Vital Sign Ontology

We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices. If properly developed and extended, we believe the VSO will find applications for the EMR, clinical informatics, and medical device communities

Biomedical Terminologies and Ontologies: Enabling Biomedical Semantic Interoperability and Standards in Europe

In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular O/T as a standard for data exchange purposes is often seen by the end-user as a function of the number of applications using that vocabulary (and, by extension, the size of the user base). Furthermore, the adoption of an O/T as an interoperability standard requires confidence in its stability and guaranteed continuity as a resource

Designing and Managing Advanced, Intelligent and Ethical Health and Social Care Ecosystems

The ongoing transformation of health systems around the world aims at personalized, preventive, predictive, participative precision medicine, supported by technology. It considers individual health status, conditions, and genetic and genomic dispositions in personal, social, occupational, environmental and behavioral contexts. In this way, it transforms health and social care from art to science by fully understanding the pathology of diseases and turning health and social care from reactive to proactive. The challenge is the understanding and the formal as well as consistent representation of the world of sciences and practices, i.e., of multidisciplinary and dynamic systems in variable context. This enables mapping between the different disciplines, methodologies, perspectives, intentions, languages, etc., as philosophy or cognitive sciences do. The approach requires the deployment of advanced technologies including autonomous systems and artificial intelligence. This poses important ethical and governance challenges. This paper describes the aforementioned transformation of health and social care ecosystems as well as the related challenges and solutions, resulting in a sophisticated, formal reference architecture. This reference architecture provides a system-theoretical, architecture-centric, ontology-based, policy-driven model and framework for designing and managing intelligent and ethical ecosystems in general and health ecosystems in particular.Peer reviewe

Ontological approach to the normative dimension of organizations: an application of Documents Acts Ontology

Modeling and knowledge representation are indispensable activities for developing information systems in the scope of modern corporations. In order to accomplish these activities, one should analyze a corporation both in terms of its physical structure and in terms its rules structure. The former we call here the descriptive dimension and the later prescriptive dimension. In this paper, we briefly discuss the descriptive dimension, and focus on the prescriptive dimension to explain the rights and obligations that corporations have to manage. After presenting background theories, we analyze the corporation through ontological principles taking advantage of theories of the so-called social ontology, namely, social acts, speech acts and document acts theory. The relevance of developing such analysis rests on the possibility of outlining a strong understanding of corporations by characterizing the nature of rights and duties obligations connected to corporative processes using Basic Formal Ontology (BFO) and Documents Acts (D-acts) Ontology. In doing this, we introduce a formal framework suitable to be applied in information systems working in the context of modern technologies like the Semantic Web

Ontological approach to the normative dimension of organizations: an application of Documents Acts Ontology

Modeling and knowledge representation are indispensable activities for developing information systems in the scope of modern corporations. In order to accomplish these activities, one should analyze a corporation both in terms of its physical structure and in terms its rules structure. The former we call here the descriptive dimension and the later prescriptive dimension. In this paper, we briefly discuss the descriptive dimension, and focus on the prescriptive dimension to explain the rights and obligations that corporations have to manage. After presenting background theories, we analyze the corporation through ontological principles taking advantage of theories of the so-called social ontology, namely, social acts, speech acts and document acts theory. The relevance of developing such analysis rests on the possibility of outlining a strong understanding of corporations by characterizing the nature of rights and duties obligations connected to corporative processes using Basic Formal Ontology (BFO) and Documents Acts (D-acts) Ontology. In doing this, we introduce a formal framework suitable to be applied in information systems working in the context of modern technologies like the Semantic Web.   http://revista.ibict.br/ciinf/article/view/402

Adding evidence type representation to DIDEO

Abstract-In this poster we present novel development and extension of the Drug-drug Interaction and Drug-drug Interaction Evidence Ontology (DIDEO). We demonstrate how reasoning over this extension of DIDEO can a) automatically create a multi-level hierarchy of evidence types from descriptions of the underlying scientific observations and b) automatically subsume individual evidence items under the correct evidence type. Thus DIDEO will enable evidence items added manually by curators to be automatically categorized into a drug-drug interaction framework with precision and minimal effort from curators. As with all previous DIDEO development this extension is consistent with OBO Foundry principles

ACGT: advancing clinico-genomic trials on cancer - four years of experience.

The challenges regarding seamless integration of distributed, heterogeneous and multilevel data arising in the context of contemporary, post-genomic clinical trials cannot be effectively addressed with current methodologies. An urgent need exists to access data in a uniform manner, to share information among different clinical and research centers, and to store data in secure repositories assuring the privacy of patients. Advancing Clinico-Genomic Trials (ACGT) was a European Commission funded Integrated Project that aimed at providing tools and methods to enhance the efficiency of clinical trials in the -omics era. The project, now completed after four years of work, involved the development of both a set of methodological approaches as well as tools and services and its testing in the context of real-world clinico-genomic scenarios. This paper describes the main experiences using the ACGT platform and its tools within one such scenario and highlights the very promising results obtained

Ontology Based Integration of Distributed and Heterogeneous Data Sources in ACGT.

In this work, we describe the set of tools comprising the Data Access Infrastructure within Advancing Clinic-genomic Trials on Cancer (ACGT), a R&D Project funded in part by the European. This infrastructure aims at improving Post-genomic clinical trials by providing seamless access to integrated clinical, genetic, and image databases. A data access layer, based on OGSA-DAI, has been developed in order to cope with syntactic heterogeneities in databases. The semantic problems present in data sources with different nature are tackled by two core tools, namely the Semantic Mediator and the Master Ontology on Cancer. The ontology is used as a common framework for semantics, modeling the domain and acting as giving support to homogenization. SPARQL has been selected as query language for the Data Access Services and the Mediator. Two experiments have been carried out in order to test the suitability of the selected approach, integrating clinical and DICOM image databases

Developing User Personas to Aid in the Design of a User-Centered Natural Product-Drug Interaction Information Resource for Researchers

Pharmacokinetic interactions between natural products and conventional drugs can adversely impact patient outcomes. These complex interactions present unique challenges that require clear communication to researchers. We are creating a public information portal to facilitate researchers’ access to credible evidence about these interactions. As part of a user-centered design process, three types of intended researchers were surveyed: drug-drug interaction scientists, clinical pharmacists, and drug compendium editors. Of the 23 invited researchers, 17 completed the survey. The researchers suggested a number of specific requirements for a natural product-drug interaction information resource, including specific information about a given interaction, the potential to cause adverse effects, and the clinical importance. Results were used to develop user personas that provided the development team with a concise and memorable way to represent information needs of the three main researcher types and a common basis for communicating the design’s rationale