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NASA NTRSDate not supplied

Why We Do What We Do: Data Reuse, Open Access and Privacy in Data Management at the Life Sciences Data Archive

As custodians of the unique and irreplaceable collections of human subject research data generated by the Human Research Program and its predecessors throughout the agency’s history, the Life Sciences Data Archive (LSDA) is charged with protecting participants’ privacy and implementing their consent decisions as it provides retrospective data for use in new studies. This active, stewardship-focused approach to data management and preservation shapes the products that LSDA provides to researchers and the responsibilities of researchers in using the data and publishing their results. This presentation reviews how federal and agency mandates shape LSDA’s data management procedures and expectations for researchers. Topics covered will include LSDA’s movement towards implementation of the FAIR (Findable, Accessible, Interoperable, Reusable) principles and the archive’s evolving data management practices; collaboration between LSDA and the Lifetime Surveillance of Astronaut Health (LSAH) project (the repository of astronaut medical data); LSDA’s response to the challenges of performing its stewardship role and maintaining trust given the public profiles of the subjects whose data it preserves; and the ever-increasing challenges to expectations of subject privacy stemming from the growing power and ubiquity of data analysis and aggregation tools.

data management↗

NASA NTRSDate not supplied

Making Heliophysics Research More Open and Accessible at the Community Coordinated Modeling Center (CCMC)

The Space Weather and Heliophysics modeling community seeks to improve our understanding of space weather events and their impact on human activities. The Community Coordinated Modeling Center’s (CCMC, https://ccmc.gsfc.nasa.gov) mission is to support the community by providing a convenient collaborative platform that brings together space weather models, model simulation data, curated datasets of solar events, and associated value-added services. Using these services, researchers and other end-users may exercise, evaluate, and intercompare contributed models, triage designated R2O models, as well as collaborate on a continuously updated archive of model run results. This presentation reports on CCMC’s ongoing efforts in making Heliophysics models and data more accessible, open, and reproducible. We will also explore interoperability within the ecosystem of CCMC services and how this ecosystem interoperates with external partner services and data streams.

space weather↗

NASA NTRSDate not supplied

Open Science for Climate at NASA

The US National Aeronautics and Space Administration (NASA) currently provides more than 75 Petabytes of open access data through NASA’s Earth Science Data and Information System (ESDIS). Many of these datasets are commonly used in WCRP research, including the Global Precipitation Measurement (GPM) mission dataset, the Soil Moisture Active Passive (SMAP) mission dataset, the IceBridge dataset, and the Atmospheric Infrared Sounder (AIRS) dataset. These datasets are essential tools for understanding patterns in precipitation, soil moisture, ice mass changes, atmospheric circulation, and their impacts on climate. NASA is also a leader in the White House OSTP’s “Federal Year of Open Science” in 2023, promoting open access and open source solutions.

Climate Data↗

NASA NTRS2018

GeneLab Analysis Working Group Kick-Off Meeting

Goals to achieve for GeneLab AWG - GL vision - Review of GeneLab AWG charter Timeline and milestones for 2018 Logistics - Monthly Meeting - Workshop - Internship - ASGSR Introduction of team leads and goals of each group Introduction of all members Q/A Three-tier Client Strategy to Democratize Data Physiological changes, pathway enrichment, differential expression, normalization, processing metadata, reproducibility, Data federation/integration with heterogeneous bioinformatics external databases The GLDS currently serves over 100 omics investigations to the biomedical community via open access. In order to expand the scope of metadata record searches via the GLDS, we designed a metadata warehouse that collects and updates metadata records from external systems housing similar data. To demonstrate the capabilities of federated search and retrieval of these data, we imported metadata records from three open-access data systems into the GLDS metadata warehouse: NCBI's Gene Expression Omnibus (GEO), EBI's PRoteomics IDEntifications (PRIDE) repository, and the Metagenomics Analysis server (MG-RAST). Each of these systems defines metadata for omics data sets differently. One solution to bridge such differences is to employ a common object model (COM) to which each systems' representation of metadata can be mapped. Warehoused metadata records are then transformed at ETL to this single, common representation. Queries generated via the GLDS are then executed against the warehouse, and matching records are shown in the COM representation (Fig. 1). While this approach is relatively straightforward to implement, the volume of the data in the omics domain presents challenges in dealing with latency and currency of records. Furthermore, the lack of a coordinated has been federated data search for and retrieval of these kinds of data across other open-access systems, so that users are able to conduct biological meta-investigations using data from a variety of sources. Such meta-investigations are key to corroborating findings from many kinds of assays and translating them into systems biology knowledge and, eventually, therapeutics.

