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NASA NTRSDate not supplied

NASA Open Science Data Repository: Biomedical FAIR Data, Analysis Tools, User Communities, and Discoveries for Deep Space Missions

Increased biomedical risks and challenges associated with deep space missions require new knowledge discovery, new health countermeasures, and development of novel ecosystems, life support, crop production, and biomedical support capabilities. To meet NASA’s Moon to Mars strategic program goals for Human and Biological Sciences, findable, accessible, interoperable, reusable (FAIR), and maximally open-access data is going to be required to enable humanity to thrive in deep space. Indeed, this cornerstone perspective on FAIR and maximally open access data was also recommended in the recent 2023-2032 Decadal Survey from the National Academies of Sciences, Engineering, and Medicine. The NASA Open Science Data Repository (OSDR) is a maximally open access and FAIR database, and meets various scientific, technical, and operational spaceflight needs. It offers public users and submitters the ability to upload, download, search, share, analyze, and visualize data across ‘omics, physiological, phenotypic, behavioral, bioimaging, video, and environmental monitoring telemetry datasets. OSDR includes NASA GeneLab, NASA Ames Life Sciences Data Archive, and the NASA Biological Institutional Scientific Collection. OSDR has >455 studies with datasets from model organisms and non-NASA human astronauts. There are ~12 datasets from the Inspiration 4 (I4) mission, spanning metagenomics, comprehensive metabolic panels, clonal hematopoiesis, spatial transcriptomics, proteomics, and cytokine panels. In the interest of data privacy, two I4 datasets have raw FASTQ and FASTA files relating to the epitranscriptome, and a new request feature is live in OSDR (with a backend review process established) which was developed based on industry norms. OSDR also recently began a collaboration with the European Space Agency (ESA) to scientifically curate and make available >200 terabytes of human and model organism space-relevant data. The OSDR submission portal is designed to ingest and curate ~25 ‘omics assay data types, and ~50 physiological-phenotypic-imaging assay data types, spanning ultrasonography, micro-computed tomography, histology, morphometric photography, rebound tonometry, gait analysis, optical coherence tomography, novel object recognition, flow cytometry, and immunohistochemistry. A suite of analysis tools are available for OSDR users including: 1) an Environmental Data Application to compare radiation, CO2, relative humidity, temperature, and other telemetry across missions and subjects, 2) the RadLab database, a collaboration between NASA, ESA, the German and Italian Space Agencies, and the Bulgarian Academy of Sciences, which compiles radiation measurements relevant to human spaceflight and provides tools for accessing and manipulating the data, and 3) a Multi-study visualization tool which enables users to look across and combine GeneLab’s omics datasets across different experiments and missions. There are ~600 volunteer OSDR Analysis Working Group (AWG) members who: 1) provide feedback on scientific standards for reuse (subject and assay metadata; processing pipelines; dataset formats and uniformed structures for machine-readability), and 2) collaborate to mine-reuse OSDR data conducting scientific analysis. OSDR has enabled 60 publications as of September 2023, many directly from AWG collaborations most notably the Cell Press package in 2020. Lastly, there are at least 15 articles which mine OSDR data part of a package of ~50 articles across Nature Portfolio with research stemming from I4, the Japan Aerospace Exploration Agency, NASA Space Biology, and the NASA Human Research Program.

