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NASA NTRSDate not supplied

pyQuARC: Open Source Library for Earth Observation Metadata Quality Assessment

Metadata quality is essential to effective data discovery and has become increasingly vital as more Earth Science data sets become available. The Common Metadata Repository (CMR) hosts metadata describing NASA’s Earth Observation data products, which are archived across 12 Distributed Active Archive Centers (DAACs). The Analysis and Review of CMR (ARC) Team, located at Marshall Space Flight Center, conducts metadata quality assessments to ensure that these data products are discoverable, accessible, and usable. To achieve these goals, the ARC team has developed a metadata quality assessment framework to evaluate metadata completeness, correctness, and consistency. ARC uses a combination of manual and automated methods to assess these three components and identify areas of improvement; the team then collaborates with the DAACs to resolve any findings. To streamline this process, ARC is currently developing a host of scripts, known as pyQuARC, to automate metadata quality assessments as much as possible. pyQuARC is an open source library for Earth Observation Metadata Quality Assessment, and the tool utilizes ARC’s metadata quality assessment framework to make basic validation checks, pinpoint inconsistencies between dataset-level (i.e. collection) and file-level (i.e. granule) metadata, and identify opportunities for more descriptive and robust information. Since pyQuARC is also customizable, other users can make modifications as needed, and future metadata standards can also be implemented. Once pyQuARC is fully developed, it will support multiple schema types to serve the broader EOSDIS metadata community. This presentation will provide an overview of pyQuARC and its process of development while showcasing the tool’s valuable features and uses.

Jenny Wood↗
NASA NTRSDate not supplied

pyQuARC: Preparing for Full Release

Metadata holds the contextual information about data and is the underlying structure for many data search portals. High quality metadata optimizes search results, allowing users to quickly retrieve the data they need. With the abundant volume and diversity of Earth observation datasets, data discovery and metadata quality are critical for end users. The Common Metadata Repository (CMR), for example, currently hosts metadata for over 9,000 Earth observation data products archived across 12 NASA Distributed Active Archive Centers (DAACs). The Analysis and Review of CMR (ARC) Team, located at Marshall Space Flight Center, assesses the completeness, correctness, and consistency of these metadata records to ensure they are accessible, usable, and discoverable. In 2021, ARC began developing pyQuARC, an open source library for Earth Observation Metadata Quality Assessment to automate this effort. The tool uses ARC’s existing metadata quality framework to provide prioritized recommendations for metadata improvement. During initial testing, pyQuARC automatically identified 58% of metadata findings when compared with a sample of manually reviewed records. Using the results from initial testing, this presentation will focus on recent advancements and improvements of the tool as the ARC team prepares for pyQuARC’s full release. It will also demonstrate pyQuARC's enrichment value, not only for the ARC team, but the broader EOSDIS metadata community as well.

Essence Raphael↗
NASA NTRSDate not supplied

ICARTT File Format Enhancements: Supporting FAIRness of Airborne and Field Campaign Data

The ICARTT (International Consortium for Atmospheric Research on Transport and Transformation) standards were developed to fulfill data management needs for the ICARTT campaign in 2004. The ICARTT file format is text-based and composed of a header with important data description information and the data section. The ICARTT format, built on the NASA Ames and GTE data formats, was created to facilitate data exchange and promote collaborations among the science teams for achieving the ICARTT campaign goals. Due to the success of the ICARTT campaign, the ICARTT file format was exposed to a broad range of airborne researchers and was adopted for use in many other field campaigns sponsored by NASA and other partner agencies. The ICARTT format standards became a NASA standard in 2010 and was amended in January 2017 providing many enhancements, including the requirement for variable standard names. Primarily designed for airborne field studies, ICARTT has been further utilized for ground-based studies. The ICARTT format can host metadata that is critical for proper use of the data, especially for in-situ measurements. However, the information that needs to be included is often in free text, meaning the information are human readable, but not machine interpretable. Furthermore, the amount and type of information provided can vary substantially between principal investigators and campaigns. To support interoperability and FAIR principles, further enhancements to the ICARTT standards are recommended. Possible recommendations include standardizing timestamps for easier data comparisons and analysis; potential use of controlled and consistent vocabulary for variable short name and certain common metadata elements; and providing guidance on variable measurement units and how they are reported.

