An Introduction to NASA’s Catalog of Archived Suborbital Earth Science Investigations (CASEI)
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Stephanie M. Wingo↗
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NASA’s Catalog of Archived Suborbital Earth Science Investigations (CASEI): Empowering Access to Airborne and Field Investigation Data
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Camille Wood↗
An Ontology-Based Archive Information Model for the Planetary Science Community
The Planetary Data System (PDS) information model is a mature but complex model that has been used to capture over 30 years of planetary science data for the PDS archive. As the de-facto information model for the planetary science data archive, it is being adopted by the International Planetary Data Alliance (IPDA) as their archive data standard. However, after seventeen years of evolutionary change the model needs refinement. First a formal specification is needed to explicitly capture the model in a commonly accepted data engineering notation. Second, the core and essential elements of the model need to be identified to help simplify the overall archive process. A team of PDS technical staff members have captured the PDS information model in an ontology modeling tool. Using the resulting knowledge-base, work continues to identify the core elements, identify problems and issues, and then test proposed modifications to the model. The final deliverables of this work will include specifications for the next generation PDS information model and the initial set of IPDA archive data standards. Having the information model captured in an ontology modeling tool also makes the model suitable for use by Semantic Web applications.
Information Model↗
Apollo Botany Experiments and Artemis: Discussion of Botany Experiment Records Digitized as Part of the Apollo Records Synthesis Project (ARSP)
The Artemis Program, with its objective of establishing a sustained human presence on the moon, has rekindled interest in lunar botany as an area of inquiry. Limited availability of collected lunar regolith samples for plant growth experiments underlines the need to leverage all existing historic datasets. As part of NASA’s Life Sciences Data Archive’s (LSDA) Apollo Records Synthesis Project (ARSP), a collection of historic Apollo era botany experiment research records from the former Space Life Sciences Archival Library (SLSAL) collection, these records have been digitized to improve access for data reuse. The records are related to post-mission quarantine experiments conducted to characterize any pathogenic effects of lunar regolith on exposed plant specimens and includes several possible dataset sources such as microscopy photos, laboratory notebooks, correspondence, data sheets, and gas chromatography results. This collection includes the output of investigations of taxa previously under-investigated in the context of space biology. An unusually phylogenetically diverse group of plants are represented in this dataset (including Pinaceae, Poeaceae, Solanaceae, Apiaceae and more). This presentation will discuss the contents of the collection, their historic context, the digitization of the collection, and the opportunities they may provide when placed in the larger corpus of lunar botany regolith experiments.
Archives↗
Biospecimen Culling: Temporal RNA Integrity Analysis Across Spaceflight Missions Dating from 1985 to 2011
The Ames Life Science Data Archive (ALSDA) at NASA Ames Research Center is managed by the Space Biosciences Division and has been operational since 1993. The ALSDA is responsible for archiving information and biospecimens collected from life science spaceflight experiments and matching ground control experiments. They are stored in the Ames biobank, which is located in the Biospecimen Storage Facility (BSF). The ALSDA also manages a Biospecimen Sharing Program, performs curation and long-term storage operations, and makes biospecimens available to the scientific community for research purposes via the Life Science Data Archive public website (https:lsda.jsc.nasa.gov). The BSF maintains both fixed and frozen spaceflight and ground tissues, collected from recent and past spaceflight missions. Due to the ever increasing demand for space to preserve current and future flight biospecimens, the ALSDA has initiated the development of a culling plan for biospecimens currently stored in the BSF. Culling enables the ALSDA to assess the quality of archived samples, and supports the development of standardized culling procedures that improve the operational efficiency of the BSF. The culling plan focuses on generating disposition recommendations for samples in the BSF, and currently is based on measuring ribonucleic acid (RNA) integrity number (RIN). The culling process includes (1) sorting and identification of candidate samples for RIN analysis, (2) completion of RIN analysis on select samples, and (3) development of disposition recommendations for specimens based on the RIN values. Furthermore, our approach allows for unique scientific opportunities, including development of a RIN-based methodology for culling, and temporal assessment of the quality of the tissues that have been stored in BSF since the 1980s. Results of this work will also support NASA open science initiatives.
