Domenico Beneventano

Semantic integration of heterogeneous information sources

Abstract Developing intelligent tools for the integration of information extracted from multiple heterogeneous sources is a challenging issue to effectively exploit the numerous sources available on-line in global information systems. In this paper, we propose intelligent, tool-supported techniques to information extraction and integration from both structured and semistructured data sources. An object-oriented language, with an underlying Description Logic, called ODLI3, derived from the standard ODMG is introduced for information extraction. ODLI3 descriptions of the source schemas are exploited first to set a Common Thesaurus for the sources. Information integration is then performed in a semiautomatic way by exploiting the knowledge in the Common Thesaurus and ODLI3 descriptions of source schemas with a combination of clustering techniques and Description Logics. This integration process gives rise to a virtual integrated view of the underlying sources for which mapping rules and integrity constraints are specified to handle heterogeneity. Integration techniques described in the paper are provided in the framework of the MOMIS system based on a conventional wrapper/mediator architecture.

Synthesizing an integrated ontology

The Mediator Environment for Multiple Information Sources (Momis) supports semiautomatic building, annotation, and extension of domain ontologies.

Description logics for semantic query optimization in object-oriented database systems

Semantic query optimization uses semantic knowledge (i.e., integrity constraints) to transform a query into an equivalent one that may be answered more efficiently. This article proposes a general method for semantic query optimization in the framework of Object-Oriented Database Systems. The method is effective for a large class of queries, including conjunctive recursive queries expressed with regular path expressions and is based on three ingredients. The first is a Description Logic, ODLRE, providing a type system capable of expressing: class descriptions, queries, views, integrity constraint rules and inference techniques, such as incoherence detection and subsumption computation. The second is a semantic expansion function for queries, which incorporates restrictions logically implied by the query and the schema (classes + rules) in one query. The third is an optimal rewriting method of a query with respect to the schema classes that rewrites a query into an equivalent one, by determining more specialized classes to be accessed and by reducing the number of factors. We implemented the method in a tool providing an ODMG-compliant interface that allows a full interaction with OQL queries, wrapping underlying Description Logic representation and techniques to the user.

Consistency checking in complex object database schemata with integrity constraints

Integrity constraints are rules that should guarantee the integrity of a database. Provided an adequate mechanism to express them is available, the following question arises: is there any way to populate a database which satisfies the constraints supplied by a database designer? That is, does the database schema, including constraints, admit at least a nonempty model? This work answers the above question in a complex object database environment, providing a theoretical framework, including the following ingredients: (1) two alternative formalisms, able to express a relevant set of state integrity constraints with a declarative style; (2) two specialized reasoners, based on the tableaux calculus, able to check the consistency of complex objects database schemata expressed with the two formalisms. The proposed formalisms share a common kernel, which supports complex objects and object identifiers, and which allow the expression of acyclic descriptions of: classes, nested relations and views, built up by means of the recursive use of record, quantified set, and object type constructors and by the intersection, union, and complement operators. Furthermore, the kernel formalism allows the declarative formulation of typing constraints and integrity rules. In order to improve the expressiveness and maintain the decidability of the reasoning activities, we extend the kernel formalism into two alternative directions. The first formalism, OLCP, introduces the capability of expressing path relations. Because cyclic schemas are extremely useful, we introduce a second formalism, OLCD, with the capability of expressing cyclic descriptions but disallowing the expression of path relations. In fact, we show that the reasoning activity in OLCDP (i.e., OLCP with cycles) is undecidable.

An information integration framework for e-commerce

One of the main challenges for e-commerce infrastructure designers is to retrieve data from different sources and create a unified view that overcomes contradictions and redundancies. Virtual catalogs, such as the Momis project, can help synthesize data and present it in a unified manner to the customer.

THE MOMIS METHODOLOGY FOR INTEGRATING HETEROGENEOUS DATA SOURCES

The Mediator Environment for Multiple Information Sources (MOMIS) aims at constructing synthesized, integrated descriptions of the information coming from multiple heterogeneous sources, in order to provide the user with a global virtual view of the sources independent from their location and the level of heterogeneity of their data. Such a global virtual view is a conceptualization of the underlying domain and then may be thought of as an ontology describing the involved sources. In this article we explore the framework’s main elements and discuss how the output of the integration process can be exploited to create a conceptualization of the underlying domain.

