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NASA Earthdata Knowledge Base

Prototype work for connecting together the main elements of Earth Observation knowledge and context in a way that is: machine-readable, human-usable and curatable. Using the latest in graph technologies and cloud managed services.

earth data↗

NASA GeneLab Platform Utilized for Space Radiation Dosimetry Biological Response Compared to Radiation Ground Studies

Ionizing radiation from Galactic Cosmic Rays (GCR) is one of the major risk factors factor that will impact health of astronauts on extended missions outside the protective effects of the Earth's magnetic field. Currently there are gaps in our knowledge of the health risks associated with chronic low dose, low dose rate ionizing radiation, specifically ions associated with high (H) atomic number (Z) and energy (E). The NASA GeneLab project (genelab.nasa.gov) aims to provide a detailed library of Omics datasets associated with biological samples exposed to HZE. The GeneLab Data System (GLDS) includes datasets from both spaceflight and ground-based studies, a majority of which involved exposure to ionizing radiation. Recently GeneLab has also assessed radiation dosimetry data with omics datasets associated with samples flown to the International Space Station (ISS). The combination of the detailed information on radiation exposure for ground-based studies and curated dosimetry information for spaceflight experiments allows GeneLab to be the first comprehensive Omics database for space related research from which an investigator can generate hypotheses to direct future experiments utilizing both ground and space biological radiation data. We demonstrate the usefulness of these datasets by analyzing multiple GeneLab datasets associated with both radiation ground-based studies and spaceflight studies. The radiation ground based studies we analyzed includes both in vivo and in vitro work with a range ions from protons to iron particles with doses from 0.1Gy to 2Gy. These datasets were compared to both in vivo and in vitro datasets from samples flown to the ISS and on shorter shuttle missions with total doses of 0.1 mGy to 30 mGys. From this analysis we were able to associate distinct biological signatures associating specific ions to specific biological response to radiation exposure in space. For example, we discovered radiation biological response related to cardiovascular effects from proton ground studies are the dominating response for samples related to cardiovascular effects on the ISS. With this work we will provide a summary of how different ions will impact different biological response in space and how this can be used in future studies to assess optimal ground experiments to simulate space radiation.

Beheshti, Afshin↗

Cross Kingdom Analysis of Data Within the GeneLab Repository Identifies a Potential Conserved Response of Life to the Stress Associated with Spaceflight

It is important to determine the health risks and potential survival for astronauts associated with long-term space missions. This entails not only understanding the impact the space environment will have on humans, but also how it will affect other organisms needed for humans to survive in space such as plants. In addition, it has been reported in the literature that hundreds of genes seem to be conserved and/or transferred between different organisms from bacteria, archaea, fungi, microorganisms, and plants to animals. Since space travel involves humans in a closed environment over a long period of time, we hypothesize that potential conserved biological factors will occur between the different organisms in that environment possibly due to transfer of genes. Determining the conserved factors that are commonly being regulated in space can shed insight into possible universal master regulators and also determine the symbiotic relationship between the organisms in space. Utilizing NASA's GeneLab Data Repository (a rapidly expanding, curated clustering of spaceflight-related ‘omics-level datasets for all organisms), we were able to uncover a novel pathway and factors that were commonly shared between humans, mice, plants, C. Elegans, and drosophilas. Through ChIP-Seq enrichment analysis techniques utilizing various GeneLab datasets from each species that were flown in space, we found the following factors to be conserved across all species: oxidative stress, DNA damage (through GABPA/NRFs and NFY), SIX5, GTF2B and glutamine synthetase. Such commonalities would likely reflect the effects of factors such as microgravity and the increased radiation exposure inherent in spaceflight on basic physical processes shared by all biological systems at the cellular level. Differences between organismal responses revealed by GeneLab's data should also help understand the unique reactions to life in space that arise from the very different lifestyles of microbes, animals and plants.