biospecimen↗
The NASA Ames Research Center Institutional Scientific Collection: History, Best Practices and Scientific Opportunities
The NASA Ames Life Sciences Institutional Scientific Collection (ISC), which is composed of the Ames Life Sciences Data Archive (ALSDA) and the Biospecimen Storage Facility (BSF), is managed by the Space Biosciences Division and has been operational since 1993. The ALSDA is responsible for archiving information and animal biospecimens collected from life science spaceflight experiments and matching ground control experiments. Both fixed and frozen spaceflight and ground tissues are stored in the BSF within the ISC. The ALSDA also manages a Biospecimen Sharing Program, performs curation and long-term storage operations, and makes biospecimens available to the scientific community for research purposes via the Life Science Data Archive public website (https:lsda.jsc.nasa.gov). As part of our best practices, a viability testing plan has been developed for the ISC, which will assess the quality of archived samples. We expect that results from the viability testing will catalyze sample use, enable broader science community interest, and improve operational efficiency of the ISC. The current viability test plan focuses on generating disposition recommendations and is based on using ribonucleic acid (RNA) integrity number (RIN) scores as a criteria for measurement of biospecimen viablity for downstream functional analysis. The plan includes (1) sorting and identification of candidate samples, (2) conducting a statiscally-based power analysis to generate representaive cohorts from the population of stored biospecimens, (3) completion of RIN analysis on select samples, and (4) development of disposition recommendations based on the RIN scores. Results of this work will also support NASA open science initiatives and guides development of the NASA Scientific Collections Directive (a policy on best practices for curation of biological collections). Our RIN-based methodology for characterizing the quality of tissues stored in the ISC since the 1980s also creates unique scientific opportunities for temporal assessment across historical missions. Support from the NASA Space Biology Program and the NASA Human Research Program is gratefully acknowledged.
ALSDA↗
Proposed US Contributions to LOFT
Proposed US Enhancements include:Tantalum X -ray collimator, Additional ground station, Large Observatory for X-Ray Timing (LOFT) instrument team participation, US science support center & data archive, and Science enabled by US hardware. High-Z material with excellent stopping power. Fabricated using a combination of laser micromachining and chemical etching. Known technology capable of producing high-aspect ratio holes and large open fractions. Reduces LOFT LAD background by a factor of 3. Telemetry formats for LOFT based upon RXTE/EDS experience. Ground system software and strategies for WFM based upon RXTE/ASM automated pipeline software. MSFC engineering trade studies supporting the Ta collimator. Burst alert triggers based upon Fermi/GBM and HETE-2. Science Enhancements Enabled by US Hardware include: Tantalum collimator: Reduces background by factor of 3. Improves sensitivity to faint sources such as AGN. Eliminates contamination by bright/variable sources. outside the LAD field of view. US Ground Station: Enables continuous telemetry of all events from the WFM. Allows LAD to observe very bright >500 mCrab sources with full event resolution.
Wilson-Hodge, Colleen↗
Translational Cell & Animal Research in Space 1965-2011
Translational Cell and Animal Research (TCAR). For nearly 50 years, the NASA Space Biology Program has funded, and Ames Research Center (ARC) has managed, a robust program of fundamental research including studies using a wide range of animal cells, tissues and organisms. Much of this research was conducted on spacecraft in microgravity environments including diverse platforms such as: Gemini Spacecraft, US Biosatellites, Apollo Command Modules, Skylabs, Russian Biosatellites, NASA Space Shuttles, NASA/Mir, and most recently, the International Space Station (ISS). During the Space Shuttle Era (1981–2011), the science of space biology took an enormous step forward with 45 missions that afforded researchers with new opportunities to conduct systematic and complex experiments aimed at a deeper understanding of how life adapts to the space environment. Beginning in the 1990s, the products of these experiments, comprised of research summaries and rare, unused biospecimens, were collected and catalogued within the ARC Life Sciences Data Archiving Office, a branch of NASA’s Life Sciences Data Archive (LSDA) managed from the NASA Johnson Spaceflight Center.
