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The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization

Abstract Background Limited universally-adopted data standards in veterinary medicine hinder data interoperability and therefore integration and comparison; this ultimately impedes the application of existing information-based tools to support advancement in diagnostics, treatments, and precision medicine. Hypothesis/Objectives A single, coherent, logic-based standard for documenting breed names in health, production, and research-related records will improve data use capabilities in veterinary and comparative medicine. Animals No live animals were used. Methods The Vertebrate Breed Ontology (VBO) was created from breed names and related information compiled from the Food and Agriculture Organization of the United Nations, breed registries, communities, and experts, using manual and computational approaches. Each breed is represented by a VBO term that includes breed information and provenance as metadata. VBO terms are classified using description logic to allow computational applications and Artificial Intelligence–readiness. Results VBO is an open, community-driven ontology representing over 19 500 livestock and companion animal breed concepts covering 49 species. Breeds are classified based on community and expert conventions (e.g., cattle breed) and supported by relations to the breed's genus and species indicated by National Center for Biotechnology Information (NCBI) Taxonomy terms. Relationships between VBO terms (e.g., relating breeds to their foundation stock) provide additional context to support advanced data analytics. VBO term metadata includes synonyms, breed identifiers/codes, and attributed cross-references to other databases. Conclusion and Clinical Importance The adoption of VBO as a standard for breed names in databases and veterinary electronic health records enhances veterinary data interoperability and computability, supporting precision medicine.

Veterinary Sciences

Ontologies at Work: Analyzing Information Requirements for Model Predictive Control in Buildings

Model Predictive Control (MPC) has shown significant potential for improving energy efficiency, indoor air quality and occupant comfort of buildings. MPC-based control algorithms have also shown the ability to shift loads and optimize for multiple objectives, including but not limited to reducing the green-house gas emissions, energy costs and peak demand. However, one of the main implementation challenges of these control algorithms is the integration and configuration effort needed to deploy a supervisory MPC controller in a building. By assigning standardized references to information sources and control points in buildings, existing studies have shown that semantic ontologies and corresponding queries have the potential to ease the deployment of such controllers. Yet, the use of semantic information to ease the deployment processes of MPC controllers is still limited. In this paper, we review three MPC experiments and synthesize the information requirements of these optimization problems. We then turn to existing and upcoming semantic ontologies such as Brick, SAREF and ASHRAE Standard 223 to represent these requirements, evaluating their potential to support the implementation of an MPC controller. This investigation concludes with a discussion of existing opportunities and open questions that the community should explore to support more streamlined MPC implementations.

Prakash, Anand Krishnan

Large Language Models for the Creation and Use of Semantic Ontologies in Buildings: Requirements and Challenges

Semantic ontologies offer a formalized, machine-readable framework for representing knowledge, enabling the structured description of complex systems. In the building domain, the adoption of ontologies like the Brick schema has transformed how buildings and their systems are modeled by providing a standardized, interoperable language. However, the complexity and the steep learning curve involved in developing and querying semantic models present substantial challenges, often requiring a workforce with specialized expertise. This paper builds on our experience in investigating how Large Language Models (LLMs) can help address these challenges, focusing on their role in constructing and querying of semantic models, particularly using the Brick Schema. Our study outlines the requirements and metrics for evaluating the scalability and effectiveness of LLM-based tools, while also discussing the current challenges and limitations in developing such tools. Ultimately, this paper aims to orient research efforts as various groups experiment with diverse techniques, while enabling more effective comparison of emerging solutions and fostering collaboration across the field.

Mulayim, Ozan Baris

What Are Ontologies and When Should They Be Used?

Data without description is at best unusable, and at worst, misused. If we do not understand the assumptions and meaning of our data, we are unable to confidently use it. Data today is largely described within a database’s schema, detailing structure and primitive datatypes as part of a relational model, but if we require assurance some data value can be correctly evaluated alongside others beyond the immediate systems in which they are defined, a more portable, richer semantics is needed. Ontologies define knowledge unambiguously across systems and establish the means to reason upon said knowledge using logical inference. They model neutral domains of information rather than data definitions from software or databases that would only serve to enrich a single system’s idiosyncrasies. In this paper, we take a casual stance to explore what ontologies are, how they are built, why they are useful, and when they should be used.

