Expanding Biological Repository Data Availability for Sharing and Knowledge Discovery
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Data↗
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Results for “FAIR data”
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High Resolution Spectrometry of Leaf and Canopy Chemistry for Biochemical Cycling
High-resolution laboratory spectrophotometer and Airborne Imaging Spectrometer (AIS) data were used to analyze forest leaf and canopy chemistry. Fundamental stretching frequencies of organic bonds in the visible, near infrared and short-wave infrared are indicative of concentrations and total content of nitrogen, phosphorous, starch and sugar. Laboratory spectrophotometer measurements showed very strong negative correlations with nitrogen (measured using wet chemistry) in the visible wavelengths. Strong correlations with green wet canopy weight in the atmospheric water absorption windows were observed in the AIS data. A fairly strong negative correlation between the AIS data at 1500 nm and total nitrogen and nitrogen concentration was evident. This relationship corresponds very closely to protein absorption features near 1500 nm.
Spanner, M. A.↗
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↗
A cost and community perspective on the barriers to microbiome data reuse
Microbiome research is becoming a mature field with a wealth of data amassed from diverse ecosystems, yet the ability to fully leverage multi-omics data for reuse remains challenging. To provide a view into researchers’ behavior and attitudes towards data reuse, we surveyed over 700 microbiome researchers to evaluate data sharing and reuse challenges. We found that many researchers are impeded by difficulties with metadata records, challenges with processing and bioinformatics, and problems with data repository submissions. We also explored the cost constraints of data reuse at each step of the data reuse process to better understand “pain points” and to provide a more quantitative perspective from sixteen active researchers. The bioinformatics and data processing step was estimated to be the most time consuming, which aligns with some of the most frequently reported challenges from the community survey. From these two approaches, we present evidence-based recommendations for how to address data sharing and reuse challenges with concrete actions for future work.
59 BASIC BIOLOGICAL SCIENCES↗
We Need A Better Way to Share Earth Observations
A more accessible, open data-sharing infrastructure will engage a broader community of contributors, helping to develop satellite data products that benefit Earth science research and applications.
Apps & Software↗
Solid rocket booster sting interference wind tunnel test analysis, appendix D
Additional analyses of wind tunnel test results from SRB sting interference test TWT 660 and HRWT 042 were conducted to evaluate the sting interference that may be present in the Space Shuttle SRB reentry aerodynamic math model. Additional wind tunnel data was obtained at higher angles of attack from test program TWT 660 and test program HRWT 042. The additional data were analyzed to evaluate the procedures used to fair the data in the development of the SRB reentry aerodynamic data Tape no. 5.
Conine, B.↗
Laying the Foundations for FAIR-er Science: ISA and the LSDA Data Submission Process in NASA's Evolving Data Management Environment
The Life Sciences Data Archive (LSDA) archives data resulting from research on the effects of spaceflight on humans and the development of countermeasures to mitigate spaceflight hazards. Archivists work with researchers to ensure that unique and high value data products and their metadata are preserved and managed to support current and future research. Currently, LSDA is updating its procedures and data submission requirements in response to the evolving data preservation environment at NASA. LSDA is implementing best practices for research data management through the establishment of clear data submission guidelines, integration of the FAIR (Findability, Accessibility, Interoperability, Reusability) principles, and use of the ISA (Investigation, Study, Assay) research metadata framework for data discoverability and transparency into the data management processes. These changes directly impact LSDA’s requirements for research data submissions. The newly revised Research Data Submission Agreement (RDSA), formerly the Data Submission Agreement (DSA), introduces ISA-compatible metadata collection standards to LSDA’s process. Adherence to LSDA’s data submission guidelines enhances the FAIR-ness of the repository’s collections for future users. This presentation will discuss (1) how submission of research data and associated metadata are impacted by current data management policies, (2) benefits of the adoption of FAIR principles and the ISA metadata framework for retrospective studies utilizing existing LSDA datasets and historic data collections, and (3) the support LSDA will provide to researchers during this transition.
