We present Open Ontologies, an open-source ontology engineering system implemented in Rust that integrates LLM-driven construction with formal OWL reasoning and ontology alignment via the Model Context Protocol. Our primary finding is that stable 1-to-1 matching is the dominant factor in ontology alignment quality: on the OAEI Anatomy track, it achieves F1 = 0.832 (P = 0.963, R = 0.733), competitive with state-of-the-art systems and exceeding all in precision. Ablation across five weight configurations shows that signal weights are irrelevant when stable matching is applied (F1 varies by less than 0.004), while removing stable matching drops F1 to 0.728. On the Conference track, the same method achieves F1 = 0.438. On tool-augmented ontology interaction, we find a surprising result: an LLM reading a raw OWL file (F1 = 0.323) performs worse than the same LLM with no file at all (F1 = 0.431), while structured MCP tool access achieves F1 = 0.717. This demonstrates that tool structure provides a qualitatively different mode of access that the LLM cannot replicate by reading raw syntax. The system ships as a single binary under the MIT licence.
Institute of Cognitive Sciences and Technologies, Italian National Research Council (ISTC-CNR)（意大利国家研究委员会认知科学与技术研究所）；University of Bologna（博洛尼亚大学）
We present the Frame-based ontology Design Outlet (FrODO), a novel method and tool for drafting ontologies from competency questions automatically. Competency questions are expressed as natural language and are a common solution for representing requirements in a number of agile ontology engineering methodologies, such as the eXtreme Design (XD) or SAMOD. FrODO builds on top of FRED. In fact, it leverages the frame semantics for drawing domain-relevant boundaries around the RDF produced by FRED from a competency question, thus drafting domain ontologies. We carried out a user-based study for a…
Background. Most tutorial ontologies focus on illustrating one aspect of ontology development, notably language features and automated reasoners, but ignore ontology development factors, such as emergent modelling guidelines and ontological principles. Yet, novices replicate examples from the exercises they carry out. Not providing good examples holistically causes the propagation of sub-optimal ontology development, which may negatively affect the quality of a real domain ontology. Results. We identified 22 requirements that a good tutorial ontology should satisfy regarding subject domain, lo…
Ontology merging is important, but not always effective. The main reason, why ontology merging is not effective, is that ontology merging is performed without considering goals. Goals define the way, in which ontologies to be merged more effectively. The paper illustrates ontology merging by means of rules, which are generated from these ontologies. This is necessary for further use in expert systems.
In ontology-based data access, databases are connected to an ontology via mappings from queries over the database to queries over the ontology. In this paper, we consider mappings from relational databases to first-order ontologies, and define an ASP-based framework for GLAV mappings with queries over the ontology in the mapping rule bodies. We show that this type of mappings can be used to express constraints and exceptions, as well as being a powerful mechanism for succinctly representing OBDA mappings. We give an algorithm for brave reasoning in this setting, and show that this problem has …
Warsaw University of Technology（华沙理工大学）；Systems Research Institute, Polish Academy of Sciences（波兰科学院系统研究所）；University of Craiova（克拉约瓦大学）
Reusing ontologies in practice is still very challenging, especially when multiple ontologies are (jointly) involved. Moreover, despite recent advances, the realization of systematic ontology quality assurance remains a difficult problem. In this work, the quality of thirty biomedical ontologies, and the Computer Science Ontology are investigated, from the perspective of a practical use case. Special scrutiny is given to cross-ontology references, which are vital for combining ontologies. Diverse methods to detect potential issues are proposed, including natural language processing and network…
The new era of the Web is known as the semantic Web or the Web of data. The semantic Web depends on ontologies that are seen as one of its pillars. The bigger these ontologies, the greater their exploitation. However, when these ontologies become too big other problems may appear, such as the complexity to charge big files in memory, the time it needs to download such files and especially the time it needs to make reasoning on them. We discuss in this paper approaches for segmenting such big Web ontologies as well as its usefulness. The segmentation method extracts from an existing ontology a …
