Alejandra Gonzalez-Beltran, Ben Tagger, Anthony Finkelstein
备注：
in Adrian Paschke, Albert Burger, Andrea Splendiani, M. Scott Marshall, Paolo Romano: Proceedings of the 3rd International Workshop on Semantic Web Applications and Tools for the Life Sciences, Berlin,Germany, December 8-10, 2010
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 from the underlying data resources metadata and a query rewriting and translation process based on reasoning, which converts a query at the domain ontology level into queries at the software infrastructure level. We present a detailed analysis of our approach as well as an extensive performance evaluation. While the implementation and evaluation was performed for the caGrid infrastructure, the approach could be applicable to other model and metadata-driven environments for data sharing.
We consider ontology-mediated queries (OMQs) based on expressive description logics of the ALC family and (unions) of conjunctive queries, studying the rewritability into OMQs based on instance queries (IQs). Our results include exact characterizations of when such a rewriting is possible and tight complexity bounds for deciding rewritability. We also give a tight complexity bound for the related problem of deciding whether a given MMSNP sentence is equivalent to a CSP.
CNRS（法国国家科学研究中心）；Université Paris Sud（巴黎南大学）；UC Santa Cruz（加州大学圣克鲁兹分校）；University of Bremen（不来梅大学）；University of Liverpool（利物浦大学）
Ontology-based data access is concerned with querying incomplete data sources in the presence of domain-specific knowledge provided by an ontology. A central notion in this setting is that of an ontology-mediated query, which is a database query coupled with an ontology. In this paper, we study several classes of ontology-mediated queries, where the database queries are given as some form of conjunctive query and the ontologies are formulated in description logics or other relevant fragments of first-order logic, such as the guarded fragment and the unary-negation fragment. The contributions o…
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…
Leipzig University（莱比锡大学）；University of Bremen（不来梅大学）
We study the evaluation of ontology-mediated queries (OMQs) on databases of bounded cliquewidth from the viewpoint of parameterized complexity theory. As the ontology language, we consider the description logics $\mathcal{ALC}$ and $\mathcal{ALCI}$ as well as the guarded two-variable fragment GF$_2$ of first-order logic. Queries are atomic queries (AQs), conjunctive queries (CQs), and unions of CQs. All studied OMQ problems are fixed-parameter linear (FPL) when the parameter is the size of the OMQ plus the cliquewidth. Our main contribution is a detailed analysis of the dependence of the runni…
In ontology-based data access, multiple data sources are integrated using an ontology and mappings. In practice, this is often achieved by a bootstrapping process, that is, the ontology and mappings are first designed to support only the most important queries over the sources and then gradually extended to enable additional queries. In this paper, we study two reasoning problems that support such an approach. The expressibility problem asks whether a given source query $q_s$ is expressible as a target query (that is, over the ontology's vocabulary) and the verification problem asks, additiona…
Millennium Institute for Foundational Research on Data（千年基础数据研究研究所）；University of Chile（智利大学）；TU Wien（维也纳工业大学）；University of Bremen（不来梅大学）；University of Edinburgh（爱丁堡大学）
We focus on ontology-mediated queries (OMQs) based on (frontier-)guarded existential rules and (unions of) conjunctive queries, and we investigate the problem of FO-rewritability, i.e., whether an OMQ can be rewritten as a first-order query. We adopt two different approaches. The first approach employs standard two-way alternating parity tree automata. Although it does not lead to a tight complexity bound, it provides a transparent solution based on widely known tools. The second approach relies on a sophisticated automata model, known as cost automata. This allows us to show that our problem …
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…
Peking University Shenzhen Graduate School（北京大学深圳研究生院）；Université du Havre（勒阿弗尔大学）；Université Paris Ouest（巴黎第十大学（巴黎西部大学））；IER Business Development Center（IER业务发展中心）
Decision support is a probabilistic and quantitative method designed for modeling problems in situations with ambiguity. Computer technology can be employed to provide clinical decision support and treatment recommendations. The problem of natural language applications is that they lack formality and the interpretation is not consistent. Conversely, ontologies can capture the intended meaning and specify modeling primitives. Disease Ontology (DO) that pertains to cancer's clinical stages and their corresponding information components is utilized to improve the reasoning ability of a decision s…
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 …
Birkbeck, University of London（伦敦大学伯贝克学院）；University of Oxford（牛津大学）；University of Warsaw（华沙大学）
We investigate the data complexity of answering queries mediated by metric temporal logic ontologies under the event-based semantics assuming that data instances are finite timed words timestamped with binary fractions. We identify classes of ontology-mediated queries answering which can be done in AC0, NC1, L, NL, P, and coNP for data complexity, provide their rewritings to first-order logic and its extensions with primitive recursion, transitive closure or datalog, and establish lower complexity bounds.
