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Why We Do What We Do: Data Reuse, Open Access, and Privacy in Data Management at the Life Sciences Data Archive
As custodian of the unique and irreplaceable collections of human subject research data generated by the Human Research Program and its predecessors throughout the agency’s history, the Life Sciences Data Archive (LSDA) is charged with protecting participants’ privacy and implementing their consent decisions as it provides retrospective data for use in new studies. This active, stewardship-focused approach to data management and preservation shapes the products that LSDA provides to researchers and the responsibilities of researchers in using the data and publishing their results. This presentation reviews how federal and agency mandates shape LSDA’s data management procedures and expectations for researchers. Topics covered will include LSDA’s movement towards implementation of the FAIR (Findable, Accessible, Interoperable, Reusable) principles and how the archive’s evolving data management practices support FAIR-ness; collaboration between LSDA and the Lifetime Surveillance of Astronaut Health (LSAH) project (the repository of astronaut medical data); LSDA’s response to the challenges of performing its stewardship role and maintaining trust given the public profiles of the subjects whose data it preserves; and the ever-increasing challenges to expectations of subject privacy stemming from the growing power and ubiquity of of data analysis and aggregation tools.
Big Federal Data Centers Implementing FAIR Data Principles: ARM Data Center Example
Atmospheric Radiation Measurement (ARM) is a multi-laboratory/multi-institutional, US Department of Energy Office of Science National User Facility. ARM’s data is currently hosted at the ARM Data Center (ADC) in Oak Ridge, Tennessee. The ADC holds more than 12,000 data products, with a total holding of more than 1.8 PB of data that dates back to 1992. This includes data from instruments, value-added products, model outputs, field campaigns, and principle investigator contributed data. In this paper, we discuss how big federal scientific data centers, such as ARM, that use modern and scalable architecture apply findable, accessible, interoperable, and reusable (FAIR) data principles to improve overall efficiency. These principles mainly emphasize machine-to-machine interactions that are directly applicable to ARM because of its data volume.
Data for: Patel et al. Carbon flux estimates are sensitive to data source: A comparison of field and lab temperature sensitivity data
This dataset contains data and code used for the paper "Carbon flux estimates are sensitive to data source: A comparison of field and lab temperature sensitivity data" [DOI COMING SOON]A large literature exists on mechanisms driving soil production of the greenhouse gases CO2 and CH4. Measurements of these gases’ fluxes are often performed using closed-chamber incubations in the laboratory or in situ, i.e., in the field. Although it is common knowledge that measurements obtained through field studies vs. laboratory incubations can diverge because of the vastly different conditions of these environments, few studies have systematically examined these patterns. It is crucial to understand the magnitude and reasons for any differences, as these data are used to parametrize and benchmark ecosystem- to global-scale models, which are then susceptible to the biases of the source data. Here, we specifically examine how greenhouse gas measurements may be influenced by whether the measurement/incubation was conducted in the field vs. laboratory, focusing on CO2 and CH4 measurements. We use Q10 of greenhouse gas flux (temperature sensitivity) for our analyses, because of the ubiquity of this metric in biological and Earth system sciences and its importance to many modeling frameworks. We predicted that laboratory measurements would be less variable, but also less representative of true field conditions. However, there was greater variability in the Q10 values calculated from lab-based measurements of CO2 fluxes, because lab experiments explore extremes rarely seen in situ, and reflect the physical and chemical disturbances occurring during sampling, transport, and incubation. Overall, respiration Q10 values were significantly greater in laboratory incubations (mean = 4.19) than field measurements (mean = 3.05), with strong influences of incubation temperature and climate region/biome. However, this was in part because field measurements typically represent total respiration (Rs), whereas lab incubations typically represent heterotrophic respiration (Rh), making direct comparisons difficult to interpret. Focusing only on Rh-derived Q10, these values showed almost identical distributions across laboratory (n = 1110) and field (n = 581) experiments, providing strong support for using the former as an experimental proxy for the latter, although we caution that geographic biases in the extant data make this conclusion tentative. Due to a smaller sample size of CH4 Q10 data, we were unable to perform a comparable robust analysis, but we expect similar interactions with soil temperature, moisture, and environmental/climatic variables. Our results here suggest the need for more concerted efforts to document and standardize these data, including sample and site metadata. This dataset contains a compressed (.zip) archive of the data and R scripts used for this manuscript. The dataset includes files in .csv format, which can be accessed and processed using MS Excel or R. This archive can also be accessed on GitHub at https://github.com/kaizadp/field_lab_q10 (DOI: 10.5281/zenodo.7106554).
