Ontologies are widely used for representing domain knowledge and meta data, playing an increasingly important role in Information Systems, the Semantic Web, Bioinformatics and many other domains. However, logical reasoning that ontologies can directly support are quite limited in learning, approximation and prediction. One straightforward solution is to integrate statistical analysis and machine learning. To this end, automatically learning vector representation for knowledge of an ontology i.e.,ontology embeddinghas been widely investigated. Numerous papers have been published on ontology embedding, but a lack of systematic reviews hinders researchers from gaining a comprehensive understanding of this field. To bridge this gap, we write this survey paper, which first introduces different kinds of semantics of ontologies and formally defines ontology embedding as well as its property of faithfulness. Based on this, it systematically categorizes and analyses a relatively complete set of over 80 papers, according to the ontologies they aim at and their technical solutions including geometric modeling, sequence modeling and graph propagation. This survey also introduces the applications of ontology embedding in ontology engineering, machine learning augmentation and life sciences, presents a new library mOWL and discusses the challenges and future directions.

OWL ontologies, whose formal semantics are rooted in Description Logic (DL), have been widely used for knowledge representation. Similar to Knowledge Graphs (KGs), ontologies are often incomplete, and maintaining and constructing them has proved challenging. While classical deductive reasoning algorithms use the precise formal semantics of an ontology to predict missing facts, recent years have witnessed growing interest in inductive reasoning techniques that can derive probable facts from an ontology. Similar to KGs, a promising approach is to learn ontology embeddings in a latent vector space, while additionally ensuring they adhere to the semantics of the underlying DL. While a variety of approaches have been proposed, current ontology embedding methods suffer from several shortcomings, especially that they all fail to faithfully model one-to-many, many-to-one, and many-to-many relations and role inclusion axioms. To address this problem and improve ontology completion performance, we propose a novel ontology embedding method named Box2EL for the DL EL++, which represents both concepts and roles as boxes (i.e., axis-aligned hyperrectangles), and models inter-concept relationships using a bumping mechanism. We theoretically prove the soundness of Box2EL and conduct an extensive experimental evaluation, achieving state-of-the-art results across a variety of datasets on the tasks of subsumption prediction, role assertion prediction, and approximating deductive reasoning.

\beginabstract High quality taxonomies play a critical role in various domains such as e-commerce, web search and ontology engineering. While there has been extensive work on expanding taxonomies from externally mined data, there has been less attention paid to enriching taxonomies by exploiting existing concepts and structure within the taxonomy. In this work, we show the usefulness of this kind of enrichment, and explore its viability with a new taxonomy completion system ICON (I mplicit CON cept Insertion). ICON generates new concepts by identifying implicit concepts based on the existing concept structure, generating names for such concepts and inserting them in appropriate positions within the taxonomy. ICON integrates techniques from entity retrieval, text summary, and subsumption prediction; this modular architecture offers high flexibility while achieving state-of-the-art performance. We have evaluated ICON on two e-commerce taxonomies, and the results show that it offers significant advantages over strong baselines including recent taxonomy completion models and the large language model, ChatGPT.

Mentions of new concepts appear regularly in texts and require automated approaches to harvest and place them into Knowledge Bases (KB), e.g., ontologies and taxonomies. Existing datasets suffer from three issues, (i) mostly assuming that a new concept is pre-discovered and cannot support out-of-KB mention discovery; (ii) only using the concept label as the input along with the KB and thus lacking the contexts of a concept label; and (iii) mostly focusing on concept placement w.r.t a taxonomy of atomic concepts, instead of complex concepts, i.e., with logical operators. To address these issues, we propose a new benchmark, adapting MedMentions dataset (PubMed abstracts) with SNOMED CT versions in 2014 and 2017 under the Diseases sub-category and the broader categories of Clinical finding, Procedure, and Pharmaceutical / biologic product. We provide usage on the evaluation with the dataset for out-of-KB mention discovery and concept placement, adapting recent Large Language Model based methods.

Discovering entity mentions that are out of a Knowledge Base (KB) from texts plays a critical role in KB maintenance, but has not yet been fully explored. The current methods are mostly limited to the simple threshold-based approach and feature-based classification, and the datasets for evaluation are relatively rare. We propose BLINKout, a new BERT-based Entity Linking (EL) method which can identify mentions that do not have corresponding KB entities by matching them to a special NIL entity. To better utilize BERT, we propose new techniques including NIL entity representation and classification, with synonym enhancement. We also apply KB Pruning and Versioning strategies to automatically construct out-of-KB datasets from common in-KB EL datasets. Results on five datasets of clinical notes, biomedical publications, and Wikipedia articles in various domains show the advantages of BLINKout over existing methods to identify out-of-KB mentions for the medical ontologies, UMLS, SNOMED CT, and the general KB, WikiData.