Ronca, April E.↗
Open Science for Plants in Space: Data Sharing, Standards, and Informatics for Reuse and Knowledge Discovery
Upcoming deep space missions rely on plants and crops for crew and ecosystem health. Access to space plant data enables scientists to gain a deeper understanding of biological responses to ionizing radiation, altered gravity, low atmospheric pressure, elevated CO2, and altered photoperiods. Open Science is the practice of making research available to all, while respecting diverse cultures, fostering collaborations with equity. 2023 is the ‘Year of Open Science’, and NASA has a 5-year Transform to Open Science (TOPS) mission designed to rapidly transform the agency toward an inclusive culture of open science. NASA’s Open Science Data Repository (OSDR) developed by NASA’s Biological and Physical Sciences Division provides access to data from space-relevant biological experiments. OSDR combines two databases, GeneLab and Ames Life Sciences Data Archive (ALSDA) to maximize access to standardized ‘omics (e.g., transcriptomics, proteomics) and phenotypic data (e.g., microscopy, biomass), respectively. OSDR started in 2014 with the creation of the first space-relevant FAIR (Findable, Accessible, Interoperable, Reusable) biological ‘omics repository (GeneLab), providing detailed metadata on investigation, sample, and assay levels. Today, GeneLab hosts 62 plant datasets which have led to 5 published peer-reviewed meta-analysis publications. Most of these publications were collaboration efforts under the OSDR Analysis Working Groups (AWGs). AWGs provide great opportunities for investigators to collaborate and set new standards for space-relevant data and metadata. The AWGs are welcoming any ASPB members interested in providing plant expertise for space biology. The addition of ALSDA to OSDR is also expanding analysis capability beyond ‘omics. Now is the time to get involved as a Subject Matter Expert as we establish the framework for modern plant data archiving through the AWGs. Investigators are invited to submit their space-relevant plant datasets to OSDR and visit the site to learn about the tools OSDR has to offer (osdr.nasa.gov/bio).
FAIR↗
Open Science for Plants in Space: Data Sharing, Standards, and Informatics for Reuse and Knowledge Discovery
Upcoming deep space missions will rely on plants for crew and ecosystem health. Open access space biology data enables scientists to examine the biological responses of plants to ionizing radiation, altered gravity, low atmospheric pressure, elevated CO2, altered photoperiods and many other abiotic stressors. Open Science is the practice of making research available to all, while respecting diverse cultures, and fostering collaborations with equity. 2023 is the ‘Year of Open Science’, and NASA has a 5-year Transform to Open Science (TOPS) initiative designed to rapidly transform the agency toward an inclusive culture of open science. NASA’s Open Science Data Repository (OSDR) within NASA’s Biological and Physical Sciences Division provides access to data from space-relevant biological experiments. OSDR combines two databases, GeneLab and Ames Life Sciences Data Archive (ALSDA) to maximize access to standardized ‘omics (e.g., transcriptomics, proteomics) and phenotypic data (e.g., microscopy, biomass), respectively. GeneLab started in 2014 with the creation of the first space-relevant FAIR (Findable, Accessible, Interoperable, Reusable) biological ‘omics repository, providing detailed metadata on investigation, sample, and assay levels. The addition of ALSDA to OSDR expands plant data analysis capabilities across both phenotypic and ‘omics data. Today, OSDR hosts 62+ plant datasets and has enabled 58 peer-reviewed publications. Most of these publications were collaboration efforts under the OSDR Analysis Working Groups (AWGs). AWGs provide great opportunities for investigators to collaborate and set new standards for space-relevant data and metadata. The AWGs welcome any ASPB members interested in contributing plant expertise for space biology, and to serve as subject matter experts as we establish the framework for modern plant data archiving. Investigators are invited to submit their space-relevant plant datasets to OSDR and visit the site to learn about the tools OSDR has to offer (osdr.nasa.gov/bio).
FAIR↗
National Space Science Data Center data archive and distribution service (NDADS) automated retrieval mail system user's guide
The National Space Science Data Center (NSSDC) has developed an automated data retrieval request service utilizing our Data Archive and Distribution Service (NDADS) computer system. NDADS currently has selected project data written to optical disk platters with the disks residing in a robotic 'jukebox' near-line environment. This allows for rapid and automated access to the data with no staff intervention required. There are also automated help information and user services available that can be accessed. The request system permits an average-size data request to be completed within minutes of the request being sent to NSSDC. A mail message, in the format described in this document, retrieves the data and can send it to a remote site. Also listed in this document are the data currently available.
Perry, Charleen M.↗
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.↗
Improved Tree-Ring Archives Will Support Earth-System Science
A steep decline in archiving could make large tree-ring datasets irrelevant. But increased spatiotemporal coverage, the addition of novel parameters at sub-annual resolution, and integration with other in situ and remote Earth observations will elevate tree-ring data as an essential component of global-change research.
