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 placement and constraints of ontologies in this ontological architecture are documented in a separate section. Each level is populated with ontological components or, in other words, ontologies. Ontologies at the same level can be related to each other, except at the foundational level, where only the ThingFO ontology is found. In addition, ontologies' terms and relationships at lower levels can be semantically enriched by ontologies' terms and relationships from the higher levels. ThingFO and ontologies at the core level such as ProcessCO, SituationCO, among others, are domain independent or neutral. ThingFO is made up of three main concepts, namely: Thing, Thing Category, and Assertion that represents human expressions about different aspects of particular and universal Things. Figure 1 shows the conceptualization of ThingFO specified in the UML language. Note that annotations of updates from the previous version (v1.2) to the current one (v1.3) can be found in Appendix A.
The present preprint specifies and defines all Terms, Properties, Relationships and Axioms of ProcessCO (Process Core Ontology). ProcessCO is an ontology devoted mainly for Work Entities and related terms, which is placed at the core level in the context of a multilayer ontological architecture called FCD-OntoArch (Foundational, Core, and Domain Ontological Architecture for Sciences). This is a five-layered ontological architecture, which considers Foundational, Core, Domain and Instance levels, where the domain level is split down in two sub-levels, namely: Top-domain and Low-domain. Ontologi…
The current preprint is an update to SituationCO v1.1 (Situation Core Ontology), which represents its new version 1.2. It specifies and defines all the terms, properties, relationships and axioms of SituationCO v1.2, being an ontology for particular and generic Situations placed at the core level in the context of a four-layered ontological architecture called FCD-OntoArch (Foundational, Core, and Domain Ontological Architecture for Sciences). This is a four-layered ontological architecture, which considers Foundational, Core, Domain and Instance levels. In turn, the domain level is split down…
GIDIS_Web, Facultad de Ingeniería, UNLPam（GIDIS_Web，UNLPam工程学院）
This preprint specifies and defines all the Terms, Properties, and Relationships of NFRsTDO (Non-Functional Requirements Top-Domain Ontology). NFRsTDO v1.2, whose UML conceptualization is shown in Figure 1 is a slightly updated version of its predecessor, namely NFRsTDO v1.1. NFRsTDO is an ontology mainly devoted to quality (non-functional) requirements and quality/cost views, which is placed at the top-domain level in the context of a multilayer ontological architecture called FCD-OntoArch (Foundational, Core, Domain, and instance Ontological Architecture for sciences). Figure 2 depicts its f…
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…
Wright State University（莱特州立大学）；Universitas Indonesia（印度尼西亚大学）
Once the conceptual overview, in terms of a somewhat informal class diagram, has been designed in the course of engineering an ontology, the process of adding many of the appropriate logical axioms is mostly a routine task. We provide a Protege plugin which supports this task, together with a visual user interface, based on established methods for ontology design pattern modeling.
Indian Institute of Technology Madras（印度理工学院马德拉斯分校）
We investigate the problem of verbalizing Web Ontology Language (OWL) axioms of domain ontologies in this paper. The existing approaches address the problem of fidelity of verbalized OWL texts to OWL semantics by exploring different ways of expressing the same OWL axiom in various linguistic forms. They also perform grouping and aggregating of the natural language (NL) sentences that are generated corresponding to each OWL statement into a comprehensible structure. However, no efforts have been taken to try out a semantic reduction at logical level to remove redundancies and repetitions, so th…
HSE University（高等经济大学）；Institute for Information Transmission Problems（信息传输问题研究所）；King’s College London（伦敦国王学院）；Steklov Mathematical Institute（斯捷克洛夫数学研究所）；Birkbeck, University of London（伦敦大学伯贝克学院）
Our concern is the problem of efficiently determining the data complexity of answering queries mediated by description logic ontologies and constructing their optimal rewritings to standard database queries. Originated in ontology-based data access and datalog optimisation, this problem is known to be computationally very complex in general, with no explicit syntactic characterisations available. In this article, aiming to understand the fundamental roots of this difficulty, we strip the problem to the bare bones and focus on Boolean conjunctive queries mediated by a simple covering axiom stat…
Modern ontology debugging methods allow efficient identification and localization of faulty axioms defined by a user while developing an ontology. The ontology development process in this case is characterized by rather frequent and regular calls to a reasoner resulting in an early user awareness of modeling errors. In such a scenario an ontology usually includes only a small number of conflict sets, i.e. sets of axioms preserving the faults. This property allows efficient use of standard model-based diagnosis techniques based on the application of hitting set algorithms to a number of given c…