Ontology Matching (OM) plays an important role in many domains such as bioinformatics and the Semantic Web, and its research is becoming increasingly popular, especially with the application of machine learning (ML) techniques. Although the Ontology Alignment Evaluation Initiative (OAEI) represents an impressive effort for the systematic evaluation of OM systems, it still suffers from several limitations including limited evaluation of subsumption mappings, suboptimal reference mappings, and limited support for the evaluation of ML-based systems. To tackle these limitations, we introduce five new biomedical OM tasks involving ontologies extracted from Mondo and UMLS. Each task includes both equivalence and subsumption matching; the quality of reference mappings is ensured by human curation, ontology pruning, etc.; and a comprehensive evaluation framework is proposed to measure OM performance from various perspectives for both ML-based and non-ML-based OM systems. We report evaluation results for OM systems of different types to demonstrate the usage of these resources, all of which are publicly available as part of the new Bio-ML track at OAEI 2022. Resource type: Ontology Matching Dataset License: CC BY 4.0 International DOI: https://doi.org/10.5281/zenodo.6510086 Documentation: https://krr-oxford.github.io/DeepOnto/#/om_resources OAEI track: https://www.cs.ox.ac.uk/isg/projects/ConCur/oaei/

The usefulness and usability of knowledge bases (KBs) is often limited by quality issues. One common issue is the presence of erroneous assertions, often caused by lexical or semantic confusion. We study the problem of correcting such assertions, and present a general correction framework which combines lexical matching, semantic embedding, soft constraint mining and semantic consistency checking. The framework is evaluated using DBpedia and an enterprise medical KB.

Materialisation is often used in RDF systems as a preprocessing step to derive all facts implied by given RDF triples and rules. Although widely used, materialisation considers all possible rule applications and can use a lot of memory for storing the derived facts, which can hinder performance. We present a novel materialisation technique that compresses the RDF triples so that the rules can sometimes be applied to multiple facts at once, and the derived facts can be represented using structure sharing. Our technique can thus require less space, as well as skip certain rule applications. Our experiments show that our technique can be very effective: when the rules are relatively simple, our system is both faster and requires less memory than prominent state-of-the-art RDF systems.

Query containment is a fundamental operation used to expedite query processing in view materialisation and query caching techniques. Since query containment has been shown to be NP-complete for arbitrary conjunctive queries on RDF graphs, we introduce a simpler form of conjunctive queries that we name f-graph queries. We first show that containment checking for f-graph queries can be solved in polynomial time. Based on this observation, we propose a novel indexing structure, named mv-index, that allows for fast containment checking between a single f-graph query and an arbitrary number of stored queries. Search is performed in polynomial time in the combined size of the query and the index. We then show how our algorithms and structures can be extended for arbitrary conjunctive queries on RDF graphs by introducing f-graph witnesses, i.e., f-graph representatives of conjunctive queries. F-graph witnesses have the following interesting property, a conjunctive query for RDF graphs is contained in another query only if its corresponding f-graph witness is also contained in it. The latter allows to use our indexing structure for the general case of conjunctive query containment. This translates in practice to microseconds or less for the containment test against hundreds of thousands of queries that are indexed within our structure.

Analytical workflows are heavily used in large and data intensive companies. An important application of such workflows in Siemens is equipment analytics when equipment KPIs and reports are computed by aggregating equipment's operational, master, and analytical data. In Siemens this data satisfies big data dimensions and this dependence poses significant challenges in authoring, reuse, and maintenance of analytical workflows by engineers and data scientists. In this work we propose to address these problems by relying on semantic technologies: we use ontologies to give a high level representation of equipment's operational and master data and offer a high level language to express KPIs over ontologies. We implemented our approach, integrated it with KNIME, and evaluated at Siemens. This is a preliminary work and we are excited about its further extensions.

The competitiveness of modern enterprises heavily depends on their ability to make the right business decisions by relying on efficient and timely analysis of the right business critical data. In large and data intensive companies such as Equinor, a Norwegian multinational oil and gas company with more than 20,000 employees, gathering such data is not a trivial task due to the growing size and complexity of corporate information sources. As a result, the data gathering task is often the most time-consuming part of the decision making process, in particular when it comes to the work processes of Equinor’s exploration geologists that should find in a timely manner new exploitable accumulations of oil or gas in given areas by analysing data about these areas. In this work we present our experience in addressing this data challenge tast at Equinor. We have developed and deployed at Equinor a semantic data access system that relies on the Ontology Based Data Access (OBDA) approach. Our system is based on our solid theoretical contributions and has been extensively evaluated at Equinor.