Babst, Flurin↗
AXAF: Current Developments and Future Plans for the Scientific Data Analysis
AXAF, the Advanced X-ray Astrophysics Facility, is one of NASA's great observatories scheduled for launch in January of 1999 by a Space Shuttle. This facility will be available to scientists in the United States and to the international astronomical community over an anticipated mission lifetime of at least 5 years. The objective of AXAF is to make astrophysical observations in the 0.09 to 10.0 keV energy range with two imaging detectors, and two sets of transmission gratings giving high spatial (0.5 arcsec) and spectral (E/(Delta)E=100-2000) resolution. The AXAF Science Center (ASC) in Cambridge, MA, USA is responsible for obtaining and reviewing observation proposals submitted by users, providing long range science planning and performing all science data calibration, data analysis, science instrument trend analysis, and science data archiving. The ASC will distribute science data products to the users. We will review here the current developments and future plans for the AXAF scientific data analysis system, its infrastructure and new key features, including the global modelling and fitting environment, integrated data analysis GUIs and new analysis tools.
Fruscione, Antonella↗
NASA Omics Archive Project
The space environment consists of a complex set of hazards including altered gravity, radiation, psychological/physiological stress, isolation, and confinement leading to complex biological responses. Advances in biotechnology capabilities offer considerable potential to provide novel insight into those responses as well as innovative diagnostic, treatment, and countermeasure solutions for astronauts as NASA begins to travel beyond low Earth orbit. Omics data (genomics, transcriptomics, proteomics, etc.) is one example that can provide NASA with critical knowledge of how a crewmember’s genetics, environment, and lifestyle can be used to develop individualized approaches for disease prevention, advance diagnostics, and improve treatment strategies. NASA ventured into the field of omics on human subjects with the successful completion of the NASA Twins Study which was the first step in mapping the multi-omic profile of astronauts to understand and mitigate the health consequences of spaceflight. The Human Research Program aims to build upon the success of the Twins Study with the NASA Omics Archive flight study, establishing a longitudinal biospecimen archive and efficiently generating a comprehensive high-quality multi-omic dataset from astronauts for the purpose of studying molecular, metabolic, and microbial changes associated with longduration spaceflight missions. The goal is to facilitate scientific and medical research community efforts to characterize and mitigate spaceflight health and performance risks. In this presentation, we will review details regarding the biospecimen and data archive to be generated by the NASA Omics Archive flight study. Data generated as part of this project will be archived in the NASA Life Sciences Portal (NLSP) and be made available for future hypothesis-driven research efforts or occupational surveillance through Institutional Review Board-approved data sharing and retrospective data requests submitted to the Life Sciences Data Archive (LSDA) team. We will also present results of a ground study performed to evaluate in-house procedures, new sample collection hardware, and vendor capabilities. The data repository generated and the samples to be archived by this study will enable future research efforts to assess an astronauts’ unique molecular and genetic profile with respect to individual spaceflight responses. Results of which will be instrumental in enabling precision health capabilities to better assess and mitigate spaceflight risks, detect disease states earlier, and actively monitor countermeasure treatments, ultimately improving clinical outcomes during future exploration class missions.
C. A. Theriot↗
Open Science for Life in Space
Understanding how biology changes in response spaceflight and how these changes affect crew and craft is important to the design of safe, robust and effective space missions. Advances in analytical technologies allow large volumes of new data to be generated from space biological experiments, and a growing library of legacy data can be re-analyzed in the context of a greater understanding of biological systems. This enables powerful insights into how biology changes during spaceflight. However, for this to be fully realized additional tools, programs, and communities must be developed. Now a developing suite of interconnected open science resources (GeneLab, the Ames Life Sciences Data Archive, the NASA Biological Institutional Science Collection, the Biospecimen Sharing Program) can be leveraged by dedicated Analysis Working Groups to accelerate the pace of discovery in the space biological sciences.
