End users of recent biomedical information systems are often unaware of the storage structure and access mechanisms of the underlying data sources and can require simplified mechanisms for writing domain specific complex queries. This research aims to assist users and their applications in formulating queries without requiring complete knowledge of the information structure of underlying data sources. To achieve this, query reformulation techniques and algorithms have been developed that can interpret ontology-based search criteria and associated domain knowledge in order to reformulate a relational query. These query reformulation algorithms exploit the semantic relationships and assertion capabilities of OWL-DL based domain ontologies for query reformulation. In this paper, this approach is applied to the integrated database schema of the EU funded Health-e-Child (HeC) project with the aim of providing ontology assisted query reformulation techniques to simplify the global access that is needed to millions of medical records across the UK and Europe.
Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within these ontologies relies on the use of automated reasoning. We have developed the Aber-OWL infrastructure that provides reasoning services for bio-ontologies. Aber-OWL consists of an ontology repository, a set of web services and web interfaces that enable ontology-based semantic access to biological data and literature. Aber-OWL is freely available at http://ab…
Answering conjunctive queries (CQs) over a set of facts extended with existential rules is a prominent problem in knowledge representation and databases. This problem can be solved using the chase algorithm, which extends the given set of facts with fresh facts in order to satisfy the rules. If the chase terminates, then CQs can be evaluated directly in the resulting set of facts. The chase, however, does not terminate necessarily, and checking whether the chase terminates on a given set of rules and facts is undecidable. Numerous acyclicity notions were proposed as sufficient conditions for c…
Our concern is the overhead of answering OWL 2 QL ontology-mediated queries (OMQs) in ontology-based data access compared to evaluating their underlying tree-shaped and bounded treewidth conjunctive queries (CQs). We show that OMQs with bounded-depth ontologies have nonrecursive datalog (NDL) rewritings that can be constructed and evaluated in LOGCFL for combined complexity, even in NL if their CQs are tree-shaped with a bounded number of leaves, and so incur no overhead in complexity-theoretic terms. For OMQs with arbitrary ontologies and bounded-leaf CQs, NDL-rewritings are constructed and e…
The World Wide Web Consortium (W3C) has published several recommendations for building and storing ontologies, including the most recent OWL 2 Web Ontology Language (OWL). These initiatives have been followed by practical implementations that popularize OWL in various domains. For example, OWL has been used for conceptual modeling in industrial engineering, and its reasoning facilities are used to provide a wealth of services, e.g. model diagnosis, automated code generation, and semantic integration. More specifically, recent studies have shown that OWL is well suited for harmonizing informati…
University of Ulm（乌尔姆大学）；National Technical University of Athens（雅典国家技术大学）
The SPARQL query language is currently being extended by the World Wide Web Consortium (W3C) with so-called entailment regimes. An entailment regime defines how queries are evaluated under more expressive semantics than SPARQLs standard simple entailment, which is based on subgraph matching. The queries are very expressive since variables can occur within complex concepts and can also bind to concept or role names. In this paper, we describe a sound and complete algorithm for the OWL Direct Semantics entailment regime. We further propose several novel optimizations such as strategies for deter…
Laboratoire de Recherche en Informatique, CNRS & Université Paris-Sud（法国国家科学研究中心与巴黎南大学计算机研究实验室）；Institute for Information Transmission Problems & MIPT（信息传输问题研究所与莫斯科物理技术学院）；Steklov Mathematical Institute & National Research University Higher School of Economics（斯捷克洛夫数学研究所与高等经济大学）
This paper investigates the impact of query topology on the difficulty of answering conjunctive queries in the presence of OWL 2 QL ontologies. Our first contribution is to clarify the worst-case size of positive existential (PE), non-recursive Datalog (NDL), and first-order (FO) rewritings for various classes of tree-like conjunctive queries, ranging from linear queries to bounded treewidth queries. Perhaps our most surprising result is a superpolynomial lower bound on the size of PE-rewritings that holds already for linear queries and ontologies of depth 2. More positively, we show that poly…
Poznan University of Technology（波兹南理工大学）；University of Cape Town（开普敦大学）
Competency Questions (CQs) are natural language questions outlining and constraining the scope of knowledge represented by an ontology. Despite that CQs are a part of several ontology engineering methodologies, we have observed that the actual publication of CQs for the available ontologies is very limited and even scarcer is the publication of their respective formalisations in terms of, e.g., SPARQL queries. This paper aims to contribute to addressing the engineering shortcomings of using CQs in ontology development, to facilitate wider use of CQs. In order to understand the relation between…
Rethinking OWL Expressivity: Semantic Units for FAIR and Cognitively Interoperable Knowledge Graphs Why OWLs don't have to understand everything they say
TIB Leibniz Information Centre for Science and Technology（TIB 莱布尼茨科学技术信息中心）
Università di Napoli Federico II（那不勒斯费德里科二世大学）；University of Bordeaux（波尔多大学）；CNRS（法国国家科学研究中心）；Bordeaux INP（波尔多国立理工学院）；LaBRI（波尔多计算机科学实验室）；Sapienza Università di Roma（罗马第一大学）；Università degli Studi di Bergamo（贝加莫大学）
