of three of these objects: 5261 Eureka and 1998 VF31 in the L5 region and 1999 UJ7 in the LA region. We also obtained JHK spectrophotometry and a visible lightcurve for 5261 Eureka. The asteroid 5261 Eureka has a visible spectrum that is classified as Sr in the Bus taxonomy, and has infrared colors consistent with the A-class asteroids. The data for 1998 VF31 have a restricted wavelength range, but are most consistent with the Sr or Sa class, though we note a marginal consistency with the D class. We can rule out a C-class classification. 1999 UJ7 has an X-class or T-class spectrum, which is unlike that of the other two Mars Trojans. The photometric data for Eureka are limited, but we can constrain the period to longer than 5 hours (likely 5.5-6 hours) and lightcurve amplitude of at least 0.15 magnitude at this viewing geometry. The spectral differences among the Mars Trojans suggests that either they did not all form at their present solar distances or that they have not always been at their present sizes.

Rivkin, A. S.↗
DOE OSTI2019

PNNL-CompBio/perseq

Per sequence functional classification and Functional annotation in addition to linking those functions to taxonomic groups presents a challenge due to many established tools performing one task and not the other creating disparate downstream data. PerSeq aims to address these challenges by performing local alignments against a reference database annotated for both aspects, function and taxonomy, to annotate sequences individually. Downstream results are merged into count tables facilitating complex analyses based on observed function or functional potential in addition to being able to separate out function by taxonomic level to determine metabolic contributions by present organisms.

Brown, Joe↗
DOE OSTI2014

Professional diversity and the productivity of cities

Attempts to understand the relationship between diversity, productivity and scale have remained limited due to the scheme-dependent nature of the taxonomies describing complex systems. We analyze the diversity of US metropolitan areas in terms of profession diversity and employment to show how this frequency distribution takes a universal scale-invariant form, common to all cities, in the limit of infinite resolution of occupational taxonomies. We show that this limit is obtained under general conditions that follow from the analysis of the variation of the occupational frequency across taxonomies at different resolutions in a way analogous to finite-size scaling in statistical physical systems. We propose a theoretical framework that derives the form and parameters of the limiting distribution of professions based on the appearance, in urban social networks, of new occupations as the result of specialization and coordination of labor. By deriving classification scheme-independent measures of functional diversity and modeling cities as social networks embedded in infrastructural space, these results show how standard economic arguments of division and coordination of labor can be articulated in detail in cities and provide a microscopic basis for explaining increasing returns to population scale observed at the level of entire metropolitan areas.

SOCIOECONOMIC SCENARIOS↗
DOE OSTI2021

Scalar Field Comparison with Topological Descriptors: Properties and Applications for Scientific Visualization

In topological data analysis and visualization, topological descriptors such as persistence diagrams, merge trees, contour trees, Reeb graphs, and Morse–Smale complexes play an essential role in capturing the shape of scalar field data. Herein we present a state–of–the–art report on scalar field comparison using topological descriptors. We provide a taxonomy of existing approaches based on visualization tasks associated with three categories of data: single fields, time–varying fields, and ensembles. These tasks include symmetry detection, periodicity detection, key event/feature detection, feature tracking, clustering, and structure statistics. Our main contributions include the formulation of a set of desirable mathematical and computational properties of comparative measures, and the classification of visualization tasks and applications that are enabled by these measures.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

Background: Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern genomics. Bacteria from different taxonomic groups, whose lifestyles and natural environments are substantially different, possess highly diverged transcriptional regulatory networks. The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches). Description: RegPrecise (http://regprecise.lbl.gov) is a web resource for collection, visualization and analysis of transcriptional regulons reconstructed by comparative genomics. We significantly expanded a reference collection of manually curated regulons we introduced earlier. RegPrecise 3.0 provides access to inferred regulatory interactions organized by phylogenetic, structural and functional properties. Taxonomy-specific collections include 781 TF regulogs inferred in more than 160 genomes representing 14 taxonomic groups of Bacteria. TF-specific collections include regulogs for a selected subset of 40 TFs reconstructed across more than 30 taxonomic lineages. Novel collections of regulons operated by RNA regulatory elements (riboswitches) include near 400 regulogs inferred in 24 bacterial lineages. RegPrecise 3.0 provides four classifications of the reference regulons implemented as controlled vocabularies: 55 TF protein families; 43 RNA motif families; ~150 biological processes or metabolic pathways; and ~200 effectors or environmental signals. Genome-wide visualization of regulatory networks and metabolic pathways covered by the reference regulons are available for all studied genomes. A separate section of RegPrecise 3.0 contains draft regulatory networks in 640 genomes obtained by an conservative propagation of the reference regulons to closely related genomes. Conclusions: RegPrecise 3.0 gives access to the transcriptional regulons reconstructed in bacterial genomes. Analytical capabilities include exploration of: regulon content, structure and function; TF binding site motifs; conservation and variations in genome-wide regulatory networks across all taxonomic groups of Bacteria. RegPrecise 3.0 was selected as a core resource on transcriptional regulation of the Department of Energy Systems Biology Knowledgebase, an emerging software and data environment designed to enable researchers to collaboratively generate, test and share new hypotheses about gene and protein functions, perform large-scale analyses, and model interactions in microbes, plants, and their communities.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2013