Barker, Richard↗

NASA’s In-Space Manufacturing Project: Update on Manufacturing Technologies and Materials to Enable More Sustainable and Safer Exploration

NASA’s In-Space Manufacturing (ISM) project seeks to develop the materials, processes, and manufacturing technologies needed to provide an on-demand manufacturing capability for deep space exploration missions. The ability to manufacture and recycle some parts on demand rather than launch them from earth has the potential to reduce logistics requirements on long duration missions and enhance crew safety. With the launch of the first 3D printer (built and operated by Made in Space through a Small Business Innovative Research – SBIR -- contract) to the International Space Station (ISS) in 2014, the ISM project demonstrated the feasibility of operating an on-demand manufacturing system in a microgravity environment. This paper will provide an update on recent advancements in ISM under three key technology areas: manufacturing, recycling, and development of a design database. ISM continues to pursue development of manufacturing technologies for space applications and use the ISS as a critical test bed to prove out these technologies before deploying them on next generation exploration systems. Activities under this focus area include: characterization of materials manufactured using the Additive Manufacturing Facility (AMF), the second generation commercial 3D-printer on ISS, also owned and operated by Made in Space; development of prototype payloads for metal manufacturing through phase II SBIR contracts with Tethers Unlimited, Made in Space, and Ultra Tech Machinery; development of a multi-material fabrication laboratory capable of processing metals and providing inspection of manufactured parts through a Broad Agency Announcement (Techshot, Interlog, and Tethers Unlimited); an in-line sensing system for ISM platforms; and development of higher strength feedstocks for 3D polymer printers. In the area of recycling, the Tethers Unlimited Refabricator payload (an integrated 3D printer and recycler for ULTEM 9085) launched to ISS in November 2018 and began operating in early 2019. This payload represents the first demonstration of on-orbit recycling; down massed specimens will assess material degradation in the polymer over multiple recycling cycles to define limits on material re-use. Other work in the recycling area includes development of common use materials intended to be reused and recycled on space missions (Tethers Unlimited and Cornerstone Research Group) and a sterilization capability for multiple-use materials (ERASMUS from Tethers Unlimited). Concurrent with manufacturing technology and materials development work is creation of a design database, a curated list of parts that can be manufactured using the suite of In-Space Manufacturing capabilities.

Tracie Prater↗

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 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.↗

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.↗

Analyzing Natural Language Context in Human-Machine Teaming using Supervised Machine Learning

Building a foundation for trustworthiness and trust verification in multi-asset teaming is the research challenge of Autonomy Teaming and TRAjectories for Complex Trusted Operational Reliability (ATTRACTOR). The Design Reference Mission (DRM) for ATTRACTOR is a search and rescue mission objective governed by a multi-member team consisting of human and machine operators. A crucial component to the effort is the communication between humans and autonomous agents throughout both planning and execution stages of the mission. Intuitive communication methods and modalities are posited as critical enablers for certifying trust and trustworthiness. This paper reports on the data collection and analysis conducted in support of the Human Informed Natural-language GANs Evaluation (HINGE)project to attain explainable and trusted communication between human-machine assets. Two identically curated image description datasets were acquired for HINGE, both consisting of two unique input modalities (typed vs. verbal) and retrieved in two distinct contexts (general vs. specific). The gathered datasets were assessed and compared using Parts-of-Speech (POS)features, sentence similarity metrics, and linguistic analysis. Then, the datasets were modeled and tested separately and in combination with one another using machine learning algorithms. The comparison and testing results reveal a superior dataset, by which a preferred context and input is understood, for generating image representations of missing persons using a Generative Adversarial Network (GAN).

Bryan A Barrows↗

Topic Modeling Tool for PeTaL (Periodic Table of Life)

A topic modeling tool is constructed for the purpose of providing insights from biology to the engineer within the framework of PeTaL (Periodic Table of Life). The machine learning text mining tools–latent Dirichlet allocation (LDA) and nonnegative matrix factorization (NMF) with Kullback-Leibler (KL) divergence—are used to provide topic clusters to the user. Topic clusters are the underlying themes of a paper. For the text modeling problem, NMF-KL is the equivalent of probabilistic latent semantic analysis. Both LDA and NMF-KL are top-performing modeling tools. These tools are used to identify biological specimens relevant to the user. Various organisms solve a particular survival problem in nature differently. The topic clusters allow people without domain expertise to find these cross-topic themes in the body of documents and then branch out and examine papers whose target organisms solve the engineer’s problem. Abstracts from the Journal of Experimental Biology were used as input for the clustering tool in addition to a curated set of articles for validation. The tool is able to accept alternate input sources.

