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All sourcesNASA NTRSDOE OSTI
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 NTRS2017

NASA's Big Earth Data Initiative Accomplishments

The goal of NASA's effort for BEDI is to improve the usability, discoverability, and accessibility of Earth Observation data in support of societal benefit areas. Accomplishments: In support of BEDI goals, datasets have been entered into Common Metadata Repository(CMR), made available via the Open-source Project for a Network Data Access Protocol (OPeNDAP), have a Digital Object Identifier (DOI) registered for the dataset, and to support fast visualization many layers have been added in to the Global Imagery Browse Services (GIBS).

CMR↗
NASA NTRSDate not supplied

A User-Focused Renovation of CERES Metadata

Production software and public data products for Clouds and the Earth’s Radiant Energy System (CERES) continue to evolve as the project extends its climate data record. The data management team for CERES is currently undertaking major renovations of both code and data products, the latter of which is, of course, in service of improving user experience. A major mode of CERES’ data product improvement is in renovating products’ metadata. Metadata standards have evolved since CERES began producing its data products in 2000. In its twentieth year, CERES essentially asked the question: how would the project design its data products if it could start all over again? With forthcoming editions, this rebirth will be realized. CERES has redesigned its metadata standards to best position itself for data discoverability. The project has used the latest standards being developed in NASA’s Earth Science Data and Information Systems (ESDIS) Project’s Unified Metadata Model (UMM) documentation; collaborated with the Atmospheric Science Data Center (ASDC) to ensure compliance with Common Metadata Repository compatibility, and continued compliance with Climate and Forecast (CF) Conventions. In doing so, the team created its own, internal document for proper metadata creation and metadata verification software that is deployed prior to all code deliveries. This presentation will discuss this redesign process, as well as needs met and those that are still outstanding in the search for an improved user experience with CERES data products.

Kathleen Dejwakh↗
NASA NTRSDate not supplied

Preserving NASA Historic and Current Mission Data and Adding Value to These for Future Researchers

The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) has been actively involved in many aspects of ensuring the long-term preservation of NASA earth science data and knowledge. This involves both the recovery and preservation of early NASA meteorological and other earth observation data, as well as preserving the more recent Earth Observation System (EOS) mission data sets which continue or have reached their end of lifetime. The GES DISC adds value to these preserved data by adding metadata and making the data available online to future researchers. The early NASA meteorological and earth observation data sets from the 1960s and 70s were originally archived on magnetic tapes, and visualizations of these data were preserved on 70-mm film. As these media have aged, their contents have been at risk of permanent loss. NASA has given the task of preserving these early data sets to the GES DISC and making these data sets easily available to the public. The data from these early missions are potentially useful to climate researchers as these are some of the only global measurements made at their time. These old data on magnetic tapes and film strips do not contain easily readable metadata, and so to add value the GES DISC has added digital metadata to them so that the data are searchable and findable. The GES DISC is also involved in preserving the data and knowledge from the EOS era missions. The GES DISC follows the guidelines developed for the preservation of data as specified in the NASA EOS Data and Information System (EOSDIS) Earth Science Data Preservation Content Specification (423-SPEC-001) document. To date, the GES DISC has consulted with the data science teams from the following missions: UARS, Earth Probe TOMS, Aura HIRDLS, and SORCE, in order to properly preserve their data and accompanying documentation. The GES DISC is also currently working with the EOS science teams from TRMM, AIRS, MLS, OMI and additional missions to ensure that the relevant documents and data sets are properly archived for future researchers. A standardized procedure for mission data preservation following 423-SPEC-001 makes preservation among the many NASA EOSDIS data centers uniform, so that these could be transitioned easily to a common EOSDIS preservation repository. This presentation will give an overview of the preservation and recovery of the old NASA historical data sets archived at the GES DISC, as well as the data and documentation preservation efforts of the EOS era missions.

James Johnson↗
NASA NTRS1988

A mass storage system for supercomputers based on Unix

The authors present the design, implementation, and utilization of a large mass storage subsystem (MSS) for the numerical aerodynamics simulation. The MSS supports a large networked, multivendor Unix-based supercomputing facility. The MSS at Ames Research Center provides all processors on the numerical aerodynamics system processing network, from workstations to supercomputers, the ability to store large amounts of data in a highly accessible, long-term repository. The MSS uses Unix System V and is capable of storing hundreds of thousands of files ranging from a few bytes to 2 Gb in size.

