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NASA NTRS2019

Using the NASA GeneLab Data System to Study the Metagenomes of Spaceships and Their Occupants

With humans pushing to live further off Earth for longer periods of time, it is increasingly important to understand the changes that occur in biological systems during spaceflight whether these be astronauts, their microbial commensals, or their plant-based life support systems. In a three-part presentation, we discuss GeneLab and recent discoveries regarding the microbiota of spacecrafts and space-flown animals. Part 1: GeneLab: Open Science for Life in Space, Jonathan Galazka, NASA Ames Research Center To accelerate the pace of discovery from precious spaceflight biological experiments, NASA as develop the GeneLab data system (genelab.nasa.gov), which allows unfettered access to omics data from spaceflight and spaceflight relevant experiments. GeneLab houses metagenomic datasets from spacecraft and relevant spacecraft models. Users can download this data and associated metadata to make new discoveries about how microbial communities may change and adapt to spaceflight.

Galazka, Jonathan M.↗

NASA NTRS2014

NASA's Astromaterials Database: Enabling Research Through Increased Access to Sample Data, Metadata and Imagery

The Astromaterials Acquisition & Curation Office at NASA's Johnson Space Center (JSC) is the designated facility for curating all of NASA's extraterrestrial samples. Today, the suite of collections includes the lunar samples from the Apollo missions, cosmic dust particles falling into the Earth's atmosphere, meteorites collected in Antarctica, comet and interstellar dust particles from the Stardust mission, asteroid particles from Japan's Hayabusa mission, solar wind atoms collected during the Genesis mission, and space‐exposed hardware from several missions. To support planetary science research on these samples, JSC's Astromaterials Curation Office hosts NASA's Astromaterials Curation digital repository and data access portal [http://curator.jsc.nasa.gov/], providing descriptions of the missions and collections, and critical information about each individual sample. Our office is designing and implementing several informatics initiatives to better serve the planetary research community. First, we are re‐hosting the basic database framework by consolidating legacy databases for individual collections and providing a uniform access point for information (descriptions, imagery, classification) on all of our samples. Second, we continue to upgrade and host digital compendia that summarize and highlight published findings on the samples (e.g., lunar samples, meteorites from Mars). We host high resolution imagery of samples as it becomes available, including newly scanned images of historical prints from the Apollo missions. Finally we are creating plans to collect and provide new data, including 3D imagery, point cloud data, micro CT data, and external links to other data sets on selected samples. Together, these individual efforts will provide unprecedented digital access to NASA's Astromaterials, enabling preservation of the samples through more specific and targeted requests, and supporting new planetary science research and collaborations on the samples.

Evans, Cindy↗

NASA NTRS2006

Data Model Management for Space Information Systems

The Reference Architecture for Space Information Management (RASIM) suggests the separation of the data model from software components to promote the development of flexible information management systems. RASIM allows the data model to evolve independently from the software components and results in a robust implementation that remains viable as the domain changes. However, the development and management of data models within RASIM are difficult and time consuming tasks involving the choice of a notation, the capture of the model, its validation for consistency, and the export of the model for implementation. Current limitations to this approach include the lack of ability to capture comprehensive domain knowledge, the loss of significant modeling information during implementation, the lack of model visualization and documentation capabilities, and exports being limited to one or two schema types. The advent of the Semantic Web and its demand for sophisticated data models has addressed this situation by providing a new level of data model management in the form of ontology tools. In this paper we describe the use of a representative ontology tool to capture and manage a data model for a space information system. The resulting ontology is implementation independent. Novel on-line visualization and documentation capabilities are available automatically, and the ability to export to various schemas can be added through tool plug-ins. In addition, the ingestion of data instances into the ontology allows validation of the ontology and results in a domain knowledge base. Semantic browsers are easily configured for the knowledge base. For example the export of the knowledge base to RDF/XML and RDFS/XML and the use of open source metadata browsers provide ready-made user interfaces that support both text- and facet-based search. This paper will present the Planetary Data System (PDS) data model as a use case and describe the import of the data model into an ontology tool. We will also describe the current effort to provide interoperability with the European Space Agency (ESA)/Planetary Science Archive (PSA) which is critically dependent on a common data model.

