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At least 19 records

INCREASING THE TRANSPARENCY AND REPRODUCIBILITY OF SPACE RADIATION SCIENCE: THE RADIATION BIOLOGY ONTOLOGY

Among the primary objectives of the Open/Open-Source Science paradigm are making scientific investigation data transparent and results reproducible [1], objectives shared by the FAIR principles [2]. To accomplish this, the conceptual framework that includes all the investigation objects needs to be accurately captured and communicated to all data consumers. A large part of this requires using metadata standards to annotate data collected. These standards should be readily accessible, informed by scientific community consensus and sufficiently specific to encompass all of the important aspects of the investigation. Starting in 2020 we have been co-leading an open consortium to develop a new metadata standard, the Radiation Biology Ontology (RBO), through the Open Biological and Biomedical Ontologies (OBO) Foundry [3]. We began by transforming many of the terms from the National Council on Radiation Protection and Measurement into concepts that can be formally related to existing OBO Foundry classes or attributes. We then identified and imported into the RBO existing OBO Foundry classes that have obvious relevance for radiation biomedicine (for example, concepts from the Environment Ontology that describe radiative processes, and concepts from the Gene Ontology dealing with molecular and cellular responses to radiation). Finally, we scrutinized datasets from investigations of radiation effects held in NASA GeneLab and LSDA repositories and added additional classes, instances, and attributes into the RBO that should be used to annotate these data. We developed the RBO using the open-source tools of GitHub and publish the RBO periodically through the NIH/NCBI BioPortal website, so systems worldwide can leverage the knowledge it contains [4]. This initial phase of concept modeling has yielded an RBO that at present has more than 300 declared concepts, with more than 3500 additional concepts imported from other OBO Foundry ontologies. While this first phase has focused on concepts for annotating samples, environments, exposures, and measurements, the next phase will center on supporting annotation of results and findings, such as concept models of molecular, cellular and tissue effects. The value of the RBO will be determined in part by our ability to engage the community in its development, and we have established a Radiobiology Informatics Consortium with unrestricted membership as the owner of the RBO in order to encourage investigators, system owners and other to join in this effort. Anyone can report issues or request new concept modeling or other features directly on GitHub. By using the BioPortal application programming interface, systems can pose dynamic queries to the latest version of the RBO for information on individual classes or entire hierarchies; this design eliminates the need for systems to be updated in order to use newer versions of the RBO. We hope to contribute to the advancement of open radiobiological science through the continued, open development of the RBO, that will provide more precise, machine-interpretable descriptions of investigations, as well as support data meta-analysis through machine learning or other artificial intelligence methods. REFERENCES [1] Open science in space. Nature Medicine, 2021. 27(9): p. 1485-1485. [2] Wilkinson, M.D., et al., The FAIR Guiding Principles for scientific data management and stewardship. Sci Data, 2016. 3: p. 160018. [3] Smith, B., et al., The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol, 2007. 25(11): p. 1251-5. [4] Whetzel, P.L., et al., BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res, 2011. 39(Web Server issue): p. W541-5.