Open Science↗
LSKnowledge: Nexus for Transformative Scientific Discoveries and Enhanced Information Retrieval in NASA Life Sciences Portal
We stand at the brink of an extraordinary transformation in the field of AI, driven by the convergence of generative AI and semantic technologies (e.g., knowledge graphs). This fusion holds immense potential and could redefine the future of scientific exploration, particularly in the realm of life sciences research. In this context, we shed light on the pivotal roles that Large Language Models (LLMs) and semantic technologies will play in advancing research, unearthing and comprehending life sciences information through innovative approaches, and empowering researchers to extract insights from NASA's extensive Life Sciences Data Archive. Within the NASA Life Sciences Portal (NLSP), the integration of LLMs and semantic technologies unlocks several advanced capabilities. First and foremost, it equips scientists with sophisticated tools to manage the ever-expanding wealth of scientific literature and data. Furthermore, it facilitates the creation of knowledge graphs that visually represent intricate relationships among biological entities, enabling comprehensive systems-level analysis. Additionally, the fusion of generative AI (including LLMs) and semantic technology can significantly benefit NASA's life sciences research by enhancing information retrieval and hypothesis generation. These tools enhance natural language understanding, facilitating knowledge discovery within NLSP. The overarching vision is to establish a cohesive knowledge ecosystem within NLSP, harnessing the power of LLMs and semantic technologies to synthesize and cross-reference data from diverse missions, disciplines, and research domains. This holistic approach ultimately deepens our understanding of how space environments impact life sciences data. To advance this initiative, we have launched LSKnowledge, aimed at enhancing the information retrieval capabilities of NLSP. In the short term, our primary goal is to develop a robust semantic search system. This system will empower HRP (Human Research Program) researchers to navigate NLSP data repositories more efficiently and precisely, catalyzing the process of hypothesis formation and scientific breakthroughs. To achieve this, we have employed pre-trained LLMs as part of a semantic search tool that can rank and highlight the most relevant records for user queries. To assess the tool's performance, we have curated a set of approximately 200 queries from subject matter experts (SMEs) and manually ranked the top records retrieved by both the current search system and the new semantic search, using SME judgments as the gold standard for relevancy. Herein, we present the results of our comparative analysis and illustrate how these findings have informed the fine-tuning of the system for enhanced performance. In the long term, our objectives include 1) retrieving publicly available information and integrating it with NLSP data to provide more precise answers to user queries, and 2) incorporating non-textual information from the NLSP database into our approach. In conclusion, the fusion of LLMs and semantic technologies within NLSP represents a pioneering stride towards reshaping the landscape of scientific discovery. This synergy not only equips researchers with powerful tools to navigate the burgeoning sea of information but also facilitates a deeper understanding of complex biological relationships, all while accelerating hypothesis generation and knowledge discovery. Through our initiative, LSKnowledge, we are committed to continually refining and expanding these capabilities, with the aim of not only enhancing information retrieval but also integrating diverse data sources to provide more precise insights. In the grand vision, NLSP strives to become the cornerstone of a comprehensive knowledge ecosystem, unraveling the enigmatic intricacies of life sciences phenomena in the context of space environments.
Life Sciences↗
HRP Data Management Plan
The purpose of Human Research Program Data Management Plan (DMP) is to define the processes and activities required for the overall management of the research data collected and managed by HRP throughout their life cycle. New updates to the Data Management Plan in 2023 include 1. CAPABILITIES AND SERVICES Data Repositories. Principal Investigators (PIs) funded by HRP may be asked to submit data to one of several NASA data repositories. HRP archives data in the NASA Life Sciences Portal (NLSP) that it considers to be unique and high value. This includes data from human subjects in space flight (ISS and commercial flights) and ground analogs to spaceflight; spaceflight tech demos involving humans; human omics data including the microbiome; parabolic flight studies; and the NASA Space Radiation Laboratory (NSRL). The Open Science Data Repository (OSDR) includes The Ames Life Sciences Data Archive (ALSDA), used to archive non-human biological data (e.g., animal) generated by the Human Research program, and GeneLab, available to HRP PIs to archive non-human omics data. Catalog for search and retrieval. A catalog of non-human HRP life science experiments, with all associated descriptions (mission, payload, hardware, and personnel related information), and biospecimens is provided on the NLSP public web site for search and retrieval. 2. IRB ROLE IN RETURN OF INDIVIDUAL RESEARCH RESULTS The NASA IRB manages the process for incidental findings and for returning results to subjects for studies for which NASA IRB is the IRB of record. Omics data, especially genomics data, may generate information significant to the health of or risk to a research subject. These data potentially hold the keys to understand lifetime risks of chronic diseases, such as cancer, as well as risks associated with exposures common in space flight. 3. UPDATE OF TERMS – IDENTIFIABLE AND ATTRIBUTABLE DATA HRP now follows Federal and NASA policy by using “identifiable” instead of “attributable” for Personally Identifiable Information (PII). 4. POLICY ABOUT INTERNAL NON-RESEARCH USE OF DATA The HRP Chief Scientist grants access to data from HRP-funded research for non-research internal use that includes program management, customer facilitation, strategic planning, and risk research planning. Typical HRP personnel granted access to HRP research data for internal use include the Element Scientist, Subject Matter Experts (SME), and Data/bioinformatics Scientists. If data accessed for Internal Use is provided to an intramural or extramural scientist for hypothesis driven research, all Federal and NASA regulations (e.g., IRB review) regarding human subject research apply.
Data Management Plan↗