A rule-based ontological framework for the classification of molecules

BACKGROUND: A variety of key activities within life sciences research involves integrating and intelligently managing large amounts of biochemical information. Semantic technologies provide an intuitive way to organise and sift through these rapidly growing datasets via the design and maintenance of ontology-supported knowledge bases. To this end, OWL-a W3C standard declarative language- has been extensively used in the deployment of biochemical ontologies that can be conveniently organised using the classification facilities of OWL-based tools. One of the most established ontologies for the chemical domain is ChEBI, an open-access dictionary of molecular entities that supplies high quality annotation and taxonomical information for biologically relevant compounds. However, ChEBI is being manually expanded which hinders its potential to grow due to the limited availability of human resources. RESULTS: In this work, we describe a prototype that performs automatic classification of chemical compounds. The software we present implements a sound and complete reasoning procedure of a formalism that extends datalog and builds upon an off-the-shelf deductive database system. We capture a wide range of chemical classes that are not expressible with OWL-based formalisms such as cyclic molecules, saturated molecules and alkanes. Furthermore, we describe a surface 'less-logician-like' syntax that allows application experts to create ontological descriptions of complex biochemical objects without prior knowledge of logic. In terms of performance, a noticeable improvement is observed in comparison with previous approaches. Our evaluation has discovered subsumptions that are missing from the manually curated ChEBI ontology as well as discrepancies with respect to existing subclass relations. We illustrate thus the potential of an ontology language suitable for the life sciences domain that exhibits a favourable balance between expressive power and practical feasibility. CONCLUSIONS: Our proposed methodology can form the basis of an ontology-mediated application to assist biocurators in the production of complete and error-free taxonomies. Moreover, such a tool could contribute to a more rapid development of the ChEBI ontology and to the efforts of the ChEBI team to make annotated chemical datasets available to the public. From a modelling point of view, our approach could stimulate the adoption of a different and expressive reasoning paradigm based on rules for which state-of-the-art and highly optimised reasoners are available; it could thus pave the way for the representation of a broader spectrum of life sciences and biomedical knowledge.</p

Ontology evaluation approach for semantic web documents

Ontology is a conceptual tool used for managing and capturing information related to domain knowledge, such as the travel, education and medical domains. Publicly available ontology repositories like Falcons and SWOOGLE enhance the growth of ontology on the Web by providing a medium for ontology developers to publish their ontologies. In order to promote ontology reuse, a suitable approach for ontology evaluation is required that deals with ontology coverage for domain representation which includes an approach for validating the ontology with a corpus of information containing terms related to domain knowledge. Since contributions in ontology evaluation were introduced in different aspects, it is important to conceptualise related information to build an evaluation approach that can help users to select ontology. This work proposed OntoUji, an ontology that conceptualises information related to ontology evaluation. From OntoUji conceptualisation, these works proceed with the development of evaluation steps that are then converted into ontology evaluation algorithms to evaluate ontology documents retrieved from selected repositories according to data-driven evaluation approach. The data-driven approach focuses on evaluating the coverage of ontology using a set of keywords provided, yet similarly involves a comparison of ontological vocabulary with a pre-defined corpus, WordNet, gained from the information retrieval approach. The evaluation is then processed using Letters Pair Similarity algorithm as the selected similarity measures technique to process the ontology coverage result. The findings showed that the OntoUji ontology conceptualization helps to define ontology evaluation steps to gain similarity result for ontology selection

Knowledge Components and Methods for Policy Propagation in Data Flows

Data-oriented systems and applications are at the centre of current developments of the World Wide Web (WWW). On the Web of Data (WoD), information sources can be accessed and processed for many purposes. Users need to be aware of any licences or terms of use, which are associated with the data sources they want to use. Conversely, publishers need support in assigning the appropriate policies alongside the data they distribute. In this work, we tackle the problem of policy propagation in data flows - an expression that refers to the way data is consumed, manipulated and produced within processes. We pose the question of what kind of components are required, and how they can be acquired, managed, and deployed, to support users on deciding what policies propagate to the output of a data-intensive system from the ones associated with its input. We observe three scenarios: applications of the Semantic Web, workflow reuse in Open Science, and the exploitation of urban data in City Data Hubs. Starting from the analysis of Semantic Web applications, we propose a data-centric approach to semantically describe processes as data flows: the Datanode ontology, which comprises a hierarchy of the possible relations between data objects. By means of Policy Propagation Rules, it is possible to link data flow steps and policies derivable from semantic descriptions of data licences. We show how these components can be designed, how they can be effectively managed, and how to reason efficiently with them. In a second phase, the developed components are verified using a Smart City Data Hub as a case study, where we developed an end-to-end solution for policy propagation. Finally, we evaluate our approach and report on a user study aimed at assessing both the quality and the value of the proposed solution