RDF↗

NASA NTRSDate not supplied

Creating a knowledge graph to connect scientific publications and datasets for improving discovery of GES DISC’s data and services

The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) archives and distributes to the public hundreds of Earth Science data collections. These collections are used in research, resulting in thousands of scientific papers published each year. As new users come to GES DISC for the data, it is important for them to understand how these data were used in the prior research. For this we are creating the Knowledge Graph that connects research paper citation and the data collection metadata. The relationships created in the graph have potential for the Web applications that utilize this information to directly connect the paper research to the GES DISC datasets and services. We will demonstrate these relationships using the Web application prototype.

Nathaniel Ross Crosby↗

NASA NTRSDate not supplied

The Radiation Biology Ontology: A New Tool Supporting FAIR Principles Across Radiation Biology Facilitating Data Discovery and Integration

Development of the Radiation Biology Ontology (RBO) was motivated by the need for a comprehensive, well-structured ontology for encoding radiation biology metadata. The primary use-cases were archiving data in the STORE database (https://www.storedb.org/), the repository for the RadoNorm Project, and in GeneLab (https://genelab.nasa.gov), NASA’s ‘omics database. The scope of radiobiology research ranges from physics to radiation oncology to socio-legal studies; no existing ontology has the necessary breadth or depth. In addition, a formal ontology has the advantage of being usable for machine learning and, importantly, for tasks like data integration, knowledge extraction from the scientific literature and for query extension and data classification. Standardisation of metadata is one of the primary objectives of the FAIR principles for open data; RBO is an important landmark for FAIR radiation biology data.

ontology↗

NASA NTRS2013

The Hopkins Ultraviolet Telescope: The Final Archive

The Hopkins Ultraviolet Telescope (HUT) was a 0.9 m telescope and moderate-resolution (Delta)lambda equals 3 A) far-ultraviolet (820-1850 Å) spectrograph that flew twice on the space shuttle, in 1990 December (Astro-1, STS-35) and 1995 March (Astro-2, STS-67). The resulting spectra were originally archived in a nonstandard format that lacked important descriptive metadata. To increase their utility, we have modified the original datareduction software to produce a new and more user-friendly data product, a time-tagged photon list similar in format to the Intermediate Data Files (IDFs) produced by the Far Ultraviolet Spectroscopic Explorer calibration pipeline. We have transferred all relevant pointing and instrument-status information from locally-archived science and engineering databases into new FITS header keywords for each data set. Using this new pipeline, we have reprocessed the entire HUT archive from both missions, producing a new set of calibrated spectral products in a modern FITS format that is fully compliant with Virtual Observatory requirements. For each exposure, we have generated quicklook plots of the fully-calibrated spectrum and associated pointing history information. Finally, we have retrieved from our archives HUT TV guider images, which provide information on aperture positioning relative to guide stars, and converted them into FITS-format image files. All of these new data products are available in the new HUT section of the Mikulski Archive for Space Telescopes (MAST), along with historical and reference documents from both missions. In this article, we document the improved data-processing steps applied to the data and show examples of the new data products.

Hopkins↗

NASA NTRSDate not supplied

Development of a Knowledge Graph for Dataset Discovery and Identification at a NASA Data Center

The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) archives and distributes hundreds of Earth Science data collections to the public. These collections are used in research, resulting in the publication of thousands of scientific papers each year. As new users come to GES DISC for data, it is important for them to understand how prior research used the data. To help researchers, a knowledge graph (KG) was designed and implemented to connect publication citations with dataset metadata. The relationships created in the graph have the potential to allow the Web applications that utilize this information to directly connect the publication to the GES DISC datasets and services. These relationships are demonstrated using a web application prototype. In addition, the graph can also make connections between publications, datasets, and measurements based on the mentions of datasets and their attributes in the publications. To demonstrate this capability, a web application was created that takes the excerpt from the publication and returns a most likely dataset and measurement pairing, ranking the results based on how often these datasets and measurements were used in prior publications.