Megan Buzanowicz↗
NASA NTRSDate not supplied

ICARTT File Format Enhancements: Supporting FAIRness and Data Discovery of Suborbital Campaign Data

Suborbital campaigns aim to accomplish a wide variety of goals and can include a variety of platforms, instruments, and parameters measured. In 2004, the ICARTT (International Consortium for Atmospheric Research on Transport and Transformation) standards were developed to fulfill data management needs for the ICARTT campaign. The ICARTT file format is text-based and composed of a header with important data description information and the data section. Built on the NASA Ames and GTE data formats, the ICARTT format was created to facilitate data exchange and promote collaborations among the science teams for achieving the ICARTT campaign goals. Due to its success and adaptation for use in many other field campaigns, the ICARTT file format became a NASA standard in 2010 and was amended in January 2017. These changes provided many enhancements, including the requirement for variable standard names. Primarily designed for airborne field studies, ICARTT has been further utilized for ground-based studies. NASA has made a commitment to build an inclusive open science community over the next decade. Open-source science strives to make publicly funded scientific research transparent, inclusive, accessible, and reproducible. The ICARTT format can host metadata that is critical for proper use of the data, particularly for in-situ measurements, and can enhance data discovery and accessibility. However, the required fields are often free text, meaning that the information is human readable, but not machine interpretable. Furthermore, the amount and type of information provided can vary significantly between principal investigators and campaigns. To support FAIR principles and interoperability, enhancements to the ICARTT standards are recommended. Possible recommendations include potential use of controlled and consistent vocabulary for variable standard name and certain common metadata elements; standardizing timestamps for easier data comparisons and analysis; and providing guidance on variable measurement units and how they are reported. Enhancing ICARTT metadata can further streamline the process to make suborbital data more readily available to the data user and improve variable-level metadata. Providing more variable-level metadata can enhance data searching and discovery, supporting NASA’s Open-Source Science Initiative (OSSI).

Megan Buzanowicz↗
DOE OSTI2023

EDX Spatial: Leveraging cloud and hybrid data management resources for spatial data

In the last few years, the National Energy Technology Laboratory has started leveraging cloud-hosted services for hosting spatial data collections published on the Energy Data eXchange (EDX). Using cloud-hosted storage and compute options offers multiple benefits for visualization and tool development through utilization of spatial data resources. The transition from on-premises services to cloud-hosted services has enabled a few key features: increased accessibility of large derivative datasets, dynamic integration of external authoritative data resources directly from outside entities through representational state transfer application programming interfaces (REST API), and the ability to produce complex mapping applications, dashboards, and online maps. As a result of the shift, NETL has launched EDX Spatial, a platform that leverages on-premises resources combined with cloud compute capabilities to enable enhanced online mapping interfaces and optimize data access. In addition, a unified workflow for handling the public release of spatial data products through EDX has been developed, including standardization of data hosting practices, metadata, symbology, and application elements. This poster reviews the opportunity of leveraging cloud-hosted and hybrid data management solutions for spatial data, and discusses the benefits and lessons learned while leveraging these services through the data repository EDX.

Morkner, Paige↗
NASA NTRSDate not supplied

Additional Metadata Guidelines to Improve the Structure and Usability of HDF and NetCDF Files

The Hierarchical Data Format (HDF) and Network Common Data Form (NetCDF) are data file formats created to aid users in the creation or use of scientific data. These file formats are useful for handling large data volumes and hosting extensive metadata as global attributes or variables and are popular with the modeling community. HDF and NetCDF files are largely used with remote sensing data and have been used to support measurements from numerous campaigns, from satellite to aircraft or ground and mobile based measurements. The files from airborne field studies, however, vary greatly in terms of the file structure and the amount and content of metadata. Information relevant to the file that can be useful to the user such as the data producer, location where data was taken, variable descriptions, or information about the instrument might not be included in the file. This metadata might be present in another file in the dataset containing the same data using the International Consortium for Atmospheric Research on Transport and Transformation (ICARTT) format. Recently, the Aerosols, Clouds, and their Interactions for Earth System Models (MACIE) group started a grassroots effort to develop a set of requirements for the HDF and NetCDF files for field studies, aiming to make the data products more interoperable and usable. Particularly, these requirements seek to make the files more compliant to Climate and Forecast (CF) metadata conventions and to standardize the file structure and the global and variable attributes. These requirements would help to ensure that HDF and NetCDF files contain adequate metadata to better support their use for research, e.g., the modeling community, and to enhance the usability and interoperability of data for research communities at large. To be presented are the details of the MACIE requirements as well as examples of the implementation of these requirements for merge files and lidar observation data files.

