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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology

Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. Here, we propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Cric searchable image database as a public platform for conventional pap smear cytology data

Amidst the current health crisis and social distancing, telemedicine has become an important part of mainstream of healthcare, and building and deploying computational tools to support screening more efficiently is an increasing medical priority. The early identification of cervical cancer precursor lesions by Pap smear test can identify candidates for subsequent treatment. However, one of the main challenges is the accuracy of the conventional method, often subject to high rates of false negative. While machine learning has been highlighted to reduce the limitations of the test, the absence of high-quality curated datasets has prevented strategies development to improve cervical cancer screening. The Center for Recognition and Inspection of Cells (CRIC) platform enables the creation of CRIC Cervix collection, currently with 400 images (1,376 × 1,020 pixels) curated from conventional Pap smears, with manual classification of 11,534 cells. This collection has the potential to advance current efforts in training and testing machine learning algorithms for the automation of tasks as part of the cytopathological analysis in the routine work of laboratories.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The 2021 update of the EPA’s adverse outcome pathway database

The EPA developed the Adverse Outcome Pathway Database (AOP-DB) to better characterize adverse outcomes of toxicological interest that are relevant to human health and the environment. Here we present the most recent version of the EPA Adverse Outcome Pathway Database (AOP-DB), version 2. AOP-DB v.2 introduces several substantial updates, which include automated data pulls from the AOP-Wiki 2.0, the integration of tissue-gene network data, and human AOP-gene data by population, semantic mapping and SPARQL endpoint creation, in addition to the presentation of the first publicly available AOP-DB web user interface. Potential users of the data may investigate specific molecular targets of an AOP, the relation of those gene/protein targets to other AOPs, cross-species, pathway, or disease-AOP relationships, or frequencies of AOP-related functional variants in particular populations, for example. Version updates described herein help inform new testable hypotheses about the etiology and mechanisms underlying adverse outcomes of environmental and toxicological concern.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A large dataset of detection and submeter-accurate 3-D trajectories of juvenile Chinook salmon

Abstract Acoustic telemetry has been used extensively to study the behavior of aquatic animals. The Juvenile Salmon Acoustic Telemetry System (JSATS) is one such system; it was developed for studying juvenile salmonids but has been used to study numerous species. A recent innovation of the JSATS system is an acoustic transmitter that is small enough to be implanted through injection or small incision that doesn’t require sutures. Use of the JSATS system involves deploying cabled acoustic receivers at hydroelectric dams, or other structures, and autonomous acoustic receivers in free-flowing sections of a river. The raw detections from acoustic-tagged fish are processed to remove potential false positives. The clean detections (5,147,996 total) are used to generate detection events and to compute 3-D trajectories (403,900 total), which are used to assign fish to a passage route through a dam. Controlled field testing involving a high-accuracy Global Positioning System receiver is done to validate the submeter accuracy of the trajectories. The JSATS dataset could be reused for expanding the understanding of near-dam fish behavior.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

CORE: A Global Aggregation Service for Open Access Papers

This paper introduces CORE, a widely used scholarly service, which provides access to the world’s largest collection of open access research publications, acquired from a global network of repositories and journals. CORE was created with the goal of enabling text and data mining of scientific literature and thus supporting scientific discovery, but it is now used in a wide range of use cases within higher education, industry, not-for-profit organisations, as well as by the general public. Through the provided services, CORE powers innovative use cases, such as plagiarism detection, in market-leading third-party organisations. CORE has played a pivotal role in the global move towards universal open access by making scientific knowledge more easily and freely discoverable. In this paper, we describe CORE’s continuously growing dataset and the motivation behind its creation, present the challenges associated with systematically gathering research papers from thousands of data providers worldwide at scale, and introduce the novel solutions that were developed to overcome these challenges. The paper then provides an in-depth discussion of the services and tools built on top of the aggregated data and finally examines several use cases that have leveraged the CORE dataset and services.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2024