open access↗

NASA NTRSDate not supplied

ASDC’s Python-Based Metadata Extraction Pipeline for Suborbital Campaigns

The FAIRness of data products, especially findability and accessibility depend on rich metadata which, when extracted, can allow for proper curation. Over the past few years, the Atmospheric Science Data Center (ASDC) suborbital science support team has developed a metadata extraction pipeline to ensure the required metadata can be retrieved systematically, effectively, and efficiently to ensure the data can be used by a broad community. The development of a pipeline has presented many, but necessary, challenges to support archival and distribution of ASDC’s 30+ suborbital missions. Though sufficient metadata is provided by instrument scientists, the metadata may not be readily machine actionable due to different formats and templates. Further complicating metadata extraction, our team has found that the nature of metadata can be quite diverse given the difference in measurement types, instruments, and measurement platforms. A metadata extraction pipeline has been developed to provide an efficient, plugin-in based, method for adding new parsers, a configuration system that lets non-developers customize how files are processed, and a system for identifying and logging metadata quality issues to ensure they are readily found and addressed. The metadata extraction pipeline identifies critical pieces of metadata that are needed to promote data FAIRness, including location, file revision, measurement start/end datetime and can be easily modified to extract further information (such as variables). Given the wide-ranging datasets, the pipeline has been modified to accommodate multiple file formats, including multiple versions of ICARTT (International Consortium for Atmospheric Research on Transport and Transformation), HDF (Hierarchical Data Format), netCDF (network Common Data Form), and multiple versions of the Ames File Format. The pipeline also supports building metadata for file formats that cannot have metadata easily extracted from them, such as PDF (Portable Document Format) and GIF (Graphics Interchange Format). The pipeline has allowed our team to maintain a consistent flow of data and metadata to archival and distribution services, ensuring the ASDC meets the needs of the suborbital science community. This presentation will highlight the ASDC’s suborbital metadata extraction pipeline, its development, how it’s been modified to support data FAIRness, and plans for maintaining the pipeline and adding new features.

Abraham Porter↗

NASA NTRS2017

Genesis Solar Wind Interstream, Coronal Hole and Coronal Mass Ejection Samples: Update on Availability and Condition

Recent refinement of analysis of ACE/SWICS data (Advanced Composition Explorer/Solar Wind Ion Composition Spectrometer) and of onboard data for Genesis Discovery Mission of 3 regimes of solar wind at Earth-Sun L1 make it an appropriate time to update the availability and condition of Genesis samples specifically collected in these three regimes and currently curated at Johnson Space Center. ACE/SWICS spacecraft data indicate that solar wind flow types emanating from the interstream regions, from coronal holes and from coronal mass ejections are elementally and isotopically fractionated in different ways from the solar photosphere, and that correction of solar wind values to photosphere values is non-trivial. Returned Genesis solar wind samples captured very different kinds of information about these three regimes than spacecraft data. Samples were collected from 11/30/2001 to 4/1/2004 on the declining phase of solar cycle 23. Meshik, et al is an example of precision attainable. Earlier high precision laboratory analyses of noble gases collected in the interstream, coronal hole and coronal mass ejection regimes speak to degree of fractionation in solar wind formation and models that laboratory data support. The current availability and condition of samples captured on collector plates during interstream slow solar wind, coronal hole high speed solar wind and coronal mass ejections are de-scribed here for potential users of these samples.

Allton, J. H.↗

NASA NTRS2019

The Value of Being a Trustworthy Repository

Today, NASA's Earth Observing System Data and Information System (EOSDIS), a system ofactive archives is attaching the CoreTrustSeal to its websites signifying that it merits theconfidence of its user community. But what value does being a trustworthy repository impart to auser? What does it mean to the owners and operators of repositories? What will it mean in thefuture? EOSDIS was started in the 1990s based on a framework of discipline-oriented, geographicallydistributed centers of expertise, named Distributed Active Archive Centers (DAACs). The functionof EOSDIS is to collect Earth Science data sensor measurements (principally those created andneeded by NASA) and manage the data and many derived digital products. EOSDIS providesmany services, including processing, curating, documenting, disseminating, and enabling datadiscovery as well as efficient use of the data. The EOSDIS has been operational over 25 years andmany lessons have been learned relative to the TRUST principles. During the tenure of EOSDIS,many changes have occurred as we have increased the size of the collection from gigabytes totens of petabytes and the distribution of the data to millions of users. We have had severalstages of system evolution that have improved EOSDIS in order to meet both stakeholder andcustomer expectations. This type of evolution is an on-going process to ensure that ourrepositories remain trustworthy. It is also important that our own community of data managersand system engineers add value in being trustworthy. This paper will discuss approaches to change within a large system of Earth Science data and services, while remaining a trustworthyrepository.