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…
Ontology Learning has been the subject of intensive study for the past decade. Researchers in this field have been motivated by the possibility of automatically building a knowledge base on top of text documents so as to support reasoning based knowledge extraction. While most works in this field have been primarily statistical (known as light-weight Ontology Learning) not much attempt has been made in axiomatic Ontology Learning (called heavy-weight Ontology Learning) from Natural Language text documents. Heavy-weight Ontology Learning supports more precise formal logic-based reasoning when c…
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…
This paper describes a new technique, called "knowledge patterns", for helping construct axiom-rich, formal ontologies, based on identifying and explicitly representing recurring patterns of knowledge (theory schemata) in the ontology, and then stating how those patterns map onto domain-specific concepts in the ontology. From a modeling perspective, knowledge patterns provide an important insight into the structure of a formal ontology: rather than viewing a formal ontology simply as a list of terms and axioms, knowledge patterns views it as a collection of abstract, modular theories (the "kno…
An Embedding-based Approach to Inconsistency-tolerant Reasoning with Inconsistent Ontologies
School of Computer Science；Engineering, Southeast University Nanjing China；School of Mathematics, Southeast University Nanjing China；School of Modern Posts \& Institute of Modern Posts, Nanjing University of Posts；Engineering, Southeast University；School of Mathematics, Southeast University
Competency Questions (CQs) are used in many ontology engineering methodologies to collect requirements and track the completeness and correctness of an ontology being constructed. Although they are frequently suggested by ontology engineering methodologies, the publicly available datasets of CQs and their formalizations in ontology query languages are very scarce. Since first efforts to automate processes utilizing CQs are being made, it is of high importance to provide large and diverse datasets to fuel these solutions. In this paper, we present BigCQ, the biggest dataset of CQ templates with…
We present a machine-readable movement writing for sleight-of-hand moves with cards -- a "Labanotation of card magic." This scheme of movement writing contains 440 categories of motion, and appears to taxonomize all card sleights that have appeared in over 1500 publications. The movement writing is axiomatized in $\mathcal{SROIQ}$(D) Description Logic, and collected formally as an Ontology of Card Sleights, a computational ontology that extends the Basic Formal Ontology and the Information Artifact Ontology. The Ontology of Card Sleights is implemented in OWL DL, a Description Logic fragment o…
Kansas State University（堪萨斯州立大学）；Michigan State University（密歇根州立大学）
Wikibase -- which is the software underlying Wikidata -- is a powerful platform for knowledge graph creation and management. However, it has been developed with a crowd-sourced knowledge graph creation scenario in mind, which in particular means that it has not been designed for use case scenarios in which a tightly controlled high-quality schema, in the form of an ontology, is to be imposed, and indeed, independently developed ontologies do not necessarily map seamlessly to the Wikibase approach. In this paper, we provide the key ingredients needed in order to combine traditional ontology mod…
In this study, we present Swift Linked Data Miner, an interruptible algorithm that can directly mine an online Linked Data source (e.g., a SPARQL endpoint) for OWL 2 EL class expressions to extend an ontology with new SubClassOf: axioms. The algorithm works by downloading only a small part of the Linked Data source at a time, building a smart index in the memory and swiftly iterating over the index to mine axioms. We propose a transformation function from mined axioms to RDF Data Shapes. We show, by means of a crowdsourcing experiment, that most of the axioms mined by Swift Linked Data Miner a…
Institute of Information Systems (IFIS)（信息系统研究所（IFIS））；University of Lübeck（吕贝克大学）
Iterated applications of belief change operators are essential for different scenarios such as that of ontology evolution where new information is not presented at once but only in piecemeal fashion within a sequence. I discuss iterated applications of so called reinterpretation operators that trace conflicts between ontologies back to the ambiguous of symbols and that provide conflict resolution strategies with bridging axioms. The discussion centers on adaptations of the classical iteration postulates according to Darwiche and Pearl. The main result of the paper is that reinterpretation oper…
Candidate axiom scoring is the task of assessing the acceptability of a candidate axiom against the evidence provided by known facts or data. The ability to score candidate axioms reliably is required for automated schema or ontology induction, but it can also be valuable for ontology and/or knowledge graph validation. Accurate axiom scoring heuristics are often computationally expensive, which is an issue if you wish to use them in iterative search techniques like level-wise generate-and-test or evolutionary algorithms, which require scoring a large number of candidate axioms. We address the …
