PIGOK: linking protein identity to gene ontology and function

Here we introduce a computer database that allows for the rapid retrieval of physicochemical properties, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes information about a protein or a list of proteins. We applied PIGOK analyzing Schizosaccharomyces pombe proteins displaying differential expression under oxidative stress and identified their biological functions and pathways. The database is available on the Internet at http://pc4-133.ludwig.ucl.ac.uk/pigok.html.

ontoReadiness: A meta-ontology for readiness certification and career portability

This paper argues the need for the information communication technology (ICT), labor exchange (job boards), and Human Capital ontology engineers (ontoEngineers) to jointly design and socialize an upper level meta-ontology for people readiness and career portability. These enticing ontology research topics have yielded "independent" results, but have yet to meet the more broader or "universal" requirement that emerging frameworks demand. This paper will focus on the need to universally develop an upper level ontology and provide the reader concepts and models that can be transformed into marketable solutions.

Ontology supported comparison in vague domains

It is problematic to use standard ontology tools when describing vague domains. Standard ontologies are designed to formally define one view of a domain, and although it is possible to define disagreeing statements, it is not advisable, as the resulting inferences could be incorrect. Two different solutions to the above problem in two different vague domains have been developed and are presented. The first domain is the knowledge base of conversational agents (chatbots). An ontological scripting language has been designed to access ontology data from within chatbot code. The solution developed is based on reifications of user statements. It enables a new layer of logics based on the different views of the users, enabling the body of knowledge to grow automatically. The second domain is competencies and competency frameworks. An ontological framework has been developed to model different competencies using the emergent standards. It enables comparison of competencies using a mix of linguistic logics and descriptive logics. The comparison results are non-binary, therefore not simple yes and no answers, highlighting the vague nature of the comparisons. The solution has been developed with small ontologies which can be added to and modified in order for the competency user to build a total picture that fits the user’s purpose. Finally these two approaches are viewed in the light of how they could aid future work in vague domains, further work in both domains is described and also in other domains such as the semantic web. This demonstrates two different approaches to achieve inferences using standard ontology tools in vague domains.

Ontology supported competency system

Traditionally representation of competencies has been very difficult using computer-based techniques. This paper introduces competencies, how they are represented, and the related concept of competency frameworks and the difficulties in using traditional ontology techniques to formalise them. A “vaguely” formalised framework has been developed within the EU project TRACE and is presented. The framework can be used to represent different competencies and competency frameworks. Through a case study using an example from the IT sector, it is shown how these can be used by individuals and organisations to specify their individual competency needs. Furthermore it is described how these representations are used for comparisons between different specifications applying ontologies and ontology toolsets. The end result is a comparison that is not binary, but tertiary, providing “definite matches”, possible / partial matches, and “no matches” using a “traffic light” analogy.

Ontology modeling for generation of clinical pathways

Purpose: Increasing costs of health care, fuelled by demand for high quality, cost-effective healthcare has drove hospitals to streamline their patient care delivery systems. One such systematic approach is the adaptation of Clinical Pathways (CP) as a tool to increase the quality of healthcare delivery. However, most organizations still rely on are paper-based pathway guidelines or specifications, which have limitations in process management and as a result can influence patient safety outcomes. In this paper, we present a method for generating clinical pathways based on organizational semiotics by capturing knowledge from syntactic, semantic and pragmatic to social level. Design/methodology/approach: The proposed modeling approach to generation of CPs adopts organizational semiotics and enables the generation of semantically rich representation of CP knowledge. Semantic Analysis Method (SAM) is applied to explicitly represent the semantics of the concepts, their relationships and patterns of behavior in terms of an ontology chart. Norm Analysis Method (NAM) is adopted to identify and formally specify patterns of behavior and rules that govern the actions identified on the ontology chart. Information collected during semantic and norm analysis is integrated to guide the generation of CPs using best practice represented in BPMN thus enabling the automation of CP. Findings: This research confirms the necessity of taking into consideration social aspects in designing information systems and automating CP. The complexity of healthcare processes can be best tackled by analyzing stakeholders, which we treat as social agents, their goals and patterns of action within the agent network. Originality/value: The current modeling methods describe CPs from a structural aspect comprising activities, properties and interrelationships. However, these methods lack a mechanism to describe possible patterns of human behavior and the conditions under which the behavior will occur. To overcome this weakness, a semiotic approach to generation of clinical pathway is introduced. The CP generated from SAM together with norms will enrich the knowledge representation of the domain through ontology modeling, which allows the recognition of human responsibilities and obligations and more importantly, the ultimate power of decision making in exceptional circumstances.

An ontology-based approach for data integration in regionally interoperable healthcare systems

In order to best utilize the limited resource of medical resources, and to reduce the cost and improve the quality of medical treatment, we propose to build an interoperable regional healthcare systems among several levels of medical treatment organizations. In this paper, our approaches are as follows:(1) the ontology based approach is introduced as the methodology and technological solution for information integration; (2) the integration framework of data sharing among different organizations are proposed(3)the virtual database to realize data integration of hospital information system is established. Our methods realize the effective management and integration of the medical workflow and the mass information in the interoperable regional healthcare system. Furthermore, this research provides the interoperable regional healthcare system with characteristic of modularization, expansibility and the stability of the system is enhanced by hierarchy structure.

Rethinking the ontology of the shareholder model of the corporation

Purpose – The purpose of this paper is to examine the critical assumptions lying behind the Anglo American model of corporate governance. Design/methodology/approach – Literature review examining the concept of a nexus of contracts underpinning agency theory which, it is argued, act as the platform for neo-liberal corporate governance focusing on shareholder wealth creation. Findings – The paper highlights the unaddressed critical challenge of why eighteenth century ownership structures are readily adopted in the twenty-first century. Social implications – A re-examination of wealth creation and wealth redistribution. Originality/value – The paper is highly original due to the fact that few contributions have been made in the area of rethinking shareholder value.