GeneLab↗

NASA NTRSDate not supplied

The NASA Open Science Data Repository: Biomedical Data, Analysis Tools, and Informatic Collaborations

Increased biomedical risks and challenges associated with deep space missions require knowledge discovery, health countermeasures, and biomedical support capabilities. Maximally open-access and reusable data is needed by developers, scientists, and engineers to develop these systems. The NASA Open Science Data Repository (OSDR) is a maximally open access and FAIR database (ie., findable, accessible, interoperable, and reusable), and meets various scientific, technical, and operational needs. It offers users and submitters the ability to upload, download, search, share, analyze, cite, and visualize data across ‘omics, physiological, phenotypic, payload, hardware, behavioral, bioimaging, video, and environmental monitoring telemetry datasets. OSDR is an expanded database, based upon the successes of NASA GeneLab. OSDR has >460 studies with datasets covering model organisms to 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 with raw files relating to the epitranscriptome, and a new request feature is live in OSDR (with a backend review process established) developed from industry norms. OSDR is collecting and curating biomedical human data from a new sub-orbital research flight and is open to more space life science/biomedical submissions from the international and commercial sectors. OSDR also recently began a collaboration with the European Space Agency (ESA) to collect and curate >200 terabytes of human and model organism data. The OSDR submission portal is designed to ingest and curate ~25 ‘omics and ~50 physiological-phenotypic-imaging assay data types. Tools available for OSDR users include: 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, and 3) a Multi-study visualization tool which enables users to look across and combine ‘omics datasets. There are ~600 volunteer OSDR Analysis Working Group (AWG) members providing feedback on scientific data/metadata standards and collaborating to mine-reuse OSDR in research. OSDR/GeneLab has enabled ~60 publications reusing data as of October 2023.

space biology↗

NASA NTRS1994

Metal-air cells comprising collapsible foam members and means for minimizing internal pressure buildup

This invention provides a prismatic zinc-air cell including, in general, a prismatic container having therein an air cathode, a separator and a zinc anode. The container has one or more oxygen access openings, and the air cathode is disposed in the container in gaseous communication with the oxygen access openings so as to allow access of oxygen to the cathode. The separator has a first side in electrolytic communication with the air cathode and a second side in electrolytic communication with the zinc anode. The separator isolates the cathode and the zinc anode from direct electrical contact and allows passage of electrolyte therebetween. An expansion chamber adjacent to the zinc anode is provided which accommodates expansion of the zinc anode during discharge of the cell. A suitable collapsible foam member generally occupies the expansion space, providing sufficient resistance tending to oppose movement of the zinc anode away from the separator while collapsing upon expansion of the zinc anode during discharge of the cell. One or more vent openings disposed in the container are in gaseous communication with the expansion space, functioning to satisfactorily minimize the pressure buildup within the container by venting gasses expelled as the foam collapses during cell discharge.

Woodruff, Glenn↗

NASA NTRS2016

GeneLab Phase 2: Integrated Search Data Federation of Space Biology Experimental Data