Salvaging Data Records with Missing Data: Data Imputation using the Multivariate t Distribution
When doing multivariate data analysis, one commonobstacle is the presence of incomplete observations, i.e., observationsfor which one or more key fields are blank. Missing datais often countered by deleting entire observations that containmissing data. The negative effects of deleting entire observationsare multiple: deleting observations reduces sample size andcan also result in biased inferences even if data is missing atrandom. In addition, knowledge contained within incompleteobservations is knowledge lost when they are deleted– and theeffort spent collecting that knowledge is effort wasted. Data imputationmethods, or methods of statistically “filling-in” missingdata, can help combat small sample sizes by using the existinginformation in partially complete observations with the end goalof producing less biased and higher confidence inferences. Whena sample from a multivariate normal population is only partiallycomplete, and the missing data meets appropriate assumptions(missing at random), robust data imputation of the missing datacan be implemented with monotone data augmentation (MDA)using the multivariate t distribution.Missing data imputation is applied to data from the NASA InstrumentCost Model (NICM) using the MDA algorithm underthe assumption of having a multivariate t distribution with fixeddegrees of freedom. A sensitivity analysis to the degrees offreedom parameter is presented to demonstrate robustness ofthe multivariate t distribution when dealing with small samplesas compared to the multivariate normal distribution.
Data-Conforming Data-Driven Control: Avoiding Premature Generalizations Beyond Data
Data-driven and adaptive control approaches face the problem of introducing sudden distributional shifts beyond the distribution of data encountered during learning. Therefore, they are prone to invalidating the very assumptions used in their own construction. This is due to the linearity of the underlying system, inherently assumed and formulated in most data-driven control approaches, which may falsely generalize the behavior of the system beyond the behavior experienced in the data. This article seeks to mitigate these problems by enforcing consistency of the newly designed closed-loop systems with data and slowing down any distributional shifts in the joint state-input space. This is achieved through incorporating affine regularization terms and linear matrix inequality constraints to data-driven approaches, resulting in convex semi-definite programs that can be efficiently solved by standard software packages. We discuss the optimality conditions of these programs and then conclude this article with a numerical example that further highlights the problem of premature generalization beyond data and shows the effectiveness of our proposed approaches in enhancing the safety of data-driven control methods.
Respiration data, microbial community assembly data, and FTICR-MS data associated with: “Disturbance Triggers Non-Linear Microbe-Environment Feedbacks. Sengupta et al., 2021, Biogeosciences”
This data package is associated with the manuscript “Disturbance Triggers Non-Linear Microbe-Environment Feedbacks, in revision in Biogeosciences (Sengupta et al. and 2021;https://bg.copernicus.org/preprints/bg-2021-51/). The study used hyporheic zone sediments as a model system to provide an integrated view of how disturbance modulates linkages among microbial ecology, biogeochemistry, and organic matter thermodynamics. Laboratory experiments exposed hyporheic sediment to varying wetting/drying dynamics. Data types include dissolved oxygen rates used to derive respiration rates, Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) data used to derive thermodynamic properties of organic matter, and microbial community assembly metrics derived from amplicon-sequence data of putatively active (cDNA) and whole community (gDNA). The outcomes of the study are condensed into a broadly applicable conceptual model linking external forcing, internal dynamics, and history. This data package is comprised of a file-level metadata (FLMD) csv, metadata csv, and seven folders that contain csv files, R scripts, xml files, and associated documentation: (1) Rates, (2) bNTI, and (3) FTICR, (4) Statistics_Analyses, (5) Raw OTU Beta dispersion Analysis, (6) bMNTD Randomizations, and (7) Data Dictionaries. The FLMD file has a description of each file included in the data package.
Solar-Geophysical Data Number 496, February 1986. Part 1: (Prompt reports). Data for January 1986,December 1985 and late data
Solar-Geophysical Data Number 498, February 1986, Part 1 (Prompt Reports), Data for January 1986, December 1985 and Late Data contains the following:detailed index for 1985-86; data for January 1986--(IUWDS alert periods (advanced and worldwide), Solar activity indices, Solar flares, Solar radio emission, Vostok inferred interplanetary magnetic field polarity, Stanford mean solar magnetic field); data for December 1985--(Solar active regions, Sudden ionospheric disturbances, Solar radio spectral observations, Cosmic ray measurements by neutron monitor, Geomagnetic indices, Radio propagation indices); late data--(Solar radio emission Nancay interferometric chart December 1985, Solar radio spectral observations Culgoora May 1985, Geomagnetic indices sudden commencements November 1985, Calcium plage data).