informatics↗

INCREASING THE TRANSPARENCY AND REPRODUCIBILITY OF SPACE RADIATION SCIENCE: THE RADIATION BIOLOGY ONTOLOGY

Among the primary objectives of the Open/Open-Source Science paradigm are making scientific investigation data transparent and results reproducible [1], objectives shared by the FAIR principles [2]. To accomplish this, the conceptual framework that includes all the investigation objects needs to be accurately captured and communicated to all data consumers. A large part of this requires using metadata standards to annotate data collected. These standards should be readily accessible, informed by scientific community consensus and sufficiently specific to encompass all of the important aspects of the investigation. Starting in 2020 we have been co-leading an open consortium to develop a new metadata standard, the Radiation Biology Ontology (RBO), through the Open Biological and Biomedical Ontologies (OBO) Foundry [3]. We began by transforming many of the terms from the National Council on Radiation Protection and Measurement into concepts that can be formally related to existing OBO Foundry classes or attributes. We then identified and imported into the RBO existing OBO Foundry classes that have obvious relevance for radiation biomedicine (for example, concepts from the Environment Ontology that describe radiative processes, and concepts from the Gene Ontology dealing with molecular and cellular responses to radiation). Finally, we scrutinized datasets from investigations of radiation effects held in NASA GeneLab and LSDA repositories and added additional classes, instances, and attributes into the RBO that should be used to annotate these data. We developed the RBO using the open-source tools of GitHub and publish the RBO periodically through the NIH/NCBI BioPortal website, so systems worldwide can leverage the knowledge it contains [4]. This initial phase of concept modeling has yielded an RBO that at present has more than 300 declared concepts, with more than 3500 additional concepts imported from other OBO Foundry ontologies. While this first phase has focused on concepts for annotating samples, environments, exposures, and measurements, the next phase will center on supporting annotation of results and findings, such as concept models of molecular, cellular and tissue effects. The value of the RBO will be determined in part by our ability to engage the community in its development, and we have established a Radiobiology Informatics Consortium with unrestricted membership as the owner of the RBO in order to encourage investigators, system owners and other to join in this effort. Anyone can report issues or request new concept modeling or other features directly on GitHub. By using the BioPortal application programming interface, systems can pose dynamic queries to the latest version of the RBO for information on individual classes or entire hierarchies; this design eliminates the need for systems to be updated in order to use newer versions of the RBO. We hope to contribute to the advancement of open radiobiological science through the continued, open development of the RBO, that will provide more precise, machine-interpretable descriptions of investigations, as well as support data meta-analysis through machine learning or other artificial intelligence methods.

knowledge↗

Precision annotation of predetermined primary sampling units on ERTS-1 MSS images

Resectioning programs were developed for projecting the boundary corners of sample units, management units, and counties into U2 RC-10 and ERTS-1 MSS images. The technique used includes corrections for earth curvature, terrain elevation, and MSS distortions. The minimum standard error obtained was about 0.15 mm or 150 meters on the ground. This technique now makes it possible to include land ownership as an integral part of forest resource sampling plans using ERTS imagery.

Vanroessel, J. W.↗

ERTS data user investigation to develop a multistage forest sampling inventory system

The author has identified the following significant results. A system to provide precision annotation of predetermined forest inventory sampling units on the ERTS-1 MSS images was developed. In addition, an annotation system for high altitude U2 photographs was completed. MSS bulk image accuracy is good enough to allow the use of one square mile sampling units. IMANCO image analyzer interpretation work for small scale images demonstrated the need for much additional analyses. Continuing image interpretation work for the next reporting period is concentrated on manual image interpretation work as well as digital interpretation system development using the computer compatible tapes.

Langley, P. G.↗

The 1981 Argentina ground data collection

Over 600 fields in the corn, soybean and wheat growing regions of the Argentine pampa were categorized by crop or cover type and ancillary data including crop calendars, historical crop production statistics and certain cropping practices were also gathered. A summary of the field work undertaken is included along with a country overview, a chronology of field trip planning and field work events, and the field work inventory of selected sample segments. LANDSAT images were annotated and used as the field work base and several hundred ground and aerial photographs were taken. These items along with segment descriptions are presented. Meetings were held with officials of the State Secretariat of Agriculture (SEAG) and the National Commission on Space Investigations (CNIE), and their support to the program are described.

Horvath, R.↗

Teaching graphics in technical communication classes

Graphic aids convey and clarify information more efficiently and accurately than words alone therefore, most technical writing includes the use of graphics. Ways of accumulating and presenting graphics illustrations on a shoestring budget are suggested. These include collecting graphics from companies, annual reports and laminating them for workshop use or putting them on a flip chart for classroom presentation, creating overhead transparencies to demonstrate different levels of effectiveness of graphic aids, and bringing in grahic artists for question/answer periods or in class workshops. Also included are an extensive handout as an introduction to graphics, sample assignments, and a selected and annotated bibliography.