Machine learning↗

OpenNEX: An open collaboration platform for the earth science community

Satellite data from the past several decades provide the most consistent record of land-surface processes that form the basis for scientific assessments of the impacts of climate variations and changes on the environment and human social-economical activities. During this time, scientific research on the characterization and assessment of environmental changes had tended to focus on large-scale land-surface changes with significant social-economic impacts. Increasingly, attention is shifting toward changes that occur more locally and that most directly relate to the everyday life of the majority of the population. In addition, there has been needs to develop management and policy decision support systems that are based on local environmental information. Almost at the same time, the advancement in sensor technology has allowed us to collect an unprecedented volume of environmental data. These data must be curated and analyzed to extract useful information for research and decision support purposes. Established in 2013 and funded by NASA, the Open NASA Earth eXchange (OpenNEX; https://opennex.org/ , Jia et al., 2019 ) project partnered with Amazon Web Services (AWS) to make available a large amount of Earth observing data, modeling results, and analysis tools on the AWS. OpenNEX provides researchers, developers, educators, and ordinary users with easy access to an integrated Earth science computational and data platform, enabling citizen scientists and application developers to realize the full value of NASA data assets and software tools. To encourage the public's engagement in this project, NASA ran virtual workshops and prize competitions. The virtual workshops provided online lectures and tutorials about how prominent scientists used the data in their research and the tutorials gave examples how to use the tools to interrogate the data in the Amazon cloud. Finally, the prize competitions allowed much wider participation in the OpenNEX project and enable testing the non-traditional projects and out-of-box ideas. OpenNEX has continued to evolve and mature. Here, we highlight new features and functionalities available to the community.

Jian Zhang↗

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↗

Using X-Ray Computed Tomography to Image Apollo Drive Tube 73002

The Apollo missions collected 382 kg of rock, regolith, and core samples from six locations on the Moon. Although most Apollo samples are well characterized, several types of samples remain wholly or largely unstudied since their return: unopened and/or sealed drive tube samples, samples frozen upon return, and samples stored in a He-purged environment. NASA selected nine teams to participate in the Apollo Next Generation Sample Analysis (ANGSA) Program to study representative samples from each of these categories. The first sample studied as part of the ANGSA program is drive tube 73002, a 4 cm diameter unopened (but unsealed) drive tube collected on a landslide deposit near Lara Crater at the Apollo 17 landing site. It was part of a ~60 cm long double drive tube, and the bottom half of the tube (73001)was sealed under vacuum on the Moon (and will be studied next). As part of the preliminary examination of sample 73002, the entire drive tube was imaged with a high resolution X-ray Computed Tomography (XCT) scan prior to opening and dissecting the sample. Additionally, >50 XCT scans have been made of “large” clasts (>4 mm) removed from the core as part of the ongoing dissection process. Here we will present both the whole drive tube XCT data showing the overall structure of sample 73002 prior to dissection, as well as XCT scans of individual clasts that reveal the types and abundance of different lithologies present within the drive tube. We will also discuss the utility of the scans as part of the curation and preliminary examination process, as well as the potential for future science returns from the XCT scans.

Ryan A Zeigler↗

NASA GeneLab Platform Utilized for Biological Response to Space Radiation in Animal Models

Ionizing radiation from Galactic Cosmic Rays (GCR) is one of the major risk factors that will impact the health of astronauts on extended missions outside the protective effects of Earth’s magnetic field. The NASA GeneLab project has detailed information on radiation exposure using animal models with curated dosimetry information for spaceflight experiments. We analyzed multiple GeneLab omics datasets associated with both ground-based and spaceflight radiation studies that included in vivo and in vitro approaches. A range of ions from protons to iron particles with doses from 0.1 Gy to 1.0 Gy for ground studies and samples flown in Low Earth Orbit (LEO) with total doses of 1.0 mGy to 30 mGy were utilized From this analysis we were able to identify distinct biological signatures associating specific ions with specific biological responses due to radiation exposure in space. For example, we discovered changes in mitochondrial function, ribosomal assembly, and immune pathways as a function of dose. We provided a summary of how the GeneLab’s rich database of omics experiments with animal models can be used to generate novel hypotheses to better understand human health risks from GCR exposures.