97 MATHEMATICS AND COMPUTING

An Ontology-Based Archive Information Model for the Planetary Science Community

The Planetary Data System (PDS) information model is a mature but complex model that has been used to capture over 30 years of planetary science data for the PDS archive. As the de-facto information model for the planetary science data archive, it is being adopted by the International Planetary Data Alliance (IPDA) as their archive data standard. However, after seventeen years of evolutionary change the model needs refinement. First a formal specification is needed to explicitly capture the model in a commonly accepted data engineering notation. Second, the core and essential elements of the model need to be identified to help simplify the overall archive process. A team of PDS technical staff members have captured the PDS information model in an ontology modeling tool. Using the resulting knowledge-base, work continues to identify the core elements, identify problems and issues, and then test proposed modifications to the model. The final deliverables of this work will include specifications for the next generation PDS information model and the initial set of IPDA archive data standards. Having the information model captured in an ontology modeling tool also makes the model suitable for use by Semantic Web applications.

Information Model

ODISEES: Ontology-Driven Interactive Search Environment for Earth Sciences

This paper discusses the Ontology-driven Interactive Search Environment for Earth Sciences (ODISEES) project currently being developed to aid researchers attempting to find usable data among an overabundance of closely related data. ODISEES' ontological structure relies on a modular, adaptable concept modeling approach, which allows the domain to be modeled more or less as it is without worrying about terminology or external requirements. In the model, variables are individually assigned semantic content based on the characteristics of the measurements they represent, allowing intuitive discovery and comparison of data without requiring the user to sift through large numbers of data sets and variables to find the desired information.

Rutherford, Matthew T.

Ontology and modeling patterns for state-based behavior representation

This paper provides an approach to capture state-based behavior of elements, that is, the specification of their state evolution in time, and the interactions amongst them. Elements can be components (e.g., sensors, actuators) or environments, and are characterized by state variables that vary with time. The behaviors of these elements, as well as interactions among them are represented through constraints on state variables. This paper discusses the concepts and relationships introduced in this behavior ontology, and the modeling patterns associated with it. Two example cases are provided to illustrate their usage, as well as to demonstrate the flexibility and scalability of the behavior ontology: a simple flashlight electrical model and a more complex spacecraft model involving instruments, power and data behaviors. Finally, an implementation in a SysML profile is provided.

state variable

An MLCommons Scientific Benchmarks Ontology

Scientific machine learning research spans diverse domains and data modalities, yet existing benchmark efforts remain siloed and lack standardization. This makes novel and transformative applications of machine learning to critical scientific use-cases more fragmented and less clear in pathways to impact. This paper introduces an ontology for scientific benchmarking developed through a unified, community-driven effort that extends the MLCommons ecosystem to cover physics, chemistry, materials science, biology, climate science, and more. Building on prior initiatives such as XAI-BENCH, FastML Science Benchmarks, PDEBench, and the SciMLBench framework, our effort consolidates a large set of disparate benchmarks and frameworks into a single taxonomy of scientific, application, and system-level benchmarks. New benchmarks can be added through an open submission workflow coordinated by the MLCommons Science Working Group and evaluated against a six-category rating rubric that promotes and identifies high-quality benchmarks, enabling stakeholders to select benchmarks that meet their specific needs. The architecture is extensible, supporting future scientific and AI/ML motifs, and we discuss methods for identifying emerging computing patterns for unique scientific workloads. The MLCommons Science Benchmarks Ontology provides a standardized, scalable foundation for reproducible, cross-domain benchmarking in scientific machine learning. A companion webpage for this work has also been developed as the effort evolves: https://mlcommons-science.github.io/benchmark/

Hawks, Ben [Fermilab] (ORCID:0000000157000288)

Semantic Analysis of Email Using Domain Ontologies and WordNet

The problem of capturing and accessing knowledge in paper form has been supplanted by a problem of providing structure to vast amounts of electronic information. Systems that can construct semantic links for natural language documents like email messages automatically will be a crucial element of semantic email tools. We have designed an information extraction process that can leverage the knowledge already contained in an existing semantic web, recognizing references in email to existing nodes in a network of ontology instances by using linguistic knowledge and knowledge of the structure of the semantic web. We developed a heuristic score that uses several forms of evidence to detect references in email to existing nodes in the Semanticorganizer repository's network. While these scores cannot directly support automated probabilistic inference, they can be used to rank nodes by relevance and link those deemed most relevant to email messages.

