Philosophy of Blockchain Technology - Ontologies

About the necessity and usefulness of developing a philosophy specific to the blockchain technology, emphasizing on the ontological aspects. After an Introduction that highlights the main philosophical directions for this emerging technology, in Blockchain Technology I explain the way the blockchain works, discussing ontological development directions of this technology in Designing and Modeling. The next section is dedicated to the main application of blockchain technology, Bitcoin, with the social implications of this cryptocurrency. There follows a section of Philosophy in which I identify the blockchain technology with the concept of heterotopia developed by Michel Foucault and I interpret it in the light of the notational technology developed by Nelson Goodman as a notational system. In the Ontology section, I present two developmental paths that I consider important: Narrative Ontology, based on the idea of order and structure of history transmitted through Paul Ricoeur's narrative history, and the Enterprise Ontology system based on concepts and models of an enterprise, specific to the semantic web, and which I consider to be the most well developed and which will probably become the formal ontological system, at least in terms of the economic and legal aspects of blockchain technology. In Conclusions I am talking about the future directions of developing the blockchain technology philosophy in general as an explanatory and robust theory from a phenomenologically consistent point of view, which allows testability and ontologies in particular, arguing for the need of a global adoption of an ontological system for develop cross-cutting solutions and to make this technology profitable. CONTENTS: Abstract Introducere Tehnologia blockchain - Proiectare - Modele Bitcoin Filosofia Ontologii - Ontologii narative - Ontologii de intreprindere Concluzii Note Bibliografie DOI: 10.13140/RG.2.2.24510.3360

A semantic web framework to integrate cancer omics data with biological knowledge

BACKGROUND: The RDF triple provides a simple linguistic means of describing limitless types of information. Triples can be flexibly combined into a unified data source we call a semantic model. Semantic models open new possibilities for the integration of variegated biological data. We use Semantic Web technology to explicate high throughput clinical data in the context of fundamental biological knowledge. We have extended Corvus, a data warehouse which provides a uniform interface to various forms of Omics data, by providing a SPARQL endpoint. With the querying and reasoning tools made possible by the Semantic Web, we were able to explore quantitative semantic models retrieved from Corvus in the light of systematic biological knowledge. RESULTS: For this paper, we merged semantic models containing genomic, transcriptomic and epigenomic data from melanoma samples with two semantic models of functional data - one containing Gene Ontology (GO) data, the other, regulatory networks constructed from transcription factor binding information. These two semantic models were created in an ad hoc manner but support a common interface for integration with the quantitative semantic models. Such combined semantic models allow us to pose significant translational medicine questions. Here, we study the interplay between a cell's molecular state and its response to anti-cancer therapy by exploring the resistance of cancer cells to Decitabine, a demethylating agent. CONCLUSIONS: We were able to generate a testable hypothesis to explain how Decitabine fights cancer - namely, that it targets apoptosis-related gene promoters predominantly in Decitabine-sensitive cell lines, thus conveying its cytotoxic effect by activating the apoptosis pathway. Our research provides a framework whereby similar hypotheses can be developed easily

A Two-Level Identity Model To Support Interoperability of Identity Information in Electronic Health Record Systems.

The sharing and retrieval of health information for an electronic health record (EHR) across distributed systems involves a range of identified entities that are possible subjects of documentation (e.g., specimen, clinical analyser). Contemporary EHR specifications limit the types of entities that can be the subject of a record to health professionals and patients, thus limiting the use of two level models in healthcare information systems that contribute information to the EHR. The literature describes several information modelling approaches for EHRs, including so called “two level models”. These models differ in the amount of structure imposed on the information to be recorded, but they generally require the health documentation process for the EHR to focus exclusively on the patient as the subject of care and this definition is often a fixed one. In this thesis, the author introduces a new identity modelling approach to create a generalised reference model for sharing archetype-constrained identity information between diverse identity domains, models and services, while permitting reuse of published standard-based archetypes. The author evaluates its use for expressing the major types of existing demographic reference models in an extensible way, and show its application for standards-compliant two-level modelling alongside heterogeneous demographics models. This thesis demonstrates how the two-level modelling approach that is used for EHRs could be adapted and reapplied to provide a highly-flexible and expressive means for representing subjects of information in allied health settings that support the healthcare process, such as the laboratory domain. By relying on the two level modelling approach for representing identity, the proposed design facilitates cross-referencing and disambiguation of certain demographics standards and information models. The work also demonstrates how it can also be used to represent additional clinical identified entities such as specimen and order as subjects of clinical documentation

Flexible web-based integration of distributed large-scale human protein interaction maps