When RDF datasets become too large to be managed by centralised systems, they are often distributed in a cluster of shared-nothing servers, and queries are answered using a distributed join algorithm. Although such solutions have been extensively studied in relational and RDF databases, we argue that existing approaches exhibit two drawbacks. First, they usually decide statically(i.e., at query compile time) how to shuffle the data, which can lead to missed opportunities for local computation. Second, they often materialise large intermediate relations whose size is determined by the entire dataset (and not the data stored in each server), so these relations can easily exceed the memory of individual servers. As a possible remedy, we present a novel distributed join algorithm for RDF. Our approach decides when to shuffle data dynamically, which ensures that query answers that can be wholly produced within a server involve only local computation. It also uses a novel flow control mechanism to ensure that every query can be answered even if each server has a bounded amount of memory that is much smaller than the intermediate relations. We complement our algorithm with a new query planning approach that balances the cost of communication against the cost of local processing at each server. Moreover, as in several existing approaches, we distribute RDF data using graph partitioning so as to maximise local computation, but we refine the partitioning algorithm to produce more balanced partitions. We show empirically that our techniques can outperform the state of the art by orders of magnitude in terms of query evaluation times, network communication, and memory use. In particular, bounding the memory use in individual servers can mean the difference between success and failure for answering queries with large answer sets.

Smart factories are equipped with machines that can sense their manufacturing environments, interact with each other, and control production processes. Smooth operation of such factories requires that the machines and engineering personnel that conduct their monitoring and diagnostics share a detailed common industrial knowledge about the factory, e.g., in the form of knowledge graphs. Creation and maintenance of such knowledge is expensive and requires automation. In this work we show how machine learning that is specifically tailored towards industrial applications can help in knowledge graph completion. In particular, we show how knowledge completion can benefit from event logs that are common in smart factories. We evaluate this on the knowledge graph from a real world-inspired smart factory with encouraging results.

Faceted search is a prominent search paradigm that became the standard in many Web applications and has also been recently proposed as a suitable paradigm for exploring and querying RDF graphs. One of the main challenges that hampers usability of faceted search systems especially in the RDF context is information overload, that is, when the size of faceted interfaces becomes comparable to the size of the data over which the search is performed. In this demo we present (an extension of) our faceted search system SemFacet and focus on features that address the information overload: ranking, aggregation, and reachability. The demo attendees will be able to try our system on an RDF graph that models online shopping over a catalogs with up to millions of products.

Rule-based diagnostics of equipment is an important task in industry. In this paper we present how semantic technologies can enhance diagnostics. In particular, we present our semantic rule language sigRL that is inspired by the real diagnostic languages used in Siemens. SigRL allows to write compact yet powerful diagnostic programs by relying on a high level data independent vocabulary, diagnostic ontologies, and queries over these ontologies. We study computational complexity of SigRL: execution of diagnostic programs, provenance computation, as well as automatic verification of redundancy and inconsistency in diagnostic programs.

Rule-based diagnostics of power generating equipment is an important task in industry. In this demo we present how semantic technologies can enhance diagnostics. In particular, we present our semantic rule language sigRL that is inspired by the real diagnostic languages in Siemens. SigRL allows to write compact yet powerful diagnostic programs by relying on a high level data independent vocabulary, diagnostic ontologies, and queries over these ontologies. We present our diagnostic system SemDia. The attendees will be able to write diagnostic programs in SemDia using sigRL over 50 Siemens turbines. We also present how such programs can be automatically verified for redundancy and inconsistency. Moreover, the attendees will see the provenance service that SemDia provides to trace the origin of diagnostic results.

In the database community Polystores is an emerging and promising approach for data federation that aims at designing a unified querying layer over multiple data models. In the Semantic Web community a similar in spirit approach of Ontology-Based Data Access (OBDA) has been recently proposed, attracted a lot of attention, and proved its success in several industrial scenarios. In this paper we discuss a semantic approach to building polystores using the OBDA paradigm. We also present our system Optique that is utilized in an industrial application of performing turbine diagnostics in Siemens.