LSDA↗
Standards and Best Practices - Two NASA Examples
Formal international standards as well as promotion of community or recommended practices have their place in ensuring "FAIRness" of data. Data management in NASA's Earth Observation System Data and Information System (EOSDIS) has benefited from both of these avenues to a significant extent. The purpose of this paper is to present one example of each of these, which promote (re)usability. The first is an ISO standard for specifying preservation content from Earth observation missions. The work on this started in 2011, informally within the Earth Science Information Partners (ESIP) in the US, while the European Space Agency (ESA) was leading an effort on Long-Term Data Preservation (LTDP). Resulting from the ESIP discussions was NASA's Preservation Content Specification, which was applied in 2012 as a requirement for NASA's new missions. ESA's Preserved Data Set Content (PDSC) document was codified into a document adopted by the Committee on Earth Observation Satellites (CEOS). It was recognized that it would be useful to combine PCS and PDSC into an ISO standard to ensure consistency in data preservation on a broader international scale. This standard, numbered ISO 19165-2 has been under development since mid-2017. The second is an example of developing recommendations for "best practices" within more limited (still fairly broad) communities. A Data Product Developers' Guide (DPDG) is currently being developed by one of NASA's Earth Science Data System Working Groups (ESDSWGs). It is for use by developers of products to be derived from Earth observation data to improve product (re)usability. One of the challenges in developing the guide is the fact that there are already many applicable standards and guides. The relevant information needs to be selected and expressed in a succinct manner, with appropriate pointers to references. The DPDG aims to compile the most applicable parts of earlier guides into a single document outlining the typical development process for Earth Science data products. Standards and best practices formally endorsed by the Earth Science Data and Information System (ESDIS) Standards Office (ESO), outputs from ESDSWGs (e.g., Dataset Interoperability Working Group, and Data Quality Working Group), and recommendations from Distributed Active Archive Centers and data producers are emphasized.
Ramapriyan, Hampapuram↗
The TOLNet 2.0 Website: How an API Can Promote Open Science and FAIR Principles
The Tropospheric Ozone Lidar Network (TOLNet) has generated over a decade of ozone vertical profile data products over North America. The science value of the TOLNet data has been demonstrated in numerous peer-reviewed publications on air quality and other ozone relevant research. To support the broad spectrum of data use, the TOLNet team launched a major effort to upgrade the web-based data repository aiming to enhance the data discoverability and to enable machine-to-machine data upload and download processes. Specifically, the TOLNet website included an application programming interface (API), which supports machine-to-machine data search and data download. The API also extracts selected variables from the files, which can be retrieved as JSON objects and used to create data displays without having to download or open the underlying files. The TOLNet science team members can also use the API for automated data upload, including a data file scanning feature to ensure data product integrity. To be presented will include a summary of key features of data repositories, an actual use case of machine-to-machine data access/use, as well as our journey to make TOLNet data more FAIR, i.e., more findable, accessible, interoperable, and (re)usable.
Crystal Gummo↗
FAIR Assessments
Presentation on Findable Accessible Interoperable and Reusable (FAIR) Assessment approaches for data.