Institute of Mathematics and Computer Science, University of Latvia（拉脱维亚大学数学与计算机科学研究所）
Ontologies are one of the core foundations of the Semantic Web. To participate in Semantic Web projects, domain experts need to be able to understand the ontologies involved. Visual notations can provide an overview of the ontology and help users to understand the connections among entities. However, the users first need to learn the visual notation before they can interpret it correctly. Controlled natural language representation would be readable right away and might be preferred in case of complex axioms, however, the structure of the ontology would remain less apparent. We propose to combi…
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…
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…
Ontology Refinement with Embeddings and LLMs: A Case Study on CASTON
University of Manchester（曼彻斯特大学）；Jönköping University（延雪平大学）；National University of Singapore（新加坡国立大学）；COMPtech i Skillingaryd AB（COMPtech i Skillingaryd AB公司）
Institute for Theoretical Computer Science（理论计算机科学研究所）；Technische Universität Dresden（德累斯顿工业大学）；Department of Computer Science（计算机科学系）；Vrije Universiteit Amsterdam（阿姆斯特丹自由大学）
The chase is a sound and complete algorithm for conjunctive query answering over ontologies of existential rules with equality. To enable its effective use, we can apply acyclicity notions; that is, sufficient conditions that guarantee chase termination. Unfortunately, most of these notions have only been defined for existential rule sets without equality. A proposed solution to circumvent this issue is to treat equality as an ordinary predicate with an explicit axiomatisation. We empirically show that this solution is not efficient in practice and propose an alternative approach. More precise…
Wright State University（莱特州立大学）；Universitas Indonesia（印度尼西亚大学）
In our experience, some ontology users find it much easier to convey logical statements using rules rather than OWL (or description logic) axioms. Based on recent theoretical developments on transformations between rules and description logics, we develop ROWL, a Protege plugin that allows users to enter OWL axioms by way of rules; the plugin then automatically converts these rules into OWL DL axioms if possible, and prompts the user in case such a conversion is not possible without weakening the semantics of the rule.
European Bioinformatics Institute（欧洲生物信息研究所）；Swiss Center for Affective Sciences, University of Geneva（日内瓦大学瑞士情感科学中心）；Royal Society of Chemistry（英国皇家化学学会）；National Institute of Standards and Technology（美国国家标准与技术研究院）；University of Maryland Baltimore County（马里兰大学巴尔的摩县分校）
The Information Artifact Ontology is an ontology in the domain of information entities. Core to the definition of what it is to be an information entity is the claim that an information entity must be `about' something, which is encoded in an axiom expressing that all information entities are about some entity. This axiom comes into conflict with ontological realism, since many information entities seem to be about non-existing entities, such as hypothetical molecules. We discuss this problem in the context of diagrams of molecules, a kind of information entity pervasively used throughout comp…
PSL University（巴黎文理研究大学）；Inria（法国国家信息与自动化研究所）；University of Bergen（卑尔根大学）；Free University of Bozen-Bolzano（博尔扎诺自由大学）；University of Milano-Bicocca（米兰比可卡大学）
Free University of Bozen-Bolzano（博尔扎诺-博岑自由大学）；Otto-von-Guericke University of Magdeburg（马格德堡奥托·冯·古里克大学）
Ontohub is a repository engine for managing distributed heterogeneous ontologies. The distributed nature enables communities to share and exchange their contributions easily. The heterogeneous nature makes it possible to integrate ontologies written in various ontology languages. Ontohub supports a wide range of formal logical and ontology languages, as well as various structuring and modularity constructs and inter-theory (concept) mappings, building on the OMG-standardized DOL language. Ontohub repositories are organised as Git repositories, thus inheriting all features of this popular versi…
Axiom pinpointing refers to the task of finding the specific axioms in an ontology which are responsible for a consequence to follow. This task has been studied, under different names, in many research areas, leading to a reformulation and reinvention of techniques. In this work, we present a general overview to axiom pinpointing, providing the basic notions, different approaches for solving it, and some variations and applications which have been considered in the literature. This should serve as a starting point for researchers interested in related problems, with an ample bibliography for d…
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 …
Indian Institute of Technology Madras（印度理工学院马德拉斯分校）
Authoring of OWL-DL ontologies is intellectually challenging and to make this process simpler, many systems accept natural language text as input. A text-based ontology authoring approach can be successful only when it is combined with an effective method for extracting ontological axioms from text. Extracting axioms from unrestricted English input is a substantially challenging task due to the richness of the language. Controlled natural languages (CNLs) have been proposed in this context and these tend to be highly restrictive. In this paper, we propose a new CNL called TEDEI (TExtual DEscri…