Real-time processing of data coming from multiple heterogeneous data streams and static databases is a typical task in many industrial scenarios such as diagnostics of large machines. A complex diagnostic task may require a collection of up to hundreds of queries over such data. Although many of these queries retrieve data of the same kind, such as temperature measurements, they access structurally different data sources. In this work we show how Semantic Technologies implemented in our system optique can simplify such complex diagnostics by providing an abstraction layer---ontology---that integrates heterogeneous data. In a nutshell, optique allows complex diagnostic tasks to be expressed with just a few high-level semantic queries. The system can then automatically enrich these queries, translate them into a collection with a large number of low-level data queries, and finally optimise and efficiently execute the collection in a heavily distributed environment. We will demo the benefits of optique on a real world scenario from Siemens.

Triple stores implementing the RL profile of OWL 2 are becoming increasingly popular. In contrast to unrestricted OWL 2, the RL profile is known to enjoy favourable computational properties for query answering, and state-of-the-art RL reasoners such as OWLim and Oracle's native inference engine of Oracle Spatial and Graph have proved extremely successful in industry-scale applications. The expressive restrictions imposed by OWL 2 RL may, however, be problematical for some applications. In this paper, we propose novel techniques that allow us (in many cases) to compute exact query answers using an off-the-shelf RL reasoner, even when the ontology is outside the RL profile. Furthermore, in the cases where exact query answers cannot be computed, we can still compute both lower and upper bounds on the exact answers. These bounds allow us to estimate the degree of incompleteness of the RL reasoner on the given query, and to optimise the computation of exact answers using a fully-fledged OWL 2 reasoner. A preliminary evaluation using the RDF Semantic Graph feature in Oracle Database has shown very promising results with respect to both scalability and tightness of the bounds.

Ontologies and ontology based systems are becoming increasingly important in meeting the demand for more powerful and flexible information systems. Requirements for such systems include the need to deal with incomplete and semi-structured information, to integrate information from heterogeneous sources, to employ richer and more flexible schemas, and for query answers to reflect both knowledge and data. Provision of such enhanced capabilities must, however, be in addition to, and not instead of, the well-established features of existing database systems, in particular their robust scalability. Achieving this is, of course, extremely challenging. In this talk I will present some recent research efforts that tackle this problem, including investigations of tractable fragments, new algorithmic techniques, new optimisations and the exploitation of relational database technology.

The ability to extract meaningful fragments from an ontology is key for ontology re-use. We propose a definition of a module that guarantees to completely capture the meaning of a given set of terms, i.e., to include all axioms relevant to the meaning of these terms, and study the problem of extracting minimal modules. We show that the problem of determining whether a subset of an ontology is a module for a given vocabulary is undecidable even for rather restricted sub-languages of OWL DL. Hence we propose two "approximations", i.e., alternative definitions of modules for a vocabulary that still provide the above guarantee, but that are possibly too strict, and that may thus result in larger modules: the first approximation is semantic and can be computed using existing DL reasoners; the second is syntactic, and can be computed in polynomial time. Finally, we report on an empirical evaluation of our syntactic approximation which demonstrates that the modules we extract are surprisingly small.

Schema statements in OWL are interpreted quite differently from analogous statements in relational databases. If these statements are meant to be interpreted as integrity constraints (ICs), OWL's interpretation may seem confusing and/or inappropriate. Therefore, we propose an extension of OWL with ICs that captures the intuition behind ICs in relational databases. We discuss the algorithms for checking IC satisfaction for different types of knowledge bases, and show that, if the constraints are satisfied, we can disregard them while answering a broad range of positive queries.

Semantic Web (SW) languages are supposed to be compatible with each other in a meaningful way, so as to facilitate machine understanding. Recent research, however, shows that the semantics of the standard SW annotation language RDF (as well as its ontological extension RDFS) and that of the standard SW ontology language OWL DL are not compatible with each other. This paper investigates some issues behind this incompatibility and proposes a novel modification of RDF(S) as a firm semantic foundation for many of the latest description logics-based SW ontology languages, including OWL DL. Furthermore, the bidirectional one-to-one mapping between RDFS(FA) axioms in strata 0-2 and OWL DL axioms has been established, which enables RDFS(FA)-agents and OWL DL-agents to communicate with each other more easily. As a result, the introduction of RDFS(FA) clarifies the vision of the semantic Web and solidifies RDF(S)'s proposed role as the base of the semantic Web

This paper proposes OWL FA, a decidable extension of OWL DL with the metamodeling architecture of RDFS(FA). It shows that the knowledge base satisfiability problem of OWL FA can be reduced to that of OWL DL, and compares the FA semantics with the recently proposed contextual semantics and Hilog semantics for OWL.

