NIAID Modeling Host Responses to Understand Severe Human Virus Infections, Multi-Omic Viral Dataset Catalog Collections

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Last updated on 2023-01-30T00:09:57+00:00 by LN Anderson

Reusable Digital Data Lifecycle Downloads for Modeling Host Responses to Understand Severe Human Virus Infections

The National Institute of Allergy and Infectious Diseases (NIAID) "Modeling Host Responses to Understand Severe Human Virus Infections" (U19AI106772) program project was a highly integrated and comprehensive systems biology research core, funded by the NIH from 2013-06-01 to 2018-05-31, investigating the complex host response to infection in a series of NIAID priority pathogens. Resulting project deliverables include an extensive and comprehensive systems biology data collection that serves to both enhance predictive modeling of infectious disease and identifying functional regulators of severe human virus pathogenicity for exploiting new developments and therapeutic interventions assisting the human host response to Category A, B, and C priority pathogens.

Omics lethal human virus (OMICS-LHV) sub-project research activities conducted at Pacific Northwest National Laboratory (PNNL) included the Proteomics, Metabolomics, and Lipidomics Core (PML) and the Computational Modeling Core (CMC), where performed proteomic, metabolomic, lipidomic, and transcriptomic data profiling leveraged world-class mass spectrometry (MS)-based capability platforms and state-of-the-art statistical and computational techniques in providing linked primary and secondary transformation viral experimental infection data.

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 lifecycle datasets and project metadata. Using a highly integrated and multidisciplinary approach, linked primary data and metadata supporting secondary normalization datasets, provide critical information necessary for research reproducibility and long-term preservation. Enabling on-demand data access for research community consumption and developer reuse, serves to support new mechanistic insights and discoveries into host-pathogen interactions for aiding future biohazard data preparedness efforts in emergency response to global health crises involving viral infection.

Accessible Secondary DOI Digital Data Downloads

    Secondary qualitative viral experimental dataset downloads contain one or more statistically processed quantitative dataset file(s) containing normalization transformation data analyses leveraging unique high-resolution instrument capabilities. In addition, all resulting primary metadata files necessary for viral infection study transparency and reuse have been included for each separate experimental DOI download (this includes: experimental designs, dataset summary, viral titer workbooks, etc.). Proteomic, metabolomic, lipidomic, and/or transcriptomics dataset downloads each have a direct relationship to a primary sample data submission corresponding to the NCBI BioProject Umbrella and MassIVE collections listed below for Ebola virus (EBOV), Influenza A virus (lAV), West Nile virus (WNV), Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV), and/ human host interferon (IFN) treatment response to infection.

    Experimental Dataset DOI Catalog Collections for Download

    50 viral experiments, 134 secondary processed data downloads, 402 supplementary dataset metadata files. Note: Each experimental download collection is comprised from comprehensive time course sample collections in replicate.

    1. Anderson, Lindsey, Eisfeld, Amie J, Waters, Katrina M, and Modeling Host Responses to Understand Severe Human Virus Infections Program Project. PNNL DataHub Omics-LHV Project Profiling of the Host Response to Ebola Virus Infection, a Processed Dataset DOI Catalog Experimental Collection. United States. 2021. PNNL DataHub (Web). DOI: 10.25584/LHVEBOV/1784282.
    2. Anderson, Lindsey, Eisfeld, Amie J, Waters, Katrina M, and Modeling Host Responses to Understand Severe Human Virus Infections Program Project. PNNL DataHub Omics-LHV Project Profiling of the Host Response to Influenza A Virus Infection, a Processed Dataset DOI Catalog Experimental Collection. United States. 2021. PNNL DataHub (Web). DOI: 10.25584/LHVFLU/1773428.
    3. Anderson, Lindsey, Eisfeld, Amie J, Waters, Katrina M, and Modeling Host Responses to Understand Severe Human Virus Infections Program Project. PNNL DataHub Omics-LHV Project Profiling of the Host Response to West Nile Virus Infection, a Processed Dataset DOI Catalog Experimental Collection. United States. 2021. PNNL DataHub (Web). DOI: 10.25584/LHVWNV/1784305.
    4. Anderson, Lindsey, Eisfeld, Amie J, Waters, Katrina M, and Modeling Host Responses to Understand Severe Human Virus Infections Program Project. PNNL DataHub Omics-LHV Project Profiling of the Host Interferon-Stimulated Response to Virus Infection, a Processed Dataset DOI Catalog Experimental Collection. United States. 2021. PNNL DataHub (Web). DOI: 10.25584/LHVIFN/1786979.
    5. Anderson, Lindsey, Eisfeld, Amie J, Waters, Katrina M, and Modeling Host Responses to Understand Severe Human Virus Infections Program Project. PNNL DataHub Omics-LHV Project Profiling of the Host Response to Middle Eastern Respiratory Syndrome coronavirus Infection, a Processed Dataset DOI Catalog Experimental Collection. United States. 2021. PNNL DataHub (Web). DOI: 10.25584/LHVMERS/1813911.