Implementing interdisciplinary sustainability education with the food-energy-water (FEW) nexus

Growth in the green jobs sector has increased demand for college graduates who are prepared to enter the workforce with interdisciplinary sustainability skills. Simultaneously, scholarly calls for interdisciplinary collaboration in the service of addressing the societal challenges of enhancing resilience and sustainability have also increased in recent years. However, developing, executing, and assessing interdisciplinary content and skills at the post-secondary level has been challenging. The objective of this paper is to offer the Food-Energy-Water (FEW) Nexus as a powerful way to achieve sustainability competencies and matriculate graduates who will be equipped to facilitate the transformation of the global society by meeting the targets set by the United Nations Sustainable Development Goals. The paper presents 10 curricular design examples that span multiple levels, including modules, courses, and programs. These modules enable clear evaluation and assessment of key sustainability competencies, helping to prepare graduates with well-defined skillsets who are equipped to address current and future workforce needs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A high-resolution large-eddy simulation framework for wildland fire predictions using TensorFlow

Background: Wildfires are becoming more severe, so we need improved tools to predict them over a wide range of conditions and scales. One approach towards this goal entails the use of coupled fire/atmosphere modelling tools. Although significant progress has been made in advancing their physical fidelity, existing tools have not taken full advantage of emerging programming paradigms and computing architectures to enable high-resolution wildfire simulations. Aims: The aim of this study was to present a new framework that enables landscape-scale wildfire simulations with physical representation of combustion at an affordable cost. Methods: We developed a coupled fire/atmosphere simulation framework using TensorFlow, which enables efficient and scalable computations on Tensor Processing Units. Key Results: Simulation results for a prescribed fire were compared with experimental data. Predicted fire behavior and statistical analysis for fire spread rate, scar area, and intermittency showed overall reasonable agreement. Scalability analysis was performed, showing close to linear scaling. Conclusions: While mesh refinement was shown to have less impact on global quantities, such as fire scar area and spread rate, it benefits predictions of intermittent fire behavior, buoyancy-driven dynamics, and small-scale turbulent motion. Implications: This new simulation framework is efficient in capturing both global quantities and unsteady dynamics of wildfires at high spatial resolutions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

El valor de los metadatos para las estaciones de recuperación de recursos del agua

Spanish: Los metadatos hacen referencia a información descriptiva (como ubicación del sensor, unidad de medida, rango de medida, fecha de calibración, fecha de limpieza, si ocurrió algún evento como episodio de lluvia/fallo operativo/vertido tóxico . . .) que es esencial para convertir los grandes volúmenes de datos que se recogen actualmente en las instalaciones de tratamiento de agua y que están sin procesar en información y recursos útiles. Con el avance de la digitalización en el sector del agua, es fundamental evitar los cementerios de datos y, por otro lado, utilizar los datos almacenados para resolver problemas actuales y futuros. Este artículo se centra en el papel crucial que tienen los metadatos para responder a desafíos futuros y posiblemente impredecibles. El objetivo de este documento es presentar el ‘reto de los metadatos’ y destacar la necesidad de tener en cuenta los metadatos cuando se recoge información como parte de las buenas prácticas de digitalización. English: Metadata refers to descriptive information (such as sensor location, measurement unit, measurement range, calibration date, cleaning date, if any event occurred such as rain event/operating failure/toxic spill, . . .) essential to convert large volumes of raw data that are currently collected at water treatment facilities into useful information and resources. With the advance of digitalization in the water sector, it is fundamental to avoid data graveyards and, on the other hand, using collected data to address current and future problems. This paper focuses on the crucial role that metadata has in responding to future and possibly unpredictable challenges. The aim of this document is to present the ‘metadata challenge’ and to highlight the need to consider metadata when collecting information as part of good digitalization practices.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Reactome and the Gene Ontology: digital convergence of data resources