ODB-Tools: A Description Logics Based Tool for Schema Validation and Semantic Query Optimization in Object Oriented Databases

ODB-Tools is a integrated environment for the object oriented database (OODB) validation, preserving taxonomy coherence and performing taxonomic inferences, and semantic query optimization. Semantic query optimization uses problem-specific knowledge (e.g. integrity constraints) for transforming a query into an equivalent one (i.e. with the same answer set) that may be answered more efficiently. The approach of the tool is based on two fundamental ingredients. The first one is the OCDL description logics proposed as a common formalism to express class descriptions, a relevant set of integrity constraints rules (IC rules) and queries. The second one are Description Logics inference techniques, exploited to evaluate the logical implications expressed by IC rules and thus to produce the semantic expansion of a given query. The optimizer tentatively applies all the possible transformations and delays the choice of beneficial transformation till the end. ODB-Tools is a ODMG 93 [1] compliant tool, both for the schema definition (ODL language) and for the query language (OQL), The tool is available in internet at http://sparc20.dsi.unimo.it and supports an on-line graphical interface developed in Java language.

MDP, a database linking drug response data to genomic information, identifies dasatinib and statins as a combinatorial strategy to inhibit YAP/TAZ in cancer cells

Targeted anticancer therapies represent the most effective pharmacological strategies in terms of clinical responses. In this context, genetic alteration of several oncogenes represents an optimal predictor of response to targeted therapy. Integration of large-scale molecular and pharmacological data from cancer cell lines promises to be effective in the discovery of new genetic markers of drug sensitivity and of clinically relevant anticancer compounds. To define novel pharmacogenomic dependencies in cancer, we created the Mutations and Drugs Portal (MDP, http://mdp.unimore.it), a web accessible database that combines the cell-based NCI60 screening of more than 50,000 compounds with genomic data extracted from the Cancer Cell Line Encyclopedia and the NCI60 DTP projects. MDP can be queried for drugs active in cancer cell lines carrying mutations in specific cancer genes or for genetic markers associated to sensitivity or resistance to a given compound. As proof of performance, we interrogated MDP to identify both known and novel pharmacogenomics associations and unveiled an unpredicted combination of two FDA-approved compounds, namely statins and Dasatinib, as an effective strategy to potently inhibit YAP/TAZ in cancer cells.

Querying a super-peer in a schema-based super-peer network

We propose a novel approach for defining and querying a super-peer within a schema-based super-peer network organized into a two-level architecture: the low level, called the peer level (which contains a mediator node), the second one, called super-peer level (which integrates mediators peers with similar content). We focus on a single super-peer and propose a method to define and solve a query, fully implemented in the SEWASIE project prototype. The problem we faced is relevant as a super-peer is a two-level data integrated system, then we are going beyond traditional setting in data integration. We have two different levels of Global as View mappings: the first mapping is at the super-peer level and maps several Global Virtual Views (GVVs) of peers into the GVV of the super-peer; the second mapping is within a peer and maps the data sources into the GVV of the peer. Moreover, we propose an approach where the integration designer, supported by a graphical interface, can implicitly define mappings by using Resolution Functions to solve data conflicts, and the Full Disjunction operator that has been recognized as providing a natural semantics for data merging queries.

Taxonomic reasoning with cycles in LOGIDATA

This paper shows the subsumption computation techniques for a LOGIDATA+ schema allowing cyclic definitions for classes. The formal framework LOGIDATACYC*, which extends LOGIDATA* to perform taxonomic reasoning in the presence of cyclic class definitions is introduced. It includes the notions of possible instances of a schema; legal instance of a schema, defined as the greatest fixed-point of possible instances; subsumption relation. On the basis of this framework, the definitions of coherent type and consistent class are introduced and the necessary algorithms to detect incoherence and compute subsumption in a LOGIDATA+ schema are given. Some examples of subsumption computation show its feasibility for schema design and validation.