Spurgeon, K. C.↗

Visualizing Multi-process CPU Utilization using CUSP

The CPU Utilization Statistics Plotter (CUSP) tool automates the interpretation of detailed CPU Utilization trace data and statistics. It puts you on the cusp of understanding how CPU resources are split among the many parallel components of a software system.CUSP combines time-sampled CPU utilization numbers and Event Log annotations to generate human-readable plots and tables. It automatically splits up large CPU usage log files around interesting events, determines and highlights just the tasks of primary relevance by evaluating their changing contribution to each plot's total CPU usage, automatically eliminates irrelevant tasks, provides context by labeling plots with names and durations of all active commands, and uses consistent color-coding to enable quick visual comparison across multiple plots.CUSP has been used to process CPU Utilization trace logs on the Mars Science Laboratory and the Mars 2020 Rover missions during flight software development and Flight Operations on the Martian surface since December 2013.

Maimone, Mark W↗

Investigation to develop a multistage forest sampling inventory system using ERTS-1 imagery

The author has identified the following significant results. The annotation system produced a RMSE of about 200 m ground distance in the MSS data system with the control data used. All the analytical MSS interpretation models tried were highly significant. However, the gains in forest sampling efficiency that can be achieved by using the models vary from zero to over 50 percent depending on the area to which they are applied and the sampling method used. Among the sampling methods tried, regression sampling yielded substantial and the most consistent gains. The single most significant variable in the interpretation model was the difference between bands 5 and 7. The contrast variable, computed by the Hadamard transform was significant but did not contribute much to the interpretation model. Forest areas containing very large timber volumes because of large tree sizes were not separable from areas of similar crown cover but containing smaller trees using ERTS image interpretation only. All correlations between space derived timber volume predictions and estimates obtained from aerial and ground sampling were relatively low but significant and stable. There was a much stronger relationship between variables derived from MSS and U2 data than between U2 and ground data.

Langley, P. G.↗

Machine Vision based Sample-Tube Localization for Mars Sample Return

A potential Mars Sample Return (MSR) architecture is being jointly studied by NASA and ESA. As currently envisioned, the MSR campaign consists of a series of 3 missions: sample cache, fetch and return to Earth. In this paper, we focus on the fetch part of the MSR, and more specifically the problem of autonomously detecting and localizing sample tubes deposited on the Martian surface. Towards this end, we study two machine-vision based approaches: First, a geometrydriven approach based on template matching that uses hardcoded filters and a 3D shape model of the tube; and second, a data-driven approach based on convolutional neural networks (CNNs) and learned features. Furthermore, we present a large benchmark dataset of sample-tube images, collected in representative outdoor environments and annotated with ground truth segmentation masks and locations. The dataset was acquired systematically across different terrain, illumination conditions and dust-coverage; and benchmarking was performed to study the feasibility of each approach, their relative strengths and weaknesses, and robustness in the presence of adverse environmental conditions.

Detry, R.↗

The graphics and data acquisition software package

A software package was developed for use with micro and minicomputers, particularly the LSI-11/DPD-11 series. The package has a number of Fortran-callable subroutines which perform a variety of frequently needed tasks for biomedical applications. All routines are well documented, flexible, easy to use and modify, and require minimal programmer knowledge of peripheral hardware. The package is also economical of memory and CPU time. A single subroutine call can perform any one of the following functions: (1) plot an array of integer values from sampled A/D data, (2) plot an array of Y values versus an array of X values; (3) draw horizontal and/or vertical grid lines of selectable type; (4) annotate grid lines with user units; (5) get coordinates of user controlled crosshairs from the terminal for interactive graphics; (6) sample any analog channel with program selectable gain; (7) wait a specified time interval, and (8) perform random access I/O of one or more blocks of a sequential disk file. Several miscellaneous functions are also provided.

Crosier, W. G.↗

Knowledge From Pictures (KFP)