Center for Semantic Web Research（语义网研究中心）；University of Chile（智利大学）；TU Wien（维也纳工业大学）；University of Edinburgh（爱丁堡大学）
Many efforts have been dedicated to identifying restrictions on ontologies expressed as tuple-generating dependencies (tgds), a.k.a. existential rules, that lead to the decidability for the problem of answering ontology-mediated queries (OMQs). This has given rise to three families of formalisms: guarded, non-recursive, and sticky sets of tgds. In this work, we study the containment problem for OMQs expressed in such formalisms, which is a key ingredient for solving static analysis tasks associated with them. Our main contribution is the development of specially tailored techniques for OMQ con…
DCC, U of Chile & IMFD Chile（智利大学计算机系与智利千年数据基金会）；University of Bremen（不来梅大学）；University of Edinburgh（爱丁堡大学）
In ontology-mediated querying, description logic (DL) ontologies are used to enrich incomplete data with domain knowledge which results in more complete answers to queries. However, the evaluation of ontology-mediated queries (OMQs) over relational databases is computationally hard. This raises the question when OMQ evaluation is efficient, in the sense of being tractable in combined complexity or fixed-parameter tractable. We study this question for a range of ontology-mediated query languages based on several important and widely-used DLs, using unions of conjunctive queries as the actual qu…
We provide an ultimately fine-grained analysis of the data complexity and rewritability of ontology-mediated queries (OMQs) based on an EL ontology and a conjunctive query (CQ). Our main results are that every such OMQ is in AC0, NL-complete, or PTime-complete and that containment in NL coincides with rewritability into linear Datalog (whereas containment in AC0 coincides with rewritability into first-order logic). We establish natural characterizations of the three cases in terms of bounded depth and (un)bounded pathwidth, and show that every of the associated meta problems such as deciding w…
With the rapid advancements in cancer research, the information that is useful for characterizing disease, staging tumors, and creating treatment and survivorship plans has been changing at a pace that creates challenges when physicians try to remain current. One example involves increasing usage of biomarkers when characterizing the pathologic prognostic stage of a breast tumor. We present our semantic technology approach to support cancer characterization and demonstrate it in our end-to-end prototype system that collects the newest breast cancer staging criteria from authoritative oncology …
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…
Tianjin University（天津大学）；Western Sydney University（西悉尼大学）；Huazhong University of Technology and Science（华中科技大学）；University of Alberta（阿尔伯塔大学）；Nankai University（南开大学）
An ontology language for ontology mediated query answering (OMQA-language) is universal for a family of OMQA-languages if it is the most expressive one among this family. In this paper, we focus on three families of tractable OMQA-languages, including first-order rewritable languages and languages whose data complexity of the query answering is in AC0 or PTIME. On the negative side, we prove that there is, in general, no universal language for each of these families of languages. On the positive side, we propose a novel property, the locality, to approximate the first-order rewritability, and …
Ontology-based data access (OBDA) is a popular approach for integrating and querying multiple data sources by means of a shared ontology. The ontology is linked to the sources using mappings, which assign views over the data to ontology predicates. Motivated by the need for OBDA systems supporting database-style aggregate queries, we propose a bag semantics for OBDA, where duplicate tuples in the views defined by the mappings are retained, as is the case in standard databases. We show that bag semantics makes conjunctive query answering in OBDA coNP-hard in data complexity. To regain tractabil…
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…
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…
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…
Ho Chi Minh City University of Technology（胡志明市理工大学）
Traditional information retrieval systems represent documents and queries by keyword sets. However, the content of a document or a query is mainly defined by both keywords and named entities occurring in it. Named entities have ontological features, namely, their aliases, classes, and identifiers, which are hidden from their textual appearance. Besides, the meaning of a query may imply latent named entities that are related to the apparent ones in the query. We propose an ontology-based generalized vector space model to semantic text search. It exploits ontological features of named entities a…
University of Oslo（奥斯陆大学）；Free University of Bozen-Bolzano（博尔扎诺自由大学）
In Ontology Based Data Access (OBDA) users pose SPARQL queries over an ontology that lies on top of relational datasources. These queries are translated on-the-fly into SQL queries by OBDA systems. Standard SPARQL-to-SQL translation techniques in OBDA often produce SQL queries containing redundant joins and unions, even after a number of semantic and structural optimizations. These redundancies are detrimental to the performance of query answering, especially in complex industrial OBDA scenarios with large enterprise databases. To address this issue, we introduce two novel notions of OBDA cons…
Institute of Information Systems (IFIS)（信息系统研究所）；University of Lübeck（吕贝克大学）
Bounded-memory computability continues to be in the focus of those areas of AI and databases that deal with feasible computations over streams---be it feasible arithmetical calculations on low-level streams or feasible query answering for declaratively specified queries on relational data streams or even feasible query answering for high-level queries on streams w.r.t. a set of constraints in an ontology such as in the paradigm of Ontology-Based Data Access (OBDA). In classical OBDA, a high-level query is answered by transforming it into a query on data source level. The transformation require…
A prominent approach to implementing ontology-mediated queries (OMQs) is to rewrite into a first-order query, which is then executed using a conventional SQL database system. We consider the case where the ontology is formulated in the description logic EL and the actual query is a conjunctive query and show that rewritings of such OMQs can be efficiently computed in practice, in a sound and complete way. Our approach combines a reduction with a decomposed backwards chaining algorithm for OMQs that are based on the simpler atomic queries, also illuminating the relationship between first-order …
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 …
University of Montpellier（蒙彼利埃大学）；University of Edinburgh（爱丁堡大学）
In the presence of inconsistencies, repair techniques thrive to restore consistency by reasoning with several repairs. However, since the number of repairs can be large, standard inconsistent tolerant semantics usually yield few answers. In this paper, we use the notion of syntactic distance between repairs following the intuition that it can allow us to cluster some repairs "close" to each other. In this way, we propose a generic framework to answer queries in a more personalise fashion.