Université de Tunis El Manar（突尼斯埃尔马纳尔大学）；Faculté des Sciences de Tunis（突尼斯理学院）；Institut Supérieur des Langues Appliquées et d’Informatique de Béja（贝贾高等应用语言与计算机学院）
This work is done as part of a master's thesis project. The goal is to integrate two or more ontologies (of the same or close domains) in a new consistent and coherent OWL ontology to insure semantic interoperability between them. To do this, we have chosen to create a bridge ontology that includes all source ontologies and their bridging axioms in a customized way. In addition, we introduced a new criterion for obtaining an ontology of better quality (having the minimum of semantic/logical conflicts). We have also proposed new terminology and definitions that clarify the unclear and misplaced…
DELE: Deductive $\mathcal{EL}^{++}$ Embeddings for Knowledge Base Completion
Mathematical Sciences \& Engineering Division, King Abdullah University of Science；KAUST Center of Excellence for Smart Health, King Abdullah University of Science；KAUST Center of Excellence for Generative AI, King Abdullah University of Science
Enriching Ontologies with Disjointness Axioms using Large Language Models
Ghent University（根特大学）；University of Tours（图尔大学）；University of Stuttgart（斯图加特大学）；University of Cagliari（卡利亚里大学）；University of Pisa（比萨大学）；University of Bologna（博洛尼亚大学）
We study the problem of rewriting a disjunctive datalog program into plain datalog. We show that a disjunctive program is rewritable if and only if it is equivalent to a linear disjunctive program, thus providing a novel characterisation of datalog rewritability. Motivated by this result, we propose weakly linear disjunctive datalog---a novel rule-based KR language that extends both datalog and linear disjunctive datalog and for which reasoning is tractable in data complexity. We then explore applications of weakly linear programs to ontology reasoning and propose a tractable extension of OWL …
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…
Facultad de Informática（信息学院）；University of the Basque Country UPV/EHU（巴斯克地区大学）
Formal ontologies are axiomatizations in a logic-based formalism. The development of formal ontologies, and their important role in the Semantic Web area, is generating considerable research on the use of automated reasoning techniques and tools that help in ontology engineering. One of the main aims is to refine and to improve axiomatizations for enabling automated reasoning tools to efficiently infer reliable information. Defects in the axiomatization can not only cause wrong inferences, but can also hinder the inference of expected information, either by increasing the computational cost of…
We propose a new mechanism for integration of OWL ontologies using semantic import relations. In contrast to the standard OWL importing, we do not require all axioms of the imported ontologies to be taken into account for reasoning tasks, but only their logical implications over a chosen signature. This property comes natural in many ontology integration scenarios, especially when the number of ontologies is large. In this paper, we study the complexity of reasoning over ontologies with semantic import relations and establish a range of tight complexity bounds for various fragments of OWL.
This paper discusses an axiomatic approach for the integration of ontologies, an approach that extends to first order logic a previous approach (Kent 2000) based on information flow. This axiomatic approach is represented in the Information Flow Framework (IFF), a metalevel framework for organizing the information that appears in digital libraries, distributed databases and ontologies (Kent 2001). The paper argues that the integration of ontologies is the two-step process of alignment and unification. Ontological alignment consists of the sharing of common terminology and semantics through a m…
Ontologies can be a powerful tool for structuring knowledge, and they are currently the subject of extensive research. Updating the contents of an ontology or improving its interoperability with other ontologies is an important but difficult process. In this paper, we focus on the presence of vague concepts, which are pervasive in natural language, within the framework of formal ontologies. We will adopt a framework in which vagueness is captured via numerical restrictions that can be automatically adjusted. Since updating vague concepts, either through ontology alignment or ontology evolution…
European Commission, Joint Research Center (JRC)（欧盟委员会联合研究中心）
In this work, we investigate a novel semantic approach for pattern discovery in trajectories that, relying on ontologies, enhances object movement information with event semantics. The approach can be applied to the detection of movement patterns and behaviors whenever the semantics of events occurring along the trajectory is, explicitly or implicitly, available. In particular, we tested it against an exacting case scenario in maritime surveillance, i.e., the discovery of suspicious container transportations. The methodology we have developed entails the formalization of the application domain…
