In the context of the emerging Semantic Web and the quest for a common logical framework underpinning its architecture, the relation of rule-based languages such as Answer Set Programming (ASP) and ontology languages such as the Web Ontology Language (OWL) has attracted a lot of attention in the literature over the past years. With its roots in Deductive Databases and Datalog though, ASP shares much more commonality with another Semantic Web standard, namely the Simple Protocol and RDF Query Language ( (...) class='Hi'>SPARQL). In this paper, we take the recent approval of the SPARQL1.1 standard by the World Wide Web consortium (W3C) as an opportunity to introduce this standard to the Logic Programming community by providing a translation of SPARQL1.1 into ASP. In this translation, we explain and highlight peculiarities of the new W3C standard. Along the way, we survey existing literature on foundations of SPARQL and SPARQL1.1, and also combinations of SPARQL with ontology and rules languages. Thereby, apart from providing the means to implement and support SPARQL natively within Logic Programming engines and particularly ASP engines, we hope to pave the way for further research on a common logical framework for Semantic Web languages, including query languages, from an ASP point of view. (shrink)

Recently, there has been growing interest in the use of ontology as a fundamental tool for representing domain-specific conceptual models to improve the semantics, accuracy, and relevance of domain users’ query results. Although the amount of data has grown steadily over the past decade, much data shares similar characteristics that can be captured by a foundational ontology. In this paper, we show how queries based on a foundational ontology can be evaluated and their performance measured. We also present a Foundational (...) Patterns benchmark to help select the most efficient triple memory and its layout. We evaluate the foundational benchmark with both generated and real datasets for state-of-the-art triple stores. (shrink)

Great progress to digitize the world’s available Biodiversity and Biogeography data have been made recently, but managing data from many different providers and research domains still remains a challenge. A review of the current landscape of metadata standards and ontologies in Biodiversity sciences suggests that existing standards, such as the Darwin Core terminology, are inadequate for describing Biodiversity data in a semantically meaningful and computationally useful way. As a contribution to fill this gap, we present an ontology-based system, called BiGe-Onto, (...) designed to manage data together from Biodiversity and Biogeography. As data sources, we use two internationally recognized repositories: the Global Biodiversity Information Facility (GBIF) and the Ocean Biogeographic Information System (OBIS). BiGe-Onto system is composed of (i) BiGe-Onto Architecture (ii) a conceptual model called BiGe-Onto specified in OntoUML, (iii) an operational version of BiGe-Onto encoded in OWL 2, and (iv) an integrated dataset for its exploitation through a SPARQL endpoint. We will show use cases that allow researchers to answer questions that manage information from both domains. (shrink)

This article aims to explore representation of the content knowledge of historical Malay manuscripts by extracting the event features using an event ontology framework. The manuscript used during the testing is Sulalatus Salatin (Sejarah Melayu ) by Abdul Ahmad Samad and it was published at University of Malaya Digital Library database. In aligning to a domain-specific ontology, the Simple Event Model (SEM) model is adopted and an event-based ontology for historical Malay manuscripts is designed. Information extraction approach is done manually (...) to extract events from the manuscript and mapped into Protégé editor. Competency questions were constructed and submitted to the Protégé editor using SPARQL to check the ontology capability of providing answers as well as to examine its correctness. Event-based ontology model assists in discovering and representing the content knowledge of historical Malay manuscripts and supports organisation of knowledge. All the main concepts are extracted from selected Malay manuscript and 17 concepts used to develop the event-based ontology model. The knowledge was verified by three domain experts in Malay manuscript. In the findings, the interrater reliability for Event and Actor instances is 84%, which means 16% of instances and its type are incorrect and need amendment. For Place, interrater reliability is 95% and 99% for Role. Meanwhile, the experts achieved 100% agreement for Time. In addition, the experts agreed that the concepts, properties and instances for Malay Manuscript Ontology and complied with the criteria of consistency, completeness, conciseness, expandability and ease of use. The development of the event-based model of an ontology-based system with a high level of semantic granularity reflects the various cultural riches and intellectual aspect stored in Malay manuscripts. This will enable systematic research of the knowledge embedded in the manuscripts and make it widely and easily accessible by everyone. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)