Richards, J.↗
NASA NTRSDate not supplied

WET Water Resources: A Google Earth Engine Python API Tool to Automate Wetland Extent Mapping Using Radar Satellite Sensors for Wetland Management and Monitoring

Wetland ecosystems are annually or seasonally wet transition zones between land and water. They provide a range of ecosystem services such as water filtration, flood mitigation, and carbon sequestration, as well as hosting biodiversity hotspots. Although they fulfill fundamental physical and natural processes, wetland extent and health are threatened by anthropogenic influences related to urbanization, population increase, pollution, and climate change. Recognizing the need to quantitatively monitor changes in these recently threatened ecosystems in a timely and cost-effective way, we developed a Google Earth Engine (GEE) Python API tool for automated wetland extent mapping using optical and radar satellite sensors that can be applied globally. The tool will significantly improve wetland change analysis and monitoring as the optical and SAR data proves high resolution (5-10 m) imagery, and SAR data is unaffected by cloud cover and light availability (day vs. night), which are common limitations for other remotely sensed sensors. The tool utilizes Copernicus Sentinel-1 C-band and NISAR L-band synthetic aperture radar (SAR) imagery. During image preprocessing, we applied a MODIS snow mask product to mask global snow coverage, which would affect land classification sensitivity. Calibration and validation were conducted through a historical change and sensitivity analysis of the Sudd watershed located in central Sudan. The tool was the first of its kind, as it enables NISAR data processing through an open-source GEE repository, further expanding and improving the utility of NASA Earth observations and contributing to NASA Open Science initiatives. We anticipate the tool will be used by researchers and practitioners interested in wetland monitoring and management..

Lori Berberian↗
NASA NTRS2016

Heuristics for Relevancy Ranking of Earth Dataset Search Results

As the Variety of Earth science datasets increases, science researchers find it more challenging to discover and select the datasets that best fit their needs. The most common way of search providers to address this problem is to rank the datasets returned for a query by their likely relevance to the user. Large web page search engines typically use text matching supplemented with reverse link counts, semantic annotations and user intent modeling. However, this produces uneven results when applied to dataset metadata records simply externalized as a web page. Fortunately, data and search provides have decades of experience in serving data user communities, allowing them to form heuristics that leverage the structure in the metadata together with knowledge about the user community. Some of these heuristics include specific ways of matching the user input to the essential measurements in the dataset and determining overlaps of time range and spatial areas. Heuristics based on the novelty of the datasets can prioritize later, better versions of data over similar predecessors. And knowledge of how different user types and communities use data can be brought to bear in cases where characteristics of the user (discipline, expertise) or their intent (applications, research) can be divined. The Earth Observing System Data and Information System has begun implementing some of these heuristics in the relevancy algorithm of its Common Metadata Repository search engine.

science data management↗
NASA NTRS2017

Relevancy Ranking of Satellite Dataset Search Results

As the Variety of Earth science datasets increases, science researchers find it more challenging to discover and select the datasets that best fit their needs. The most common way of search providers to address this problem is to rank the datasets returned for a query by their likely relevance to the user. Large web page search engines typically use text matching supplemented with reverse link counts, semantic annotations and user intent modeling. However, this produces uneven results when applied to dataset metadata records simply externalized as a web page. Fortunately, data and search provides have decades of experience in serving data user communities, allowing them to form heuristics that leverage the structure in the metadata together with knowledge about the user community. Some of these heuristics include specific ways of matching the user input to the essential measurements in the dataset and determining overlaps of time range and spatial areas. Heuristics based on the novelty of the datasets can prioritize later, better versions of data over similar predecessors. And knowledge of how different user types and communities use data can be brought to bear in cases where characteristics of the user (discipline, expertise) or their intent (applications, research) can be divined. The Earth Observing System Data and Information System has begun implementing some of these heuristics in the relevancy algorithm of its Common Metadata Repository search engine.

science data management↗
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 NTRS2017

Knowledge Base for Distributed Spacecraft Mission Design Using the Trade-Space Analysis Tool for Constellations (TAT-C)