Behnke, Jeanne↗

NASA NTRS2018

Analysis and Review of NASA Earth Science Metadata: How Automation Plays a Role

The Analysis and Review of the Common Metadata Repository (CMR ARC) Team reviews all EOSDIS metadata. The team’s objective is to achieve consistency, correctness, and completeness for all metadata records in the CMR, as well as improve the discoverability of NASA's Earth Science data within the CMR framework. This work is currently being completed at Marshall Space Flight Center. CMR makes a single discovery point possible for NASA's Earth Science data users. The CMR team, in collaboration with three other core metadata teams, contributes to the stewardship of NASA's Earth Science data through a process of continual curation and the ongoing development of the Unified Metadata Model (UMM). A key tool now used in the curation process, referred to as the NASA CMR Dashboard, is an online curation dashboard developed in collaboration with software development company, Element 84. This tool facilitates the review of Earth Science metadata records and subsequent stakeholder collaboration on the resolution of identified issues. A key capability of the new tool is a suite of automated compliance checks written in Python 3.6 that verify the integrity of various metadata elements across multiple standards.

Staton, Patrick↗

NASA NTRS2011

Apollo Lunar Sample Integration into Google Moon: A New Approach to Digitization

The Google Moon Apollo Lunar Sample Data Integration project is part of a larger, LASER-funded 4-year lunar rock photo restoration project by NASA s Acquisition and Curation Office [1]. The objective of this project is to enhance the Apollo mission data already available on Google Moon with information about the lunar samples collected during the Apollo missions. To this end, we have combined rock sample data from various sources, including Curation databases, mission documentation and lunar sample catalogs, with newly available digital photography of rock samples to create a user-friendly, interactive tool for learning about the Apollo Moon samples

Dawson, Melissa D.↗

NASA NTRS2018

NASA's GeneLab: An Integrated Omics Data Commons and Workbench

GeneLab (http://genelab.nasa.gov) is a NASA initiative designed to accelerate “open science” biomedical research in support of the human exploration of space and the improvement of life on earth. The GeneLab Data Systems (GLDS) were developed to help investigators corroborate findings from “omics” (genomics, transcriptomics, proteomics, and metabolomics) assays and translate them into systems biology knowledge and, eventually, therapeutics, including countermeasures to support life in space. Phase I of the project (completed) emphasized developing key capabilities for submission, curation, storage, search, and retrieval of omics data from biomedical research in and of space environments. The development focus for Phase II (completed) was federated data search and retrieval of these kinds of data from other open-access repositories. The last phase of the project (in work) entails developing an omics analysis tool set, and a portal to visualize processed omics data, emphasizing integration with the data repository and search functions developed during the prior phases. The final product will be an open-access system where users can individually or collaboratively publish, search, integrate, analyze, and visualize omics data.

genome↗

NASA NTRS2018

NASA's GeneLab: An Integrated Omics Data Commons and Workbench

GeneLab (http://genelab.nasa.gov) is a NASA initiative designed to accelerate "open science" biomedical research in support of the human exploration of space and the improvement of life on earth. The GeneLab Data Systems (GLDS) were developed to help investigators corroborate findings from "omics" (genomics, transcriptomics, proteomics, and metabolomics) assays and translate them into systems biology knowledge and, eventually, therapeutics, including countermeasures to support life in space. Phase I of the project (completed) emphasized developing key capabilities for submission, curation, storage, search, and retrieval of omics data from biomedical research in and of space environments. The development focus for Phase II (completed) was federated data search and retrieval of these kinds of data from other open-access repositories. The last phase of the project (in work) entails developing an omics analysis tool set, and a portal to visualize processed omics data, emphasizing integration with the data repository and search functions developed during the prior phases. The final product will be an open-access system where users can individually or collaboratively publish, search, integrate, analyze, and visualize omics data.

