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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research

Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database, a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project’s interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team’s modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB’s expandability and flexible architecture allow it to serve as an example ecosystems database.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2015

GeneLab: A Systems Biology Platform for Spaceflight Omics Data

NASA's mission includes expanding our understanding of biological systems to improve life on Earth and to enable long-duration human exploration of space. Resources to support large numbers of spaceflight investigations are limited. NASA's GeneLab project is maximizing the science output from these experiments by: (1) developing a unique public bioinformatics database that includes space bioscience relevant "omics" data (genomics, transcriptomics, proteomics, and metabolomics) and experimental metadata; (2) partnering with NASA-funded flight experiments through bio-sample sharing or sample augmentation to expedite omics data input to the GeneLab database; and (3) developing community-driven reference flight experiments. The first database, GeneLab Data System Version 1.0, went online in April 2015. V1.0 contains numerous flight datasets and has search and download capabilities. Version 2.0 will be released in 2016 and will link to analytic tools. In 2015 Genelab partnered with two Biological Research in Canisters experiments (BBRIC-19 and BRIC-20) which examine responses of Arabidopsis thaliana to spaceflight. GeneLab also partnered with Rodent Research-1 (RR1), the maiden flight to test the newly developed rodent habitat. GeneLab developed protocols for maxiumum yield of RNA, DNA and protein from precious RR-1 tissues harvested and preserved during the SpaceX-4 mission, as well as from tissues from mice that were frozen intact during spaceflight and later dissected. GeneLab is establishing partnerships with at least three planned flights for 2016. Organism-specific nationwide Science Definition Teams (SDTs) will define future GeneLab dedicated missions and ensure the broader scientific impact of the GeneLab missions. GeneLab ensures prompt release and open access to all high-throughput omics data from spaceflight and ground-based simulations of microgravity and radiation. Overall, GeneLab will facilitate the generation and query of parallel multi-omics data, and deep curation of metadata for integrative analysis, allowing researchers to uncover cellular networks as observed in systems biology platforms. Consequently, the scientific community will have access to a more complete picture of functional and regulatory networks responsive to the spaceflight environment.. Analysis of GeneLab data will contribute fundamental knowledge of how the space environment affects biological systems, and enable emerging terrestrial benefits resulting from mitigation strategies to prevent effects observed during exposure to space. As a result, open access to the data will foster new hypothesis-driven research for future spaceflight studies spanning basic science to translational science.

proteomics↗
DOE OSTI2025

Increasing the Scale of the Mass Spectrometry Query Language Compendium with Explainable AI

A significant bottleneck in metabolomics data interpretation is the effective use of domain knowledge to assign structural information based on fragmentation patterns. The mass spectrometry query language (MassQL) aims to make this process accessible and applicable across multiple analysis platforms. While advanced computational methods are capable of predicting compound structures from fragmentation data, AI/ML approaches often rely on complex, opaque criteria that are difficult to interpret or modify. As a result, their predictive patterns cannot be readily translated into human-readable rules, such as those used in MassQL. Here, in this study, we introduce ChemEcho, a machine learning embedding method that converts tandem mass spectrometry data into sparse feature vectors containing peak and neutral mass subformulae to enhance explainable AI/ML-based methods. An advantage of this approach is that decision trees trained using these feature vectors can be directly translated to MassQL. Using a battery of decision trees trained using ChemEcho embeddings to predict molecular attributes, we generated over 1500 MassQL queries for 765 molecular features and evaluated their precision and recall. From these queries, the 50 highest-performing queries were integrated into the MassQL compendium. This set of generated MassQL queries included environmentally and biologically relevant classes such as PFAS and molecules containing phosphate or sulfate substructures. To illustrate the impact these queries would have on a typical metabolomics experiment, these MassQL queries were applied to a public metabolomics data set─resulting in a marked increase in the structural information derived from tandem mass spectra. Access and reuse of these queries is expected to enhance structural annotation in untargeted experiments, leading to more specific claims and advancing many applications in metabolomics.

Harwood, Thomas V. [USDOE Joint Genome Institute (↗
NASA NTRS2012

Systems and methods for an extensible business application framework

Method and systems for editing data from a query result include requesting a query result using a unique collection identifier for a collection of individual files and a unique identifier for a configuration file that specifies a data structure for the query result. A query result is generated that contains a plurality of fields as specified by the configuration file, by combining each of the individual files associated with a unique identifier for a collection of individual files. The query result data is displayed with a plurality of labels as specified in the configuration file. Edits can be performed by querying a collection of individual files using the configuration file, editing a portion of the query result, and transmitting only the edited information for storage back into a data repository.

