OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists’ toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment. Results We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy’s capability for enriching, modifying and querying biomedical ontologies. Conclusions Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses

Subset reasoning for event-based systems

In highly dynamic domains such as the Internet of Things (IoT), smart industries, smart manufacturing, pervasive health or social media, data is being continuously generated. By combining this generated data with background knowledge and performing expressive reasoning upon this combination, meaningful decisions can be made. Furthermore, this continuously generated data typically originates from multiple heterogeneous sources. Ontologies are ideal for modeling the domain and facilitates the integration of heterogeneous produced data with background knowledge. Furthermore, expressive ontology reasoning allows to infer implicit facts and enables intelligent decision making. The data produced in these domains is often volatile. Time-critical systems, such as IoT Nurse Call systems, require timely processing of the produced IoT data. However, there is still a mismatch between volatile data and expressive ontology reasoning, since the incoming data frequency is often higher than the reasoning time. For this reason, we present an approximation technique that allows to extract a subset of data to speed-up the reasoning process. We demonstrate this technique in a Nurse Call proof of concept where the locations of the nurses are tracked and the most suited nurse is selected when the patient launches a call and in an extension of an existing benchmark. We managed to speed up the reasoning process up to 10 times for small datasets and up to more than 1000 times for large datasets

Building Data Warehouses with Semantic Web Data

The Semantic Web (SW) deployment is now a realization and the amount of semantic annotations is ever increasing thanks to several initiatives that promote a change in the current Web towards the Web of Data, where the semantics of data become explicit through data representation formats and standards such as RDF/(S) and OWL. However, such initiatives have not yet been accompanied by e cient intelligent applications that can exploit the implicit semantics and thus, provide more insightful analysis. In this paper, we provide the means for e ciently analyzing and exploring large amounts of semantic data by combining the inference power from the annotation semantics with the analysis capabilities provided by OLAP-style aggregations, navigation, and reporting. We formally present how semantic data should be organized in a well-de ned conceptual MD schema, so that sophisticated queries can be expressed and evaluated. Our proposal has been evaluated over a real biomedical scenario, which demonstrates the scalability and applicability of the proposed approach

A method to generate a modular ifcOWL ontology

Building Information Modeling (BIM) and Semantic Web technologies are becoming more and more popular in the Architecture Engineering Construction (AEC) and Facilities Management (FM) industry to support information management, information exchange and data interoperability. One of the key integration gateways between BIM and Semantic Web is represented by the ifcOWL ontology, i.e. the Web Ontology Language (OWL) version of the IFC standard, being one of reference technical standard for AEC/FM. Previous studies have shown how a recommended ifcOWL ontology can be automatically generated by converting the IFC standard from the official EXPRESS schema. However, the resulting ifcOWL is a large monolithic ontology that presents serious limitations for real industrial applications in terms of usability and performance (i.e. querying and reasoning). Possible enhancements to reduce the complexity and the data size consist in (1) modularization of ifcOWL making it easier to use subsets of the entire ontology, and (2) rethinking the contents and structure of an ontology for AEC/FM to better fit in the semantic web scope and make its usage more efficient. The second approach can be enabled by the first one, since it would make it easier to replace some of the ifcOWL modules with new optimized ontologies for the AEC-FM industry. This paper focuses on the first approach presenting a method to automatically generate a modular ifcOWL ontology. The method aims at minimizing the dependencies between modules to better exploit the modularization. The results are compared with simpler and more straight-forward solutions