A process model in platform independent and neutral formal representation for design engineering automation

An engineering design process as part of product development (PD) needs to satisfy ever-changing customer demands by striking a balance between time, cost and quality. In order to achieve a faster lead-time, improved quality and reduced PD costs for increased profits, automation methods have been developed with the help of virtual engineering. There are various methods of achieving Design Engineering Automation (DEA) with Computer-Aided (CAx) tools such as CAD/CAE/CAM, Product Lifecycle Management (PLM) and Knowledge Based Engineering (KBE). For example, Computer Aided Design (CAD) tools enable Geometry Automation (GA), PLM systems allow for sharing and exchange of product knowledge throughout the PD lifecycle. Traditional automation methods are specific to individual products and are hard-coded and bound by the proprietary tool format. Also, existing CAx tools and PLM systems offer bespoke islands of automation as compared to KBE. KBE as a design method incorporates complete design intent by including re-usable geometric, non-geometric product knowledge as well as engineering process knowledge for DEA including various processes such as mechanical design, analysis and manufacturing. It has been recognised, through an extensive literature review, that a research gap exists in the form of a generic and structured method of knowledge modelling, both informal and formal modelling, of mechanical design process with manufacturing knowledge (DFM/DFA) as part of model based systems engineering (MBSE) for DEA with a KBE approach. There is a lack of a structured technique for knowledge modelling, which can provide a standardised method to use platform independent and neutral formal standards for DEA with generative modelling for mechanical product design process and DFM with preserved semantics. The neutral formal representation through computer or machine understandable format provides open standard usage. This thesis provides a contribution to knowledge by addressing this gap in two-steps: • In the first step, a coherent process model, GPM-DEA is developed as part of MBSE which can be used for modelling of mechanical design with manufacturing knowledge utilising hybrid approach, based on strengths of existing modelling standards such as IDEF0, UML, SysML and addition of constructs as per author’s Metamodel. The structured process model is highly granular with complex interdependencies such as activities, object, function, rule association and includes the effect of the process model on the product at both component and geometric attributes. • In the second step, a method is provided to map the schema of the process model to equivalent platform independent and neutral formal standards using OWL/SWRL ontology for system development using Protégé tool, enabling machine interpretability with semantic clarity for DEA with generative modelling by building queries and reasoning on set of generic SWRL functions developed by the author. Model development has been performed with the aid of literature analysis and pilot use-cases. Experimental verification with test use-cases has confirmed the reasoning and querying capability on formal axioms in generating accurate results. Some of the other key strengths are that knowledgebase is generic, scalable and extensible, hence provides re-usability and wider design space exploration. The generative modelling capability allows the model to generate activities and objects based on functional requirements of the mechanical design process with DFM/DFA and rules based on logic. With the help of application programming interface, a platform specific DEA system such as a KBE tool or a CAD tool enabling GA and a web page incorporating engineering knowledge for decision support can consume relevant part of the knowledgebase

A Syntax for Rules in OWL 2

Abstract. Being able to extend an OWL ontology with some form of rules is a feature that many ontology developers consider as very impor-tant. Nevertheless, working with rules in practice can be difficult since the tool support is not as good as for handling ontologies without rules. Furthermore, the existing rule syntaxes are not very well aligned with the new OWL 2 standard. We propose, therefore, an extension to OWL 2 for representing rules, which is directly inspired by (DL Safe) SWRL rules, but uses and extends the succinct and human-readable functional-style syntax of OWL 2. We also propose an OWL/XML version of the syntax to allow for easy XML serialization. Support for parsing such rules has been added to the new OWL API 3.0 and reasoning over ontologies ex-tended with these rules is possible with the two OWL 2 reasoners Pellet and HermiT. In HermiT, these rules can also be used in conjunction with Description Graphs.