Bell, David G.↗
NASA NTRS2000

Mass Storage Performance Information System

The purpose of this task is to develop a data warehouse to enable system administrators and their managers to gather information by querying the data logs of the MDSDS. Currently detailed logs capture the activity of the MDSDS internal to the different systems. The elements to be included in the data warehouse are requirements analysis, data cleansing, database design, database population, hardware/software acquisition, data transformation, query and report generation, and data mining.

Scheuermann, Peter↗
DOE OSTI2018

ENRESA's Spent Nuclear Fuel and Special Waste Database - 18115

Empresa Nacional de Residuos Radiactivos S.A. (ENRESA, by its initials in Spanish) Spent Nuclear Fuel (SNF) and Special Waste (SW) database development was initiated in a common effort between ENRESA and UNESA (the Spanish Association of the Electricity Industry) as a consequence of new regulatory requirements in the frame of radioactive waste management plans. Although these requirements were only mandatory for operators of nuclear power plants, ENRESA deemed necessary to have a centralized database which collected the data from the plant operators. The most relevant features of this database are: - The information collected covers not only the general characteristics of the SNF and SW but also the operation details needed for their characterization. - An application, named Gestion de Elementos Combustibles y Residuos Especiales (GECYRE, by its initials in Spanish) has been implemented for easing the queries and the generation of predefined reports. - An agile data transfer scheme, based on XML files, is used for an effective communication between ENRESA and the operators. The database is currently in production phase since 2014. During this phase it has demonstrated its effectiveness as an information repository to address the SNF and SW interim storage projects in Spain foreseen in the near future. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
NASA NTRS1994

Using Induction to Refine Information Retrieval Strategies

Conceptual information retrieval systems use structured document indices, domain knowledge and a set of heuristic retrieval strategies to match user queries with a set of indices describing the document's content. Such retrieval strategies increase the set of relevant documents retrieved (increase recall), but at the expense of returning additional irrelevant documents (decrease precision). Usually in conceptual information retrieval systems this tradeoff is managed by hand and with difficulty. This paper discusses ways of managing this tradeoff by the application of standard induction algorithms to refine the retrieval strategies in an engineering design domain. We gathered examples of query/retrieval pairs during the system's operation using feedback from a user on the retrieved information. We then fed these examples to the induction algorithm and generated decision trees that refine the existing set of retrieval strategies. We found that (1) induction improved the precision on a set of queries generated by another user, without a significant loss in recall, and (2) in an interactive mode, the decision trees pointed out flaws in the retrieval and indexing knowledge and suggested ways to refine the retrieval strategies.

Baudin, Catherine↗
DOE OSTI2017

Synthetic Transaction Test Generator for Websites

Python script for querying a list of web sites and their details from Splunk and dynamically creating tests for monitoring uptime. The data generated from this script is then sent back to Splunk for creating reports and alerts.

Brown, Justin↗
DOE OSTI2017

Synthetic Transaction Test Generator for Websites

Python script for querying a list of web sites and their details from Splunk and dynamically creating tests for monitoring uptime. The data generated from this script is then sent back to Splunk for creating reports and alerts.

Source record↗
NASA NTRS2006

CAPRI: A Geometric Foundation for Computational Analysis and Design

CAPRI is a software building tool-kit that refers to two ideas; (1) A simplified, object-oriented, hierarchical view of a solid part integrating both geometry and topology definitions, and (2) programming access to this part or assembly and any attached data. A complete definition of the geometry and application programming interface can be found in the document CAPRI: Computational Analysis PRogramming Interface appended to this report. In summary the interface is subdivided into the following functional components: 1. Utility routines -- These routines include the initialization of CAPRI, loading CAD parts and querying the operational status as well as closing the system down. 2. Geometry data-base queries -- This group of functions allow all top level applications to figure out and get detailed information on any geometric component in the Volume definition. 3. Point queries -- These calls allow grid generators, or solvers doing node adaptation, to snap points directly onto geometric entities. 4. Calculated or geometrically derived queries -- These entry points calculate data from the geometry to aid in grid generation. 5. Boundary data routines -- This part of CAPRI allows general data to be attached to Boundaries so that the boundary conditions can be specified and stored within CAPRI s data-base. 6. Tag based routines -- This part of the API allows the specification of properties associated with either the Volume (material properties) or Boundary (surface properties) entities. 7. Geometry based interpolation routines -- This part of the API facilitates Multi-disciplinary coupling and allows zooming through Boundary Attachments. 8. Geometric creation and manipulation -- These calls facilitate constructing simple solid entities and perform the Boolean solid operations. Geometry constructed in this manner has the advantage that if the data is kept consistent with the CAD package, therefore a new design can be incorporated directly and is manufacturable. 9. Master Model access This addition to the API allows for the querying of the parameters and dimensions of the model. The feature tree is also exposed so it is easy to see where the parameters are applied. Calls exist to allow for the modification of the parameters and the suppression/unsuppression of nodes in the tree. Part regeneration is performed by a single API call and a new part becomes available within CAPRI (if the regeneration was successful). This is described in a separate document. Components 1-7 are considered the CAPRI base level reader.