Ontology operations, e.g., aligning and merging, were studied and implemented extensively in different settings, such as, categorical operations, relation algebras, typed graph grammars, with different concerns. However, aligning and merging operations in the settings share some generic properties, e.g., idempotence, commutativity, associativity, and representativity, labeled by (I), (C), (A), and (R), respectively, which are defined on an ontology merging system $(\mathfrak{O},\sim,\merge)$, where $\mathfrak{O}$ is a set of the ontologies concerned, $\sim$ is a binary relation on $\mathfrak{O…
King Abdullah University of Science and Technology (KAUST)（阿卜杜拉国王科技大学）
Motivation: Ontologies are widely used in biology for data annotation, integration, and analysis. In addition to formally structured axioms, ontologies contain meta-data in the form of annotation axioms which provide valuable pieces of information that characterize ontology classes. Annotations commonly used in ontologies include class labels, descriptions, or synonyms. Despite being a rich source of semantic information, the ontology meta-data are generally unexploited by ontology-based analysis methods such as semantic similarity measures. Results: We propose a novel method, OPA2Vec, to gene…
U.S. Customs and Border Protection（美国海关和边境保护局）；National Center for Ontological Research（国家本体论研究中心）；University at Buffalo（布法罗大学）；CUBRC, Inc.（CUBRC公司）；Institute for Artificial Intelligence and Data Science（人工智能与数据科学研究所）
This paper discloses the potential of OWL (Web Ontology Language) ontologies for generation of rules. The main purpose of this paper is to identify new types of rules, which may be generated from OWL ontologies. Rules, generated from OWL ontologies, are necessary for the functioning of the Semantic Web Expert System. It is expected that the Semantic Web Expert System (SWES) will be able to process ontologies from the Web with the purpose to supplement or even to develop its knowledge base.
This paper argues that certain ontology design problems are profitably addressed by treating ontologies as theories and by defining a set of operations that create new ontologies, including their constraints, out of other ontologies. The paper first shows how to use the operations in the context of ontology reuse, how to take advantage of the operations to compare different ontologies, or different versions of an ontology, and how the operations may help design mediated schemas in a bottom up fashion. The core of the paper discusses how to compute the operations for lightweight ontologies and …
Philosophers frequently struggle with the relation of metaphysics to the everyday world, with its practical value, and with its relation to empirical science. This paper distinguishes several different models of the relation between philosophical ontology and applied (scientific) ontology that have been advanced in the history of philosophy. Adoption of a strong participation model for the philosophical ontologist in science is urged, and requirements and consequences of the participation model are explored. This approach provides both a principled view and justification of the role of the phi…
RheinMain University of Applied Sciences（莱茵美因应用科学大学）
When ontologies cover overlapping topics, the overlap can be represented using ontology alignments. These alignments need to be continuously adapted to changing ontologies. Especially for large ontologies this is a costly task often consisting of manual work. Finding changes that do not lead to an adaption of the alignment can potentially make this process significantly easier. This work presents an approach to finding these changes based on RDF embeddings and common classification techniques. To examine the feasibility of this approach, an evaluation on a real-world dataset is presented. In t…
Tel-Aviv University（特拉维夫大学）；Ben Gurion University of the Negev（本·古里安大学内盖夫分校）
An ontology is a formal representation of domain knowledge, which can be interpreted by machines. In recent years, ontologies have become a major tool for domain knowledge representation and a core component of many knowledge management systems, decision support systems and other intelligent systems, inter alia, in the context of agriculture. A review of the existing literature on agricultural ontologies, however, reveals that most of the studies, which propose agricultural ontologies, are lacking an explicit evaluation procedure. This is undesired because without well-structured evaluation pr…
