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All sources NASA NTRS DOE OSTI

DOE OSTI2021

Simplifying and Visualizing the Ontology of Systems Engineering Models

The credibility of an engineering model is of critical importance in large-scale projects. How concerned should an engineer be when reusing someone else's model when they may not know the author or be familiar with the tools that were used to create it? In this report, the authors advance engineers' capabilities for assessing models through examination of the underlying semantic structure of a model--the ontology. This ontology defines the objects in a model, types of objects, and relationships between them. In this study, two advances in ontology simplification and visualization are discussed and are demonstrated on two systems engineering models. These advances are critical steps toward enabling engineering models to interoperate, as well as assessing models for credibility. For example, results of this research show an 80% reduction in file size and representation size, dramatically improving the throughput of graph algorithms applied to the analysis of these models. Finally, four future problems are outlined in ontology research toward establishing credible models--ontology discovery, ontology matching, ontology alignment, and model assessment.

42 ENGINEERING↗

NASA NTRSDate not supplied

New developments in space radiation research at NASA: Annotating data using a novel radiation biology ontology

Like many interdisciplinary sciences, data producers and consumers in the field of radiation biology often use a wide variety of terminology to describe their experiments and data. Furthermore, space systems and technologies are rapidly evolving, and a shared understanding and common terminology for these is also lacking. The efficiency of research organizations can be enhanced by standardizing metadata through the use of knowledge resources like ontologies. Employing a sophisticated model such as a formal ontology to standardize metadata enables automated data acquisition processes and supports more complete, accurate meta-analysis through more efficient and complete data discovery and retrieval, particularly when using multiple data sources. Thus, we developed the Radiation Biology Ontology (RBO) in order to improved radiation biology metadata uniformity and transparency. We used open-source software (the Ontology Development Kit, Protégé and WebProtégé) and worked within the OBO Foundry framework, which includes a set of ontology development principles and practices for ontology consistency, uniformity, and accountability. The RBO has now been incorporated into two radiation research data repositories, NASA’s GeneLab omics database (https://genelab.nasa.gov), and the European Commission STORE database (https://www.storedb.org/). Continuous build integration tools allowed our international RBO collaboration to be more efficient and focus its efforts on semantic model design. Currently, the RBO contains over 300 annotated classes and individuals specific to the study of radiation on biological systems, as well as imports of many additional classes from other OBO Foundry ontologies that relate to and/or provide context for these RBO entities. We publish the RBO through the OBO Foundry, so that it is available for browsing, download, and querying through NCBI Bioportal web site and application programming interface. The NASA Ames Life Science Data Archive (ALSDA) is also in the process of adopting use of the RBO, taking NASA one step closer to a knowledge-based system for space biology data. It is our hope that the global communities of radiation research Investigators, data curators and data analysts can similarly leverage the RBO and will contribute to its further development.

radiation↗

NASA NTRS2011

Ontological Modeling for Integrated Spacecraft Analysis

Current spacecraft work as a cooperative group of a number of subsystems. Each of these requiresmodeling software for development, testing, and prediction. It is the goal of my team to create anoverarching software architecture called the Integrated Spacecraft Analysis (ISCA) to aid in deploying the discrete subsystems' models. Such a plan has been attempted in the past, and has failed due to the excessive scope of the project. Our goal in this version of ISCA is to use new resources to reduce the scope of the project, including using ontological models to help link the internal interfaces of subsystems' models with the ISCA architecture.I have created an ontology of functions specific to the modeling system of the navigation system of a spacecraft. The resulting ontology not only links, at an architectural level, language specificinstantiations of the modeling system's code, but also is web-viewable and can act as a documentation standard. This ontology is proof of the concept that ontological modeling can aid in the integration necessary for ISCA to work, and can act as the prototype for future ISCA ontologies.

ontological modeling↗

DOE OSTI2024

Multiple aspects maintenance ontology-based intelligent maintenance optimization framework for safety-critical systems