    Relevant Source Code

    1. Kelly G. Stratton & Lisa M. Bramer. (2018). pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data (0.10.0). Zenodo. DOI: 10.5281/zenodo.6108668. URL: https://github.com/pmartR/pmartR/tree/v1.0.0
    2. Matthew Monroe, Cameron Casey, Grant Fujimoto, Christopher Wilkins, Joon-Yong Lee, Cameron Giberson, & Michael Degan. (2022). LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data. DOI: 10.5281/zenodo.6459463. URL: https://github.com/PNNL-Comp-Mass-Spec/LIQUID

    Linked Open Primary Data Downloads

    Primary Sequencing Data - 2,555 total primary datasets

    The Gene Expression Omnibus (GEO) is a public domain community data repository, supported by the NIH, promoting the free exchange of MIAME-compliant gene expression profile and array-based data.Primary transcriptome Agilent and Affymetrix microarray experimental data collections (txt and txt.gz) and associated metadata are openly available and have been submitted to the NCBI BioProject Umbrella: PRJNA274402 corresponding to dataset sub-project collection uploads to GEO under the SuperSeries: GSE65575,  and link to primary publication data accessions where possible.

    Primary Mass Spectrometry Data - 21,194 total primary datasets

    The Mass Spectrometry Interactive Virtual Environment (MassIVE) is a public domain community data repository, developed by the NIH-funded Center for Computational Mass Spectrometry, promoting the free exchange of mass spectrometry data.

    Reusable FAIRsharing DOI Repository Standards

    Primary Data Archive

    Mass Spectrometry - proteomics, metabolomics, lipidomics

    Sequencing - transcriptomics, microarray

    Secondary Data Archive

    Multi-Omic Integrations - transcriptomics, proteomics, metabolomics, lipidomics, experimental metadata

    Software & Source Code

    Data Processing Analysis Tools

     

      Acknowledgment of Federal Funding

      The data described here was funded in whole or in part by the National Institute of Allergy and Infectious Diseases, of the National Institutes of Health under award number U19AI106772 and is a contribution of the "Modeling Host Responses to Understand Severe Human Virus Infections" Project at Pacific Northwest National Laboratory. Data generated by the Omics-LHV Core for proteomics, metabolomics, and lipidomics analyses for were performed at Pacific Northwest National Laboratory in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy’s (DOE) Office, operating under the Battelle Memorial Institute for the DOE under contract number DE-AC05-76RLO1830. 

      Citation Policy

      In efforts to enable discovery, reproducibility, and reuse of NIH-funded project dataset citations, we ask that all reuse of project data and metadata download materials acknowledge all primary and secondary dataset citations where applicable and direct corresponding journal articles (Grant U19AI106772) where allowable in accordance with best practices outlined by the FORCE11 Joint Declaration of Data Citation Principles in alignment with NIH acknowledgement requirements (NOT-OD-21-013).

      Data Licensing

      CC BY-SA 4.0 (secondary dataset download DOIs), CC0 1.0 (project metadata and PNNL DataHub policy default)

       

        Project status

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        English
        Datasets (49)
        Publications (20)
        People (2)

        Lindsey Anderson’s research has been dedicated to the identification and characterization of novel, targeted and non-targeted, functional metabolic interactions using a high-throughput systems biology and computational biology approach. Her expertise in functional metabolism and multidisciplinary...

        Dr. Katrina Waters is the division director for Biological Sciences at the Pacific Northwest National Laboratory. Waters has a Ph.D. in biochemistry and more than 15 years of experience in microarray and proteomics data analysis. Her research interests are focused on the integration of genomics...

        Data Sources (4)
        Methods (1)
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        Software (2)