The GeneLab project is a science initiative to maximize the scientific return of omics data collected from spaceflight and from ground simulations of microgravity and radiation experiments, supported by a data system for a public bioinformatics repository and collaborative analysis tools for these data. The mission of GeneLab is to maximize the utilization of the valuable biological research resources aboard the ISS by collecting genomic, transcriptomic, proteomic and metabolomic (so-called omics) data to enable the exploration of the molecular network responses of terrestrial biology to space environments using a systems biology approach. All GeneLab data are made available to a worldwide network of researchers through its open-access data system. GeneLab is currently being developed by NASA to support Open Science biomedical research in order to enable the human exploration of space and improve life on earth. Open access to Phase 1 of the GeneLab Data Systems (GLDS) was implemented in April 2015. Download volumes have grown steadily, mirroring the growth in curated space biology research data sets (61 as of June 2016), now exceeding 10 TB/month, with over 10,000 file downloads since the start of Phase 1. For the period April 2015 to May 2016, most frequently downloaded were data from studies of Mus musculus (39) followed closely by Arabidopsis thaliana (30), with the remaining downloads roughly equally split across 12 other organisms (each 10 of total downloads). GLDS Phase 2 is focusing on interoperability, supporting data federation, including integrated search capabilities, of GLDS-housed data sets with external data sources, such as gene expression data from NIHNCBIs Gene Expression Omnibus (GEO), proteomic data from EBIs PRIDE system, and metagenomic data from Argonne National Laboratory's MG-RAST. GEO and MG-RAST employ specifications for investigation metadata that are different from those used by the GLDS and PRIDE (e.g., ISA-Tab). The GLDS Phase 2 system will implement a Google-like, full-text search engine using a Service-Oriented Architecture by utilizing publicly available RESTful web services Application Programming Interfaces (e.g., GEO Entrez Programming Utilities) and a Common Metadata Model (CMM) in order to accommodate the different metadata formats between the heterogeneous bioinformatics databases. GLDS Phase 2 completion with fully implemented capabilities will be made available to the general public in September 2017.

Space Biology↗

NASA NTRSDate not supplied

Exploring Blockchain to Support Open Science Practices

Open science aims to foster transparent sharing of scientific processes including open access, incentivization, provenance, open source code and tools, metrics, and resource sharing. However, effective management of these processes remains a challenge. This paper explores the application of blockchain technology to address these key aspects of open science. Blockchain offers a decentralized and secureplatform for information exchange and verification. By leveraging blockchain, open science can enhance transparency and reproducibility. In this paper, we present an implementation of blockchain for Earth science data synchronization across organizations, enabling tracking of data copying, citation, anddownload. The findings highlight the potential of blockchain in supporting open science objectives.

Iksha Gurung↗

NASA NTRS2016

Web Map Apps using NASA's Earth Observing Fleet

Through the miracle of open web mapping services for satellite imagery, a garden of new applications has sprouted to monitor the planet across a variety of domains. The Global Imagery Browse Services (GIBS) provide free and open access to full resolution imagery captured by NASAs Earth observing fleet. Spanning 15+ years and running through as recently as a few hours ago, GIBS aims to provide a general-purpose window into NASA's vast archive of the planet. While the vast nature of this archive can be daunting, many domain-specific applications have been built to meet the needs of their respective communities. This presentation will demonstrate a diverse set of these new applications which can take planetarium visitors into (virtual) orbit, guide fire resource managers to hotspots, help anglers find their next catch, illustrate global air quality patterns to local regulators, and even spur a friendly competition to find clouds which are shaped the most like cats. We hope this garden will continue to grow and will illustrate upcoming upgrades to GIBS which may open new pathways for development. data visualization, web services, open access

data visualization↗

NASA NTRSDate not supplied

NASA EOSDIS 20 Years of Data Usage and User Assessment in Support of Open Science Initiative

NASA EOS Data and Information System (EOSDIS) has been distributing data to world-wide users free with open access. Since the launch of NASA’s Terra satellite in 1999, more than 10,000 distinct EOS data products have been archived and distributed by NASA-funded Earth Science data centers encompassed by the EOSDIS. As of September 30, 2022, more than 90 PB of data archived by EOSDIS have been made available to public users and during FY 2023 over 60 PB have been distributed to public users worldwide. Over these twenty and more years, it has shown significant increase in the distribution of various data products. This has been possible due to free and open access of the data thereby a step towards open science initiative. The purposes of this study are 1) to perform a comprehensive investigation of the archive and distribution patterns of EOSDIS data products for last 20 years, 2) to identify and characterize the global user community for those data, 3) analyze the increased demand for data products, 4) evaluate distribution of higher level products because those are the ones most frequently used in the studies of natural disasters by public users (those data requestors not involved directly in the production or validation of the data products.) and contribute globally to the advance scientific understanding of the Earth-Atmosphere Systems. Funded by the Earth Science Data and Information System (ESDIS) Project, the ESDIS Metrics System (EMS) collects archive, distribution, and user information from EOSDIS data centers. The information (comprising all data products including heritage datasets going back to the 1990s) is stored in a relational database from which it can be analyzed in many ways. We present several metrics analyses that include data distribution patterns for all, as well as the most frequently requested data products; and user characterizations by country, domain, and Earth Science discipline (e.g., Land, Ocean, Cryosphere) of the requested products. Due to the enormous quantity of data handled by EOSDIS data centers and requirements of future data systems to archive increasing amounts of Earth Science data from future and current Earth Science missions effectively, the results of this study can provide insight on how the user communities have accessed the data and provide guidance for open science initiative.

