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 evaluated in LOGCFL. We show experimentally feasibility and scalability of our rewritings compared to previously proposed NDL-rewritings. On the negative side, we prove that answering OMQs with tree-shaped CQs is not fixed-parameter tractable if the ontology depth or the number of leaves in the CQs is regarded as the parameter, and that answering OMQs with a fixed ontology (of infinite depth) is NP-complete for tree-shaped and LOGCFL for bounded-leaf CQs.
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 rela…
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…
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…
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…
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…
The vision of the Semantic Web is becoming a reality with billions of RDF triples being distributed over multiple queryable end-points (e.g. Linked Data). Although there has been a body of work on RDF triples persistent storage, it seems that, considering reasoning dependent queries, the problem of providing an efficient, in terms of performance, scalability and data redundancy, partitioning of the data is still open. In regards to recent data partitioning studies, it seems reasonable to think that data partitioning should be guided considering several directions (e.g. ontology, data, applicat…
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…
The RDF data model facilitates integration of diverse data available in structured and semi-structured formats. To obtain an RDF graph with a low amount of errors and internal redundancy, the chosen ontology must be consistently applied. However, with each addition of new diverse data the ontology must evolve thereby increasing its complexity, which could lead to accumulation of unintended erroneous composites. Thus, there is a need for a gatekeeping system that compares the intended content described in the ontology with the actual content of the resource. Here we present Empusa, a tool that …
LIRMM, CNRS（法国国家科学研究中心LIRMM实验室）；Birkbeck, University of London（伦敦大学伯贝克学院）；Steklov Mathematical Institute, Moscow（莫斯科斯捷克洛夫数学研究所）
We give solutions to two fundamental computational problems in ontology-based data access with the W3C standard ontology language OWL 2 QL: the succinctness problem for first-order rewritings of ontology-mediated queries (OMQs), and the complexity problem for OMQ answering. We classify OMQs according to the shape of their conjunctive queries (treewidth, the number of leaves) and the existential depth of their ontologies. For each of these classes, we determine the combined complexity of OMQ answering, and whether all OMQs in the class have polynomial-size first-order, positive existential, and…
University of Bremen（不来梅大学）；University of Liverpool（利物浦大学）
We introduce and study several notions of approximation for ontology-mediated queries based on the description logics ALC and ALCI. Our approximations are of two kinds: we may (1) replace the ontology with one formulated in a tractable ontology language such as ELI or certain TGDs and (2) replace the database with one from a tractable class such as the class of databases whose treewidth is bounded by a constant. We determine the computational complexity and the relative completeness of the resulting approximations. (Almost) all of them reduce the data complexity from coNP-complete to PTime, in…
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…
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…
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…
Despite its scientific, political, and practical value, comprehensive information about human languages, in all their variety and complexity, is not readily obtainable and searchable. One reason is that many language data are collected as audio and video recordings which imposes a challenge to document indexing and retrieval. Annotation of multimedia data provides an opportunity for making the semantics explicit and facilitates the searching of multimedia documents. We have developed OntoELAN, an ontology-based linguistic multimedia annotator that features: (1) support for loading and displayi…