The old maxim goes: 'A picture is worth a thousand words'. The objective of the research reported in this paper is to demonstrate this idea as it relates to the knowledge acquisition process and the automated development of an expert system's rule base. A prototype tool, the Knowledge From Pictures (KFP) tool, has been developed which configures an expert system's rule base by an automated analysis of and reasoning about a 'picture', i.e., a graphical representation of some target system to be supported by the diagnostic capabilities of the expert system under development. This rule base, when refined, could then be used by the expert system for target system monitoring and fault analysis in an operational setting. Most people, when faced with the problem of understanding the behavior of a complicated system, resort to the use of some picture or graphical representation of the system as an aid in thinking about it. This depiction provides a means of helping the individual to visualize the bahavior and dynamics of the system under study. An analysis of the picture augmented with the individual's background information, allows the problem solver to codify knowledge about the system. This knowledge can, in turn, be used to develop computer programs to automatically monitor the system's performance. The approach taken is this research was to mimic this knowledge acquisition paradigm. A prototype tool was developed which provides the user: (1) a mechanism for graphically representing sample system-configurations appropriate for the domain, and (2) a linguistic device for annotating the graphical representation with the behaviors and mutual influences of the components depicted in the graphic. The KFP tool, reasoning from the graphical depiction along with user-supplied annotations of component behaviors and inter-component influences, generates a rule base that could be used in automating the fault detection, isolation, and repair of the system.

Truszkowski, Walt↗

Expedition Memory: Towards Agent-based Web Services for Creating and Using Mars Exploration Data.

Explorers ranging over kilometers of rugged, sometimes "feature-less" terrain for over a year could be overwhelmed by tracking and sharing what they have done and learned. An automated system based on the existing Mobile Agents design [ I ] and Mars Exploration Rover experience [2], could serve as an "expedition memory" that would be indexed by voice as wel1 as a web interface, linking people, places, activities, records (voice notes, photographs, samples). and a descriptive scientific ontology. This database would be accessible during EVAs by astronauts, annotated by the remote science team, linked to EVA plans, and allow cross indexing between sites and expeditions. We consider the basic problem, our philosophical approach, technical methods, and uses of the expedition memory for facilitating long-term collaboration between Mars crews and Earth support teams. We emphasize that a "memory" does not mean a database per se, but an interactive service that combines different resources, and ultimately could be like a helpful librarian.

Clancey, William J.↗

Experimental philosophy leading to a small scale digital data base of the conterminous United States for designing experiments with remotely sensed data

Research using satellite remotely sensed data, even within any single scientific discipline, often lacked a unifying principle or strategy with which to plan or integrate studies conducted over an area so large that exhaustive examination is infeasible, e.g., the U.S.A. However, such a series of studies would seem to be at the heart of what makes satellite remote sensing unique, that is the ability to select for study from among remotely sensed data sets distributed widely over the U.S., over time, where the resources do not exist to examine all of them. Using this philosophical underpinning and the concept of a unifying principle, an operational procedure for developing a sampling strategy and formal testable hypotheses was constructed. The procedure is applicable across disciplines, when the investigator restates the research question in symbolic form, i.e., quantifies it. The procedure is set within the statistical framework of general linear models. The dependent variable is any arbitrary function of remotely sensed data and the independent variables are values or levels of factors which represent regional climatic conditions and/or properties of the Earth's surface. These factors are operationally defined as maps from the U.S. National Atlas (U.S.G.S., 1970). Eighty-five maps from the National Atlas, representing climatic and surface attributes, were automated by point counting at an effective resolution of one observation every 17.6 km (11 miles) yielding 22,505 observations per map. The maps were registered to one another in a two step procedure producing a coarse, then fine scale registration. After registration, the maps were iteratively checked for errors using manual and automated procedures. The error free maps were annotated with identification and legend information and then stored as card images, one map to a file. A sampling design will be accomplished through a regionalization analysis of the National Atlas data base (presently being conducted). From this analysis a map of homogeneous regions of the U.S.A. will be created and samples (LANDSAT scenes) assigned by region.

Labovitz, M. L.↗

Laser ranging data analysis

Results of the near real-time analysis of Lageos laser ranging data are reported. The data was analyzed in terms of range bias, time bias, and internal precision; and estimates for the Earth orientation parameters X sub p, Y sub p, and UT1 are obtained. The results of these analyses are reported in a variety of formats. Sample copies of the weekly summaries from the second half of 1988 are included along with an annotated distribution list of the weekly summaries. Annual summaries for 1987 and 1988 are also included.

