Coherent Integration of Databases by Abductive Logic Programming

We introduce an abductive method for a coherent integration of independent data-sources. The idea is to compute a list of data-facts that should be inserted to the amalgamated database or retracted from it in order to restore its consistency. This method is implemented by an abductive solver, called Asystem, that applies SLDNFA-resolution on a meta-theory that relates different, possibly contradicting, input databases. We also give a pure model-theoretic analysis of the possible ways to `recover' consistent data from an inconsistent database in terms of those models of the database that exhibit as minimal inconsistent information as reasonably possible. This allows us to characterize the `recovered databases' in terms of the `preferred' (i.e., most consistent) models of the theory. The outcome is an abductive-based application that is sound and complete with respect to a corresponding model-based, preferential semantics, and -- to the best of our knowledge -- is more expressive (thus more general) than any other implementation of coherent integration of databases

MultiView : a methodology for supporting multiple view schemata in object-oriented databases

It has been widely recognized that object-oriented database (OODB) technology needs to be extended to provide a mechanism similar to views in relational database systems. We define an object-oriented view to be an arbitrarily complex virtual schema graph with possibly restructured generalization and decomposition hierarchies - rather than just one virtual class as has been proposed in the literature. In this paper, we propose a methodology, called MultiView, for supporting multiple such view schemata. MultiView breaks the schema design task into the following independent and well-defined subtasks: (1) the customization of type descriptions and object sets of existing classes by deriving virtual classes, (2) the integration of all derived classes into one consistent global schema graph, and (3) the definition of arbitrarily complex view schemata on this augmented global schema. For the first task of MultiView, we define a set of object algebra operators that can be used by the view definer for class customization. For the second task of MultiView, we propose an algorithm that automatically integrates these newly derived virtual classes into the global schema. We solve the third task of MultiView by first letting the view definer explicitly select the desired view classes from the global schema using a view definition language and then by automatically generating a view class hierarchy for these selected classes. In addition, we present algorithms that verify the closure property of a view and, if found to be incomplete, transform it into a closed, yet minimal, view. In this paper, we introduce the fundamental concept of view independence and show MultiView to be view independent. We also outline implementation techniques for realizing MultiView with existing OODB technology

DNA barcoding and taxonomy: dark taxa and dark texts

Both classical taxonomy and DNA barcoding are engaged in the task of digitizing the living world. Much of the taxonomic literature remains undigitized. The rise of open access publishing this century and the freeing of older literature from the shackles of copyright have greatly increased the online availability of taxonomic descriptions, but much of the literature of the mid- to late-twentieth century remains offline (‘dark texts’). DNA barcoding is generating a wealth of computable data that in many ways are much easier to work with than classical taxonomic descriptions, but many of the sequences are not identified to species level. These ‘dark taxa’ hamper the classical method of integrating biodiversity data, using shared taxonomic names. Voucher specimens are a potential common currency of both the taxonomic literature and sequence databases, and could be used to help link names, literature and sequences. An obstacle to this approach is the lack of stable, resolvable specimen identifiers. The paper concludes with an appeal for a global ‘digital dashboard’ to assess the extent to which biodiversity data are available online. This article is part of the themed issue ‘From DNA barcodes to biomes’