genome↗

NASA NTRS2017

NASA's GeneLab: An Integrated Omics Data Commons and Workbench

Berrios, Daniel C.↗

NASA NTRS2018

GeneLab: Omics Database for Spaceflight Experiments

Motivation - To curate and organize expensive spaceflight experiments conducted aboard space stations and maximize the scientific return of investment, while democratizing access to vast amounts of spaceflight related omics data generated from several model organisms. Results - The GeneLab Data System (GLDS) is an open access database containing fully coordinated and curated "omics" (genomics, transcriptomics, proteomics, metabolomics) data, detailed metadata and radiation dosimetry for a variety of model organisms. GLDS is supported by an integrated data system allowing federated search across several public bioinformatics repositories. Archived datasets can be queried using full-text search (e.g., keywords, Boolean and wildcards) and results can be sorted in multifactorial manner using assistive filters. GLDS also provides a collaborative platform built on GenomeSpace for sharing files and analyses with collaborators. It currently houses 172 datasets and supports standard guidelines for submission of datasets, MIAME (for microarray), ENCODE Consortium Guidelines (for RNA-seq) and MIAPE Guidelines (for proteomics).

omics↗

NASA NTRS2018

Air Quality Satellite Monitoring by TROPOMI on Sentinel-5P

The recently launched Sentinel satellite mission, the Sentinel-5 Precursor (Sentinel-5P), is one of the European Space Agency's (ESA) new mission family – Sentinels. The sole payload on Sentinel-5P is the TROPOspheric Monitoring Instrument (TROPOMI), a nadir-viewing 108⁰ field-of-view push-broom grating hyperspectral spectrometer, covering the wavelengths of ultraviolet-visible (270 nm - 495 nm), near infrared (675 nm - 775 nm), and shortwave infrared (2305 nm - 2385 nm). Sentinel-5P is the first of the Atmospheric Composition Sentinels, and is providing measurements of atmospheric chemistry, aerosols, and clouds at high spatial, temporal, and spectral resolution. The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) supports over a thousand data collections in the focus areas of Atmospheric Composition, Water & Energy Cycles, and Climate Variability. Sentinel-5P TROPOMI Level-1B (L1B) and Level-2 (L2) products are curated at the GES DISC. Sentinel-5P data are provided by the European Union and the European Space Agency (ESA) through an agreement between ESA and NASA. Through its convenient and enhanced tools/services, such as OPeNDAP and L2 Subsetting, GES DISC offers the air quality remote sensing user community facile solutions for using complex Earth science data and applications. This presentation will demonstrate up-to-date TROPOMI products including EarthView (EV) radiance, solar irradiance, Aerosol Index, Carbon Monoxide, Total column Ozone, Nitrogen Dioxide, and cloud, as well as easy ways to access, visualize and subset TROPOMI data.

TROPOMI↗

NASA NTRSDate not supplied

Senteniel-6 Radio Occultation Product Released by NASA GES DISC to Supplement Satellite Remote Sensing Datasets for PBL Study

The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) curates hyperspectral atmospheric sounder remote sensing and numerical model reanalysis datasets which have been utilized in the Planetary Boundary Layer (PBL) research and applications. The hyperspectral sounder remote-sensing datasets include the Atmospheric Infrared Sounder (AIRS) on the Aqua satellite to the Cross-track Infrared Sounder (CrIS) on Suomi--National Polar- orbiting Partnership (NPP) and National Oceanic and Atmospheric Administration -20 (N NOAA-20)/ Joint Polar-orbiting Satellite System -1 (JPSS-1). The Modern-Era Retrospective analysis for Research and Applications Version 2 (MERRA-2) global reanalysis product provides a data record commencing in 1980. The sounder remote sensing and reanalysis datasets include temperature, water vapor, and trace gas profile down to the PBL, and also have a derived PBL height as well. A nearly 10-year (June 2006 to December 2015) seasonal and annual PBL height climatology dataset from COSMIC Global Navigation Satellite System (GNSS) radio occultation (RO) measurement is also available from the GES DISC. In collaboration with Sentinel-6 Project, the GES DISC is implementing curation activities for GNSS RO products from the Sentinel-6A/Sentinel-6 Michael Freilich satellite launched on November 21, 2020. Sentinel-6A RO products provide refractivity, temperature, and humidity profile with finer vertical resolution, leveraging PBL research and application as a supplement to the hyperspectral sounder remote sensing and reanalysis products. The public release of Sentinel- 6A RO products is scheduled for mid-October of 2021. In this presentation, we will introduce all Senitnel-6A products and services, and demonstrate use cases studying the PBL by combining these products with other GES DISC archived data products.

