José Francisco Aldana Montes

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MOTIVATION In addition to existing bioinformatics software, a lot of new tools are being developed world wide to supply services for an ever growing, widely dispersed and heterogeneous collection of biological data. The integration of these resources under a common platform is a challenging task. To this end, several groups are developing integration(More)
In this work we present GOAL (Genetics for Ontology Alignments) a new approach to compute the optimal ontology alignment function for a given ontology input set. Although this problem could be solved by an exhaustive search when the number of similarity measures is low, our method is expected to scale better for a high number of measures. Our approach is a(More)
MOTIVATION Life Sciences have emerged as a key domain in the Linked Data community because of the diversity of data semantics and formats available through a great variety of databases and web technologies. Thus, it has been used as the perfect domain for applications in the web of data. Unfortunately, bioinformaticians are not exploiting the full potential(More)
In this work we present an architecture for XML-based mediator systems and a framework for helping systems developers in the construction of mediator-services for the integration of heterogeneous data sources. A unique feature of our architecture is its capability to manage (proprietary) user’s software tools and algorithms, modelled as Extended Value Added(More)
Recommender Systems have become a significant area in the context of web personalization, given the large amount of available data. Ontologies can be widely taken advantage of in recommender systems, since they provide a means of classifying and discovering of new information about the items to recommend, about user profiles and even about their context. We(More)
With the increasing development of real applications using semantic Web technologies, it is necessary to provide scalable and efficient ontology querying and reasoning systems. In this paper we present ECQ (Extended Conjunctive Queries), a simple but powerful query language for OWL. ECQ supports Tbox reasoning and complex queries, going beyond conjunctive(More)
SUMMARY We present Systems Biology Metabolic Modeling Assistant (SBMM Assistant), a tool built using an ontology-based mediator, and designed to facilitate metabolic modeling through the integration of data from repositories that contain valuable metabolic information. This software can be used for the visualization, design and management of metabolic(More)
Protein-protein interactions can be considered the basic skeleton for living organism self-organization and homeostasis. Impressive quantities of experimental data are being obtained and computational tools are essential to integrate and to organize this information. This paper presents Protopia, a biological tool that offers a way of searching for proteins(More)
The analysis of information in the biological domain is usually focused on the analysis of data from single on-line data sources. Unfortunately, studying a biological process requires having access to disperse, heterogeneous, autonomous data sources. In this context, an analysis of the information is not possible without the integration of such data. KA-SB(More)