Berrios, Daniel C.

Ontology-Driven Information Integration

Ontology-driven information integration (ODII) is a method of computerized, automated sharing of information among specialists who have expertise in different domains and who are members of subdivisions of a large, complex enterprise (e.g., an engineering project, a government agency, or a business). In ODII, one uses rigorous mathematical techniques to develop computational models of engineering and/or business information and processes. These models are then used to develop software tools that support the reliable processing and exchange of information among the subdivisions of this enterprise or between this enterprise and other enterprises.

Tissot, Florence

A Hyperbolic Ontology Visualization Tool for Model Application Programming Interface Documentation

Spacecraft modeling, a critically important portion in validating planned spacecraft activities, is currently carried out using a time consuming method of mission to mission model implementations and integration. A current project in early development, Integrated Spacecraft Analysis (ISCA), aims to remedy this hindrance by providing reusable architectures and reducing time spent integrating models with planning and sequencing tools. The principle objective of this internship was to develop a user interface for an experimental ontology-based structure visualization of navigation and attitude control system modeling software. To satisfy this, a number of tree and graph visualization tools were researched and a Java based hyperbolic graph viewer was selected for experimental adaptation. Early results show promise in the ability to organize and display large amounts of spacecraft model documentation efficiently and effectively through a web browser. This viewer serves as a conceptual implementation for future development but trials with both ISCA developers and end users should be performed to truly evaluate the effectiveness of continued development of such visualizations.

mission operations system (MOS)

An Ontological Approach to Integrate Commercial Space Operations with an In-time Aviation Safety Management System (IASMS)

The emergence of commercial space operations (CSO) is one of many Advanced Air Mobility domains that pose major challenges to in-time safety assurance because of the different architectures used by the operators and other agents. The National Academies recognized the need to improve integration of disparate architectures and recommended that an In-time Aviation Safety Management System(IASMS) be developed to provide seamless connectivity across interacting architectures and enable in-time safety assurance. An ontological approach to integrating CSO with IASMS involves in-time Services, Functions, and Capabilities design to manage operational risks and inform changes to design. The resulting integrated architecture provides a common basis for risk management and in-time safety assurance.

K Ellis

Automated model generation and parameter estimation of building energy models using an ontology-based framework

This study presents a methodology for automated model generation and parameter estimation of building energy models using semantic modeling and Bayesian estimation. Semantic modeling techniques are used to represent the system components and their interactions, facilitating the automatic generation of a simulation model from dynamic component models. The proposed approach is applied to a case study of a ventilation system where a simulation model is generated, calibrated, and assessed through different performance metrics. These metrics demonstrate the accuracy and reliability of both model point estimates and probabilistic prediction intervals across all model outputs. Overall, the proposed methodology offers a systematic and automated approach to model development and calibration in building energy systems, with potential applications in building performance analysis, monitoring, and optimization.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI

Ontologies for Intelligent Data Science

As anyone even vaguely aware of current technology can tell you, machine learning (ML) and artificial intelligence (AI) have made exceptional breakthroughs in recent years. Generative artificial intelligence (GAI) emerged circa 2022 dominated by Large Language Models (LLMs) and generative tools for images emerged at about the same time.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION

Intelligent resource discovery using ontology-based resource profiles

Successful resource discovery across heterogeneous repositories is strongly dependent on the semantic and syntactic homogeneity of the associated resource descriptions. Ideally, resource descriptions are easily extracted from pre-existing standardized sources, expressed using standard syntactic and semantic structures, and managed and accessed within a distributed, flexible, and scaleable software framework.

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