Ontology-based data integration

About: Ontology-based data integration is a research topic. Over the lifetime, 11065 publications have been published within this topic receiving 216888 citations.

Creating the gene ontology resource: design and implementation.

Abstract: The exponential growth in the volume of accessible biological information has generated a confusion of voices surrounding the annotation of molecular information about genes and their products. The Gene Ontology (GO) project seeks to provide a set of structured vocabularies for specific biological domains that can be used to describe gene products in any organism. This work includes building three extensive ontologies to describe molecular function, biological process, and cellular component, and providing a community database resource that supports the use of these ontologies. The GO Consortium was initiated by scientists associated with three model organism databases: SGD, the Saccharomyces Genome database; FlyBase, the Drosophila genome database; and MGD/GXD, the Mouse Genome Informatics databases. Additional model organism database groups are joining the project. Each of these model organism information systems is annotating genes and gene products using GO vocabulary terms and incorporating these annotations into their respective model organism databases. Each database contributes its annotation files to a shared GO data resource accessible to the public at http://www.geneontology.org/. The GO site can be used by the community both to recover the GO vocabularies and to access the annotated gene product data sets from the model organism databases. The GO Consortium supports the development of the GO database resource and provides tools enabling curators and researchers to query and manipulate the vocabularies. We believe that the shared development of this molecular annotation resource will contribute to the unification of biological information.

PROMPT: Algorithm and Tool for Automated Ontology Merging and Alignment

Abstract: Researchers in the ontology-design field have developed the content for ontologies in many domain areas. Recently, ontologies have become increasingly common on the WorldWide Web where they provide semantics for annotations in Web pages. This distributed nature of ontology development has led to a large number of ontologies covering overlapping domains. In order for these ontologies to be reused, they first need to be merged or aligned to one another. The processes of ontology alignment and merging are usually handled manually and often constitute a large and tedious portion of the sharing process. We have developed and implemented PROMPT, an algorithm that provides a semi-automatic approach to ontology merging and alignment. PROMPT performs some tasks automatically and guides the user in performing other tasks for which his intervention is required. PROMPT also determines possible inconsistencies in the state of the ontology, which result from the user’s actions, and suggests ways to remedy these inconsistencies. PROMPT is based on an extremely general knowledge model and therefore can be applied across various platforms. Our formative evaluation showed that a human expert followed 90% of the suggestions that PROMPT generated and that 74% of the total knowledge-base operations invoked by the user were suggested by PROMPT.

Determining semantic similarity among entity classes from different ontologies

Abstract: Semantic similarity measures play an important role in information retrieval and information integration. Traditional approaches to modeling semantic similarity compute the semantic distance between definitions within a single ontology. This single ontology is either a domain-independent ontology or the result of the integration of existing ontologies. We present an approach to computing semantic similarity that relaxes the requirement of a single ontology and accounts for differences in the levels of explicitness and formalization of the different ontology specifications. A similarity function determines similar entity classes by using a matching process over synonym sets, semantic neighborhoods, and distinguishing features that are classified into parts, functions, and attributes. Experimental results with different ontologies indicate that the model gives good results when ontologies have complete and detailed representations of entity classes. While the combination of word matching and semantic neighborhood matching is adequate for detecting equivalent entity classes, feature matching allows us to discriminate among similar, but not necessarily equivalent entity classes.

Linking data to ontologies

Abstract: Many organizations nowadays face the problem of accessing existing data sources by means of flexible mechanisms that are both powerful and efficient. Ontologies are widely considered as a suitable formal tool for sophisticated data access. The ontology expresses the domain of interest of the information system at a high level of abstraction, and the relationship between data at the sources and instances of concepts and roles in the ontology is expressed by means of mappings. In this paper we present a solution to the problem of designing effective systems for ontology-based data access. Our solution is based on three main ingredients. First, we present a new ontology language, based on Description Logics, that is particularly suited to reason with large amounts of instances. The second ingredient is a novel mapping language that is able to deal with the so-called impedance mismatch problem, i.e., the problem arising from the difference between the basic elements managed by the sources, namely data, and the elements managed by the ontology, namely objects. The third ingredient is the query answering method, that combines reasoning at the level of the ontology with specific mechanisms for both taking into account the mappings and efficiently accessing the data at the sources.

An ontology for context-aware pervasive computing environments

Abstract: This document describes COBRA-ONT, an ontology for supporting pervasive context-aware systems. COBRA-ONT, expressed in the Web Ontology Language OWL, is a collection of ontologies for describing places, agents and events and their associated properties in an intelligent meeting-room domain. This ontology is developed as a part of the Context Broker Architecture (CoBrA), a broker-centric agent architecture that provides knowledge sharing, context reasoning and privacy protection supports for pervasive context-aware systems. We also describe an inference engine for reasoning with information expressed using the COBRA-ONT ontology and the ongoing research in using the DAML-Time ontology for context reasoning.