Nathaniel Crosby↗

NASA NTRS2010

Public Participation in Earth Science from the ISS

The Gateway to Astronaut Photography of Earth (GAPE) is an online database (http://eol.jsc.nasa.gov) of terrestrial astronaut photography that enables the public to experience the astronaut s view from orbit. This database of imagery includes all NASA human-directed missions from the Mercury program of the early 1960 s to the current International Space Station (ISS). To date, the total number of images taken by astronauts is 1,025,333. Of the total, 621,316 images have been "cataloged" (image geographic center points determined and descriptive metadata added). The remaining imagery provides an opportunity for the citizen-scientist to become directly involved with NASA through cataloging of astronaut photography, while simultaneously experiencing the wonder and majesty of our home planet as seen by astronauts on board the ISS every day. We are currently developing a public cataloging interface for the GAPE website. When complete, the citizen-scientist will be able to access a selected subset of astronaut imagery. Each candidate will be required to pass a training tutorial in order to receive certification as a cataloger. The cataloger can then choose from a selection of images with basic metadata that is sorted by difficulty levels. Some guidance will be provided (template/pull down menus) for generation of geographic metadata required from the cataloger for each photograph. Each cataloger will also be able to view other contributions and further edit that metadata if they so choose. After the public inputs their metadata the images will be posted to an internal screening site. Images with similar geographic metadata and centerpoint coordinates from multiple catalogers will be reviewed by NASA JSC Crew Earth Observations (CEO) staff. Once reviewed and verified, the metadata will be entered into the GAPE database with the contributors identified by their chosen usernames as having cataloged the frame.

Willis, Kimberly J.↗

NASA NTRSDate not supplied

NASA GeneLab: Open Science for Life in Space

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 350 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab Sequencing Lab. The GLDS contains rich metadata about each experiment and has integrated radiation dosimetry data from experiments flown on the Space Shuttle, International Space Station, and Free Flying spacecrafts. With the increasing amount and complexity of omics data being generated, GeneLab utilizes community-defined, common models for metadata and terminology so that omics data and results are discoverable and reliably reproducible. GeneLab uses the ISA-Tab specification and semantic model for organizing and representing omics metadata. In addition to metadata standards, data files must be open-source file or common exchange formats to ensure accessibility and usability by all users. To ease data ingestion and transfer, the web-based submission tool allows PIs a user-friendly user interface to curate, organize, and publish their space relevant omics data. In the more recent years, data curation and submission portal has incorporated the FAIR principles making data findable, accessible, interoperable, and reusable. To increase reusability of data, GeneLab has implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 200 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. To train the next generation of scientists, NASA offers training programs such as GeneLab 4 High School (GL4HS) and GeneLab 4 Universities. NLM Curation at a Scale Workshop 2022 | NASA GeneLab (GL4U) to teach students bioinformatics and computational biology methods to analyze omics data. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.

GeneLab↗

NASA NTRS2019

GeneLab: Open Science for Life in Space

Galazka, Jonathan M.↗

NASA NTRS1991

Contents of the JPL Distributed Active Archive Center (DAAC) archive, version 2-91

The Distributed Active Archive Center (DAAC) archive at the Jet Propulsion Laboratory (JPL) includes satellite data sets for the ocean sciences and global change research to facilitate multidisciplinary use of satellite ocean data. Parameters include sea surface height, surface wind vector, sea surface temperature, atmospheric liquid water, and surface pigment concentration. The Jet Propulsion Laboratory DAAC is an element of the Earth Observing System Data and Information System (EOSDIS) and will be the United States distribution site for the Ocean Topography Experiment (TOPEX)/POSEIDON data and metadata.

Smith, Elizabeth A.↗

NASA NTRS1994

JPL Physical Oceanography Distributed Active Archive Center (PO.DAAC) data availability, version 1-94

The Physical Oceanography Distributed Active Archive Center (PO.DAAC) archive at the Jet Propulsion Laboratory (JPL) includes satellite data sets for the ocean sciences and global-change research to facilitate multidisciplinary use of satellite ocean data. Parameters include sea-surface height, surface-wind vector, sea-surface temperature, atmospheric liquid water, and integrated water vapor. The JPL PO.DAAC is an element of the Earth Observing System Data and Information System (EOSDIS) and is the United States distribution site for Ocean Topography Experiment (TOPEX)/POSEIDON data and metadata.

