Using Ontologies for Semantic Data Integration

While big data analytics is considered as one of the most important paths to competitive advantage of today’s enterprises, data scientists spend a comparatively large amount of time in the data preparation and data integration phase of a big data project. This shows that data integration is still a major challenge in IT applications. Over the past two decades, the idea of using semantics for data integration has become increasingly crucial, and has received much attention in the AI, database, web, and data mining communities. Here, we focus on a specific paradigm for semantic data integration, called Ontology-Based Data Access (OBDA). The goal of this paper is to provide an overview of OBDA, pointing out both the techniques that are at the basis of the paradigm, and the main challenges that remain to be addressed

Declarative Ajax Web Applications through SQL++ on a Unified Application State

Implementing even a conceptually simple web application requires an inordinate amount of time. FORWARD addresses three problems that reduce developer productivity: (a) Impedance mismatch across the multiple languages used at different tiers of the application architecture. (b) Distributed data access across the multiple data sources of the application (SQL database, user input of the browser page, session data in the application server, etc). (c) Asynchronous, incremental modification of the pages, as performed by Ajax actions. FORWARD belongs to a novel family of web application frameworks that attack impedance mismatch by offering a single unifying language. FORWARD's language is SQL++, a minimally extended SQL. FORWARD's architecture is based on two novel cornerstones: (a) A Unified Application State (UAS), which is a virtual database over the multiple data sources. The UAS is accessed via distributed SQL++ queries, therefore resolving the distributed data access problem. (b) Declarative page specifications, which treat the data displayed by pages as rendered SQL++ page queries. The resulting pages are automatically incrementally modified by FORWARD. User input on the page becomes part of the UAS. We show that SQL++ captures the semi-structured nature of web pages and subsumes the data models of two important data sources of the UAS: SQL databases and JavaScript components. We show that simple markup is sufficient for creating Ajax displays and for modeling user input on the page as UAS data sources. Finally, we discuss the page specification syntax and semantics that are needed in order to avoid race conditions and conflicts between the user input and the automated Ajax page modifications. FORWARD has been used in the development of eight commercial and academic applications. An alpha-release web-based IDE (itself built in FORWARD) enables development in the cloud.Comment: Proceedings of the 14th International Symposium on Database Programming Languages (DBPL 2013), August 30, 2013, Riva del Garda, Trento, Ital

Reasoning and Change Management in Modular Ontologies

The benefits of modular representations are well known from many areas of computer science. In this paper, we concentrate on the benefits of modular ontologies with respect to local containment of terminological reasoning. We define an architecture for modular ontologies that supports local reasoning by compiling implied subsumption relations. We further address the problem of guaranteeing the integrity of a modular ontology in the presence of local changes. We propose a strategy for analyzing changes and guiding the process of updating compiled information

Implementation and Deployment of a Library of the High-level Application Programming Interfaces (SemSorGrid4Env)

The high-level API service is designed to support rapid development of thin web applications and mashups beyond the state of the art in GIS, while maintaining compatibility with existing tools and expectations. It provides a fully configurable API, while maintaining a separation of concerns between domain experts, service administrators and mashup developers. It adheres to REST and Linked Data principles, and provides a novel bridge between standards-based (OGC O&M) and Semantic Web approaches. This document discusses the background motivations for the HLAPI (including experiences gained from any previously implemented versions), before moving onto specific details of the final implementation, including configuration and deployment instructions, as well as a full tutorial to assist mashup developers with using the exposed observation data

The SP theory of intelligence: benefits and applications

This article describes existing and expected benefits of the "SP theory of intelligence", and some potential applications. The theory aims to simplify and integrate ideas across artificial intelligence, mainstream computing, and human perception and cognition, with information compression as a unifying theme. It combines conceptual simplicity with descriptive and explanatory power across several areas of computing and cognition. In the "SP machine" -- an expression of the SP theory which is currently realized in the form of a computer model -- there is potential for an overall simplification of computing systems, including software. The SP theory promises deeper insights and better solutions in several areas of application including, most notably, unsupervised learning, natural language processing, autonomous robots, computer vision, intelligent databases, software engineering, information compression, medical diagnosis and big data. There is also potential in areas such as the semantic web, bioinformatics, structuring of documents, the detection of computer viruses, data fusion, new kinds of computer, and the development of scientific theories. The theory promises seamless integration of structures and functions within and between different areas of application. The potential value, worldwide, of these benefits and applications is at least $190 billion each year. Further development would be facilitated by the creation of a high-parallel, open-source version of the SP machine, available to researchers everywhere.Comment: arXiv admin note: substantial text overlap with arXiv:1212.022

Composition and Inversion of Schema Mappings

In the recent years, a lot of attention has been paid to the development of solid foundations for the composition and inversion of schema mappings. In this paper, we review the proposals for the semantics of these crucial operators. For each of these proposals, we concentrate on the three following problems: the definition of the semantics of the operator, the language needed to express the operator, and the algorithmic issues associated to the problem of computing the operator. It should be pointed out that we primarily consider the formalization of schema mappings introduced in the work on data exchange. In particular, when studying the problem of computing the composition and inverse of a schema mapping, we will be mostly interested in computing these operators for mappings specified by source-to-target tuple-generating dependencies

Community next steps for making globally unique identifiers work for biocollections data

Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets. For data associated with biocollections, the biodiversity community has long recognized that an essential part of establishing and preserving linkages is to apply globally unique identifiers at the point when data are generated in the field and to persist these identifiers downstream, but this is seldom implemented in practice. There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses. In order to further progress towards a broader community consensus, a group of biocollections and informatics experts assembled in Stockholm in October 2014 to discuss community next steps to overcome current roadblocks. The workshop participants divided into four groups focusing on: identifier practice in current field biocollections; identifier application for legacy biocollections; identifiers as applied to biodiversity data records as they are published and made available in semantically marked-up publications; and cross-cutting identifier solutions that bridge across these domains. The main outcome was consensus on key issues, including recognition of differences between legacy and new biocollections processes, the need for identifier metadata profiles that can report information on identifier persistence missions, and the unambiguous indication of the type of object associated with the identifier. Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided

A Comparative Genomics Approach to Using High-Throughput Gene Expression Data to Study Limb Regeneration in Ambystoma Mexicanum and Danio Rerio: Developing a More Completely Annotated Database

Axolotl (Ambystoma mexicanum) and the zebrafish (Danio rerio) represent organisms extensively studied because of their remarkable capability of fully regenerating completely functional tissues after a traumatic event takes place. However, the research conducted with regards to the genomics of these two organisms has remained fairly independent of each other. The intent of this study is to bridge this gap and connect genes between axolotl and the zebrafish by use a “Rosetta stone” framework to develop a database comparing gene expression data obtained from both microarraybased experiments and high-throughput DNA sequencing of axolotl and zebrafish mRNA and miRNA. Using gene data of this variety, accessed from a variety of private and public resources, 78 axolotl genes were matched to human genes and found to have homologous zebrafish genes. The function of these genes were organized and discussed from a variety of perspectives, including general gene ontologies, specific mechanisms and functions, expression during regeneration at specific times post amputation, and expression in normal regenerating specimens as compared to specimens exposed to the toxin TCDD. Specific proteins and protein functionalities that appear most frequently or novel significance included ribosomal proteins and mitochondrial processes, neurite regeneration, the presences of proteins NADH ubiquinone oxidoreductase, histone, cystatin, and cathepsin, cell differentiation, apoptosis and cellular maintenance, and the structure of the extracellular matrix