Free University of Bozen-Bolzano（博岑-博尔扎诺自由大学）；University of Liverpool（利物浦大学）；University of Bremen（不来梅大学）；Birkbeck, University of London（伦敦大学伯贝克学院）
The question whether an ontology can safely be replaced by another, possibly simpler, one is fundamental for many ontology engineering and maintenance tasks. It underpins, for example, ontology versioning, ontology modularization, forgetting, and knowledge exchange. What safe replacement means depends on the intended application of the ontology. If, for example, it is used to query data, then the answers to any relevant ontology-mediated query should be the same over any relevant data set; if, in contrast, the ontology is used for conceptual reasoning, then the entailed subsumptions between co…
Predicting Failures of LLMs to Link Biomedical Ontology Terms to Identifiers Evidence Across Models and Ontologies
Department of Neurology（神经学系）；Rehabilitation University of Illinois at Chicago Chicago, IL, USA（伊利诺伊大学芝加哥分校康复学院）；Lab for Applied Artificial Intelligence（应用人工智能实验室）；Engineering Program（工程学院）
Electronic Research Institute（电子研究所）；Al-Azhar University（爱资哈尔大学）
This Ontologies are widely used as a means for solving the information heterogeneity problems on the web because of their capability to provide explicit meaning to the information. They become an efficient tool for knowledge representation in a structured manner. There is always more than one ontology for the same domain. Furthermore, there is no standard method for building ontologies, and there are many ontology building tools using different ontology languages. Because of these reasons, interoperability between the ontologies is very low. Current ontology tools mostly use functions to build…
Ontology engineering is a hard and error-prone task, in which small changes may lead to errors, or even produce an inconsistent ontology. As ontologies grow in size, the need for automated methods for repairing inconsistencies while preserving as much of the original knowledge as possible increases. Most previous approaches to this task are based on removing a few axioms from the ontology to regain consistency. We propose a new method based on weakening these axioms to make them less restrictive, employing the use of refinement operators. We introduce the theoretical framework for weakening DL…
We propose a system for automated essay grading using ontologies and textual entailment. The process of textual entailment is guided by hypotheses, which are extracted from a domain ontology. Textual entailment checks if the truth of the hypothesis follows from a given text. We enact textual entailment to compare students answer to a model answer obtained from ontology. We validated the solution against various essays written by students in the chemistry domain.
University of Liverpool（利物浦大学）；University of Bremen（不来梅大学）
We study the problem of learning description logic (DL) ontologies in Angluin et al.'s framework of exact learning via queries. We admit membership queries ("is a given subsumption entailed by the target ontology?") and equivalence queries ("is a given ontology equivalent to the target ontology?"). We present three main results: (1) ontologies formulated in (two relevant versions of) the description logic DL-Lite can be learned with polynomially many queries of polynomial size; (2) this is not the case for ontologies formulated in the description logic EL, even when only acyclic ontologies are…
Otto von Guericke University Magdeburg（马格德堡奥托·冯·格里克大学）；University of Zurich（苏黎世大学）；University of St Gallen（圣加仑大学）
In ontology development, there is a gap between domain ontologies which mostly use the web ontology language, OWL, and foundational ontologies written in first-order logic, FOL. To bridge this gap, we present Gavel, a tool that supports the development of heterogeneous 'FOWL' ontologies that extend OWL with FOL annotations, and is able to reason over the combined set of axioms. Since FOL annotations are stored in OWL annotations, FOWL ontologies remain compatible with the existing OWL infrastructure. We show that for the OWL domain ontology OBI, the stronger integration with its FOL top-level …
Rewriting-based approaches for answering queries over an OWL 2 DL ontology have so far been developed mainly for Horn fragments of OWL 2 DL. In this paper, we study the possibilities of answering queries over non-Horn ontologies using datalog rewritings. We prove that this is impossible in general even for very simple ontology languages, and even if PTIME = NP. Furthermore, we present a resolution-based procedure for $\SHI$ ontologies that, in case it terminates, produces a datalog rewriting of the ontology. Our procedure necessarily terminates on DL-Lite_{bool}^H ontologies---an extension of …
