Ontology-based protein-protein interactions extraction from literature using the hidden vector state model

This paper proposes a novel framework of incorporating protein-protein interactions (PPI) ontology knowledge into PPI extraction from biomedical literature in order to address the emerging challenges of deep natural language understanding. It is built upon the existing work on relation extraction using the Hidden Vector State (HVS) model. The HVS model belongs to the category of statistical learning methods. It can be trained directly from un-annotated data in a constrained way whilst at the same time being able to capture the underlying named entity relationships. However, it is difficult to incorporate background knowledge or non-local information into the HVS model. This paper proposes to represent the HVS model as a conditionally trained undirected graphical model in which non-local features derived from PPI ontology through inference would be easily incorporated. The seamless fusion of ontology inference with statistical learning produces a new paradigm to information extraction.

A formal model of the Semantic Web Service Ontology (WSMO)

Semantic Web Service, one of the most significant research areas within the Semantic Web vision, has attracted increasing attention from both the research community and industry. The Web Service Modelling Ontology (WSMO) has been proposed as an enabling framework for the total/partial automation of the tasks (e.g., discovery, selection, composition, mediation, execution, monitoring, etc.) involved in both intra- and inter-enterprise integration of Web services. To support the standardisation and tool support of WSMO, a formal model of the language is highly desirable. As several variants of WSMO have been proposed by the WSMO community, which are still under development, the syntax and semantics of WSMO should be formally defined to facilitate easy reuse and future development. In this paper, we present a formal Object-Z formal model of WSMO, where different aspects of the language have been precisely defined within one unified framework. This model not only provides a formal unambiguous model which can be used to develop tools and facilitate future development, but as demonstrated in this paper, can be used to identify and eliminate errors present in existing documentation.

Sensing presence (PreSense) ontology : user modelling in the semantic sensor web

Increasingly, people's digital identities are attached to, and expressed through, their mobile devices. At the same time digital sensors pervade smart environments in which people are immersed. This paper explores different perspectives in which users' modelling features can be expressed through the information obtained by their attached personal sensors. We introduce the PreSense Ontology, which is designed to assign meaning to sensors' observations in terms of user modelling features. We believe that the Sensing Presence ( PreSense ) Ontology is a first step toward the integration of user modelling and "smart environments". In order to motivate our work we present a scenario and demonstrate how the ontology could be applied in order to enable context-sensitive services. © 2012 Springer-Verlag.

Ontology augmentation:combining semantic web and text resources

This work investigates the process of selecting, extracting and reorganizing content from Semantic Web information sources, to produce an ontology meeting the specifications of a particular domain and/or task. The process is combined with traditional text-based ontology learning methods to achieve tolerance to knowledge incompleteness. The paper describes the approach and presents experiments in which an ontology was built for a diet evaluation task. Although the example presented concerns the specific case of building a nutritional ontology, the methods employed are domain independent and transferrable to other use cases. © 2011 ACM.

Ontology-based knowledge capture and sharing in enterprise organisations

Despite years of effort in building organisational taxonomies, the potential of ontologies to support knowledge management in complex technical domains is under-exploited. The authors of this chapter present an approach to using rich domain ontologies to support sense-making tasks associated with resolving mechanical issues. Using Semantic Web technologies, the authors have built a framework and a suite of tools which support the whole semantic knowledge lifecycle. These are presented by describing the process of issue resolution for a simulated investigation concerning failure of bicycle brakes. Foci of the work have included ensuring that semantic tasks fit in with users’ everyday tasks, to achieve user acceptability and support the flexibility required by communities of practice with differing local sub-domains, tasks, and terminology.

Cross ontology query answering on the semantic web:an initial evaluation

PowerAqua is a Question Answering system, which takes as input a natural language query and is able to return answers drawn from relevant semantic resources found anywhere on the Semantic Web. In this paper we provide two novel contributions: First, we detail a new component of the system, the Triple Similarity Service, which is able to match queries effectively to triples found in different ontologies on the Semantic Web. Second, we provide a first evaluation of the system, which in addition to providing data about PowerAqua's competence, also gives us important insights into the issues related to using the Semantic Web as the target answer set in Question Answering. In particular, we show that, despite the problems related to the noisy and incomplete conceptualizations, which can be found on the Semantic Web, good results can already be obtained.