Lalit Wanchoo↗

NASA NTRSDate not supplied

Using OPeNDAP In The Cloud to Connect NASA Data Centers and Support Open Data Access

NASA DAACs (Distributed Active Archive Centers), including the Goddard Earth Sciences Data Information and Services Center (GES DISC), are currently transitioning from on-premises servers to a shared Earthdata Cloud in order to build more interoperability, cross-collaboration, and streamlined services between their data centers. Migrating its on-premises OPeNDAP service to the cloud is a critical component of making this interconnectedness between NASA DAACs possible. To improve their cloud services, GES DISC is leveraging open-source platforms like Github to collect user feedback, create use cases, and develop resources to enable real-time learning for users about OPeNDAP in the cloud. This presentation gives an overview of the OPeNDAP in the cloud, resources developed to access this service, and considerations for improved user guidance and experience to further support NASA's commitment to the Open-Source Science Initiative (OSSI).

Christopher Battisto↗

NASA NTRS2004

Development of Laser-Polarized Noble Gas Magnetic Resonance Imaging (MRI) Technology

We are developing technology for laser-polarized noble gas nuclear magnetic resonance (NMR), with the aim of enabling it as a novel biomedical imaging tool for ground-based and eventually space-based application. This emerging multidisciplinary technology enables high-resolution gas-space magnetic resonance imaging (MRI)-e.g., of lung ventilation, perfusion, and gas-exchange. In addition, laser-polarized noble gases (3He and 1BXe) do not require a large magnetic field for sensitive NMR detection, opening the door to practical MRI with novel, open-access magnet designs at very low magnetic fields (and hence in confined spaces). We are pursuing two specific aims in this technology development program. The first aim is to develop an open-access, low-field (less than 0.01 T) instrument for MRI studies of human gas inhalation as a function of subject orientation, and the second aim is to develop functional imaging of the lung using laser-polarized He-3 and Xe-129.

Walsworth, Ronald L.↗

NASA NTRSDate not supplied

Improving Access to the GEOS Composition Forecast Model with API Development and Ingestion into Google Earth Engine

The GEOS Composition Forecast (GEOS-CF) model produces forecast and historical estimates of atmospheric composition and meteorology fields, which provide useful insight into air quality issues and events. In a year for which Canadian wildfires created adverse air quality conditions in the eastern United States, access to model fields such as PM2.5 are in high demand. The GEOS-CF team at the NASA Global Modeling and Assimilation Office (GMAO) first developed in-house solutions to improve data access via the CF API, and recently partnered with Google to ingest a collated set of model diagnostics into the Google Earth Engine (GEE) data repository. GEOS-CF model output is also being ingested into AWS storage. Creating these various open access points to GEOS-CF model diagnostics provides the public with an opportunity to easily interact with air quality information. Users are able to use a temporally consistent global grid of air quality fields in machine learning applications, mapping tools, and data informatics. Hosting GEOS-CF forecasts and the historical timeseries of these chemistry and meteorology fields in GEE allows users to create dynamic JavaScript-based air quality applications in the GEE code editor. GEOS-CF users can also access the model output via the GEE Python application programming interface (API), making it easy to perform various analyses with Python. This presentation will show two examples of accessing the GEOS-CF model through GEE. The first is an example application made in the GEE code editor which allows users to view time series plots and downscaled maps of surface level NO2. The second example exhibits using the GEE Python API to create a machine learning model to temporally gap-fill between air quality observations. These examples are an introduction to the many possible benefits of having open access to the GEOS-CF model through multiple platforms.