Haimes, Robert↗
NASA NTRS1981

Use of an engineering data management system in the analysis of space shuttle orbiter tiles

The use of an engineering data management system to facilitate the extensive stress analyses of the space shuttle orbiter thermal protection system is demonstrated. The methods used to gather, organize, and store the data; to query data interactively; to generate graphic displays of the data; and to access, transform, and prepare the data for input to a stress analysis program are described. Information related to many separate tiles can be accessed individually from the data base which has a natural organization from an engineering viewpoint. The flexible user features of the system facilitate changes in data content and organization which occur during the development and refinement of the tile analysis procedure. Additionally, the query language supports retrieval of data to satisfy a variety of user-specified conditions.

Giles, G. L.↗
DOE OSTI2021

GRIP: Constraint-based Explanation of Missing Answers for Graph Queries

Abstract: A useful feature in graph query engines is to clarify “Why certain entities (nodes, attribute values or edges) are missing” in query answers. This task is even more challenging when the relevant data is already missing in the underlying data source. Missing data, on the other hand, can be inferred by enforcing data constraints for graphs. We demonstrate GRIP, a system that exploits data constraints to clarify missing answers for graph queries. (1) Constraint-based ex- planation. Given a desired yet missing entity in the query answer, GRIP ensures to generate finite and minimal sequences of data con- strains (an “explanation”) that should be consecutively enforced to ?? to ensure its occurrence for the same query. (2) Answering “why” and“how” questions. Users can query GRIP with both“Why”(“Why” the element is missing) and “How” questions (“How” to refine the graph to include the missing answer). GRIP engine supports run- time generation of explanations by incrementally maintaining a set of bi-directional search trees. (3) Interactive exploration. GRIP provides a user-friendly GUI to support interactive ad visual exploration of explanations, including both automated generation and step-by-step inspection of graph manipulations.

graphs↗
DOE OSTI2020

Data-Consistent Inversion for Stochastic Input-to-Output Maps

Data-consistent inversion is a recently developed measure-theoretic framework for solving a stochastic inverse problem involving models of physical systems. The goal is to construct a probability measure on model inputs (i.e., parameters of interest) whose associated push-forward measure matches (i.e., is consistent with) a probability measure on the observable outputs of the model (i.e., quantities of interest). Previous implementations required the map from parameters of interest to quantities of interest to be deterministic. This work generalizes this framework for maps that are stochastic, i.e., contain uncertainties and variation not explainable by variations in uncertain parameters of interest. Generalizations of previous theorems of existence, uniqueness, and stability of the data-consistent solution are provided while new theoretical results address the stability of marginals on parameters of interest. A notable aspect of the algorithmic generalization is the ability to query the solution to generate independent identically distributed samples of the parameters of interest without requiring knowledge of the so-called stochastic parameters. This work therefore extends the applicability of the data-consistent inversion framework to a much wider class of problems. This includes those based on purely experimental and field data where only a subset of conditions are either controllable or can be documented between experiments while the underlying physics, measurement errors, and any additional covariates are either uncertain or not accounted for by the researcher. Finally, numerical examples demonstrate application of this approach to systems with stochastic sources of uncertainties embedded within the modeling of a system and a numerical diagnostic is summarized that is useful for determining if a key assumption is verified among competing choices of stochastic maps.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2010

Route Generation for a Synthetic Character (BOT) Using a Partial or Incomplete Knowledge Route Generation Algorithm in UT2004 Virtual Environment

This paper presents a new Route Generation Algorithm that accurately and realistically represents human route planning and navigation for Military Operations in Urban Terrain (MOUT). The accuracy of this algorithm in representing human behavior is measured using the Unreal Tournament(Trademark) 2004 (UT2004) Game Engine to provide the simulation environment in which the differences between the routes taken by the human player and those of a Synthetic Agent (BOT) executing the A-star algorithm and the new Route Generation Algorithm can be compared. The new Route Generation Algorithm computes the BOT route based on partial or incomplete knowledge received from the UT2004 game engine during game play. To allow BOT navigation to occur continuously throughout the game play with incomplete knowledge of the terrain, a spatial network model of the UT2004 MOUT terrain is captured and stored in an Oracle 11 9 Spatial Data Object (SOO). The SOO allows a partial data query to be executed to generate continuous route updates based on the terrain knowledge, and stored dynamic BOT, Player and environmental parameters returned by the query. The partial data query permits the dynamic adjustment of the planned routes by the Route Generation Algorithm based on the current state of the environment during a simulation. The dynamic nature of this algorithm more accurately allows the BOT to mimic the routes taken by the human executing under the same conditions thereby improving the realism of the BOT in a MOUT simulation environment.