Sampling and Analysis of Impact Crater Residues found on the Wide Field Planetary Camera-2 Radiator

After nearly 16 years on orbit, the Wide Field Planetary Camera-2 (WFPC-2) was recovered from the Hubble Space Telescope in May 2009 during the 12 day shuttle mission designated STS-125. During that exposure to the low Earth orbit environment, the WFPC-2 radiator was struck by approximately 700 impactors producing crater features 300 micrometers and larger in size. Following an optical inspection of these features in 2009, an agreement was reached for the joint NASA-ESA examination and characterization of crater residues, the remnants of the projectile, in 2011. Active examination began in 2012, with 486 of the impact features being cored at NASA Johnson Space Center fs (JSC) Space Exposed Hardware cleanroom and curation facility. The core samples were subsequently divided between NASA and ESA. NASA's analysis was conducted at JSC fs Astromaterials Research and Exploration Science (ARES) Division, using scanning electron microscopy (SEM)/ energy dispersive X-ray spectrometry (EDS) methods, and ESA's analysis was conducted at the Natural History Museum (NHM) again using SEM/EDS, and at the University of Surrey Ion Beam Centre (IBC) using ion beam analysis (IBA) with a scanned proton microbeam. As detailed discussion of the joint findings remains premature at this point, this paper reports on the coring technique developed; the practical taxonomy developed to classify residues as belonging either to anthropogenic "orbital debris" or micrometeoroids; and the protocols for examination of crater residues. Challenges addressed in coring were the relative thickness of the surface to be cut, protection of the impact feature from contamination while coring, and the need to preserve the cleanroom environment so as to preclude or minimize cross-contamination. Classification criteria are summarized, including the assessment of surface contamination and surface cleaning. Finally, we discuss the analytical techniques used to examine the crater residues. We employed EDS from either electron excitation (SEM-EDS) and, in a minority of cases for cores assessed as "difficult" targets, proton excitation (IBA). All samples were documented by electron imagery: backscattered electron imagery in the SEM, and where appropriate, secondary electron imagery during IBA.

Kearsley, A. T.↗
DOE OSTI2015

Microbial species delineation using whole genome sequences

Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required.

Biochemistry & Molecular Biology↗
NASA NTRS1993

Previous experience in manned space flight: A survey of human factors lessons learned

Previous experience in manned space flight programs can be used to compile a data base of human factors lessons learned for the purpose of developing aids in the future design of inhabited spacecraft. The objectives are to gather information available from relevant sources, to develop a taxonomy of human factors data, and to produce a data base that can be used in the future for those people involved in the design of manned spacecraft operations. A study is currently underway at the Johnson Space Center with the objective of compiling, classifying, and summarizing relevant human factors data bearing on the lessons learned from previous manned space flights. The research reported defines sources of data, methods for collection, and proposes a classification for human factors data that may be a model for other human factors disciplines.

Chandlee, George O.↗
DOE OSTI2020

taxadb: A high‐performance local taxonomic database interface

Abstract A familiar and growing challenge in ecological and evolutionary research is that of establishing consistent taxonomy when combining data from separate sources. While this problem is already well understood and numerous naming authorities have been created to address the issue, most researchers lack a fast, consistent, and intuitive way to retrieve taxonomic names. We present taxadb R package which creates a local database, managed automatically from within R, to provide fast operations on millions of taxonomic names. taxadb provides access to established naming authorities to resolve synonyms, taxonomic identifiers, and hierarchical classification in a consistent and intuitive data format. taxadb makes operation on millions of taxonomic names fast and manageable.

Norman, Kari E. A.↗
DOE OSTI2021

IoT Intrusion Detection Taxonomy, Reference Architecture, and Analyses

This paper surveys the deep learning (DL) approaches for intrusion-detection systems (IDSs) in Internet of Things (IoT) and the associated datasets toward identifying gaps, weaknesses, and a neutral reference architecture. A comparative study of IDSs is provided, with a review of anomaly-based IDSs on DL approaches, which include supervised, unsupervised, and hybrid methods. All techniques in these three categories have essentially been used in IoT environments. To date, only a few have been used in the anomaly-based IDS for IoT. For each of these anomaly-based IDSs, the implementation of the four categories of feature(s) extraction, classification, prediction, and regression were evaluated. We studied important performance metrics and benchmark detection rates, including the requisite efficiency of the various methods. Four machine learning algorithms were evaluated for classification purposes: Logistic Regression (LR), Support Vector Machine (SVM), Decision Tree (DT), and an Artificial Neural Network (ANN). Therefore, we compared each via the Receiver Operating Characteristic (ROC) curve. The study model exhibits promising outcomes for all classes of attacks. The scope of our analysis examines attacks targeting the IoT ecosystem using empirically based, simulation-generated datasets (namely the Bot-IoT and the IoTID20 datasets).

97 MATHEMATICS AND COMPUTING↗