Source record↗

NASA NTRS2013

Sally Ride EarthKAM - Automated Image Geo-Referencing Using Google Earth Web Plug-In

Sally Ride EarthKAM is an educational program funded by NASA that aims to provide the public the ability to picture Earth from the perspective of the International Space Station (ISS). A computer-controlled camera is mounted on the ISS in a nadir-pointing window; however, timing limitations in the system cause inaccurate positional metadata. Manually correcting images within an orbit allows the positional metadata to be improved using mathematical regressions. The manual correction process is time-consuming and thus, unfeasible for a large number of images. The standard Google Earth program allows for the importing of KML (keyhole markup language) files that previously were created. These KML file-based overlays could then be manually manipulated as image overlays, saved, and then uploaded to the project server where they are parsed and the metadata in the database is updated. The new interface eliminates the need to save, download, open, re-save, and upload the KML files. Everything is processed on the Web, and all manipulations go directly into the database. Administrators also have the control to discard any single correction that was made and validate a correction. This program streamlines a process that previously required several critical steps and was probably too complex for the average user to complete successfully. The new process is theoretically simple enough for members of the public to make use of and contribute to the success of the Sally Ride EarthKAM project. Using the Google Earth Web plug-in, EarthKAM images, and associated metadata, this software allows users to interactively manipulate an EarthKAM image overlay, and update and improve the associated metadata. The Web interface uses the Google Earth JavaScript API along with PHP-PostgreSQL to present the user the same interface capabilities without leaving the Web. The simpler graphical user interface will allow the public to participate directly and meaningfully with EarthKAM. The use of similar techniques is being investigated to place ground-based observations in a Google Mars environment, allowing the MSL (Mars Science Laboratory) Science Team a means to visualize the rover and its environment.

Andres, Paul M.↗

NASA NTRS2016

Managing Sustainable Data Infrastructures: The Gestalt of EOSDIS

EOSDIS epitomizes a System of Systems, whose many varied and distributed parts are integrated into a single, highly functional organized science data system. A distributed architecture was adopted to ensure discipline-specific support for the science data, while also leveraging standards and establishing policies and tools to enable interdisciplinary research, and analysis across multiple scientific instruments. The EOSDIS is composed of system elements such as geographically distributed archive centers used to manage the stewardship of data. The infrastructure consists of underlying capabilities connections that enable the primary system elements to function together. For example, one key infrastructure component is the common metadata repository, which enables discovery of all data within the EOSDIS system. EOSDIS employs processes and standards to ensure partners can work together effectively, and provide coherent services to users.

remote sensing↗

NASA NTRS2016

Outcomes of a NASA Workshop to Develop a Portfolio of Low Latency Datasets for Time-Sensitive Applications

It is widely accepted that time-sensitive remote sensing data serve the needs of decision makers in the applications communities and yet to date, a comprehensive portfolio of NASA low latency datasets has not been available. This paper will describe the NASA low latency, or Near-Real Time (NRT), portfolio, how it was developed and plans to make it available online through a portal that leverages the existing EOSDIS capabilities such as the Earthdata Search Client (https:search.earthdata.nasa.gov), the Common Metadata Repository (CMR) and the Global Imagery Browse Service (GIBS). This paper will report on the outcomes of a NASA Workshop to Develop a Portfolio of Low Latency Datasets for Time-Sensitive Applications (27-29 September 2016 at NASA Langley Research Center, Hampton VA). The paper will also summarize findings and recommendations from the meeting outlining perceived shortfalls and opportunities for low latency research and application science.