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…
In ontology-based data access (OBDA), ontologies have been successfully employed for querying possibly unstructured and incomplete data. In this paper, we advocate using ontologies not only to formulate queries and compute their answers, but also for modifying queries by relaxing or restraining them, so that they can retrieve either more or less answers over a given dataset. Towards this goal, we first illustrate that some domain knowledge that could be naturally leveraged in OBDA can be expressed using complex role inclusions (CRI). Queries over ontologies with CRI are not first-order (FO) re…
Bosch Center for Artificial Intelligence（博世人工智能中心）；Oslo Metropolitan University（奥斯陆城市大学）；University of Oslo（奥斯陆大学）；Nanjing University（南京大学）；City, University of London（伦敦城市大学）
Industrial analytics that includes among others equipment diagnosis and anomaly detection heavily relies on integration of heterogeneous production data. Knowledge Graphs (KGs) as the data format and ontologies as the unified data schemata are a prominent solution that offers high quality data integration and a convenient and standardised way to exchange data and to layer analytical applications over it. However, poor design of ontologies of high degree of mismatch between them and industrial data naturally lead to KGs of low quality that impede the adoption and scalability of industrial analy…
Currently, the text document retrieval systems have many challenges in exploring the semantics of queries and documents. Each query implies information which does not appear in the query but the documents related with the information are also expected by user. The disadvantage of the previous spreading activation algorithms could be many irrelevant concepts added to the query. In this paper, a proposed novel algorithm is only activate and add to the query named entities which are related with original entities in the query and explicit relations in the query.
RWTH Aachen University（亚琛工业大学）；Fraunhofer FIT（弗劳恩霍夫应用信息技术研究所）；ZBMED - Information Center for Life Sciences（ZB MED——生命科学信息中心）；University of Cologne（科隆大学）
Structured and unstructured data and facts about drugs, genes, protein, viruses, and their mechanism are spread across a huge number of scientific articles. These articles are a large-scale knowledge source and can have a huge impact on disseminating knowledge about the mechanisms of certain biological processes. A domain-specific knowledge graph~(KG) is an explicit conceptualization of a specific subject-matter domain represented w.r.t semantically interrelated entities and relations. A KG can be constructed by integrating such facts and data and be used for data integration, exploration, and…
University of Warsaw（华沙大学）；Cardiff University（卡迪夫大学）
We study the problem of finite entailment of ontology-mediated queries. Going beyond local queries, we allow transitive closure over roles. We focus on ontologies formulated in the description logics ALCOI and ALCOQ, extended with transitive closure. For both logics, we show 2EXPTIME upper bounds for finite entailment of unions of conjunctive queries with transitive closure. We also provide a matching lower bound by showing that finite entailment of conjunctive queries with transitive closure in ALC is 2EXPTIME-hard.
Free University of Bozen-Bolzano（博尔扎诺自由大学）；University of Liverpool（利物浦大学）；Birkbeck, University of London（伦敦大学伯贝克学院）
Our aim is to investigate ontology-based data access over temporal data with validity time and ontologies capable of temporal conceptual modelling. To this end, we design a temporal description logic, TQL, that extends the standard ontology language OWL 2 QL, provides basic means for temporal conceptual modelling and ensures first-order rewritability of conjunctive queries for suitably defined data instances with validity time.