Abstract Maintenance optimization is a process for improving the efficiency of maintenance strategies and activities, considering various aspects of the target system and components, such as the probabilities of system failures and the cost of repair and replacement of a failed component. The improvement of maintenance optimization algorithms generally requires information from various data sources. For example, it may require the system risk information derived from risk analysis tools or the residual lifetime of a component from fault prognosis tools. The requirements of data acquisition (DAQ) and aggregation pose new challenges for maintenance management systems (MMSs) that implement and use these maintenance optimization algorithms. This paper proposes a multiple aspects maintenance ontology-based framework to facilitate DAQ from MMSs, online monitoring systems, fault detection and discrimination tools, risk assessment tools, decision-making tools, and component identification tools, and accelerate the implementation and verification of contemporary maintenance optimization models and algorithms. The proposed framework consists of a multi-aspect maintenance ontology with critical information for maintenance optimization and application interfaces for collecting information from various data sources, such as fault prognosis tools, online monitoring tools, risk assessment tools, and decision-making algorithms. In addition, this paper proposes a heuristic method for integrating concepts and properties from other existing ontologies into the proposed framework when the existing ontology is not fully compatible with the ontology under construction. Finally, the paper verifies the proposed ontology framework using a feedwater system designed for nuclear power plants with valves and filters as the components under maintenance.

Diao, Xiaoxu (ORCID:0000000346726352)↗

DOE OSTI2020

Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project

An important need exists to better understand and stratify kidney disease according to its underlying pathophysiology in order to develop more precise and effective therapeutic agents. National collaborative efforts such as the Kidney Precision Medicine Project are working towards this goal through the collection and integration of large, disparate clinical, biological and imaging data from patients with kidney disease. Ontologies are powerful tools that facilitate these efforts by enabling researchers to organize and make sense of different data elements and the relationships between them. Ontologies are critical to support the types of big data analysis necessary for kidney precision medicine, where heterogeneous clinical, imaging and biopsy data from diverse sources must be combined to define a patient’s phenotype. Here, the development of two new ontologies — the Kidney Tissue Atlas Ontology and the Ontology of Precision Medicine and Investigation — will support the creation of the Kidney Tissue Atlas, which aims to provide a comprehensive molecular, cellular and anatomical map of the kidney. These ontologies will improve the annotation of kidney-relevant data, and eventually lead to new definitions of kidney disease in support of precision medicine.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Post-composing ontology terms for efficient phenotyping in plant breeding

Abstract Ontologies are widely used in databases to standardize data, improving data quality, integration, and ease of comparison. Within ontologies tailored to diverse use cases, post-composing user-defined terms reconciles the demands for standardization on the one hand and flexibility on the other. In many instances of Breedbase, a digital ecosystem for plant breeding designed for genomic selection, the goal is to capture phenotypic data using highly curated and rigorous crop ontologies, while adapting to the specific requirements of plant breeders to record data quickly and efficiently. For example, post-composing enables users to tailor ontology terms to suit specific and granular use cases such as repeated measurements on different plant parts and special sample preparation techniques. To achieve this, we have implemented a post-composing tool based on orthogonal ontologies providing users with the ability to introduce additional levels of phenotyping granularity tailored to unique experimental designs. Post-composed terms are designed to be reused by all breeding programs within a Breedbase instance but are not exported to the crop reference ontologies. Breedbase users can post-compose terms across various categories, such as plant anatomy, treatments, temporal events, and breeding cycles, and, as a result, generate highly specific terms for more accurate phenotyping.

Mathematical & Computational Biology↗

NASA NTRS2004

An Ontology for Requesting Distant Robotic Action: A Case Study in Naming and Action Identification for Planning on the Mars Exploration Rover Mission

This paper focuses on the development and use of the abbreviated names as well as an emergent ontology associated with making requests for action of a distant robotic rover during the 2003-2004 NASA Mars Exploration Rover (MER) mission, run by the Jet Propulsion Laboratory. The infancy of the domain of Martian telerobotic science, in which specialists request work from a rover moving through the landscape, as well as the need to consider the interdisciplinary teams involved in the work required an empirical approach. The formulation of this ontology is grounded in human behavior and work practice. The purpose of this paper is to identify general issues for an ontology of action (specifically for requests for action), while maintaining sensitivity to the users, tools and the work system within a specific technical domain. We found that this ontology of action must take into account a dynamic environment, changing in response to the movement of the rover, changes on the rover itself, as well as be responsive to the purposeful intent of the science requestors. Analysis of MER mission events demonstrates that the work practice and even robotic tool usage changes over time. Therefore, an ontology must adapt and represent both incremental change and revolutionary change, and the ontology can never be more than a partial agreement on the conceptualizations involved. Although examined in a rather unique technical domain, the general issues pertain to the control of any complex, distributed work system as well as the archival record of its accomplishments.