Sean Leavor↗
NASA NTRSDate not supplied

Extending CF Conventions to Enhance Data FAIRness for Atmospheric Composition Observations

The Hierarchical Data Format (HDF) and Network Common Data Form (NetCDF) are data file formats created to aid users in the creation or use of scientific data. These file formats are useful for handling large data volumes and hosting extensive metadata as global, group, or variable attributes and are popular with the modeling community. HDF and NetCDF files are widely used with atmospheric remote sensing data and have been used to support measurements from numerous field campaigns, from satellite to aircraft or ground and mobile based measurements. The files from airborne field studies, however, vary greatly in terms of the file structure and the amount and content of their metadata. Information relevant to the file that can be useful to the user such as the data producer, location where data was taken, variable descriptions, or information about the instrument might not be included in the file. Recently, the Measurements of Aerosols, Clouds, and their Interactions for Earth System Models (MACIE) group started a grassroots effort to develop a CF-based template for the HDF and NetCDF files for field studies, with the aim of making the data products more interoperable and usable. This template seeks to make the files more compliant to Climate and Forecast (CF) metadata conventions and to standardize the file structure and the global and variable attributes. The template would help to ensure that HDF and NetCDF files contain adequate metadata to better support their use for research, e.g., the modeling community, and to enhance the usability and interoperability of data for research communities at large. The draft template has been applied to recent field studies for various instruments and their merge files in support of the Atmosphere Observing System (AOS) project. The details of the revised template are to be presented, as well as examples of the implementation of these requirements for merge files and lidar observation data files and issues revealed during the implementation process.

Sean Leavor↗
DOE OSTI2026

Beyond microbial abundance: metadata integration enhances disease prediction in human microbiome studies

Multiple studies have highlighted the interaction of the human microbiome with physiological systems such as the gut, immune, liver, and skin, via key axes. Advances in sequencing technologies and high-performance computing have enabled the analysis of large-scale metagenomic data, facilitating the use of machine learning to predict disease likelihood from microbiome profiles. However, challenges such as compositionality, high dimensionality, sparsity, and limited sample sizes have hindered the development of actionable models. One strategy to improve these models is by incorporating key metadata from both the human host and sample collection/processing protocols. This remains challenging due to sparsity and inconsistency in metadata annotation and availability. In this paper, we introduce a machine learning-based pipeline for predicting human disease states by integrating host and protocol metadata with microbiome abundance profiles from 68 different studies, processed through a consistent pipeline. Our findings indicate that metadata can enhance machine learning predictions, particularly at higher taxonomic ranks like Kingdom and Phylum, though this effect diminishes at lower ranks. Our study leverages a large collection of microbiome datasets comprising 11,208 samples, therefore enhancing the robustness and statistical confidence of our findings. This work is a critical step toward utilizing microbiome and metadata for predicting diseases such as gastrointestinal infections, diabetes, cancer, and neurological disorders.

Mathematics and Computing↗
DOE OSTI2021

Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes

Although secondary metabolites are typically associated with competitive or pathogenic interactions, the high bioactivity of endophytic fungi in the Xylariales, coupled with their abundance and broad host ranges spanning all lineages of land plants and lichens, suggests that enhanced secondary metabolism might facilitate symbioses with phylogenetically diverse hosts. Here, we examined secondary metabolite gene clusters (SMGCs) across 96 Xylariales genomes in two clades (Xylariaceae s.l. and Hypoxylaceae), including 88 newly sequenced genomes of endophytes and closely related saprotrophs and pathogens. We paired genomic data with extensive metadata on endophyte hosts and substrates, enabling us to examine genomic factors related to the breadth of symbiotic interactions and ecological roles. All genomes contain hyperabundant SMGCs; however, Xylariaceae have increased numbers of gene duplications, horizontal gene transfers (HGTs) and SMGCs. Enhanced metabolic diversity of endophytes is associated with a greater diversity of hosts and increased capacity for lignocellulose decomposition. Our results suggest that, as host and substrate generalists, Xylariaceae endophytes experience greater selection to diversify SMGCs compared with more ecologically specialised Hypoxylaceae species. Altogether, our results provide new evidence that SMGCs may facilitate symbiosis with phylogenetically diverse hosts, highlighting the importance of microbial symbioses to drive fungal metabolic diversity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

PNNL DataHub Project: Omics Lethal Human Viruses Project Profiling of the Host Response to Ebola Virus Infection, Processed Experimental Dataset Catalog