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 …
We study a logic-based approach to versioning of ontologies. Under this view, ontologies provide answers to queries about some vocabulary of interest. The difference between two versions of an ontology is given by the set of queries that receive different answers. We investigate this approach for terminologies given in the description logic EL extended with role inclusions and domain and range restrictions for three distinct types of queries: subsumption, instance, and conjunctive queries. In all three cases, we present polynomial-time algorithms that decide whether two terminologies give the …
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）；Faculté des Sciences Économiques et de Gestion de Tunis（突尼斯经济与管理科学学院）；Faculté des Sciences juridique Économique et de Gestion de Jendouba（坚杜拜法律经济与管理科学学院）
This work is done as part of a research master's thesis project. The goal is to generate SPARQL queries based on user-supplied keywords to query RDF graphs. To do this, we first transformed the input ontology into an RDF graph that reflects the semantics represented in the ontology. Subsequently, we stored this RDF graph in the Neo4j graphical database to ensure efficient and persistent management of RDF data. At the time of the interrogation, we studied the different possible and desired interpretations of the request originally made by the user. We have also proposed to carry out a sort of t…
Univ. 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（波尔多大学计算机科学研究所）；IIT Bombay（印度理工学院孟买分校）；University of Bayreuth（拜罗伊特大学）
Testing containment of queries is a fundamental reasoning task in knowledge representation. We study here the containment problem for Conjunctive Regular Path Queries (CRPQs), a navigational query language extensively used in ontology and graph database querying. While it is known that containment of CRPQs is expspace-complete in general, we focus here on severely restricted fragments, which are known to be highly relevant in practice according to several recent studies. We obtain a detailed overview of the complexity of the containment problem, depending on the features used in the regular ex…
University of Toronto, Faculty of Information（多伦多大学信息学院）
This paper reconstructs the Freebase data dumps to understand the underlying ontology behind Google's semantic search feature. The Freebase knowledge base was a major Semantic Web and linked data technology that was acquired by Google in 2010 to support the Google Knowledge Graph, the backend for Google search results that include structured answers to queries instead of a series of links to external resources. After its shutdown in 2016, Freebase is contained in a data dump of 1.9 billion Resource Description Format (RDF) triples. A recomposition of the Freebase ontology will be analyzed in r…
Entity-based semantic search has been widely adopted in modern search engines to improve search accuracy by understanding users' intent. In e-commerce, an accurate and complete product type (PT) ontology is essential for recognizing product entities in queries and retrieving relevant products from catalog. However, finding product types (PTs) to construct such an ontology is usually expensive due to the considerable amount of human efforts it may involve. In this work, we propose an active learning framework that efficiently utilizes domain experts' knowledge for PT discovery. We also show the…
The temporal phenomena have many facets that are studied by different communities. In Semantic Web, large heterogeneous data are handled and produced. These data often have informal, semi-formal or formal temporal information which must be interpreted by software agents. In this paper we present Human Time Ontology (HuTO) an RDFS ontology to annotate and represent temporal data. A major contribution of HuTO is the modeling of non-convex intervals giving the ability to write queries for this kind of interval. HuTO also incorporates normalization and reasoning rules to explicit certain informati…
We introduce novel mathematical models and algorithms to generate (shortest or k different) explanations for biomedical queries, using answer set programming. We implement these algorithms and integrate them in BIOQUERY-ASP. We illustrate the usefulness of these methods with some complex biomedical queries related to drug discovery, over the biomedical knowledge resources PHARMGKB, DRUGBANK, BIOGRID, CTD, SIDER, DISEASE ONTOLOGY and ORPHADATA. To appear in Theory and Practice of Logic Programming (TPLP).
University of Liverpool（利物浦大学）；University of Bremen（不来梅大学）
We study the complexity of ontology-mediated querying when ontologies are formulated in the guarded fragment of first-order logic (GF). Our general aim is to classify the data complexity on the level of ontologies where query evaluation w.r.t. an ontology O is considered to be in PTime if all (unions of conjunctive) queries can be evaluated in PTime w.r.t. O and coNP-hard if at least one query is coNP-hard w.r.t. O. We identify several large and relevant fragments of GF that enjoy a dichotomy between PTime and coNP, some of them additionally admitting a form of counting. In fact, almost all on…
Presently, a very large number of public and private data sets are available around the local governments. In most cases, they are not semantically interoperable and a huge human effort is needed to create integrated ontologies and knowledge base for smart city. Smart City ontology is not yet standardized, and a lot of research work is needed to identify models that can easily support the data reconciliation, the management of the complexity and reasoning. In this paper, a system for data ingestion and reconciliation smart cities related aspects as road graph, services available on the roads, …