Abstract Motivation Gene Ontology Causal Activity Models (GO-CAMs) assemble individual associations of gene products with cellular components, molecular functions and biological processes into causally linked activity flow models. Pathway databases such as the Reactome Knowledgebase create detailed molecular process descriptions of reactions and assemble them, based on sharing of entities between individual reactions into pathway descriptions. Results To convert the rich content of Reactome into GO-CAMs, we have developed a software tool, Pathways2GO, to convert the entire set of normal human Reactome pathways into GO-CAMs. This conversion yields standard GO annotations from Reactome content and supports enhanced quality control for both Reactome and GO, yielding a nearly seamless conversion between these two resources for the bioinformatics community. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

TranSyT , an innovative framework for identifying transport systems

The importance and rate of development of genome-scale metabolic models have been growing for the last few years, increasing the demand for software solutions that automate several steps of this process. However, since TRIAGE’s release, software development for the automatic integration of transport reactions into models has stalled. Here, in this paper, we present the Transport Systems Tracker (TranSyT). Unlike other transport systems annotation software, TranSyT does not rely on manual curation to expand its internal database, which is derived from highly curated records retrieved from the Transporters Classification Database and complemented with information from other data sources. TranSyT compiles information regarding transporter families and proteins, and derives reactions into its internal database, making it available for rapid annotation of complete genomes. All transport reactions have GPR associations and can be exported with identifiers from four different metabolite databases. TranSyT is currently available as a plugin for merlin v4.0 and an app for KBase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Standardized naming of microbiome samples in Genomes OnLine Database

The power of next-generation sequencing has resulted in an explosive growth in the number of projects aiming to understand the metagenomic diversity of complex microbial environments. The interdisciplinary nature of this microbiome research community, along with the absence of reporting standards for microbiome data and samples, poses a significant challenge for follow-up studies. Commonly used names of metagenomes and metatranscriptomes in public databases currently lack the essential information necessary to accurately describe and classify the underlying samples, which makes a comparative analysis difficult to conduct and often results in misclassified sequences in data repositories. The Genomes OnLine Database (GOLD) (https:// gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute has been at the forefront of addressing this challenge by developing a standardized nomenclature system for naming microbiome samples. GOLD, currently in its twenty-fifth anniversary, continues to enrich the research community with hundreds of thousands of metagenomes and metatranscriptomes with well-curated and easy-to-understand names. Through this manuscript, we describe the overall naming process that can be easily adopted by researchers worldwide. Additionally, we propose the use of this naming system as a best practice for the scientific community to facilitate better interoperability and reusability of microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants

Abstract FatPlants, an open-access, web-based database, consolidates data, annotations, analysis results, and visualizations of lipid-related genes, proteins, and metabolic pathways in plants. Serving as a minable resource, FatPlants offers a user-friendly interface for facilitating studies into the regulation of plant lipid metabolism and supporting breeding efforts aimed at increasing crop oil content. This web resource, developed using data derived from our own research, curated from public resources, and gleaned from academic literature, comprises information on known fatty-acid-related proteins, genes, and pathways in multiple plants, with an emphasis on Glycine max, Arabidopsis thaliana, and Camelina sativa. Furthermore, the platform includes machine-learning based methods and navigation tools designed to aid in characterizing metabolic pathways and protein interactions. Comprehensive gene and protein information cards, a Basic Local Alignment Search Tool search function, similar structure search capacities from AphaFold, and ChatGPT-based query for protein information are additional features. Database URL: https://www.fatplants.net/

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The Unified Phenotype Ontology : a framework for cross-species integrative phenomics

Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and interpreting these data to inform biological hypotheses. A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed. We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative analysis environment that provides users with access to over 250 000 uniformly annotated and publicly available genomes with curated metadata. PATRIC offers web-based visualization and comparative analysis tools, a private workspace in which users can analyze their own data in the context of the public collections, services that streamline complex bioinformatic workflows and command-line tools for bulk data analysis. Over the past several years, as genomic and other omics-related experiments have become more cost-effective and widespread, we have observed considerable growth in the usage of and demand for easy-to-use, publicly available bioinformatic tools and services. Here we report the recent updates to the PATRIC resource, including new web-based comparative analysis tools, eight new services and the release of a command-line interface to access, query and analyze data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

eDNAjoint: An R package for interpreting paired or semi‐paired environmental DNA and traditional survey data in a Bayesian framework