Callum Wayman↗

NASA NTRSDate not supplied

Improving Access to the GEOS Composition Forecast Model with API Development and Ingestion into Google Earth Engine

The GEOS Composition Forecast (GEOS-CF) model produces forecast and historical estimates of atmospheric composition and meteorology fields, which provide useful insight into air quality issues and events. In a year for which Canadian wildfires created adverse air quality conditions in the eastern United States, access to model fields such as PM2.5 are in high demand. The GEOS-CF team at the NASA Global Modeling and Assimilation Office (GMAO) first developed in-house solutions to improve data access via the CF API, and recently partnered with Google to ingest a collated set of model diagnostics into the Google Earth Engine (GEE) data repository. GEOS-CF model output is also being ingested into AWS storage. Creating these various open access points to GEOS-CF model diagnostics provides the public with an opportunity to easily interact with air quality information. Users are able to use a temporally consistent global grid of air quality fields in machine learning applications, mapping tools, and data informatics. Hosting GEOS-CF forecasts and the historical timeseries of these chemistry and meteorology fields in GEE allows users to create dynamic JavaScript-based air quality applications in the GEE code editor. GEOS-CF users can also access the model output via the GEE Python application programming interface (API), making it easy to perform various analyses with Python. This presentation will show two examples of accessing the GEOS-CF model through GEE. The first is an example application made in the GEE code editor which allows users to view time series plots and downscaled maps of surface level NO 2 . The second example exhibits using the GEE Python API to create a machine learning model to temporally gap-fill between air quality observations. These examples are an introduction to the many possible benefits of having open access to the GEOS-CF model through multiple platforms.

Callum Wayman↗

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 NTRS2015

GeneLab: A Systems Biology Platform for Spaceflight Omics Data

NASA's mission includes expanding our understanding of biological systems to improve life on Earth and to enable long-duration human exploration of space. Resources to support large numbers of spaceflight investigations are limited. NASA's GeneLab project is maximizing the science output from these experiments by: (1) developing a unique public bioinformatics database that includes space bioscience relevant "omics" data (genomics, transcriptomics, proteomics, and metabolomics) and experimental metadata; (2) partnering with NASA-funded flight experiments through bio-sample sharing or sample augmentation to expedite omics data input to the GeneLab database; and (3) developing community-driven reference flight experiments. The first database, GeneLab Data System Version 1.0, went online in April 2015. V1.0 contains numerous flight datasets and has search and download capabilities. Version 2.0 will be released in 2016 and will link to analytic tools. In 2015 Genelab partnered with two Biological Research in Canisters experiments (BBRIC-19 and BRIC-20) which examine responses of Arabidopsis thaliana to spaceflight. GeneLab also partnered with Rodent Research-1 (RR1), the maiden flight to test the newly developed rodent habitat. GeneLab developed protocols for maxiumum yield of RNA, DNA and protein from precious RR-1 tissues harvested and preserved during the SpaceX-4 mission, as well as from tissues from mice that were frozen intact during spaceflight and later dissected. GeneLab is establishing partnerships with at least three planned flights for 2016. Organism-specific nationwide Science Definition Teams (SDTs) will define future GeneLab dedicated missions and ensure the broader scientific impact of the GeneLab missions. GeneLab ensures prompt release and open access to all high-throughput omics data from spaceflight and ground-based simulations of microgravity and radiation. Overall, GeneLab will facilitate the generation and query of parallel multi-omics data, and deep curation of metadata for integrative analysis, allowing researchers to uncover cellular networks as observed in systems biology platforms. Consequently, the scientific community will have access to a more complete picture of functional and regulatory networks responsive to the spaceflight environment.. Analysis of GeneLab data will contribute fundamental knowledge of how the space environment affects biological systems, and enable emerging terrestrial benefits resulting from mitigation strategies to prevent effects observed during exposure to space. As a result, open access to the data will foster new hypothesis-driven research for future spaceflight studies spanning basic science to translational science.

proteomics↗