Automatic annotation of bioinformatics workflows with biomedical ontologies

Legacy scientific workflows, and the services within them, often present scarce and unstructured (i.e. textual) descriptions. This makes it difficult to find, share and reuse them, thus dramatically reducing their value to the community. This paper presents an approach to annotating workflows and their subcomponents with ontology terms, in an attempt to describe these artifacts in a structured way. Despite a dearth of even textual descriptions, we automatically annotated 530 myExperiment bioinformatics-related workflows, including more than 2600 workflow-associated services, with relevant ontological terms. Quantitative evaluation of the Information Content of these terms suggests that, in cases where annotation was possible at all, the annotation quality was comparable to manually curated bioinformatics resources.Comment: 6th International Symposium on Leveraging Applications (ISoLA 2014 conference), 15 pages, 4 figure

Km4City Ontology Building vs Data Harvesting and Cleaning for Smart-city Services

Presently, a very large number of public and private data sets are available from local governments. In most cases, they are not semantically interoperable and a huge human effort would be needed to create integrated ontologies and knowledge base for smart city. Smart City ontology is not yet standardized, and a lot of research work is needed to identify models that can easily support the data reconciliation, the management of the complexity, to allow the data reasoning. In this paper, a system for data ingestion and reconciliation of smart cities related aspects as road graph, services available on the roads, traffic sensors etc., is proposed. The system allows managing a big data volume of data coming from a variety of sources considering both static and dynamic data. These data are mapped to a smart-city ontology, called KM4City (Knowledge Model for City), and stored into an RDF-Store where they are available for applications via SPARQL queries to provide new services to the users via specific applications of public administration and enterprises. The paper presents the process adopted to produce the ontology and the big data architecture for the knowledge base feeding on the basis of open and private data, and the mechanisms adopted for the data verification, reconciliation and validation. Some examples about the possible usage of the coherent big data knowledge base produced are also offered and are accessible from the RDF-Store and related services. The article also presented the work performed about reconciliation algorithms and their comparative assessment and selection

Relation Ontology II

Conceived as follow-up to recent efforts destined to supply .owl ontologies with relational tools of greater complexity, the present article focuses on four main paths, all of them consisting in providing biomedical ontologies with formal means to express (1) deviations from normality, (2) topological connectedness, (3) inherence and (4) causality and function

On Pain and the Privation Theory of Evil

The paper argues that pain is not a good counter-example to the privation theory of evil. Objectors to the privation thesis see pain as too real to be accounted for in privative terms. However, the properties for which pain is intuitively thought of as real, i.e. its localised nature, intensity, and quality are features of the senso-somatic aspect of pain. This is a problem for the objectors because, as findings of modern science clearly demonstrate, the senso-somatic aspect of pain is neurologically and clinically separate from the emotional-psychological aspect of suffering. The intuition that what seems so real in pain is also the source of pain’s negative value thus falls apart. As far as the affective aspect of pain, i.e. ”painfulness’ is concerned, it cannot refute the privation thesis either. For even if this is indeed the source of pain’s badness, the affective aspect is best accounted for in privative terms of loss and negation. The same holds for the effect of pain on the aching person

Creating Intelligent Computational Edge through Semantic Mediation

This research proposes semantic mediation based on reasoning and the first order logic for mediating the best possible configuration of Computational Edge, relevant for software applications which may benefit for running computations with proximity to their data sources. The mediation considers the context in which these applications exist and exploits the semantic of that context for decision making on where computational elements should reside and which data they should use. The application of semantic mediation could address the initiative to accommodate algorithms from predictive and learning technologies, push AI towards computational edges and potentially contribute towards creating a computing continuum

Extension of Ontologies Assisted by Automated Reasoning Systems

A method to extend ontologies with the assistance of automated reasoning systems and preserving a kind of completeness with respect to their associate conceptualizations is presented. The use of such systems makes feasible the ontological insertion of new concepts, but it is necessary to re-interpret the older ones with respect to new ontological commitments.We illustrate the method extending a well-known ontology about spatial relationships, the called Region Connection Calculus.Ministerio de Educación y Ciencia TIN2004-0388

Intellectual Property, Globalization, and Left-Libertarianism

Intellectual property has become the apple of discord in today’s moral and political debates. Although it has been approached from many different perspectives, a final conclusion has not been reached. In this paper I will offer a new way of thinking about intellectual property rights (IPRs), from a left-libertarian perspective. My thesis is that IPRs are not (natural) original rights, aprioric rights, as it is usually argued. They are derived rights hence any claim for intellectual property is weaker than the correlative duties attached to self-ownership and world-ownership rights, which are of crucial importance in any left-libertarian view. Moreover, IPRs lack priority in front of these two original rights and should be overridden by stronger claims of justice. Thus, as derived rights, IPRs should not benefit of strong enforcement like any original rights especially if it could be in the latters’ detriment