Abstract Environmental DNA (eDNA) sampling is increasingly used in surveys of species distribution as a potentially sensitive and efficient monitoring method. Yet access to modelling tools designed specifically for interpreting this new data type lags behind its ubiquity. While occupancy modelling software has dominated the analytical landscape for eDNA data analysis of single species, this type of model may not always be the most appropriate. The rate of eDNA detection often corresponds to species density, rather than just occupancy, and researchers often have access to observations from non‐genetic sampling methods at the same sites. To provide users access to a modelling framework designed to maximize the use of all available data, we developed an R package, eDNAjoint . The package provides an easy‐to‐use interface for fitting a ‘joint’ model that integrates data from paired or semi‐paired eDNA and traditional surveys in a Bayesian framework. The model can be used to estimate parameters like the probability of a false positive eDNA detection and mean catch rate at a site, and the package allows access to multiple model variations and Bayesian prior customization. Additional functionality can be used for model selection, summarising posteriors and comparing the relative sensitivities of the two survey methods. We demonstrate the use of eDNAjoint by fitting a variation of the model with site‐level covariates that scale the sensitivity of eDNA sampling relative to traditional sampling. The example workflow uses binary eDNA and seine count data for the endangered tidewater goby ( Eucyclogobius newberryi ) from a study by Schmelzle and Kinziger (2016). This use case includes a prior sensitivity analysis and an evaluation of the relationship between detection rates and environmental variables. eDNAjoint has the potential to greatly increase the range of users who will be able to rigorously analyse eDNA and traditional survey data in a Bayesian framework, understand if and how eDNA can improve monitoring practices, and gain confidence in the interpretability of eDNA data.

Keller, Abigail G. [Department of Environment Scie↗
DOE OSTI2024

Development of learning objectives to support undergraduate virology curriculum guidelines

It has become increasingly important for microbiology educators to help students learn critical concepts of the discipline. This is particularly true in virology, where current challenges include increasing rates of vaccine hesitancy, misinformation about the COVID-19 pandemic, and controversy surrounding research on pathogens with pandemic potential. Having students learn virology can attract more people to the field and increase the number of people who can engage in meaningful discourse about issues relating to the discipline. However, the limited number of virologists who teach undergraduates, combined with the fact that many institutions lack stand-alone virology courses, results in virology often being taught as a limited number of lectures within an undergraduate microbiology course (if it is covered at all), which may or may not be taught by an individual trained as a virologist. To provide a framework to teach virology to undergraduate students, a team of virology educators, with support from the American Society for Virology (ASV), developed curriculum guidelines for use in a stand-alone undergraduate virology course or a virology section within another course. These guidelines are available at the ASV website (https://asv.org/curriculum-guidelines/). To assist educators in implementing these guidelines, we created examples of measurable learning objectives. This perspective provides details about the virology curriculum guidelines and learning objectives and accompanies the perspective by Boury et al. in this issue of the Journal of Microbiology & Biology Education about the recent revision of the microbiology curriculum guidelines overseen by the American Society for Microbiology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

COVID-19 Knowledge Graph -- Dataset for SMCDC 2021 Challenge 2

This repository contains the data for the 2021 Smoky Mountains Computational Sciences Data Challenge (SMCDC21) Challenge 2 -- Finding Novel Links in COVID-19 Knowledge Graph. The total size of all files in this repository is 285MB. Challenge website: https://smc-datachallenge.ornl.gov/2021-challenge-2/ More information about the challenge and the data: https://github.com/ORNL/smcdc-2021-covid-kg

60 APPLIED LIFE SCIENCES↗