Patrick Lambrix

SAMBO-A system for aligning and merging biomedical ontologies

Due to the recent explosion of the amount of on-line accessible biomedical data and tools, finding and retrieving the relevant information is not an easy task. The vision of a Semantic Web for life sciences alleviates these difficulties. A key technology for the Semantic Web is ontologies. In recent years many biomedical ontologies have been developed and many of these ontologies contain overlapping information. To be able to use multiple ontologies they have to be aligned or merged. In this paper we propose a framework for aligning and merging ontologies. Further, we developed a system for aligning and merging biomedical ontologies (SAMBO) based on this framework. The framework is also a first step towards a general framework that can be used for comparative evaluations of alignment strategies and their combinations. In this paper we evaluated different strategies and their combinations in terms of quality and processing time and compared SAMBO with two other systems.

Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX

MOTIVATION Analysis and simulation of pathway data is of high importance in bioinformatics. Standards for representation of information about pathways are necessary for integration and analysis of data from various sources. Recently, a number of representation formats for pathway data, SBML, PSI MI and BioPAX, have been proposed. RESULTS In this paper we compare these formats and evaluate them with respect to their underlying models, information content and possibilities for easy creation of tools. The evaluation shows that the main structure of the formats is similar. However, SBML is tuned towards simulation models of molecular pathways while PSI MI is more suitable for representing details about particular interactions and experiments. BioPAX is the most general and expressive of the formats. These differences are apparent in allowed information and the structure for representation of interactions. We discuss the impact of these differences both with respect to information content in existing databases and computational properties for import and analysis of data.

Evaluation of ontology development tools for bioinformatics

Ontologies are being used nowadays in many areas, including bioinformatics. To assist users in developing and maintaining ontologies a number of tools have been developed. In this paper we compare four such tools, Protégé-2000, Chimaera, DAG-Edit and OilEd. As test ontologies we have used ontologies from the Gene Ontology Consortium. No system is preferred in all situations, but each system has its own strengths and weaknesses.

Evaluation of ontology merging tools in bioinformatics.

Ontologies are being used nowadays in many areas, including bioinformatics. One of the issues in ontology research is the aligning and merging of ontologies. Tools have been developed for ontology merging, but they have not been evaluated for their use in bioinformatics. In this paper we evaluate two of the most well-known ontology merging tools with a bioinformatics perspective. As test ontologies we have used Gene Ontology and Signal-Ontology.

Using Partial Reference Alignments to Align Ontologies

In different areas ontologies have been developed and many of these ontologies contain overlapping information. Often we would therefore want to be able to use multiple ontologies. To obtain good results, we need to find the relationships between terms in the different ontologies, i.e. we need to align them. Currently, there already exist a number of ontology alignment systems. In these systems an alignment is computed from scratch. However, recently, some situations have occurred where a partial reference alignment is available, i.e. some of the correct mappings between terms are given or have been obtained. In this paper we investigate whether and how a partial reference alignment can be used in ontology alignment. We use partial reference alignments to partition ontologies, to compute similarities between terms and to filter mapping suggestions. We test the approaches on previously developed gold standards and discuss the results.

A Framework for Part-of Hierarchies in Terminological Logics

There is a growing recognition that part-whole hierarchies are a very general form of representation, widely used by humans in commonsense reasoning. This paper develops a terminological logic, and related inference mechanisms for representing and reasoning about composite concepts and individuals. A basic terminological logic language is extended with constructs for describing composite concepts in terms of their parts and the relationships between them. A part-of hierarchy is defined, based on the relationship of compositional inclusion. This part-of hierarchy is analogous to, but different from, the “is-a” hierarchy. Compositional inferencing is defined as a process which infers the existence of a whole, based on the existence of the required parts, where the parts are in the necessary relationship to each other. Three stable states are defined with respect to compositional inferencing - compositional extensions, credulous compositional extensions and skeptical compositional conclusions. This framework significantly enhances and is complementary to, knowledge representation and reasoning based on is-a hierarchies.

A tool for evaluating ontology alignment strategies

Ontologies are an important technology for the Semantic Web. In different areas ontologies have already been developed and many of these ontologies contain overlapping information. Often we would therefore want to be able to use multiple ontologies. To obtain good results, we need to find the relationships between terms in the different ontologies, i.e. we need to align them. Currently, there exist a number of systems that support users in aligning ontologies, but not many comparative evaluations have been performed and there exists little support to perform such evaluations. However, the study of the properties, the evaluation and comparison of the alignment strategies and their combinations, would give us valuable insight in how the strategies could be used in the best way. In this paper we propose the KitAMO framework for comparative evaluation of ontology alignment strategies and their combinations and present our current implementation. We evaluate the implementation with respect to performance. We also illustrate how the system can be used to evaluate and compare alignment strategies and their combinations in terms of performance and quality of the proposed alignments. Further, we show how the results can be analyzed to obtain deeper insights into the properties of the strategies.

Alignment of biomedical ontologies using life science literature

In recent years many biomedical ontologies have been developed and many of these ontologies contain overlapping information. To be able to use multiple ontologies they have to be aligned. In this paper we propose strategies for aligning ontologies based on life science literature. We propose a basic algorithm as well as extensions that take the structure of the ontologies into account. We evaluate the strategies and compare them with strategies implemented in the alignment system SAMBO. We also evaluate the combination of the proposed strategies and the SAMBO strategies.

Formalisations of Capabilities for BDI-Agents

Intentional agent systems are increasingly being used in a wide range of complex applications. Capabilities has recently been introduced into some of these systems as a software engineering mechanism to support modularity and reusability while still allowing meta-level reasoning. This paper presents possible formalisations of capabilities within the framework of beliefs, goals and intentions and indicates how capabilities can affect agent reasoning about its intentions. We define a style of agent commitment which we refer to as a self-aware agent which allows an agent to modify its goals and intentions as its capabilities change. We also indicate which aspects of the specification of a BDI interpreter are affected by the introduction of capabilities and give some indications of additional reasoning which could be incorporated into an agent system on the basis of both the theoretical analysis and the existing implementation.

A method for recommending ontology alignment strategies

In different areas ontologies have been developed and many of these ontologies contain overlapping information. Often we would therefore want to be able to use multiple ontologies. To obtain good results, we need to find the relationships between terms in the different ontologies, i.e. we need to align them. Currently, there already exist a number of different alignment strategies. However, it is usually difficult for a user that needs to align two ontologies to decide which of the different available strategies are the most suitable. In this paper we propose a method that provides recommendations on alignment strategies for a given alignment problem. The method is based on the evaluation of the different available alignment strategies on several small selected pieces from the ontologies, and uses the evaluation results to provide recommendations. In the paper we give the basic steps of the method, and then illustrate and discuss the method in the setting of an alignment problem with two well-known biomedical ontologies. We also experiment with different implementations of the steps in the method.