Wales, Roxana C.↗

DOE OSTI2025

The Unified Phenotype Ontology : a framework for cross-species integrative phenomics

Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and interpreting these data to inform biological hypotheses. A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed. We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Towards Next-Generation Urban Decision Support Systems through AI-Powered Construction of Scientific Ontology Using Large Language Models—A Case in Optimizing Intermodal Freight Transportation

The incorporation of Artificial Intelligence (AI) models into various optimization systems is on the rise. However, addressing complex urban and environmental management challenges often demands deep expertise in domain science and informatics. This expertise is essential for deriving data and simulation-driven insights that support informed decision-making. In this context, we investigate the potential of leveraging the pre-trained Large Language Models (LLMs) to create knowledge representations for supporting operations research. By adopting ChatGPT-4 API as the reasoning core, we outline an applied workflow that encompasses natural language processing, Methontology-based prompt tuning, and Generative Pre-trained Transformer (GPT), to automate the construction of scenario-based ontologies using existing research articles and technical manuals of urban datasets and simulations. From these ontologies, knowledge graphs can be derived using widely adopted formats and protocols, guiding various tasks towards data-informed decision support. The performance of our methodology is evaluated through a comparative analysis that contrasts our AI-generated ontology with the widely recognized pizza ontology, commonly used in tutorials for popular ontology software. We conclude with a real-world case study on optimizing the complex system of multi-modal freight transportation. Our approach advances urban decision support systems by enhancing data and metadata modeling, improving data integration and simulation coupling, and guiding the development of decision support strategies and essential software components.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

NASA NTRSDate not supplied

Increasing Data Discovery and Re-Use: The Space Life Sciences Ontology

Two of the most important goals of the adoption of the FAIR principles are increasing the ability of agents to find and re-use research data. Achieving these goals for space life sciences research is even more pressing, given the relatively expensive and scarce nature of these data. We have reported in the past on the progress made by exemplar life sciences data systems towards implementing FAIR, showing gaps particularly in the “interoperability area” of the principles; the lack of common conceptual models for space life science research is one reason for this gap. There were few available resources that define, annotate, categorize or otherwise relate various kinds of metadata describing the acquisition, nature, and intent of investigational space life sciences data. To address this gap, NASA is working with the Open Biological and Biomedical Ontology Foundry (https://obofoundry.org/) to develop the Space Life Science Ontology (SLSO) that is intended to support archival and other kinds of systems that operate using these data. The scope of the ontology includes concepts regarding those aspects of investigation design and execution specific or unique to space environments, such as types of specialized equipment, operating organizations, and documentation. The ontology is continually being developed and published to the life science community (https://github.com/nasa/LSDAO/); at the time of this publication, the SLSO newly and uniquely defines 30 types (classes), 90 properties, and 14 relations specific to space life sciences metadata. In addition, the SLSO reuses (imports) some 2,360 types (classes), 49 properties, and 393 relations from other ontologies that are relevant to these kinds of metadata. In addition to its role as a common conceptualization for space biomedical research activities, the SLSO can also be used to provide automated support for traditionally difficult and expensive activities such as data curation and cross-system data integration and analysis.

fair↗

DOE OSTI2023

Ontologizing health systems data at scale: making translational discovery a reality

Common data models solve many challenges of standardizing electronic health record (EHR) data but are unable to semantically integrate all of the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68–99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2021

ECO: the Evidence and Conclusion Ontology, an update for 2022

The Evidence and Conclusion Ontology (ECO) is a community resource that provides an ontology of terms used to capture the type of evidence that supports biomedical annotations and assertions. Consistent capture of evidence information with ECO allows tracking of annotation provenance, establishment of quality control measures, and evidence-based data mining. ECO is in use by dozens of data repositories and resources with both specific and general areas of focus. ECO is continually being expanded and enhanced in response to user requests as well as our aim to adhere to community best-practices for ontology development. The ECO support team engages in multiple collaborations with other ontologies and annotating groups. Here we report on recent updates to the ECO ontology itself as well as associated resources that are available through this project. ECO project products are freely available for download from the project website (https://evidenceontology.org/) and GitHub (https://github.com/evidenceontology/evidenceontology). ECO is released into the public domain under a CC0 1.0 Universal license.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