The University of Jordan（约旦大学）；Brunel University – West London（布鲁内尔大学西伦敦校区）
Ontologies are key enablers for sharing precise and machine-understandable semantics among different applications and parties. Yet, for ontologies to meet these expectations, their quality must be of a good standard. The quality of an ontology is strongly based on the design method employed. This paper addresses the design problems related to the modelling of ontologies, with specific concentration on the issues related to the quality of the conceptualisations produced. The paper aims to demonstrate the impact of the modelling paradigm adopted on the quality of ontological models and, conseque…
The sharing of ontologies between diverse communities of discourse allows them to compare their own information structures with that of other communities that share a common terminology and semantics - ontology sharing facilitates interoperability between online knowledge organizations. This paper demonstrates how ontology sharing is formalizable within the conceptual knowledge model of Information Flow (IF). Information Flow indirectly represents sharing through a specifiable, ontology extension hierarchy augmented with synonymic type equivalencing - two ontologies share terminology and meani…
Research Center on Spatial Cognition, University of Bremen（不来梅大学空间认知研究中心）；University of Birmingham（伯明翰大学）；DFKI GmbH Bremen（德国人工智能研究中心不来梅分中心）；Infoterm（国际术语信息中心）；University of Toronto（多伦多大学）
The Distributed Ontology Language (DOL) is currently being standardized within the OntoIOp (Ontology Integration and Interoperability) activity of ISO/TC 37/SC 3. It aims at providing a unified framework for (1) ontologies formalized in heterogeneous logics, (2) modular ontologies, (3) links between ontologies, and (4) annotation of ontologies. This paper presents the current state of DOL's standardization. It focuses on use cases where distributed ontologies enable interoperability and reusability. We demonstrate relevant features of the DOL syntax and semantics and explain how these integrat…
Virginia Commonwealth University（弗吉尼亚联邦大学）；University of Sydney（悉尼大学）
Ontologies have been known for their semantic representation of knowledge. ontologies cannot automatically evolve to reflect updates that occur in respective domains. To address this limitation, researchers have called for automatic ontology generation from unstructured text corpus. Unfortunately, systems that aim to generate ontologies from unstructured text corpus are domain-specific and require manual intervention. In addition, they suffer from uncertainty in creating concept linkages and difficulty in finding axioms for the same concept. Knowledge Graphs (KGs) has emerged as a powerful mod…
Faculty of Information Technology（信息技术学院）；Faculty of Computer Science（计算机科学学院）；Monash University（莫纳什大学）；University of Lyon（里昂大学）
Ontologies form the basic interest in various computer science disciplines such as semantic web, information retrieval, database design, etc. They aim at providing a formal, explicit and shared conceptualization and understanding of common domains between different communities. In addition, they allow for concepts and their constraints of a specific domain to be explicitly defined. However, the distributed nature of ontology development and the differences in viewpoints of the ontology engineers have resulted in the so called "semantic heterogeneity" between ontologies. Semantic heterogeneity …
Embedding Ontologies via Incorporating Extensional and Intensional Knowledge
School of Computer Science and Engineering, Southeast University（东南大学计算机科学与工程学院）；Department of Computer Science, The University of Manchester（曼彻斯特大学计算机科学系）；China Mobile Research Institute（中国移动研究院）
University of A Coruña（拉科鲁尼亚大学）；University of Montpellier（蒙彼利埃大学）
Biomedical researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms. We developed a new …
National Center for Ontological Research（国家本体论研究中心）；U.S. Customs & Border Protection（美国海关与边境保护局）；University at Buffalo（布法罗大学）；Institute for Artificial Intelligence and Data Science（人工智能与数据科学研究所）
Understanding large ontologies is still an issue, and has an impact on many ontology engineering tasks. We describe a novel method for identifying and extracting conceptual components from domain ontologies, which are used to understand and compare them. The method is applied to two corpora of ontologies in the Cultural Heritage and Conference domain, respectively. The results, which show good quality, are evaluated by manual inspection and by correlation with datasets and tool performance from the ontology alignment evaluation initiative.