Controlled Query Evaluation (CQE) has been recently studied in the context of Semantic Web ontologies. The goal of CQE is concealing some query answers so as to prevent external users from inferring confidential information. In general, there exist multiple, mutually incomparable ways of concealing answers, and previous CQE approaches choose in advance which answers are visible and which are not. In this paper, instead, we study a dynamic CQE method, namely, we propose to alter the answer to the current query based on the evaluation of previous ones. We aim at a system that, besides being able…
The Web of Data is an open environment consisting of a great number of large inter-linked RDF datasets from various domains. In this environment, organizations and companies adopt the Linked Data practices utilizing Semantic Web (SW) technologies, in order to publish their data and offer SPARQL endpoints (i.e., SPARQL-based search services). On the other hand, the dominant standard for information exchange in the Web today is XML. The SW and XML worlds and their developed infrastructures are based on different data models, semantics and query languages. Thus, it is crucial to develop interoper…
Rapid growth of documents, web pages, and other types of text content is a huge challenge for the modern content management systems. One of the problems in the areas of information storage and retrieval is the lacking of semantic data. Ontologies can present knowledge in sharable and repeatedly usable manner and provide an effective way to reduce the data volume overhead by encoding the structure of a particular domain. Metadata in relational databases can be used to extract ontology from database in a special domain. According to solve the problem of sharing and reusing of data, approaches ba…
SPARQL is the standard query language for RDF graphs. In its strict instantiation, it only offers querying according to the RDF semantics and would thus ignore the semantics of data expressed with respect to (RDF) schemas or (OWL) ontologies. Several extensions to SPARQL have been proposed to query RDF data modulo RDFS, i.e., interpreting the query with RDFS semantics and/or considering external ontologies. We introduce a general framework which allows for expressing query answering modulo a particular semantics in an homogeneous way. In this paper, we discuss extensions of SPARQL that use reg…
So-called combined approaches answer a conjunctive query over a description logic ontology in three steps: first, they materialise certain consequences of the ontology and the data; second, they evaluate the query over the data; and third, they filter the result of the second phase to eliminate unsound answers. Such approaches were developed for various members of the DL-Lite and the EL families of languages, but none of them can handle ontologies containing nominals. In our work, we bridge this gap and present a combined query answering approach for ELHO---a logic that contains all features o…
We address the problem of answering Web ontology queries efficiently. An ontology is formalized as a Deductive Ontology Base (DOB), a deductive database that comprises the ontology's inference axioms and facts. A cost-based query optimization technique for DOB is presented. A hybrid cost model is proposed to estimate the cost and cardinality of basic and inferred facts. Cardinality and cost of inferred facts are estimated using an adaptive sampling technique, while techniques of traditional relational cost models are used for estimating the cost of basic facts and conjunctive ontology queries.…
In the current era, many disciplines are seen devoted towards ontology development for their domains with the intention of creating, disseminating and managing resource descriptions of their domain knowledge into machine understandable and processable manner. Ontology construction is a difficult group activity that involves many people with the different expertise. Generally, domain experts are not familiar with the ontology implementation environments and implementation experts do not have all the domain knowledge. We have designed Collaborative Business Intelligence Ontology (CBIOnt) for BI4…
The relatively recent adoption of Knowledge Graphs as an enabling technology in multiple high-profile artificial intelligence and cognitive applications has led to growing interest in the Semantic Web technology stack. Many semantics-related tools, however, are focused on serving experts with a deep understanding of semantic technologies. For example, triplification of relational data is available but there is no open source tool that allows a user unfamiliar with OWL/RDF to import data into a semantic triple store in an intuitive manner. Further, many tools require users to have a working und…
The ever-increasing amount of data in biomedical research, and in cancer research in particular, needs to be managed to support efficient data access, exchange and integration. Existing software infrastructures, such caGrid, support access to distributed information annotated with a domain ontology. However, caGrid's current querying functionality depends on the structure of individual data resources without exploiting the semantic annotations. In this paper, we present the design and development of an ontology-based querying functionality that consists of: the generation of OWL2 ontologies fr…
The logic-based machine-understandable framework of the Semantic Web often challenges naive users when they try to query ontology-based knowledge bases. Existing research efforts have approached this problem by introducing Natural Language (NL) interfaces to ontologies. These NL interfaces have the ability to construct SPARQL queries based on NL user queries. However, most efforts were restricted to queries expressed in English, and they often benefited from the advancement of English NLP tools. However, little research has been done to support querying the Arabic content on the Semantic Web b…