Solar-geophysical data number 499, March 1986. Part 1: (Prompt reports). Data for February 1986, January 1986 and late data
Solar-Geophysical Data Number 499, March 1986, Part 1 (Prompt Reports); Data for February 1986, January 1986 and Late Data, contains the following: Detailed index for 1985 to 1986; Data for February 1986--(IUWDS alert periods (Advance and worldwide), Solar activity indices, Solar flares, Solar radio emission, Vostok inferred interplanetary magnetic field polarity, Stanford mean solar magnetic field); data for January 1986--(Solar active regions, Sudden ionospheric disturbances, Solar radio spectral observations, Cosmic ray measurements by neutron monitor, Geomagnetic indices, Radio propagation indices); Late data-(Solar active regions, Solar radio spectral observations Culgoora, Cosmic ray measurements by neutron monitor, Calcium plage data).
Sensitivity of mesoscale-model forecast skill to some initial-data characteristics, data density, data position, analysis procedure and measurement error
The effects of horizontal and vertical data resolution, data density, data location, different objective analysis algorithms, and measurement error on mesoscale-forecast accuracy are studied with observing-system simulation experiments. Domain-averaged errors are shown to generally decrease with time. It is found that the vertical distribution of error growth depends on the initial vertical distribution of the error itself. Larger gravity-inertia wave noise is produced in forecasts with coarser vertical data resolution. The use of a low vertical resolution observing system with three data levels leads to more forecast errors than moderate and high vertical resolution observing systems with 8 and 14 data levels. Also, with poor vertical resolution in soundings, the initial and forecast errors are not affected by the horizontal data resolution.
Semantic Web Data Discovery of Earth Science Data at NASA Goddard Earth Sciences Data and Information Services Center (GES DISC)
Mirador is a web interface for searching Earth Science data archived at the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC). Mirador provides keyword-based search and guided navigation for providing efficient search and access to Earth Science data. Mirador employs the power of Google's universal search technology for fast metadata keyword searches, augmented by additional capabilities such as event searches (e.g., hurricanes), searches based on location gazetteer, and data services like format converters and data sub-setters. The objective of guided data navigation is to present users with multiple guided navigation in Mirador is an ontology based on the Global Change Master directory (GCMD) Directory Interchange Format (DIF). Current implementation includes the project ontology covering various instruments and model data. Additional capabilities in the pipeline include Earth Science parameter and applications ontologies.
NASA Earth Observing System Data and Information System (EOSDIS): A U.S. Network of Data Centers Serving Earth Science Data: A Network Member of ICSU WDS
NASA's Earth Observing System Data and Information System (EOSDIS) has been in operation since August 1994, and serving a diverse user community around the world with Earth science data from satellites, aircraft, field campaigns and research investigations. The ESDIS Project, responsible for EOSDIS is a Network Member of the International Council for Sciences (ICSU) World Data System (WDS). Nine of the 12 Distributed Active Archive Centers (DAACs), which are part of EOSDIS, are Regular Members of the ICSUWDS. This poster presents the EOSDIS mission objectives, key characteristics of the DAACs that make them world class Earth science data centers, successes, challenges and best practices of EOSDIS focusing on the years 2014-2016, and illustrates some highlights of accomplishments of EOSDIS. The highlights include: high customer satisfaction, growing archive and distribution volumes, exponential growth in number of products distributed to users around the world, unified metadata model and common metadata repository, flexibility provided to uses by supporting data transformations to suit their applications, near-real-time capabilities to support various operational and research applications, and full resolution image browse capabilities to help users select data of interest. The poster also illustrates how the ESDIS Project is actively involved in several US and international data system organizations.
Nuclear Data Sheets for A=188☆
Evaluated nuclear structure and decay data for all nuclei with mass number A=188 (Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au, Hg, Tl, Pb, Bi, Po) are presented. The experimental data are compiled and evaluated, and best values for level and gamma-ray energies, quantum numbers, lifetimes, gamma-ray intensities, and other nuclear properties are recommended. Inconsistencies and discrepancies that exist in the literature are noted. This work supersedes the earlier evaluation by Balraj Singh (2002Si10), published in Nuclear Data Sheets 95, 387 (2002). The gamma-ray transition probabilities were calculated using the ENSDF analysis program ruler (www-nds.iaea.org/public/ensdf{sub p}gm/). However, the reader should be warned that the program may produce incorrect results when dealing with non-symmetric uncertainties.