STFC Daresbury Laboratory（科学技术设施委员会达斯伯里实验室）；Institute of Chemical Process Fundamentals of the Czech Academy of Sciences（捷克科学院化学过程基础研究所）；WearHealth UG（威尔健康有限责任公司）；Goldbeck Consulting Ltd（戈德贝克咨询有限公司）；Osthus GmbH（奥斯特胡斯有限公司）；Fraunhofer Institute for Manufacturing Technology and Advanced Materials（弗劳恩霍夫制造技术与先进材料研究所）
The Virtual Materials Marketplace (VIMMP) project, which develops an open platform for providing and accessing services related to materials modelling, is presented with a focus on its ontology development and data technology aspects. Within VIMMP, a system of marketplace-level ontologies is developed to characterize services, models, and interactions between users; the European Materials and Modelling Ontology (EMMO) is employed as a top-level ontology. The ontologies are used to annotate data that are stored in the ZONTAL Space component of VIMMP and to support the ingest and retrieval of da…
Institute of Mathematics, Novosibirsk State University（新西伯利亚国立大学数学研究所）；Institute of Informatics Systems, Novosibirsk State University（新西伯利亚国立大学信息系统研究所）
We introduce an extension to the Protege ontology editor, which allows for discovering concept definitions, which are not explicitly present in axioms, but are logically implied by an ontology. The plugin supports ontologies formulated in the Description Logic EL, which underpins the OWL 2 EL profile of the Web Ontology Language and despite its limited expressiveness captures most of the biomedical ontologies published on the Web. The developed tool allows to verify whether a concept can be defined using a vocabulary of interest specified by a user. In particular, it allows to decide whether s…
In this paper we discuss various problems, associated to temporal phenomena. These problems include persistence and change, the integration of objects and processes, and truth-makers for temporal propositions. We propose an approach which interprets persistence as a phenomenon emanating from the activity of the mind, and which, additionally, postulates that persistence, finally, rests on personal identity. The General Formal Ontology (GFO) is a top level ontology being developed at the University of Leipzig. Top level ontologies can be roughly divided into 3D-ontologies, and 4D-ontologies. GFO…
The project of the Ontology Web Search Engine is presented in this paper. The main purpose of this paper is to develop such a project that can be easily implemented. Ontology Web Search Engine is software to look for and index ontologies in the Web. OWL (Web Ontology Languages) ontologies are meant, and they are necessary for the functioning of the SWES (Semantic Web Expert System). SWES is an expert system that will use found ontologies from the Web, generating rules from them, and will supplement its knowledge base with these generated rules. It is expected that the SWES will serve as a univ…
Aristotle University of Thessaloniki（塞萨洛尼基亚里士多德大学）
Semantic Web Rule Language (SWRL) combines OWL (Web Ontology Language) ontologies with Horn Logic rules of the Rule Markup Language (RuleML) family. Being supported by ontology editors, rule engines and ontology reasoners, it has become a very popular choice for developing rule-based applications on top of ontologies. However, SWRL is probably not go-ing to become a WWW Consortium standard, prohibiting industrial acceptance. On the other hand, SPIN (SPARQL Inferencing Notation) has become a de-facto industry standard to rep-resent SPARQL rules and constraints on Semantic Web models, building o…
The construction of an ontology of scientific knowledge objects, presented here, is part of the development of an approach oriented towards the visualization of scientific knowledge. It is motivated by the fact that the concepts that are used to organize scientific knowledge (theorem, law, experience, proof, etc.) appear in existing ontologies but that none of these ontologies is centered on this topic and presents them in a simple and easily understandable organization. This ontology has been constructed by 1) selecting concepts that appear in high level ontologies or in ontologies of knowled…
Huazhong University of Technology & Science（华中科技大学）；Western Sydney University（西悉尼大学）；University of Alberta（阿尔伯塔大学）
Existential rules, also known as data dependencies in Databases, have been recently rediscovered as a promising family of languages for Ontology-based Query Answering. In this paper, we prove that disjunctive embedded dependencies exactly capture the class of recursively enumerable ontologies in Ontology-based Conjunctive Query Answering (OCQA). Our expressive completeness result does not rely on any built-in linear order on the database. To establish the expressive completeness, we introduce a novel semantic definition for OCQA ontologies. We also show that neither the class of disjunctive tu…
Karlsruhe Institute of Technology (KIT)（卡尔斯鲁厄理工学院）