FAIR↗
LinkML: an open data modeling framework
Background Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, nonstandardized spreadsheets, or data repositories. This lack of structure challenges interoperability, making data integration, validation, and reuse difficult. Findings LinkML (Linked Data Modeling Language) is an open framework that simplifies the process of authoring, validating, and sharing data. LinkML can describe a range of data structures, from flat, list-based models to complex, interrelated, and normalized models that utilize polymorphism and compound inheritance. It offers an approachable syntax that is not tied to any one technical architecture and can be integrated seamlessly with many existing frameworks. The LinkML syntax provides a standard way to describe schemas, classes, and relationships, allowing modelers to build well-defined, stable, and optionally ontology-aligned data structures. Once defined, LinkML schemas may be imported into other LinkML schemas. These key features make LinkML an accessible platform for interdisciplinary collaboration and a reliable way to define and share data semantics. Conclusions LinkML helps reduce heterogeneity, complexity, and the proliferation of single-use data models while simultaneously enabling compliance with FAIR (Findable, Accessible, Interoperable, and Reusable) data standards. LinkML has seen increasing adoption in various fields, including biology, chemistry, biomedicine, microbiome research, finance, electrical engineering, transportation, and commercial software development. In short, LinkML makes implicit models explicitly computable and allows data to be standardized at their origin. LinkML documentation and code are available at https://linkml.io/.
AI-ready data↗
Applications of VAS and TOVS to tropical cyclones
The results of the attempts to use VAS (visible IR spin scan radiometer atmospheric sounder) data for predicting tropical cyclones are reported. VAS, mounted on a GEO platform, has 14 detectors for upwelling radiance. The McIDAS software was, by the 1983 hurricane season, upgraded to providing imagery and mass, motion and moisture patterns using the satellite data, which also permitted determinations of accurate temperature and moisture profiles. Comparisons made between VAS and radiosonde data revealed fairly close agreement of satellite and in-situ conditions during the 1983 season. When combined with data from the Tiros operational vertical sounder (TOVS) to define wind streamlines and predict the path of a hurricane from data fed into numerical models, sufficiently good agreement was obtained to initiate plans to forecast a hurricane trajectory during the 1984 season.
Velden, C. S.↗
Measuring Interfacial Tension Between Immiscible Liquids
Glass capillary tube technique measures interfacial tension between two immiscible liquids. Yields useful data over fairly wide range of interfacial tensions, both for pairs of liquids having equal densities and pairs of liquids having unequal densities. Data on interfacial tensions important in diverse industrial chemical applications, including enhanced extraction of oil; printing; processing foods; and manufacture of paper, emulsions, foams, aerosols, detergents, gel encapsulants, coating materials, fertilizers, pesticides, and cosmetics.
Rashidnia, Nasser↗
The Earth Radiation Budget (ERB) experiment - An overview
The development of ERB observational systems is traced from its beginnings in the late 1950's through to the current ERB on the Nimbus 7 satellite. The instruments comprising the current 22-channel ERB experiment are described in some detail. Noteworthy are the inclusion in one solar channel, of a self-calibrating cavity to measure the solar constant and the use of biaxial scanning telescopes to determine the angular reflection and emission model required for processing the narrow-angle radiometric data. A fairly detailed description of the prelaunch and in-flight calibrations is given along with an analysis of the radiometric performance of the instruments. The data processing system is traced with the aid of a schematic flow diagram showing the steps required to produce the many tape and microfilm products archived. Future plans for improving the quality and accuracy of the data products are discussed. Finally, the upcoming Earth Radiation Budget Experiment (ERBE) is briefly mentioned. It will be capable of simultaneously measuring the radiation budget from three satellites, each having a different equator crossing time and angle.