Opportunities for multi-point measurements, greater revisit frequency, failure robustness, and improved cost effectiveness motivate consideration of Distributed Spacecraft Missions (DSMs) for future Earth science missions. However, careful analysis is required to assess the distributed sensing capabilities of a constellation compared to more mature monolithic spacecraft while also considering other important dimensions such as cost and risk. The large combinatorial DSM design space limits existing mission analysis tools and exploration methods which emphasize monolithic design variables. The Trade-space Analysis Tool for Constellations (TAT-C) under development at Goddard seeks to enumerate and evaluate alternative mission architectures to minimize cost and maximize scientific return for pre-defined goals during pre-phase A analysis.Similar to other model-centric engineering efforts, efficient data management is a significant challenge for DSM mission analysis. In TAT-C, a Knowledge Base (KB) is envisioned as a cumulative central repository of information and meta-information about DSMs. Initial KB concepts store related data for reuse within or across mission analyses; however, over time, the KB is envisioned to be an important layer to coordinate actions of both human analysts and automated design agents to search a large design space for desirable mission alternatives. Preliminary KB research builds on a modern web technology stack to provide the following functionality: 1) storage of trade-space search requests which set requirements and constraints for DSM concepts, 2) storage of analysis results which quantify performance metrics for evaluated DSM concepts, 3) a RESTful application programming interface (API) for scripted access to data from TAT-C modules, 4) web-based graphical user interface (GUI) for manual access to underlying data, and 5) access control and management restrictions relevant to data protection and security. These efforts have culminated in a prototype KB used by the research team during TAT-C development to assess opportunities for future work.

Pattern Recognition↗
NASA NTRS2011

Deep Space Network-Wide Portal Development: Planning Service Pilot Project

The Deep Space Network (DSN) is an international network of antennas that supports interplanetary spacecraft missions and radio and radar astronomy observations for the exploration of the solar system and the universe. DSN provides the vital two-way communications link that guides and controls planetary explorers, and brings back the images and new scientific information they collect. In an attempt to streamline operations and improve overall services provided by the Deep Space Network a DSN-wide portal is under development. The project is one step in a larger effort to centralize the data collected from current missions including user input parameters for spacecraft to be tracked. This information will be placed into a principal repository where all operations related to the DSN are stored. Furthermore, providing statistical characterization of data volumes will help identify technically feasible tracking opportunities and more precise mission planning by providing upfront scheduling proposals. Business intelligence tools are to be incorporated in the output to deliver data visualization.

project development↗
NASA NTRSDate not supplied

An Automated Approach to Labelling Datasets in Earth Science Publications

NASA Data Active Archive Centers, orDAACs, ingest, store, and distribute dataacquired from satellites, ground systems as well asreanalysis models. Many authors use this datain their research. However, most of the datasets usedin Earth Science Publications are not citedcorrectly or not cited at all. Thus, there is no directlink between the datasets used and thescientific publications which reference them. Thisleads to issues with reproducibility of theresults, attribution of the research results, anddiscovery of new datasets. This project began byexploring various methods of automatically labellingGoddard Earth Sciences Data andInformation Services Center (GES DISC) datasets usingSupervised Machine Learning and EarthData Search Common Metadata Repository (CMR) queries.The ultimate goal was to create alibrary of citations that utilized automated citationlabeling to directly link the researchpublications to the data they use. Supervised MachineLearning approaches struggled due to thelimited amount of labelled training data to learnfrom. Increasing the volume of training data isdifficult as it requires subject matter experts todevote time to manually reviewing journalarticles and determining the datasets used. The CMRqueries were inconsistent because theunderlying metadata is continuously being updated.Thus, it is hard to generalize theeffectiveness of the CMR results as they are dependenton the internal state of CMR. Theseapproaches helped inform the decision to transitionthe project into using a Knowledge Graph.Another key aspect of this project focused on theautomated extraction of features (platform,instrument, variables, etc) and explicit citationsfrom within Earth Science Publications. Theseautomated extractions were used to classify researchpapers based on their platform/instrumentcouples. This information was input into the CitationManagement System for GES DISC. Theseplatform/instrument couples also provide an additionalfacet that can be searched on the GESDISC website.

Edward Jahoda↗
NASA NTRS2018

GeneLab: Omics Database for Spaceflight Experiments

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

omics↗
NASA NTRS1993

Toxic substances registry system: Index of material safety data sheets

The Material Safety Data Sheets (MSDS's) listed in this index reflect product inventories and associated MSDS's which were submitted to the Toxic Substances Registry database maintained by the Base Operations Contractor at the Kennedy Space Center. The purpose of this index is to provide KSC government, contractor, and tenant organizations a means to access information on the hazards associated with these chemicals. The Toxic Substance Registry Service (TSRS) was established to manage information dealing with the storage and use of toxic and otherwise hazardous materials at KSC. As a part of this service, the BOC Environmental Health Services maintains a central repository of MSDS's which were provided to TSRS. The data on the TSRS are obtained from NASA, contractor, and tenant organizations who use or store hazardous materials at KSC. It is the responsibility of these organizations to conduct inventories, obtain MSDS's, distribute Hazard Communication information to their employees, and otherwise implement compliance with appropriate Federal, State, and NASA Hazard Communication and Worker Right-to-Know regulations and policies.