Ontologies order and interconnect knowledge of a certain field in a formal and semantic way so that they are machine-parsable. They try to define allwhere acceptable definition of concepts and objects, classify them, provide properties as well as interconnect them with relations (e.g. "A is a special case of B"). More precisely, Tom Gruber defines Ontologies as a "specification of a conceptualization; [...] a description (like a formal specification of a program) of the concepts and relationships that can exist for an agent or a community of agents." [1] An Ontology is made of Individuals whic…
A semantic approach to mapping the Provenance Ontology to Basic Formal Ontology
National Center for Ontological Research（国家本体论研究中心）；Conceptual Systems（概念系统公司）；University at Buffalo（布法罗大学）；Summit Knowledge Solutions（顶峰知识解决方案公司）；University of Vienna（维也纳大学）；Institute for Artificial Intelligence and Data Science（人工智能与数据科学研究所）
Ontologies provide a formal description of concepts and their relationships in a knowledge domain. The goal of ontology alignment is to identify semantically matching concepts and relationships across independently developed ontologies that purport to describe the same knowledge. In order to handle the widest possible class of ontologies, many alignment algorithms rely on terminological and structural meth- ods, but the often fuzzy nature of concepts complicates the matching process. However, one area that should provide clear matching solutions due to its mathematical nature, is units of meas…
University of Cape Town（开普敦大学）；Poznan University of Technology（波兹南理工大学）
Emerging ontology authoring methods to add knowledge to an ontology focus on ameliorating the validation bottleneck. The verification of the newly added axiom is still one of trying and seeing what the reasoner says, because a systematic testbed for ontology authoring is missing. We sought to address this by introducing the approach of test-driven development for ontology authoring. We specify 36 generic tests, as TBox queries and TBox axioms tested through individuals, and structure their inner workings in an `open box'-way, which cover the OWL 2 DL language features. This is implemented as a…
The Multilingual Semantic Web has been in focus for over a decade. Multilingualism in Linked Data and RDF has shown substantial adoption, but this is unclear for ontologies since the last review 15 years ago. One of the design goals for OWL was internationalisation, with the aim that an ontology is usable across languages and cultures. Much research to improve on multilingual ontologies has taken place in the meantime, and presumably multilingual linked data could use multilingual ontologies. Therefore, this review seeks to (i) elucidate and compare the modelling options for multilingual ontol…
This preprint specifies and defines all terms, properties, relationships and axioms of ThingFO (Thing Foundational Ontology) v1.3, which is a slightly updated version of its predecessor, ThingFO v1.2. It is an ontology for particular and universal Things placed at the foundational level in the context of a five-tier ontological architecture named FCD-OntoArch (Foundational, Core, Domain and instance Ontological Architecture for sciences). Figure 2 depicts its five tiers, which entail Foundational, Core, Top-Domain, Low-Domain and Instance levels. Two guidelines and three rules that guide the p…
Despite the large-scale uptake of semantic technologies in the biomedical domain, little is known about common modelling practices in published ontologies. OWL ontologies are often published only in the crude form of sets of axioms leaving the underlying design opaque. However, a principled and systematic ontology development life cycle is likely to be reflected in regularities of the ontology's emergent syntactic structure. To develop an understanding of this emergent structure, we propose to reverse-engineer ontologies taking a syntax-directed approach for identifying and analysing regularit…
RV College of Engineering（RV工程学院）；IBM Research（IBM研究院）；IIT Guwahati（印度理工学院古瓦哈蒂分校）
Ontologies comprising of concepts, their attributes, and relationships are used in many knowledge based AI systems. While there have been efforts towards populating domain specific ontologies, we examine the role of document structure in learning ontological relationships between concepts in any document corpus. Inspired by ideas from hypernym discovery and explainability, our method performs about 15 points more accurate than a stand-alone R-GCN model for this task.
Modeling an ontology is a hard and time-consuming task. Although methodologies are useful for ontologists to create good ontologies, they do not help with the task of evaluating the quality of the ontology to be reused. For these reasons, it is imperative to evaluate the quality of the ontology after constructing it or before reusing it. Few studies usually present only a set of criteria and questions, but no guidelines to evaluate the ontology. The effort to evaluate an ontology is very high as there is a huge dependence on the evaluator's expertise to understand the criteria and questions in…