Protein-protein interactions constitute the backbone of many molecular processes. This has motivated the recent construction of several large-scale human protein-protein interaction maps [1-10]. Although these maps clearly offer a wealth of information, their use is challenging: complexity, rapid growth, and fragmentation of interaction data hamper their usability. To overcome these hurdles, we have developed a publicly accessible database termed UniHI (Unified Human Interactome) for integration of human protein-protein interaction data. This database is designed to provide biomedical researchers a common platform for exploring previously disconnected human interaction maps. UniHI offers researchers flexible integrated tools for accessing comprehensive information about the human interactome. Several features included in the UniHI allow users to perform various types of network-oriented and functional analysis. At present, UniHI contains over 160,000 distinct interactions between 17,000 unique proteins from ten major interaction maps derived by both computational and experimental approaches [1-10]. Here we describe the details of the implementation and maintenance of UniHI and discuss the challenges that have to be addressed for a successful integration of interaction data

The de novo FAIRification process of a registry for vascular anomalies

Contains fulltext : 237199.pdf (Publisher’s version ) (Open Access

An Analysis of Service Ontologies

Services are increasingly shaping the world’s economic activity. Service provision and consumption have been profiting from advances in ICT, but the decentralization and heterogeneity of the involved service entities still pose engineering challenges. One of these challenges is to achieve semantic interoperability among these autonomous entities. Semantic web technology aims at addressing this challenge on a large scale, and has matured over the last years. This is evident from the various efforts reported in the literature in which service knowledge is represented in terms of ontologies developed either in individual research projects or in standardization bodies. This paper aims at analyzing the most relevant service ontologies available today for their suitability to cope with the service semantic interoperability challenge. We take the vision of the Internet of Services (IoS) as our motivation to identify the requirements for service ontologies. We adopt a formal approach to ontology design and evaluation in our analysis. We start by defining informal competency questions derived from a motivating scenario, and we identify relevant concepts and properties in service ontologies that match the formal ontological representation of these questions. We analyze the service ontologies with our concepts and questions, so that each ontology is positioned and evaluated according to its utility. The gaps we identify as the result of our analysis provide an indication of open challenges and future work

A Design Theory for Secure Semantic E-Business Processes (SSEBP)

This dissertation develops and evaluates a Design theory. We follow the design science approach (Hevener, et al., 2004) to answer the following research question: "How can we formulate a design theory to guide the analysis and design of Secure Semantic eBusiness processes (SSeBP)?" Goals of SSeBP design theory include (i) unambiguously represent information and knowledge resources involved in eBusiness processes to solve semantic conflicts and integrate heterogeneous information systems; (ii) analyze and model business processes that include access control mechanisms to prevent unauthorized access to resources; and (iii) facilitate the coordination of eBusiness process activities-resources by modeling their dependencies. Business processes modeling techniques such as Business Process Modeling Notation (BPMN) (BPMI, 2004) and UML Activity Diagrams (OMG, 2003) lack theoretical foundations and are difficult to verify for correctness and completeness (Soffer and Wand, 2007). Current literature on secure information systems design methods are theoretically underdeveloped and consider security as a non-functional requirement and as an afterthought (Siponen et al. 2006, Mouratidis et al., 2005). SSeBP design theory is one of the first attempts at providing theoretically grounded guidance to design richer secure eBusiness processes for secure and coordinated seamless knowledge exchange among business partners in a value chain. SSeBP design theory allows for the inclusion of non-repudiation mechanisms into the analysis and design of eBusiness processes which lays the foundations for auditing and compliance with regulations such as Sarbanes-Oxley. SSeBP design theory is evaluated through a rigorous multi-method evaluation approach including descriptive, observational, and experimental evaluation. First, SSeBP design theory is validated by modeling business processes of an industry standard named Collaborative Planning, Forecasting, and Replenishment (CPFR) approach. Our model enhances CPFR by incorporating security requirements in the process model, which is critically lacking in the current CPFR technical guidelines. Secondly, we model the demand forecasting and capacity planning business processes for two large organizations to evaluate the efficacy and utility of SSeBP design theory to capture the realistic requirements and complex nuances of real inter-organizational business processes. Finally, we empirically evaluate SSeBP, against enhanced Use Cases (Siponen et al., 2006) and UML activity diagrams, for informational equivalence (Larkin and Simon, 1987) and its utility in generating situational awareness (Endsley, 1995) of the security and coordination requirements of a business process. Specific contributions of this dissertation are to develop a design theory (SSeBP) that presents a novel and holistic approach that contributes to the IS knowledge base by filling an existing research gap in the area of design of information systems to support secure and coordinated business processes. The proposed design theory provides practitioners with the meta-design and the design process, including the system components and principles to guide the analysis and design of secure eBusiness processes that are secure and coordinated