The classification of gene products in the molecular biology domain: Realism, objectivity, and the limitations of the Gene Ontology

Background: Controlled vocabularies in the molecular biology domain exist to facilitate data integration across database resources. One such tool is the Gene Ontology (GO), a classification designed to act as a universal index for gene products from any species. The Gene Ontology is used extensively in annotating gene products and analysing gene expression data, yet very little research exists from a library and information science perspective exploring the design principles, philosophy and social role of ontologies in biology. Aim: To explore how molecular biologists, in creating the Gene Ontology, devised guidelines and rules for determining which scientific concepts are included in the ontology, and the criteria for how these concepts are represented. Methods: A domain analysis approach was used to devise a mixed methodology to study the design of the Gene Ontology. Concept analysis of a GO term and a critical discourse analysis of GO developer mailing list texts were used to test whether ontological realism is a tenable basis for constructing objective ontologies. A comparison of the current GO vocabulary construction guidelines and a study of the reasons why GO terms are removed from the ontology further explored the justifications for the design of the Gene Ontology. Finally, a content analysis of published GO papers examined how authors use and cite GO data and terminology. Results: Gene Ontology terms can be presented according to different epistemologies for concepts, indicating that ontological realism is not the only way objective ontologies can be designed. Social roles and the exercise of power were found to play an important role in determining ontology content, and poor synonym control, a lack of clear warrant for deciding terminology and arbitrary decisions to delete and invent new terms undermine the objectivity and universal applicability of the Gene Ontology. Authors exhibited poor compliance with GO data citation policies, and in re-wording and misquoting GO terminology, risk exacerbating the semantic problems this controlled vocabulary was designed to solve. Conclusions: The failure of the Gene Ontology to define what is meant by a molecular function, the exercise of power by GO developers in clearing contentious concepts from the ontology, and the strict adherence to ontological realism, which marginalises social and subjective ways of classifying scientific concepts, limits the utility of the ontology as a tool to unify the molecular biology domain. These limitations to the Gene Ontology design could be overcome with the development of lighter, pluralistic, user-controlled ‘open ontologies’ for gene products that can work alongside more traditional, ‘top-down’ developed vocabularies

An Ontology for Product-Service Systems

Industries are transforming their business strategy from a product-centric to a more service-centric nature by bundling products and services into integrated solutions to enhance the relationship between their customers. Since Product- Service Systems design research is currently at a rudimentary stage, the development of a robust ontology for this area would be helpful. The advantages of a standardized ontology are that it could help researchers and practitioners to communicate their views without ambiguity and thus encourage the conception and implementation of useful methods and tools. In this paper, an initial structure of a PSS ontology from the design perspective is proposed and evaluated

Pemilihan kerjaya di kalangan pelajar aliran perdagangan sekolah menengah teknik : satu kajian kes

This research is a survey to determine the career chosen of form four student in commerce streams. The important aspect of the career chosen has been divided into three, first is information about career, type of career and factor that most influence students in choosing a career. The study was conducted at Sekolah Menengah Teknik Kajang, Selangor Darul Ehsan. Thirty six form four students was chosen by using non-random sampling purpose method as respondent. All information was gather by using questionnaire. Data collected has been analyzed in form of frequency, percentage and mean. Results are performed in table and graph. The finding show that information about career have been improved in students career chosen and mass media is the main factor influencing students in choosing their career

Semantics for incident identification and resolution reports

In order to achieve a safe and systematic treatment of security protocols, organizations release a number of technical briefings describing how to detect and manage security incidents. A critical issue is that this document set may suffer from semantic deficiencies, mainly due to ambiguity or different granularity levels of description and analysis. An approach to face this problem is the use of semantic methodologies in order to provide better Knowledge Externalization from incident protocols management. In this article, we propose a method based on semantic techniques for both, analyzing and specifying (meta)security requirements on protocols used for solving security incidents. This would allow specialist getting better documentation on their intangible knowledge about them.Ministerio de Economía y Competitividad TIN2013-41086-

Run-time risk management in adaptive ICT systems

We will present results of the SERSCIS project related to risk management and mitigation strategies in adaptive multi-stakeholder ICT systems. The SERSCIS approach involves using semantic threat models to support automated design-time threat identification and mitigation analysis. The focus of this paper is the use of these models at run-time for automated threat detection and diagnosis. This is based on a combination of semantic reasoning and Bayesian inference applied to run-time system monitoring data. The resulting dynamic risk management approach is compared to a conventional ISO 27000 type approach, and validation test results presented from an Airport Collaborative Decision Making (A-CDM) scenario involving data exchange between multiple airport service providers

Capturing Scientific Knowledge on Medical Risk Factors

In this paper, we describe a model for representing scientific knowledge of risk factors in medicine in an explicit format which enables its use for automated reasoning. The resulting model supports linking the conclusions of up-to-date clinical research with data relating to individual patients. This model, which we have implemented as an ontology-based system using Linked Data, enables the capture of risk factor knowledge and serves as a translational research tool to apply that knowledge to assist with patient treatment, lifestyle, and education. Knowledge captured using this model can be disseminated for other intelligent systems to use for a variety of purposes, for example, to explore the state of the available medical knowledge

Enterprise application reuse: Semantic discovery of business grid services

Web services have emerged as a prominent paradigm for the development of distributed software systems as they provide the potential for software to be modularized in a way that functionality can be described, discovered and deployed in a platform independent manner over a network (e.g., intranets, extranets and the Internet). This paper examines an extension of this paradigm to encompass ‘Grid Services’, which enables software capabilities to be recast with an operational focus and support a heterogeneous mix of business software and data, termed a Business Grid - "the grid of semantic services". The current industrial representation of services is predominantly syntactic however, lacking the fundamental semantic underpinnings required to fulfill the goals of any semantically-oriented Grid. Consequently, the use of semantic technology in support of business software heterogeneity is investigated as a likely tool to support a diverse and distributed software inventory and user. Service discovery architecture is therefore developed that is (a) distributed in form, (2) supports distributed service knowledge and (3) automatically extends service knowledge (as greater descriptive precision is inferred from the operating application system). This discovery engine is used to execute several real-word scenarios in order to develop and test a framework for engineering such grid service knowledge. The examples presented comprise software components taken from a group of Investment Banking systems. Resulting from the research is a framework for engineering servic

Informaticology: combining Computer Science, Data Science, and Fiction Science

Motivated by an intention to remedy current complications with Dutch terminology concerning informatics, the term informaticology is positioned to denote an academic counterpart of informatics where informatics is conceived of as a container for a coherent family of practical disciplines ranging from computer engineering and software engineering to network technology, data center management, information technology, and information management in a broad sense. Informaticology escapes from the limitations of instrumental objectives and the perspective of usage that both restrict the scope of informatics. That is achieved by including fiction science in informaticology and by ranking fiction science on equal terms with computer science and data science, and framing (the study of) game design, evelopment, assessment and distribution, ranging from serious gaming to entertainment gaming, as a chapter of fiction science. A suggestion for the scope of fiction science is specified in some detail. In order to illustrate the coherence of informaticology thus conceived, a potential application of fiction to the ontology of instruction sequences and to software quality assessment is sketched, thereby highlighting a possible role of fiction (science) within informaticology but outside gaming