Jacobowitz, H.↗
Meteoroid and debris special investigation group; status of 3-D crater analysis from binocular imagery
During the 3 month deintegration of the LDEF, the M&D SIG generated approximately 5000 digital color stereo image pairs of impact related features from all space exposed surfaces. Currently, these images are being processed at JSC to yield more accurate feature information. Work is currently underway to determine the minimum number of data points necessary to parametrically define impact crater morphologies in order to minimize the man-hour intensive task of tie point selection. Initial attempts at deriving accurate crater depth and diameter measurements from binocular imagery were based on the assumption that the crater geometries were best defined by paraboloid. We made no assumptions regarding the crater depth/diameter ratios but instead allowed each crater to define its own coefficients by performing a least-squares fit based on user-selected tiepoints. Initial test cases resulted in larger errors than desired, so it was decided to test our basic assumptions that the crater geometries could be parametrically defined as paraboloids. The method for testing this assumption was to carefully slice test craters (experimentally produced in an appropriate aluminum alloy) vertically through the center resulting in a readily visible cross-section of the crater geometry. Initially, five separate craters were cross-sectioned in this fashion. A digital image of each cross-section was then created, and the 2-D crater geometry was then hand-digitized to create a table of XY position for each crater. A 2nd order polynomial (parabolic) was fitted to the data using a least-squares approach. The differences between the fit equation and the actual data were fairly significant, and easily large enough to account for the errors found in the 3-D fits. The differences between the curve fit and the actual data were consistent between the caters. This consistency suggested that the differences were due to the fact that a parabola did not sufficiently define the generic crater geometry. Fourth and 6th order equations were then fitted to each crater cross-section, and significantly better estimates of the crater geometry were obtained with each fit. Work is presently underway to determine the best way to make use of this new parametric crater definition.
Sapp, Clyde A.↗
The Challenges of Releasing Human Data for Analysis
The NASA Johnson Space Center s (NASA JSC) Committee for the Protection of Human Subjects (CPHS) recently approved the formation of two human data repositories: the Lifetime Surveillance of Astronaut Health Repository (LSAH-R) for clinical data and the Life Sciences Data Archive Repository (LSDA-R) for research data. The establishment of these repositories forms the foundation for the release of data and information beyond the scope for which the data was originally collected. The release of clinical and research data and information is primarily managed by two NASA groups: the Evidence Base Working Group (EBWG), consisting of members of both repositories, and the LSAH Policy Board. The goal of unifying these repositories and their processes is to provide a mutually supportive approach to handling medical and research data, to enhance the use of medical and research data to reduce risk, and to promote the understanding of space physiology, countermeasures and other mitigation strategies. Over the past year, both repositories have received over 100 data and information requests from a wide variety of requesters. The disposition of these requests has highlighted the challenges faced when attempting to make data collected on a unique set of subjects available beyond the original intent for which the data were collected. As the EBWG works through each request, many considerations must be factored into account when deciding what data can be shared and how - from the Privacy Act of 1974 and the Health Insurance Portability and Accountability Act (HIPAA), to NASA s Health Information Management System (10HIMS) and Human Experimental and Research Data Records (10HERD) access requirements. Additional considerations include the presence of the data in the repositories and vetting requesters for legitimacy of their use of the data. Additionally, fair access must be ensured for intramural, as well as extramural investigators. All of this must be considered in the formulation of the charters, policies and workflows for the human data repositories at NASA.
Fitts, Mary↗
Open Science for Life in Space: Bioimaging, Data Sharing, and Tools for Knowledge Discovery
Precious space-flown biological experiments have both multi-omic and phenotypic data which NASA strives to make maximally open access for reuse. Currently a number of these space-relevant bioimaging datasets are being reused for AI/ML approaches. NASA Ames Life Science Data Archive and NASA GeneLab are working to make all current and future bioimaging data even more accessible and reusable. Standards for collection and curation are being implemented to enable scientists worldwide access to these data for further discovery and use.
data science↗
Formation and characterization of simulated small droplet icing clouds
Two pneumatic two-fluid atomizers operating at high liquid and gas pressures produced water sprays that simulated small droplet clouds for use in studying icing effects on aircraft performance. To measure median volume diameter, MVD or D sub v.5, of small droplet water sprays, a scattered-light scanning instrument was developed. Drop size data agreed fairly well with calculated values at water and nitrogen pressures of 60 and 20 psig, respectively, and at water and nitrogen pressures of 250 and 100 psig, respectively, but not very well at intermediate values of water and nitrogen pressure. MVD data were correlated with D sub 0, W sub N, and W sub w, i.e., orifice diameter, nitrogen, and water flowrate, respectively, to give the expression for MVD in microns.
Ingebo, R. D.↗