Ebola virus (EBOV) is high risk biological agent, classified as a Category A priority pathogen (Flaviviridae) by the National Institute of Allergy and Infectious Diseases (NIAID), known to cause hemorrhagic fever with high mortality rates in humans. Lethal host-pathogen invasion mechanisms and the cellular intricacies behind these fatal infections still remain unclear. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013-2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. Herein, PNNL sub-projects provide a never before released comprehensive infectious disease collection of primary and secondary transformation multi-Omics data profiling a series of priority pathogen primary experimental studies for enhanced open-access to viral Omics datasets and project lifecycle metadata. Secondary host-pathogen viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics (P), metabolomics (M), lipidomics (L), and transcriptomics (T) dataset downloads each have a direct relationship to a primary sample submission corresponding to a specific Ebola virus [NCBITAXON:186536] (Zaire/Makona or Zaire/Mayinga) experimental infection study. Human host samples types include peripheral blood mononuclear cells isolated from blood plasma ["PBMC", BTO:0001025], human hepatoma carcinoma cells ["HUH", BTO:0001950], human umbilical vein endothelial cells ["HUVEC", BTO:0001949], immortalized human hepatocyte cells ["IHH", BTO:0006147], and human histiocytic lymphoma cells ["U937", BTO:0001412].

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

PNNL DataHub Project: Omics Lethal Human Viruses Project Profiling of the Host Response to Influenza A Virus Infection, Processed Experimental Dataset Catalog

Influenza A virus (IAV) is a high risk biological agent, classified as a Category C priority pathogen (Orthomyxoviridae) by the National Institute of Allergy and Infectious Diseases (NIAID), and is known to cause severe respiratory disease with high mortality rates in humans. Lethal host-pathogen invasion mechanisms and the cellular intricacies behind these fatal infections still remain unclear. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013-2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. Herein, PNNL sub-projects provide a never before released comprehensive infectious disease collection of primary and secondary transformation multi-Omics data profiling a series of priority pathogen primary experimental studies for enhanced open-access to viral Omics datasets and project lifecycle metadata. Secondary host-pathogen viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics (P), metabolomics (M), lipidomics (L), and transcriptomics (T) dataset downloads each have a direct relationship to a primary sample submission corresponding to a specific Influenza A virus [NCBITAXON:11320] experimental infection study. Host sample types include human lung adenocarcinoma cells ["Calu-3", BTO:0002750] and whole mouse lung [BTO:0000763] tissue collections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

PNNL DataHub Project: Omics Lethal Human Viruses Project Profiling of the Host Interferon-Stimulated Response to Virus Infection, Processed Experimental Dataset Catalog

Human Interferon (IFN) alpha, beta, and gamma participate in the body's natural immune response to lethal virus infection and disease.The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013 - 2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013-2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. Herein, PNNL sub-projects provide a never before released comprehensive infectious disease collection of primary and secondary transformation multi-Omics data profiling a series of priority pathogen primary experimental studies for enhanced open-access to viral Omics datasets and project lifecycle metadata. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics (T) dataset downloads each have a direct relationship to a primary sample submission corresponding to a specific Human Interferon (IFN), interferon alpha (IFNα), interferon beta (IFNβ), and/or interferon gamma (IFNγ) stimulated response to an experimental virus infection treatment study. Host sample types include cerebellum ["CB", BTO:0000232], cortical neurons ["CN", BTO:0004102], cortex ["CT", BTO:0000233], dendritic cells ["DC", BTO:0002042], granule cell neurons ["GCN", BTO:0003393], lymph node ["LN", BTO:0000784], and serum ["SE", BTO:0001239] from mouse (Mus musculus) tissue collections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Omics Lethal Human Viruses Project Profiling of the Host Response to MERS-CoV Infection, Processed Experimental Dataset Catalog

Middle East Respiratory Syndrome coronavirus (MERS-CoV) is classified as a Category C priority pathogen (Coronaviridae) by the National Institute of Allergy and Infectious Diseases (NIAID), and is known to cause severe respiratory disease with high mortality rates in humans. Lethal host-pathogen invasion mechanisms and the cellular intricacies behind these fatal infections still remain unclear. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013-2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. Herein, PNNL sub-projects provide a never before released comprehensive infectious disease collection of primary and secondary transformation multi-Omics data profiling a series of priority pathogen primary experimental studies for enhanced open-access to viral Omics datasets and project lifecycle metadata. Secondary host-pathogen viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics (P), metabolomics (M), lipidomics (L), and transcriptomics (T) dataset downloads each have a direct relationship to a primary sample submission corresponding to a specific MERS-CoV [NCBITAXON:1335626] experimental infection study. Host sample types include human lung adenocarcinoma cells ["Calu-3", BTO:0002750], human bronchial epithelial cells ["Calu-3 clone 2B4"; BTO:0002022], primary human fibroblasts ["FB"; BTO:0000452], primary human airway epithelial cells ["HAE"; BTO:0005571], human microvascular endothelial cells ["HMVE"; BTO:0003123], and whole mouse lung [BTO:0000763] tissue collections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