Classical logics and Datalog-related logics have both been proposed as underlying formalisms for the Semantic Web. Although these two different formalism groups have some commonalities, and look similar in the context of expressively-impoverished languages like RDF, their differences become apparent at more expressive language levels. After considering some of these differences, we argue that, although some of the characteristics of Datalog have their utility, the open environment of the Semantic Web is better served by standard logics.

Although the OWLWeb Ontology Language adds considerable expressive power to the Semantic Web it does have expressive limitations, particularly with respect to what can be said about properties. Wepresent ORL (OWL Rules Language), a Horn clause rules extension to OWL that overcomes many of these limitations. ORL extends OWL in a syntactically and semantically coherent manner: the basic syntax for ORL rules is an extension of the abstract syntax for OWL DL and OWLLite; ORL rules are given formal meaning via an extension of the OWLDL model-theoretic semantics; ORL rules are given an XML syntax basedon the OWL XML presentation syntax; and a mapping from ORL rules to RDF graphs is given based on the OWL RDF/XML exchange syntax. Wediscuss the expressive power of ORL, showing that the ontology consistency problem is undecidable, provide several examples of ORLusage, and discuss how reasoning support for ORL might be provided.

We show how to interoperate, semantically and inferentially, between the leading Semantic Web approaches to rules (RuleML Logic Programs) and ontologies (OWL/DAML+OIL Description Logic) via analyzing their expressive intersection. To do so, we define a new intermediate knowledge representation (KR) contained within this intersection: Description Logic Programs (DLP), and the closely related Description Horn Logic (DHL) which is an expressive fragment of first-order logic (FOL). DLP provides a significant degree of expressiveness, substantially greater than the RDF-Schema fragment of Description Logic. We show how to perform DLP-fusion: the bidirectional translation of premises and inferences (including typical kinds of queries) from the DLP fragment of DL to LP, and vice versa from the DLP fragment of LP to DL. In particular, this translation enables one to "build rules on top of ontologies": it enables the rule KR to have access to DL ontological definitions for vocabulary primitives (e.g., predicates and individual constants) used by the rules. Conversely, the DLP-fusion technique likewise enables one to "build ontologies on top of rules": it enables ontological definitions to be supplemented by rules, or imported into DL from rules. It also enables available efficient LP inferencing algorithms/implementations to be exploited for reasoning over large-scale DL ontologies.

The Semantic Web is vitally dependent on a formal meaning for the constructs of its languages. For Semantic Web languages to work well together their formal meanings must employ a common view (or thesis) of representation, otherwise it will not be possible to reconcile documents written in different languages. The thesis of representation underlying RDF and RDFS is particularly troublesome in this regard, as it has several unusual aspects, both semantic and syntactic. A more-standard thesis of representation would result in the ability to reuse existing results and tools in the Semantic Web.

An important objective of the Semantic Web is to make Electronic Commerce interactions more flexible and automated. To achieve this, standardization of ontologies, message content and message protocols will be necessary.In this paper we investigate how Semantic and Web Services technologies can be used to support service advertisement and discovery in e-commerce. In particular, we describe the design and implementation of a service matchmaking prototype which uses a DAML-S based ontology and a Description Logic reasoner to compare ontology based service descriptions. We also present the results of initial experiments testing the performance of this prototype implementation in a realistic agent based e-commerce scenario.

Article Share on Enabling knowledge representation on the Web by extending RDF schema Authors: Jeen Broekstra Aidministrator Nederland bv, Holland Aidministrator Nederland bv, HollandView Profile , Michel Klein Vrije Universiteit Amsterdam, Holland Vrije Universiteit Amsterdam, HollandView Profile , Stefan Decker Department of Computer Science, Stanford University, Stanford Department of Computer Science, Stanford University, StanfordView Profile , Dieter Fensel Vrije Universiteit Amsterdam, Holland Vrije Universiteit Amsterdam, HollandView Profile , Frank van Harmelen Vrije Universiteit Amsterdam, Holland Vrije Universiteit Amsterdam, HollandView Profile , Ian Horrocks Department of Computer Science, University of Manchester, UK Department of Computer Science, University of Manchester, UKView Profile Authors Info & Claims WWW '01: Proceedings of the 10th international conference on World Wide WebMay 2001 Pages 467–478https://doi.org/10.1145/371920.372105Online:01 April 2001Publication History 50citation1,138DownloadsMetricsTotal Citations50Total Downloads1,138Last 12 Months20Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access