Source record↗

Lunar Instrument Data Integration Into the Virtual Reality Mission Simulation System for Decision Communication and Situational Awareness

In situ resource utilization (ISRU) technologies are a key advancement required to make human habitation on the Moon and Mars viable. The upcoming Volatiles Investigating Polar Exploration Rover (VIPER) mission will provide crucial correlations between volatiles and lunar geology to understand the water content available for ISRU on the moon. The mission will require the coordination of multi-disciplinary teams across the country making real time decisions based on rover instrument data. The virtual reality Mission Simulation System (vMSS) is a virtual reality platform designed at MIT by the Resource Exploration and Science of our Cosmic Environment (RESOURCE) team to provide teams with a collaboration interface for planetary missions like VIPER. Herein we determine the integration pathway for analog based datasets that are examples of VIPER's two main instruments, the near-infrared volatile spectrometer subsystem (NIRVSS) and the neutron spectrometer subsystem (NSS), into vMSS to provide the most valuable visualization tools. Focusing on improving situational awareness, decision making, reducing task load and incorporating comments from scientists working previous analogs and on the current VIPER mission, we recommend critical elements to implement into vMSS and the best approaches for data visualization. We present a review of relevant analogs and state of the art mission software. We have developed a design concept and path to flight of analysed instrument data integrated with data maps that allow for virtual manipulation and annotation between non-co-located team members. We focus on pre-mission mapping of a priori data for improved situational awareness, layering of analysed instrument data, correlative mapping and interactive capabilities for in-mission decision making, as well as archiving and annotation tools for post-mission analysis. Finally, we lay out the roadmap for the future development of immersive sample site visualization capabilities and the use of integrated instrument data in vMSS with automated temporal and geospatial planning.

Cody Alison Paige↗

The usefulness of Skylab/EREP S-190 and S-192 imagery in multistage forest surveys

The author has identified the following significant results. The RMSE of point location achieved with the annotation system on S190A imagery was 100 m and 90 m in the x and y direction, respectively. Potential gains in sampling precision attributable to space derived imagery ranged from 4.9 to 43.3 percent depending on the image type, interpretation method, time of year, and sampling method applied. Seasonal variation was significant. S190A products obtained in September yielded higher gains than those obtained in June. Using 100 primary sample units as a base under simple random sampling, the revenue made available for incorporating space acquired data into the sample design to estimate timber volume was as high as $39,400.00.

Langley, P. G.↗

The application of large numbers of pleasure boats to collect synoptic sea-truth for ERTS-1 overpasses

The author has identified the following significant results. In order to interpret and annotate current circulation and suspended sediment concentration maps derived from ERTS-1 digital tapes, the University of Delaware has been collecting water samples and other data from boats and helicopters. In order to increase the number of samples at the exact time of the ERTS-1 pass over Delaware Bay, pleasure craft were organized to obtain samples of the entire test site. On the ERTS-1 pass of July second, scientists were stationed at three public boat launches along the Bay to hand out sampling packets to interested boaters. The packets contained two litre sampling bottles, a map, data card, and a pen. The boaters were asked to fill the two bottles between 11 and 11:15 a.m., mark their location on the map, and fill out the data card. Forty-nine packets were handed out of which 40 were returned (82%). Only four of the 40 were not in the alloted time range. This gave 36 real time data points covering approximately 30 nautical miles. The samples are being analyzed for sediment concentration, particle size, and salinity. Participating boaters will receive a copy of an ERTS image of the Delaware Bay and a summary report of the project. Because of the success of the project, future use of pleasure boaters is being planned.

Klemas, V.↗

MISR Level 1A CCD Science data, all cameras (MIL1A_V1)

The Level 1A data are raw MISR data that are decommutated, reformatted 12-bit Level 0 data shifted to byte boundaries, i.e., reversal of square-root encoding applied and converted to 16 bit, and annotated (e.g., with time information). These data are used by the Level 1B1 processing algorithm to generate calibrated radiances. The science data output preserves the spatial sampling rate of the Level 0 raw MISR CCD science data. CCD data are collected during routine science observations of the sunlit portion of the Earth. Each product represents one 'granule' of data. A 'granule' is defined to be the smallest unit of data required for MISR processing. Also, included in the Level 1A product are pointers to calibration coefficient files provided for Level 1B processing. [Location=GLOBAL] [Temporal_Coverage: Start_Date=2000-02-24; Stop_Date=] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180].

CCD↗