Shuttle Entry Air Data System concepts applied to Space Shuttle Orbiter flight pressure data to determine air data - STS 1-4
The Shuttle Entry Air Data System (SEADS) is the implementation of a new concept in air data systems, with application to entry vehicles. This concept incorporates an array of flush orifices in the nose and forward fuselage of the vehicle and a new flowfield modeling concept for the analysis of flight data and the determination of the required air data parameters. Although the SEADS has not been fully demonstrated, a developmental analysis capability has been assembled and demonstrated. This analytical capability has been used to analyze selected Development Flight Instrumentation (DFI) pressure data from STS-1 through STS-4 and determine angle of attack and freestream dynamic pressure. The results of this study verify the potential of the SEADS as a highly fault tolerant operational air data system. In addition, the transition of SEADS from its present status as an experimental system to an operational system is shown to be readily achievable.
National Space Science Data Center and World Data Center A for Rockets and Satellites - Ionospheric data holdings and services
The activities and services of the National Space Science data Center (NSSDC) and the World Data Center A for Rockets and Satellites (WDC-A-R and S) are described with special emphasis on ionospheric physics. The present catalog/archive system is explained and future developments are indicated. In addition to the basic data acquisition, archiving, and dissemination functions, ongoing activities include the Central Online Data Directory (CODD), the Coordinated Data Analysis Workshopps (CDAW), the Space Physics Analysis Network (SPAN), advanced data management systems (CD/DIS, NCDS, PLDS), and publication of the NSSDC News, the SPACEWARN Bulletin, and several NSSD reports.
Identifying Improvements to Airborne and Field Data Stewardship from Data User and Producer Needs (Findings from the March 2022 Airborne and Field Data Workshop)
Workshop Purpose: to gather valuable feedback from data users and data producers in order to improve the acquisition and use of NASA’s airborne and field data. Workshop Goals: - Identify new ways to improve the discovery, access, and reuse of NASA’s airborne and field data - Intentionally include the airborne community in future planning to ensure the community needs are met - Understand how NASA can better help researchers realize the full value of airborne and field data - Enable Open Source Science and determine what this means for airborne and field data communities
The Hourly GHI, DHI and DNI: Intercomparison of the CERES-Based Data and the NSRDB Data through Comparison with the Ground-Based BSRN Data
The NASA Clouds and the Earth’s Radiant Energy System (CERES) SYN1deg(Ed4.1) provides hourly global horizontal irradiance (GHI), diffuse horizontal irradiance (DHI) and direct horizontal irradiance (DirHI) at 1-degree latitude by 1-degree longitude resolution, and the time span is from March 2000 to near present. While the GHI agrees well with the ground-based Baseline Surface Radiation Network (BSRN) data, the DHI and DirHI are, respectively, positively and negatively biased against the BSRN data, and so is the direct normal irradiance (DNI) derived simply by dividing the DirHI by the cosine of the hourly solar zenith angle (SZA). We found that the biases tend to be well-defined functions of cos(SZA) and the cloud fraction (CLFR). We thus performed a bias-correction on the hourly DHI and DNI in the latitude-cos(SZA)-CLFR phase space, and therefrom, we derived the hourly global tilted irradiance (GTI) at a number of tilt angles using the isotropic diffuse irradiance model, and the results agree well with the GTI derived from the original BSRN near-instantaneous records. Meanwhile, the National Renewable Energy Laboratory (NREL) has produced the National Solar Radiation Database (NSRDB) with finer spatiotemporal resolution using its Physical Solar Model (PSM) and surface-based measured data, model results and satellite-based data as inputs. Now the NSRDB data covers not only the United States and its neighboring regions, but Europe, Africa, Asia and Oceania. The available temporal resolutions are 5, 10, 15, 30 and 60 minutes and the spatial resolutions are 2, 4 and 10 km, depending on the selected region. In this presentation, we compare both the CERES-based and NSRDB GHI, DHI and DNI with their BSRN counterparts and show how finer spatial resolution may give us an advantage in data accuracy and usability.
The Planetary Data System Web Catalog Interface--Another Use of the Planetary Data System Data Model
The Planetary Data System Data Model consists of a set of standardized descriptions of entities within the Planetary Science Community. These can be real entities in the space exploration domain such as spacecraft, instruments, and targets; conceptual entities such as data sets, archive volumes, and data dictionaries; or the archive data products such as individual images, spectrum, series, and qubes.