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

Scientific Knowledge Object Patterns

Web technology is revolutionizing the way diverse scientific knowledge is produced and disseminated. In the past few years, a handful of discourse representation models have been proposed for the externalization of the rhetoric and argumentation captured within scientific publications. However, there hasn’t been a unified interoperable pattern that is commonly used in practice by publishers and individual users yet. In this paper, we introduce the Scientific Knowledge Object Patterns (SKO Patterns) towards a general scientific discourse representation model, especially for managing knowledge in emerging social web and semantic web. © ACM, 2011. This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version is going to be published in "Proceedings of 15th European Conference on Pattern Languages of Programs", (2011) http://portal.acm.org/event.cfm?id=RE197&CFID=8795862&CFTOKEN=1476113

Machine Science in Biomedicine: Practicalities, Pitfalls and Potential

Machine Science, or Data-driven Research, is a new and interesting scientific methodology that uses advanced computational techniques to identify, retrieve, classify and analyse data in order to generate hypotheses and develop models. In this paper we describe three recent biomedical Machine Science studies, and use these to assess the current state of the art with specific emphasis on data mining, data assessment, costs, limitations, skills and tool support

Ontology-based knowledge representation of experiment metadata in biological data mining

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes

Business Process Innovation using the Process Innovation Laboratory

Most organizations today are required not only to establish effective business processes but they are required to accommodate for changing business conditions at an increasing rate. Many business processes extend beyond the boundary of the enterprise into the supply chain and the information infrastructure therefore is critical. Today nearly every business relies on their Enterprise System (ES) for process integration and the future generations of enterprise systems will increasingly be driven by business process models. Consequently process modeling and improvement will become vital for business process innovation (BPI) in future organizations. There is a significant body of knowledge on various aspect of process innovation, e.g. on conceptual modeling, business processes, supply chains and enterprise systems. Still an overall comprehensive and consistent theoretical framework with guidelines for practical applications has not been identified. The aim of this paper is to establish a conceptual framework for business process innovation in the supply chain based on advanced enterprise systems. The main approach to business process innovation in this context is to create a new methodology for exploring process models and patterns of applications. The paper thus presents a new concept for business process innovation called the process innovation laboratory a.k.a. the Ð-Lab. The Ð-Lab is a comprehensive framework for BPI using advanced enterprise systems. The Ð-Lab is a collaborative workspace for experimenting with process models and an explorative approach to study integrated modeling in a controlled environment. The Ð-Lab facilitates innovation by using an integrated action learning approach to process modeling including contemporary technological, organizational and business perspectivesNo; keywords