The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web

Research in life sciences is increasingly being conducted in a digital and online environment. In particular, life scientists have been pioneers in embracing new computational tools to conduct their investigations. To support the sharing of digital objects produced during such research investigations, we have witnessed in the last few years the emergence of specialized repositories, e.g., DataVerse and FigShare. Such repositories provide users with the means to share and publish datasets that were used or generated in research investigations. While these repositories have proven their usefulness, interpreting and reusing evidence for most research results is a challenging task. Additional contextual descriptions are needed to understand how those results were generated and/or the circumstances under which they were concluded. Because of this, scientists are calling for models that go beyond the publication of datasets to systematically capture the life cycle of scientific investigations and provide a single entry point to access the information about the hypothesis investigated, the datasets used, the experiments carried out, the results of the experiments, the people involved in the research, etc. In this paper we present the Research Object (RO) suite of ontologies, which provide a structured container to encapsulate research data and methods along with essential metadata descriptions. Research Objects are portable units that enable the sharing, preservation, interpretation and reuse of research investigation results. The ontologies we present have been designed in the light of requirements that we gathered from life scientists. They have been built upon existing popular vocabularies to facilitate interoperability. Furthermore, we have developed tools to support the creation and sharing of Research Objects, thereby promoting and facilitating their adoption.Comment: 20 page

Developing Ontological Theories for Conceptual Models using Qualitative Research

Conceptual modelling is believed to be at the core of the IS discipline. There have been attempts to develop theoretical foundations for conceptual models, in particular ontological models as axiomatic reference systems. Although the notion of ontology has become popular in modelling theories, criticism has risen as to its philosophical presuppositions. Taking on this criticism, we discuss the task of developing socially constructed ontologies for modelling domains and outline how to enhance the expressiveness of ontological modelling theories by developing them via qualitative research methods such as Grounded Theory

Ontology as Product-Service System: Lessons Learned from GO, BFO and DOLCE

This paper defends a view of the Gene Ontology (GO) and of Basic Formal Ontology (BFO) as examples of what the manufacturing industry calls product-service systems. This means that they are products (the ontologies) bundled with a range of ontology services such as updates, training, help desk, and permanent identifiers. The paper argues that GO and BFO are contrasted in this respect with DOLCE, which approximates more closely to a scientific theory or a scientific publication. The paper provides a detailed overview of ontology services and concludes with a discussion of some implications of the product-service system approach for the understanding of the nature of applied ontology. Ontology developer communities are compared in this respect with developers of scientific theories and of standards (such as W3C). For each of these we can ask: what kinds of products do they develop and what kinds of services do they provide for the users of these products

A model for digital preservation repository risk relationships

The paper introduces the Preserved Object and Repository Risk Ontology (PORRO), a model that relates preservation functionality with associated risks and opportunities for their mitigation. Building on work undertaken in a range of EU and UK funded research projects (including the Digital Curation Centre , DigitalPreservationEurope and DELOS ), this ontology illustrates relationships between fundamental digital library goals and their parameters; associated rights and responsibilities; practical activities and resources involved in their accomplishment; and risks facing digital libraries and their collections. Its purpose is to facilitate a comprehensive understanding of risk causality and to illustrate opportunities for mitigation and avoidance. The ontology reflects evidence accumulated from a series of institutional audits and evaluations, including a specific subset of digital libraries in the DELOS project which led to the definition of a digital library preservation risk profile. Its applicability is intended to be widespread, and its coverage expected to evolve to reflect developments within the community. Attendees will gain an understanding of the model and learn how they can utilize this online resource to inform their own risk management activities

A Semantic-Based Information Management System to Support Innovative Product Design

International competition and the rapidly global economy, unified by improved communication and transportation, offer to the consumers an enormous choice of goods and services. The result is that companies now require quality, value, time to market and innovation to be successful in order to win the increasing competition. In the engineering sector this is traduced in need of optimization of the design process and in maximization of re-use of data and knowledge already existing in the company. The “SIMI-Pro” (Semantic Information Management system for Innovative Product design) system addresses specific deficiencies in the conceptual phase of product design when knowledge management, if applied, is often sectorial. Its main contribution is in allowing easy, fast and centralized collection of data from multiple sources and in supporting the retrieval and re-use of a wide range of data that will help stylists and engineers shortening the production cycle. SIMI-Pro will be one of the first prototypes to base its information management and its knowledge sharing system on process ontology and it will demonstrate how the use of centralized network systems, coupled with Semantic Web technologies, can improve inter-working activities and interdisciplinary knowledge sharing

Towards an ontology of common sense

Philosophers from Plotinus to Paul Churchland have yielded to the temptation to embrace doctrines which contradict the core beliefs of common sense. Philosophical realists have on the other hand sought to counter this temptation and to vindicate those core beliefs. The remarks which follow are to be understood as a further twist of the wheel in this never-ending battle. They pertain to the core beliefs of common sense concerning the external reality that is given in everyday experience -the beliefs of folk physics, as we might call them. Just as critics of Churchland et al. have argued that the folk-psychological ontology of beliefs, desires, etc. yields the best explanation we can have of the order of cognitive phenomena conceived from the perspective of first-person experience, so we shall argue that (1) the commonsensical ontology of folk physics yields the best explanation we can have of our externally directed cognitive experience and that (2) an ontology of mesoscopic things, events and processes must play a role, in particular, in our best scientific theory of human action

Ibuanyidanda Neotic Propaedeutic Principle as an Afrocentric Environmental Prognosis to the Problems of Climate Change in the Twenty First Century

The activities of man and other beings on a daily basis have been the primordial antecedence for the negative changes experienced in the environment today. Nature in its rudimentary state was harmless and friendly to man and its inhabitants. But owing to the egocentric approaches of man towards the environment, fundamentally for the purpose of earning a living and advancing development, man manipulates every available resources to his favor including the environment. These egomaniacal demeanor has propelled the once harmless nature to react against human beings, causing socio-economic and psychological damages. Climate change to this end has been defined as a change in oceans, land surfaces and ice sheets occurring overtime scales of decades or longer. It expresses itself in the evidence differentiation from the usual sun radiation, volcanoes, internal virility in climate system or human system. The twenty first century is facing the boomerang of the human seeds sown on the climate. It becomes imperative for Africans to align with the rest of the world in fashioning out an approach to tackle climate change and other related environmental issues, and curb the present and predicted damages. To this end the paper proposes Innocent Asouzu’s complementary Noetic Propaedeutic principle as the viable prognosis towards fostering environmental peace, mutual co-existence with all other beings within the horizon to bring about solution to climate change. The paper explores the philosophical methods of analysis and prescription in its research