Hanold, Gregg T.↗
NASA NTRS1988

Semantic based man-machine interface for real-time communication

A flight expert system (FLES) was developed to assist pilots in monitoring, diagnosing and recovering from in-flight faults. To provide a communications interface between the flight crew and FLES, a natural language interface (NALI) was implemented. Input to NALI is processed by three processors: (1) the semantics parser; (2) the knowledge retriever; and (3) the response generator. First the semantic parser extracts meaningful words and phrases to generate an internal representation of the query. At this point, the semantic parser has the ability to map different input forms related to the same concept into the same internal representation. Then the knowledge retriever analyzes and stores the context of the query to aid in resolving ellipses and pronoun references. At the end of this process, a sequence of retrievel functions is created as a first step in generating the proper response. Finally, the response generator generates the natural language response to the query. The architecture of NALI was designed to process both temporal and nontemporal queries. The architecture and implementation of NALI are described.

Ali, M.↗
NASA NTRS2005

NASA Interactive Forms Type Interface - NIFTI

A flexible database query, update, modify, and delete tool was developed that provides an easy interface to Oracle forms. This tool - the NASA interactive forms type interface, or NIFTI - features on-the- fly forms creation, forms sharing among users, the capability to query the database from user-entered criteria on forms, traversal of query results, an ability to generate tab-delimited reports, viewing and downloading of reports to the user s workstation, and a hypertext-based help system. NIFTI is a very powerful ad hoc query tool that was developed using C++, X-Windows by a Motif application framework. A unique tool, NIFTI s capabilities appear in no other known commercial-off-the- shelf (COTS) tool, because NIFTI, which can be launched from the user s desktop, is a simple yet very powerful tool with a highly intuitive, easy-to-use graphical user interface (GUI) that will expedite the creation of database query/update forms. NIFTI, therefore, can be used in NASA s International Space Station (ISS) as well as within government and industry - indeed by all users of the widely disseminated Oracle base. And it will provide significant cost savings in the areas of user training and scalability while advancing the art over current COTS browsers. No COTS browser performs all the functions NIFTI does, and NIFTI is easier to use. NIFTI s cost savings are very significant considering the very large database with which it is used and the large user community with varying data requirements it will support. Its ease of use means that personnel unfamiliar with databases (e.g., managers, supervisors, clerks, and others) can develop their own personal reports. For NASA, a tool such as NIFTI was needed to query, update, modify, and make deletions within the ISS vehicle master database (VMDB), a repository of engineering data that includes an indentured parts list and associated resource data (power, thermal, volume, weight, and the like). Since the VMDB is used both as a collection point for data and as a common repository for engineering, integration, and operations teams, a tool such as NIFTI had to be designed that could expedite the creation of database query/update forms which could then be shared among users.

Jain, Bobby↗
NASA NTRS1981

Use of an engineering data management system in the analysis of Space Shuttle Orbiter tiles

This paper demonstrates the use of an engineering data management system to facilitate the extensive stress analyses of the Space Shuttle Orbiter thermal protection system. Descriptions are given of the approach and methods used (1) to gather, organize, and store the data, (2) to query data interactively, (3) to generate graphic displays of the data, and (4) to access, transform, and prepare the data for input to a stress analysis program. The relational information management system was found to be well suited to the tile analysis problem because information related to many separate tiles could be accessed individually from a data base having a natural organization from an engineering viewpoint. The flexible user features of the system facilitated changes in data content and organization which occurred during the development and refinement of the tile analysis procedure. Additionally, the query language supported retrieval of data to satisfy a variety of user-specified conditions.

Giles, G. L.↗
DOE OSTI2020

Sign-OPT: A Query-Efficient Hard-label Adversarial Attack

We study the most practical problem setup for evaluating adversarial robustness of a machine learning system with limited access: the hard-label black-box attack setting for generating adversarial examples, where limited model queries are allowed and only the decision is provided to a queried data input. Several algorithms have been proposed for this problem but they typically require huge amount (>20,000) of queries for attacking one example. Among them, one of the state-of-the-art approaches (Cheng et al., 2019) showed that hard-label attack can be modeled as an optimization problem where the objective function can be evaluated by binary search with additional model queries, thereby a zeroth order optimization algorithm can be applied. In this paper, we adopt the same optimization formulation but propose to directly estimate the sign of gradient at any direction instead of the gradient itself, which enjoys the benefit of single query. Using this single query oracle for retrieving sign of directional derivative, we develop a novel query-efficient Sign-OPT approach for hard-label black-box attack. We provide a convergence analysis of the new algorithm and conduct experiments on several models on MNIST, CIFAR-10 and ImageNet. We find that Sign-OPT attack consistently requires 5X to 10X fewer queries when compared to the current state-of-the-art approaches, and usually converges to an adversarial example with smaller perturbation.

Cheng, Minhao↗