AquaLog : an ontology-driven question answering system for organizational semantic intranets

The semantic web vision is one in which rich, ontology-based semantic markup will become widely available. The availability of semantic markup on the web opens the way to novel, sophisticated forms of question answering. AquaLog is a portable question-answering system which takes queries expressed in natural language and an ontology as input, and returns answers drawn from one or more knowledge bases (KBs). We say that AquaLog is portable because the configuration time required to customize the system for a particular ontology is negligible. AquaLog presents an elegant solution in which different strategies are combined together in a novel way. It makes use of the GATE NLP platform, string metric algorithms, WordNet and a novel ontology-based relation similarity service to make sense of user queries with respect to the target KB. Moreover it also includes a learning component, which ensures that the performance of the system improves over the time, in response to the particular community jargon used by end users.

AquaLog : an ontology-driven question answering system to interface the semantic web

The semantic web (SW) vision is one in which rich, ontology-based semantic markup will become widely available. The availability of semantic markup on the web opens the way to novel, sophisticated forms of question answering. AquaLog is a portable question-answering system which takes queries expressed in natural language (NL) and an ontology as input, and returns answers drawn from one or more knowledge bases (KB). AquaLog presents an elegant solution in which different strategies are combined together in a novel way. AquaLog novel ontology-based relation similarity service makes sense of user queries.

Extracting significant words from corpora for ontology extraction

We show a new method for term extraction from a domain relevant corpus using natural language processing for the purposes of semi-automatic ontology learning. Literature shows that topical words occur in bursts. We find that the ranking of extracted terms is insensitive to the choice of population model, but calculating frequencies relative to the burst size rather than the document length in words yields significantly different results.

Experimental and theoretical studies on six-membered ring hydrogen bond systems in crystalline drug substances

DUE TO COPYRIGHT RESTRICTIONS ONLY AVAILABLE FOR CONSULTATION AT ASTON UNIVERSITY LIBRARY AND INFORMATION SERVICES WITH PRIOR ARRANGEMENT

Experimental and theoretical studies on molecular geometry and polymorphism in crystalline drug substances

DUE TO COPYRIGHT RESTRICTIONS ONLY AVAILABLE FOR CONSULTATION AT ASTON UNIVERSITY LIBRARY AND INFORMATION SERVICES WITH PRIOR ARRANGEMENT

Ontologies for crisis management:a review of state of the art in ontology design and usability

The growing use of a variety of information systems in crisis management both by non-governmental organizations (NGOs) and emergency management agencies makes the challenges of information sharing and interoperability increasingly important. The use of semantic web technologies is a growing area and is a technology stack specifically suited to these challenges. This paper presents a review of ontologies, vocabularies and taxonomies that are useful in crisis management systems. We identify the different subject areas relevant to crisis management based on a review of the literature. The different ontologies and vocabularies available are analysed in terms of their coverage, design and usability. We also consider the use cases for which they were designed and the degree to which they follow a variety of standards. While providing comprehensive ontologies for the crisis domain is not feasible or desirable there is considerable scope to develop ontologies for the subject areas not currently covered and for the purposes of interoperability.

Issues in learning an ontology from text

Ontology construction for any domain is a labour intensive and complex process. Any methodology that can reduce the cost and increase efficiency has the potential to make a major impact in the life sciences. This paper describes an experiment in ontology construction from text for the animal behaviour domain. Our objective was to see how much could be done in a simple and relatively rapid manner using a corpus of journal papers. We used a sequence of pre-existing text processing steps, and here describe the different choices made to clean the input, to derive a set of terms and to structure those terms in a number of hierarchies. We describe some of the challenges, especially that of focusing the ontology appropriately given a starting point of a heterogeneous corpus. Results - Using mainly automated techniques, we were able to construct an 18055 term ontology-like structure with 73% recall of animal behaviour terms, but a precision of only 26%. We were able to clean unwanted terms from the nascent ontology using lexico-syntactic patterns that tested the validity of term inclusion within the ontology. We used the same technique to test for subsumption relationships between the remaining terms to add structure to the initially broad and shallow structure we generated. All outputs are available at http://thirlmere.aston.ac.uk/~kiffer/animalbehaviour/ webcite. Conclusion - We present a systematic method for the initial steps of ontology or structured vocabulary construction for scientific domains that requires limited human effort and can make a contribution both to ontology learning and maintenance. The method is useful both for the exploration of a scientific domain and as a stepping stone towards formally rigourous ontologies. The filtering of recognised terms from a heterogeneous corpus to focus upon those that are the topic of the ontology is identified to be one of the main challenges for research in ontology learning.