PNNL DataHub Project: Omics Lethal Human Viruses Project Profiling of the Host Response to West Nile Virus Infection, Processed Experimental Dataset Catalog

West Nile virus (WNV) is classified as a Category B priority pathogen (mosquito-borne Flavivirus) by the National Institute of Allergy and Infectious Diseases (NIAID), and are known to cause severe infections in humans where lethal host-associated mechanisms are not clearly defined. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013 - 2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013-2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. Herein, PNNL sub-projects provide a never before released comprehensive infectious disease collection of primary and secondary transformation multi-Omics data profiling a series of priority pathogen primary experimental studies for enhanced open-access to viral Omics datasets and project lifecycle metadata. Secondary host-pathogen viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics (P), metabolomics (M), lipidomics (L), and transcriptomics (T) dataset downloads each have a direct relationship to a primary sample submission corresponding a specific West Nile virus [NCBITAXON:11082] (WNV-NY99 382) experimental infection study. Host sample types include cerebellum ["CB", BTO:0000232], cortical neurons ["CN", BTO:0004102], cortex ["CT", BTO:0000233], dendritic cells ["DC", BTO:0002042], granule cell neurons ["GCN", BTO:0003393], lymph node ["LN", BTO:0000784], and serum ["SE", BTO:0001239] from mouse (Mus musculus) tissue collections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses

High-throughput sequencing has generated an unprecedented volume of data. However, researcher-submitted data in repositories requires extensive curation and quality control for reuse. These tasks are hindered by the multiplicity of repositories, the sheer volume of the data, and the complexity of virus (meta)data curation. To address these challenges, VirJenDB offers a user-friendly platform to facilitate versioned, community-driven curation, and ontology development. Virus sequences were ingested from 16 sources, including ~200 fields of metadata or standards, covering taxonomy, sample, and host information. Up to 85 metadata fields have undergone at least one round of curation, and are linked to 15.4 million virus sequences, with 88 % from those infecting eukaryotes and the remaining infecting prokaryotes. Subsets were created, including a novel collection of 0.91 million viral operational taxonomic unit (vOTU) sequences across all viruses, while keeping the original sequences from each vOTU to facilitate downstream analyses, e.g. sequence variation. The VirJenDB web portal (https://www.virjendb.org) provides HTTPS and Application Programming Interface (API) access to the sequence datasets and metadata, offering a search engine, filtering, download, visualizations, and documentation. VirJenDB aims to connect the phage and eukaryotic virus research communities by supporting webtool integration, meta-analyses, and metadata schema extensions.

Saghaei, Shahram↗
DOE OSTI2026

covariance libs

This dataset contains covariance libraries created for SCALE. These will be distributed by providing documentation and metadata in GitLab repos hosted by ORNL (code.ornl.gov/scale/data/cov-libs), and the main datasets are hosted in S3-based ORNL servers. The data are also contained in Constellation. More documentation can be found in PUB ID 263037.

Brown, Jesse [ORNL] (ORCID:0000000207694100)↗
DOE OSTI2021

Omics-Lethal Human Viruses, Influenza A Experiment ICL105

The purpose of this experiment was to evaluate the host epigenetic response to Influenza A (H5N1) viral infection from human lung adenocarcinoma cells (Calu-3) high throughput sequencing (ChIP-Seq) sample data. Host-associated viral downloads contain one or more primary host-pathogen experimental study metadata design workbooks (supporting metadata only).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Omics-Lethal Human Viruses, Influenza A Experiment ICL106

The purpose of this experiment was to evaluate the human host epigenetic response to Influenza A H5N1 virus and MERS-CoV viral infection from human lung adenocarcinoma cell (Calu-3) high throughput sequencing (MeDIP-Seq) sample data. Host-associated viral downloads contain one or more primary host-pathogen experimental study metadata design workbooks (supporting metadata only).

59 BASIC BIOLOGICAL SCIENCES↗