FAIRmaterials: Ontology Tools with Data FAIRification in Development

The bilingual FAIRmaterials package simplifies the creation and visualization of materials and data science ontologies. FAIRmaterials, available in the Python and R languages, addresses the complexities associated with traditional ontology editors based on manual user input such as Protege with an intuitive workflow and easy-to-use templates, making it accessible to users both experienced and inexperienced with ontologies. The FAIRmaterials package is its ability to programatically convert simple and structured CSV inputs into rich, well-defined ontologies. This capability is designed to support the findability, accessibility, interoperability, and reusability (FAIR) of research data and serve as a tool in the process of data FAIRification. Its additional features, such as automated ontology merging, static visualizations, and comprehensive documentation for outputs extend its utility, making it a valuable tool for any researcher engaged in knowledge management.

Bradley, Alexander Harding [Case Western Reserve U↗

NASA NTRS1996

Theory and ontology for sharing temporal knowledge

Using current technology, the sharing or re-using of knowledge-bases is very difficult, if not impossible. ARPA has correctly recognized the problem and funded a knowledge sharing initiative. One of the outcomes of this project is a formal language called Knowledge Interchange Format (KIF) for representing knowledge that could be translated into other languages. Capturing and representing design knowledge and reasoning with them have become very important for NASA who is a pioneer of innovative design of unique products. For upgrading an existing design for changing technology, needs, or requirements, it is essential to understand the design rationale, design choices, options and other relevant information associated with the design. Capturing such information and presenting them in the appropriate form are part of the ongoing Design Knowledge Capture project of NASA. The behavior of an object and various other aspects related to time are captured by the appropriate temporal knowledge. The captured design knowledge will be represented in such a way that various groups of NASA who are interested in various aspects of the design cycle should be able to access and use the design knowledge effectively. To facilitate knowledge sharing among these groups, one has to develop a very well defined ontology. Ontology is a specification of conceptualization. In the literature several specific domains were studied and some well defined ontologies were developed for such domains. However, very little, or no work has been done in the area of representing temporal knowledge to facilitate sharing. During the ASEE summer program, I have investigated several temporal models and have proposed a theory for time that is flexible to accommodate the time elements, such as, points and intervals, and is capable of handling the qualitative and quantitative temporal constraints. I have also proposed a primitive temporal ontology using which other relevant temporal ontologies can be built. I have investigated various issues of sharing knowledge and have proposed a formal framework for modeling the concept of knowledge sharing. This work may be implemented and tested in the software environment supplied by Knowledge Based System, Inc.

Loganantharaj, Rasiah↗

NASA NTRS2016

Ontologies for Aviation Data Management

Managing complex aviation data can be a significant challenge for any enterprise – whether a government agency, airline, airframe manufacturer, or aviation service provider. To handle this challenge, data models are typically developed to characterize and manage the data generated, used, and stored by a given enterprise. Unfortunately, different data providers employ qualitatively different data models, and this gives rise to problems exchanging data across organizational boundaries. Over the past decade, these problems have motivated data producers and consumers to look toward standardized data exchange models to address data interoperability. In this paper we examine some of these standardized data exchange models and compare them with a new type of data model based on ontologies. Ontology models have emerged in recent years from a confluence of research in the artificial intelligence, semantic web, and information science communities. This paper introduces ontology models, provides several use cases for ontologies relevant to aviation data management, and summarizes state of the art aviation prototype applications that utilize ontologies.

artificial intelligence↗

NASA NTRSDate not supplied

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↗

DOE OSTI2021

Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)

Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5,000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a 10-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2009

Scientific Digital Libraries, Interoperability, and Ontologies

Scientific digital libraries serve complex and evolving research communities. Justifications for the development of scientific digital libraries include the desire to preserve science data and the promises of information interconnectedness, correlative science, and system interoperability. Shared ontologies are fundamental to fulfilling these promises. We present a tool framework, some informal principles, and several case studies where shared ontologies are used to guide the implementation of scientific digital libraries. The tool framework, based on an ontology modeling tool, was configured to develop, manage, and keep shared ontologies relevant within changing domains and to promote the interoperability, interconnectedness, and correlation desired by scientists.

Information Model↗