Rule-based information integration

In this report, we show the process of information integration. We specifically discuss the language used for integration. We show that integration consists of two phases, the schema mapping phase and the data integration phase. We formally define transformation rules, conversion, evolution and versioning. We further discuss the integration process from a data point of view

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

Bioinformatics service reconciliation by heterogeneous schema transformation

This paper focuses on the problem of bioinformatics service reconciliation in a generic and scalable manner so as to enhance interoperability in a highly evolving field. Using XML as a common representation format, but also supporting existing flat-file representation formats, we propose an approach for the scalable semi-automatic reconciliation of services, possibly invoked from within a scientific workflows tool. Service reconciliation may use the AutoMed heterogeneous data integration system as an intermediary service, or may use AutoMed to produce services that mediate between services. We discuss the application of our approach for the reconciliation of services in an example bioinformatics workflow. The main contribution of this research is an architecture for the scalable reconciliation of bioinformatics services

Composition with Target Constraints

It is known that the composition of schema mappings, each specified by source-to-target tgds (st-tgds), can be specified by a second-order tgd (SO tgd). We consider the question of what happens when target constraints are allowed. Specifically, we consider the question of specifying the composition of standard schema mappings (those specified by st-tgds, target egds, and a weakly acyclic set of target tgds). We show that SO tgds, even with the assistance of arbitrary source constraints and target constraints, cannot specify in general the composition of two standard schema mappings. Therefore, we introduce source-to-target second-order dependencies (st-SO dependencies), which are similar to SO tgds, but allow equations in the conclusion. We show that st-SO dependencies (along with target egds and target tgds) are sufficient to express the composition of every finite sequence of standard schema mappings, and further, every st-SO dependency specifies such a composition. In addition to this expressive power, we show that st-SO dependencies enjoy other desirable properties. In particular, they have a polynomial-time chase that generates a universal solution. This universal solution can be used to find the certain answers to unions of conjunctive queries in polynomial time. It is easy to show that the composition of an arbitrary number of standard schema mappings is equivalent to the composition of only two standard schema mappings. We show that surprisingly, the analogous result holds also for schema mappings specified by just st-tgds (no target constraints). This is proven by showing that every SO tgd is equivalent to an unnested SO tgd (one where there is no nesting of function symbols). Similarly, we prove unnesting results for st-SO dependencies, with the same types of consequences.Comment: This paper is an extended version of: M. Arenas, R. Fagin, and A. Nash. Composition with Target Constraints. In 13th International Conference on Database Theory (ICDT), pages 129-142, 201

Semantic processing of EHR data for clinical research

There is a growing need to semantically process and integrate clinical data from different sources for clinical research. This paper presents an approach to integrate EHRs from heterogeneous resources and generate integrated data in different data formats or semantics to support various clinical research applications. The proposed approach builds semantic data virtualization layers on top of data sources, which generate data in the requested semantics or formats on demand. This approach avoids upfront dumping to and synchronizing of the data with various representations. Data from different EHR systems are first mapped to RDF data with source semantics, and then converted to representations with harmonized domain semantics where domain ontologies and terminologies are used to improve reusability. It is also possible to further convert data to application semantics and store the converted results in clinical research databases, e.g. i2b2, OMOP, to support different clinical research settings. Semantic conversions between different representations are explicitly expressed using N3 rules and executed by an N3 Reasoner (EYE), which can also generate proofs of the conversion processes. The solution presented in this paper has been applied to real-world applications that process large scale EHR data.Comment: Accepted for publication in Journal of Biomedical Informatics, 2015, preprint versio