Source record↗
NASA NTRSDate not supplied

Citizen Science Approach for Searching and Curating Literature of the Effects of Spaceflight on Cardiovascular Outcomes in Rodents and Humans

The spaceflight environment causes significant changes to the structure and function of the cardiovascular system, including fluid redistribution, alterations in blood pressure, and changes in cardiac output. The goal of this project is to quantitatively summarize the data on the effects of actual or simulated microgravity and radiation exposure resulting from spaceflight on the cardiovascular system. As the first step, a group of investigators approached through a collaboration of the Ames Life Science Data Archive (ALSDA) Analysis Working Group developed a list of relevant cardiovascular search terms. Based on these, medical librarians generated and executed the search strategy in Medline, CINAHL, Embase and NASA repositories. In parallel, we recruited students and young professionals from various space industry-affiliated organizations, resulting in ~100 individuals joining. With this program we aimed to reach students and young people underrepresented in STEM, including first-generation, female, minorities, disadvantaged backgrounds, fostered individuals, etc. These individuals completed a virtual training course on the nature and methodologies of the project. Following this, the participants were structured into teams with more senior/experienced individuals designated as team leaders. Currently, the teams are screening approximately 15,000 studies using the systematic review tool, Covidence. Teams will be extracting and curating data for meta-analysis of the cardiovascular spaceflight literature, but also extracting, submitting, and curating appropriate datasets into the new ALSDA submission portal and repository. This effort will result in collaborative publications based upon the literature meta-analyses, and a number of publicly accessible datasets for reuse, modeling, machine learning, and knowledge graph-type approaches. This approach reduces the length of time to complete title/abstract screening time from 1-2 years needed for this volume of studies, to 3-4 months, while also providing a unique, open-access educational experience to space research and training in knowledge synthesis tools to interested individuals.

space biology↗
NASA NTRS2008

Estimating Software-Development Costs With Greater Accuracy

COCOMOST is a computer program for use in estimating software development costs. The goal in the development of COCOMOST was to increase estimation accuracy in three ways: (1) develop a set of sensitivity software tools that return not only estimates of costs but also the estimation error; (2) using the sensitivity software tools, precisely define the quantities of data needed to adequately tune cost estimation models; and (3) build a repository of software-cost-estimation information that NASA managers can retrieve to improve the estimates of costs of developing software for their project. COCOMOST implements a methodology, called '2cee', in which a unique combination of well-known pre-existing data-mining and software-development- effort-estimation techniques are used to increase the accuracy of estimates. COCOMOST utilizes multiple models to analyze historical data pertaining to software-development projects and performs an exhaustive data-mining search over the space of model parameters to improve the performances of effort-estimation models. Thus, it is possible to both calibrate and generate estimates at the same time. COCOMOST is written in the C language for execution in the UNIX operating system.

Baker, Dan↗
NASA NTRSDate not supplied

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↗
NASA NTRS2015

Climate Data Initiative: A Geocuration Effort to Support Climate Resilience

Curation is traditionally defined as the process of collecting and organizing information around a common subject matter or a topic of interest and typically occurs in museums, art galleries, and libraries. The task of organizing data around specific topics or themes is a vibrant and growing effort in the biological sciences but to date this effort has not been actively pursued in the Earth sciences. In this paper, we introduce the concept of geocuration and define it as the act of searching, selecting, and synthesizing Earth science data/metadata and information from across disciplines and repositories into a single, cohesive, and useful collection. We present the Climate Data Initiative (CDI) project as a prototypical example. The CDI project is a systematic effort to manually curate and share openly available climate data from various federal agencies. CDI is a broad multi-agency effort of the U.S. government and seeks to leverage the extensive existing federal climate-relevant data to stimulate innovation and private-sector entrepreneurship to support national climate-change preparedness. We describe the geocuration process used in the CDI project, lessons learned, and suggestions to improve similar geocuration efforts in the future.

Metada↗