Feng Ding↗

NASA NTRSDate not supplied

Scientific Content Curation in an Open Science Era

Today’s open science environment, in combination with the Big Data era, means more scientific data, software, tools, documentation, publications and other resources are available than ever. The promise of the open science era is that scientists will spend less time reinventing the wheel and more time doing actionable research. Yet navigating this vast and complex information landscape can feel overwhelming to scientists trying to get their bearings. In this presentation, we define and discuss the importance of scientific content curation for enhancing discovery and use of scientific data and information. We also share two examples of scientific content curation in action: the Catalog of Archived Suborbital Earth Science Investigations (CASEI) and the Science Discovery Engine (SDE).

Kaylin Bugbee↗

NASA NTRSDate not supplied

Multi-Decadal Nitrogen Dioxide and Derived Products from Satellites (MINDS) Datasets Released by NASA GES DISC and Their Applications for Air Quality

Nitrogen dioxide (NO2), a pervasive air pollutant, comes from vehicles, power plants, industrial emissions, and off-road sources such as construction or lawn and gardening equipment. The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) curates many remote sensing datasets with NO2 retrievals, which have been utilized for air quality research and applications. The remotely-sensed datasets include those generated by the Ozone Monitoring Instrument (OMI) on the Aura satellite, the TROPOspheric Monitoring Instrument (TROPOMI) onboard the Copernicus Sentinel-5 Precursor (S5P), and the Ozone Mapping and Profiling Suite (OMPS) Nadir-Mapper (NM) instrument on the Suomi National Polar-orbiting Partnership (S- NPP). In collaboration with the NASA Making Earth System Data Records for Use in Research Environments (MEaSUREs) Multi-Decadal Nitrogen Dioxide and Derived Products from Satellites (MINDS) project, the GES DISC recently released MINDS datasets. The NASA MEaSUREs MINDS project aims to develop long-term NO2 global data records by adapting a consistent retrieval algorithm to multiple instrument measurements. Long-term data records will be achieved by applying consistent retrieval approaches to multiple satellite instruments, including OMI (2004 - ); the Global Ozone Monitoring Experiment (GOME, 1995-2011) onboard the second European Remote Sensing satellite (ERS-2); the Scanning Imaging Spectrometer for Atmospheric Cartography (SCIAMACHY, 2002-2012) onboard the ENVIronmental SATellite (ENVISAT); GOME-2 on the Meteorological Operational satellites (MetOp-A and MetOp-B, 2006 - ); and TROPOMI onboard the Copernicus S5P (2017 - ). The long-term record (1995 to present) of MINDS datasets makes them very useful for air quality trend studies. Some MINDS datasets with high spatial resolution of only a few kilometers can be used for air quality research and applications at regional scales. In this presentation, we will introduce all of the MINDS products and services, and demonstrate use cases of MINDS data for studying air quality. We will also present a few other NO2 datasets acquired from NASA’s Health and Air Quality Applied Sciences Team (HAQAST), to be archived and distributed by the GES DISC, and highlight some of their applications for air quality and health.

Feng Ding↗

NASA NTRS2020

Accelerating Space Life Sciences: Successes and Challenges of Biospecimen and Data Sharing

NASA's current human space flight research is directed towards enabling human space exploration beyond Low Earth Orbit (LEO). To that end, NASA Space Flight Payload Projects; Rodent Research, Cell Science, and Microbial Labs, flown on the International Space Station (ISS), benefit the global life sciences and commercial space communities. Verified data sets, science results, peer-reviewed publications, and returned biospecimens, collected and analyzed for flight and ground investigations, are all part of the knowledge base collected by NASA's Human Exploration and Operations Mission Directorate's Space Life and Physical Sciences Research and Applications (SLPSRA) Division, specifically the Human Research and Space Biology Programs. These data and biospecimens are made available through the public Life Sciences Data Archive (LSDA) website to promote basic discovery, pre-clinical and clinical science.The NASA Institutional Scientific Collection (ISC), stores flight and ground biospecimens from Space Shuttle and ISS programs. These specimens are curated and managed by the Ames Life Sciences Data Archive (ALSDA), an internal node of NASA's LSDA. The ISC stores over 30,000 specimens from experiments dating from 1984 to present. Currently available specimens include tissues from the circulatory, digestive, endocrine, excretory, integumentary, muscular, neurosensory, reproductive, respiratory and skeletal systems.NASA's biospecimen collection represents a unique and limited resource of unique spaceflight payload and ground control research subjects. These specimens are harvested according to well established SOPs that maintain their quality and integrity. Once the primary scientific objectives have been met, the remaining specimens are made available to provide secondary opportunities for complementary studies or new investigations to broaden research without large expenditures of time or resources. Website: https://lsda.jsc.nasa.gov/