remote sensing↗

NASA NTRS2012

Long-Lasting Science Returns from the Apollo Heat Flow Experiments

The Apollo astronauts deployed geothermal heat flow instruments at landing sites 15 and 17 as part of the Apollo Lunar Surface Experiments Packages (ALSEP) in July 1971 and December 1972, respectively. These instruments continuously transmitted data to the Earth until September 1977. Four decades later, the data from the two Apollo sites remain the only set of in-situ heat flow measurements obtained on an extra-terrestrial body. Researchers continue to extract additional knowledge from this dataset by utilizing new analytical techniques and by synthesizing it with data from more recent lunar orbital missions such as the Lunar Reconnaissance Orbiter. In addition, lessons learned from the Apollo experiments help contemporary researchers in designing heat flow instruments for future missions to the Moon and other planetary bodies. For example, the data from both Apollo sites showed gradual warming trends in the subsurface from 1971 to 1977. The cause of this warming has been debated in recent years. It may have resulted from fluctuation in insolation associated with the 18.6-year-cycle precession of the Moon, or sudden changes in surface thermal environment/properties resulting from the installation of the instruments and the astronauts' activities. These types of reanalyses of the Apollo data have lead a panel of scientists to recommend that a heat flow probe carried on a future lunar mission reach 3 m into the subsurface, approx 0.6 m deeper than the depths reached by the Apollo 17 experiment. This presentation describes the authors current efforts for (1) restoring a part of the Apollo heat flow data that were left unprocessed by the original investigators and (2) designing a compact heat flow instrument for future robotic missions to the Moon. First, at the conclusion of the ALSEP program in 1977, heat flow data obtained at the two Apollo sites after December 1974 were left unprocessed and not properly archived through NASA. In the following decades, heat flow data from January 1975 through February 1976, as well as the metadata necessary for processing the data (the data reduction algorithm, instrument calibration data, etc.), were somehow lost. In 2010, we located 450 original master archival tapes of unprocessed data from all the ALSEP instruments for a period of April through June 1975 at the Washington National Records Center. We are currently extracting the heat flow data packets from these tapes and processing them. Second, on future lunar missions, heat flow probes will likely be deployed by a network of small robotic landers, as recommended by the latest Decadal Survey of the National Academy of Science. In such a scenario, the heat flow probe must be a compact system, and that precludes use of heavy excavation equipment such as a rotary drill for reaching the 3-m target depth. The new heat flow system under development uses a pneumatically driven penetrator. It utilizes a stem that winds out of a reel and pushes its conical tip into the regolith. Simultaneously, gas jets, emitted from the cone tip, loosen and blow away the soil. Lab experiments have demonstrated its effectiveness in lunar vacuum.

Nagihara, S.↗

NASA NTRS2014

NASA GeneLab Concept of Operations

NASA's GeneLab aims to greatly increase the number of scientists that are using data from space biology investigations on board ISS, emphasizing a systems biology approach to the science. When completed, GeneLab will provide the integrated software and hardware infrastructure, analytical tools and reference datasets for an assortment of model organisms. GeneLab will also provide an environment for scientists to collaborate thereby increasing the possibility for data to be reused for future experimentation. To maximize the value of data from life science experiments performed in space and to make the most advantageous use of the remaining ISS research window, GeneLab will apply an open access approach to conducting spaceflight experiments by generating, and sharing the datasets derived from these biological studies in space.Onboard the ISS, a wide variety of model organisms will be studied and returned to Earth for analysis. Laboratories on the ground will analyze these samples and provide genomic, transcriptomic, metabolomic and proteomic data. Upon receipt, NASA will conduct data quality control tasks and format raw data returned from the omics centers into standardized, annotated information sets that can be readily searched and linked to spaceflight metadata. Once prepared, the biological datasets, as well as any analysis completed, will be made public through the GeneLab Space Bioinformatics System webb as edportal. These efforts will support a collaborative research environment for spaceflight studies that will closely resemble environments created by the Department of Energy (DOE), National Center for Biotechnology Information (NCBI), and other institutions in additional areas of study, such as cancer and environmental biology. The results will allow for comparative analyses that will help scientists around the world take a major leap forward in understanding the effect of microgravity, radiation, and other aspects of the space environment on model organisms. These efforts will speed the process of scientific sharing, iteration, and discovery.

Space Life Science↗

NASA NTRS2011

Improvements in Space Geodesy Data Discovery at the CDDIS

The Crustal Dynamics Data Information System (CDDIS) supports data archiving and distribution activities for the space geodesy and geodynamics community. The main objectives of the system are to store space geodesy and geodynamics related data products in a central data bank. to maintain information about the archival of these data, and to disseminate these data and information in a timely manner to a global scientific research community. The archive consists of GNSS, laser ranging, VLBI, and DORIS data sets and products derived from these data. The CDDIS is one of NASA's Earth Observing System Data and Information System (EOSDIS) distributed data centers; EOSDIS data centers serve a diverse user community and arc tasked to provide facilities to search and access science data and products. Several activities are currently under development at the CDDIS to aid users in data discovery, both within the current community and beyond. The CDDIS is cooperating in the development of Geodetic Seamless Archive Centers (GSAC) with colleagues at UNAVCO and SIO. TIle activity will provide web services to facilitate data discovery within and across participating archives. In addition, the CDDIS is currently implementing modifications to the metadata extracted from incoming data and product files pushed to its archive. These enhancements will permit information about COOlS archive holdings to be made available through other data portals such as Earth Observing System (EOS) Clearinghouse (ECHO) and integration into the Global Geodetic Observing System (GGOS) portal.

Noll, C.↗