Collaborative Semantic Content Management: an Ongoing Case Study for Imaging Applications

This paper presents a collaborative solution for knowledge management, implemented as a semantic content management system (CMS) with the purpose of knowledge sharing between users with different backgrounds. The CMS is enriched with semantic annotations, enabling content to be categorized, retrieved and published on the Web thanks to the Linked Open Data (LOD) principle which enables the linking of data inside existing resources using a standardized URI mechanism. Annotations are done collaboratively as a social process. Users with different backgrounds express their knowledge using structured natural language. The user knowledge is captured thanks to an ontologic approach and it can be further transformed into RDF(S) classes and properties. Ontologies are at the heart of our CMS and they naturally co-evolve with their communities of use to provide a new way of knowledge sharing inside the network. The ontology is modeled following the so-called DOGMA (Developing Ontology-Grounded Methods and Applications) paradigm, grounded in natural language. The approach will be demonstrated on a use case concerning the semantic annotation of anatomical data (e.g. medical images).257-26

Initial specification of the evaluation tasks "Use cases to bridge validation and benchmarking" PROMISE Deliverable 2.1

Evaluation of multimedia and multilingual information access systems needs to be performed from a usage oriented perspective. This document outlines use cases from the three use case domains of the PROMISE project and gives some initial pointers to how their respective characteristics can be extrapolated to determine and guide evaluation activities, both with respect to benchmarking and to validation of the usage hypotheses. The use cases will be developed further during the course of the evaluation activities and workshops projected to occur in coming CLEF conferences

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

Towards an Ontology-Based Phenotypic Query Model

Clinical research based on data from patient or study data management systems plays an important role in transferring basic findings into the daily practices of physicians. To support study recruitment, diagnostic processes, and risk factor evaluation, search queries for such management systems can be used. Typically, the query syntax as well as the underlying data structure vary greatly between different data management systems. This makes it difficult for domain experts (e.g., clinicians) to build and execute search queries. In this work, the Core Ontology of Phenotypes is used as a general model for phenotypic knowledge. This knowledge is required to create search queries that determine and classify individuals (e.g., patients or study participants) whose morphology, function, behaviour, or biochemical and physiological properties meet specific phenotype classes. A specific model describing a set of particular phenotype classes is called a Phenotype Specification Ontology. Such an ontology can be automatically converted to search queries on data management systems. The methods described have already been used successfully in several projects. Using ontologies to model phenotypic knowledge on patient or study data management systems is a viable approach. It allows clinicians to model from a domain perspective without knowing the actual data structure or query language

Toward an ontology of identity-related constructs in addiction, with examples from nicotine and tobacco research.

We aimed to create a basic set of definitions and relationships for identity-related constructs, as part of the Addiction Ontology and E-Cigarette Ontology projects, that could be used by researchers with diverse theoretical positions and so facilitate evidence synthesis and interoperability. We reviewed the use of identity-related constructs in psychological and social sciences and how these have been applied to addiction with a focus on nicotine and tobacco research. We, then, used an iterative process of adaptation and review to arrive at a basic set of identity-related classes with labels, definitions and relationships that could provide a common framework for research. We propose that 'identity' be used to refer to 'a cognitive representation by a person or group of themselves', with 'self-identity' referring to an individual's identity and 'group identity' referring to an identity held by a social group. Identities can then be classified at any level of granularity based on the content of the representations (e.g. 'tobacco smoker identity', 'cigarette smoker identity' and 'vaper identity'). We propose distinguishing identity from 'self-appraisal' to capture the distinction between the representation of oneself (e.g. as an 'ex-smoker') and (i) the importance and (ii) the positive or negative evaluation that we attach to what is represented. We label an identity that is appraised as enduring as a 'core identity', related to 'strong identity' because of the appraisal as important. Identities that are appraised positively or negatively involve 'positive self-appraisal' and 'negative self-appraisal' respectively. This allows us to create 'logically defined classes' of identity by combining them (e.g. 'positive core cigarette smoker identity' to refer to a cigarette smoker self-identity that is both positive and important). We refer to the totality of self-identities of a person as a 'composite self-identity'. An ontology of identity constructs may assist in improving clarity when discussing theories and evidence relating to this construct in addiction research. [Abstract copyright: © 2022 The Authors. Addiction published by John Wiley & Sons Ltd on behalf of Society for the Study of Addiction.

Linked Registries: Connecting Rare Diseases Patient Registries through a Semantic Web Layer

Patient registries are an essential tool to increase current knowledge regarding rare diseases. Understanding these data is a vital step to improve patient treatments and to create the most adequate tools for personalized medicine. However, the growing number of disease-specific patient registries brings also new technical challenges. Usually, these systems are developed as closed data silos, with independent formats and models, lacking comprehensive mechanisms to enable data sharing. To tackle these challenges, we developed a Semantic Web based solution that allows connecting distributed and heterogeneous registries, enabling the federation of knowledge between multiple independent environments. This semantic layer creates a holistic view over a set of anonymised registries, supporting semantic data representation, integrated access, and querying. The implemented system gave us the opportunity to answer challenging questions across disperse rare disease patient registries. The interconnection between those registries using Semantic Web technologies benefits our final solution in a way that we can query single or multiple instances according to our needs. The outcome is a unique semantic layer, connecting miscellaneous registries and delivering a lightweight holistic perspective over the wealth of knowledge stemming from linked rare disease patient registries

Toward an ontology of identity-related constructs in addiction, with examples from nicotine and tobacco research

Background and aims We aimed to create a basic set of definitions and relationships for identity-related constructs, as part of the Addiction Ontology and E-Cigarette Ontology projects, that could be used by researchers with diverse theoretical positions and so facilitate evidence synthesis and interoperability. Methods We reviewed the use of identity-related constructs in psychological and social sciences and how these have been applied to addiction with a focus on nicotine and tobacco research. We, then, used an iterative process of adaptation and review to arrive at a basic set of identity-related classes with labels, definitions and relationships that could provide a common framework for research. Results We propose that ‘identity’ be used to refer to ‘a cognitive representation by a person or group of themselves’, with ‘self-identity’ referring to an individual's identity and ‘group identity’ referring to an identity held by a social group. Identities can then be classified at any level of granularity based on the content of the representations (e.g. ‘tobacco smoker identity’, ‘cigarette smoker identity’ and ‘vaper identity’). We propose distinguishing identity from ‘self-appraisal’ to capture the distinction between the representation of oneself (e.g. as an ‘ex-smoker’) and (i) the importance and (ii) the positive or negative evaluation that we attach to what is represented. We label an identity that is appraised as enduring as a ‘core identity’, related to ‘strong identity’ because of the appraisal as important. Identities that are appraised positively or negatively involve ‘positive self-appraisal’ and ‘negative self-appraisal’ respectively. This allows us to create ‘logically defined classes’ of identity by combining them (e.g. ‘positive core cigarette smoker identity’ to refer to a cigarette smoker self-identity that is both positive and important). We refer to the totality of self-identities of a person as a ‘composite self-identity’. Conclusions An ontology of identity constructs may assist in improving clarity when discussing theories and evidence relating to this construct in addiction research