Scott, Ryan T.↗

NASA NTRS2017

NASA Ames Institutional Scientific Collection (ISC)

NASA's current human space flight research is directed towards enabling human space exploration beyond Low Earth Orbit (LEO). The Space Flight Payload Projects; Rodent Research, Cell Science, and Microbial Labs, flown on the International Space Station (ISS), benefit both the global life sciences and commercial space communities. Verified data sets, science results, peer-reviewed publications, and returned biospecimens, collected and analyzed for flight and ground investigations, are all part of the knowledge base within NASA’s Human Exploration and Operations Mission Directorate’s Space Life and Physical Sciences Research and Applications (SLPSRA) Division, specifically the Human Research and Space Biology Programs. These data and biospecimens are made available through the public LSDA website. The Ames Institutional Scientific Collection (ISC), or ARC Biobank, stores flight and ground biospecimens from Space Shuttle and ISS programs. These specimens are curated and managed by the Ames Life Sciences Data Archive (ALSDA), an internal node of NASA's Life Sciences Data Archive (LSDA). The ARC Biolbank stores over 15,000 specimens from experiments dating from 1984 to present. Currently available specimens include tissues from the circulatory, digestive, endocrine, excretory, integumentary, muscular, neurosensory, reproductive, respiratory and skeletal systems. The most recent contributions include RNA, DNA and protein extracts from Rodent Research 1 and tissues from Rodent Research 4. NASA's biospecimen collection represents a unique and limited resource. The use of these biospecimens maximizes utilization and scientific return from these unique spaceflight payload and ground control research subjects. These biospecimens are harvested following complex, costly NASA research activities to meet primary scientific objectives. Once the primary scientific objectives have been met, the remaining specimens are made available to provide secondary opportunities for complementary studies or new investigations to broaden research without large expenditures of time or resources. Innovative ways of sharing this information ultimately advances the frontiers of human space exploration as well as scientific understanding of the effects of gravity on life on earth.

French, Alison J.↗

NASA NTRSDate not supplied

Maximizing Spaceflight Biological Data with Omics Analytics: The NASA GeneLab Database

NASA’s GeneLab includes an open-access repository of some 250+ omics datasets generated by biological experiments relevant to spaceflight including simulated cosmic radiation and microgravity. In order to maximize the intelligibility of these data, particularly for users with limited bioinformatics background, GeneLab has become a knowledgebase platform converting raw genetic and proteomic signatures found in flight samples into biological and physiological meanings. A large community of more than 100 scientists has rallied behind GeneLab and organized into four Analysis Working Groups (AWGs: Animal, Plant, Microbe, and Multi-Omics). Together, the AWGs have gained scientific recognition worldwide by establishing a consortium in charge of adopting new complex standards for data analysis workflows and omics sample processing in a rapidly evolving field. We will demonstrate the usage of the repository with smart search capability, an online controlled-access toolshed "Galaxy" to process user data with vetted standard workflows, a workspace for data sharing and a data submission portal with ontology control for better metadata curation. The GeneLab visualization portal will also be demonstrated, showing how anyone without formal training in bioinformatics can now browse the space biology omics data to discover new biology and potential solutions to improve life in space.

Sylvain Vincent Costes↗

NASA NTRSDate not supplied

GeneLab: The NASA System Biology Platform for Space Omics Repository, Analysis and Visualization

GeneLab↗