Afshin Beheshti↗

Chemical Reactivity of In-Situ Lunar Dust

Is in-situ lunar dust less, the same, or more chemically reactivity reactive than the Apollo samples currently stored in curation facilities here on Earth? This question has been debated extensively across the community of scientists that have focused on lunar dust biotoxicity. A definitive answer will further mitigate exploration risks to future human explorers on the Moon and will provide useful information for astrobiologists and space biologists as well.

Lunar Dust↗

NASA GeneLab Platform Utilized for Space Radiation Dosimetry Biological Response Compared to Radiation Ground Studies

Ionizing radiation from Galactic Cosmic Rays (GCR) is one of the major risk factors that will impact the health of astronauts on extended missions outside the protective effects of Earth’s magnetic field. The NASA GeneLab project has detailed information on radiation exposure using animal models with curated dosimetry information for spaceflight experiments. We analyzed multiple GeneLab omics datasets associated with both ground-based and spaceflight radiation studies that included in vivo and in vitro approaches. A range of ions from protons to iron particles with doses from 0.1 Gy to 1.0 Gy for ground studies and samples flown in Low Earth Orbit (LEO) with total doses of 1.0 mGy to 30 mGy were utilized From this analysis we were able to identify distinct biological signatures associating specific ions with specific biological responses due to radiation exposure in space. For example, we discovered changes in mitochondrial function, ribosomal assembly, and immune pathways as a function of dose. We provided a summary of how the GeneLab’s rich database of omics experiments with animal models can be used to generate novel hypotheses to better understand human health risks from GCR exposures.

Afshin Beheshti↗

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

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.

GeneLab↗

Chemical Reactivity of In-Situ Lunar Dust for Biotoxicity Assessment

How does the chemical reactivity of in-situ lunar dust compare to Apollo samples currently stored in curation facilities here on Earth? Essential investigations of this question will help us to further mitigate exploration risks for future human explorers on the Moon and will also provide critical information for astrobiologists and space biologists using the Moon for scientific inquiry. Apollo 14 dust biotoxicity studies, carried out by the NASA Lunar Airborne Dust Toxicity Assessment Group (LADTAG), included numerous cellular and animal experiments. Intratracheal instillation and inhalation studies in rats both showed Apollo 14 dust to be intermediate in toxicity compared to low-tox titanium dusts and high-tox quartz dusts of similar particle sizes. The collective results were used in models to establish a safe exposure limit for astronauts. Although LADTAG took extensive steps to preserve what chemical reactivity may still have existed in the samples, it is simply unknown if they possessed true in-situ chemical reactivity or if that reactivity has decayed. Initial gas loss on collection and other alterations, and even intermittent exposure to Earth-normal conditions during subsequent decades of handling, obscure a forensic reconstruction of the initial state. Because a mineral dust’s chemical reactivity influences its biotoxicity, researchers have developed methods to “activate” lunar dust and simulants. Past studies that modeled impact processes and radiation in the lunar environment suggest that in-situ lunar dust is likely to be more chemically reactive than Earth-exposed samples. Because of these results, in-situ measurements are warranted. Since the lunar surface is heterogeneous, dust biotoxicity is expected to vary from site to site due to particle size, mineralogy, physical characteristics, degree of space weathering, and chemical reactivity. This circumstance dictates dust assessments at a suite of lunar sites enabled by CLPS opportunities. Dose, location, and duration of particle exposure will also affect biological responses. In-situ chemical reactivity measurements can inform cross-cutting collaborative research campaigns such as astrobiology studies examining regolith interactions with organisms and its ability to preserve chemical and structural biomarkers, as well as space biology investigations that examine regolith-microbe interactions relating to life support systems, plant growth, biomining, and development of regolith biocomposites.

Jon C Rask↗

NASA’s Global Change Master Directory (GCMD) Keyword Viewer Beta

The Global Change Master Directory (GCMD) Keyword Viewer is a web-based client that allows metadata curators and ontologists to search for and navigate the GCMD keywords in a user-friendly and human-readable tree structure. The Keyword Viewer is built on top of the Keyword Management Systems (KMS) API, which provides machine-to-machine access to the keywords.

Tyler B Stevens↗