Instituto de energía solar

Professors and researchers from the Universidad Politécnica de Madrid's Facultad de Informática, Víctor Maojo, José Crespo, Miguel García Remesal, David Pérez del Rey and Diana de la Iglesia, and from Rutgers University, Casimir Kulikowski, have published an article in the Methods of Information in Medicine journal. This paper criticizes biomedical ontologies based purely on philosophical ideas and states a host of potential scientific constraints.

One critical aspect is the inadequacy of the Aristotelian approaches to various aspects of computational ontologies: accept a priori an alleged external ontological reality, failure to consider aspects such as organization and emergence in biology, fundamental differences in the ontologies philosophical foundation of classic and modern scientific theories and finally, to address other issues as the representation of graphic forms and structures and volumes.

The authors of this article highlight the problems of using these philosophical methodologies in biomedicine from the scientific point of view. This is the first article published in the area of biomedicine and biomedical informatics with a critical analysis of these philosophical approaches. The proposal of the topic suggests the need to evaluate scientifically the Aristotelian ontology base.

For example, the authors discuss recent philosophical approaches made to build ontologies of shapes and graphic or visual structures (two and three dimensions). The researchers suggest that it consider it appropriate scientific knowledge on these topics since Gauss, Euler, Riemann, and decades of research in image processing. The authors include numerous references in scientific papers (such as Monod, Lorenz or Feynman). This discussion is reminiscent of the attempt, cyclically repeated with little success, to introduce classical philosophical ideas in the scientific world.

Epistemological debate

The authors have raised the interest in biomedical ontologies. It has published another article in response to the criticisms published in the same journal issue; ten well-known authors reply the professor and his collaborators.

Two of these researchers, philosophers, made extremely harsh comments arguing the validity of the philosophical ideas presented in the field of computational ontologies and their contribution to modern science. Others, on the other hand, claimed that ontology formalization confined to classical philosophy is unsuitable for computational models. The journal's editors have also written an editorial on the topic explaining, without taking sides, the elements of the discussion to help readers to form a sound opinion. Controversy is the order of the day.

Computational ontologies are conceptualizations of a domain used as a framework for exchanging information between semantically heterogeneous computer systems and knowledge bases. Their development has facilitated the semantic web.

The pioneering researchers in the field decided to name this technique "ontologies", borrowing the name from philosophy. Ontologies, with this definition, are very popular in several fields for processing huge quantities of data and knowledge.

For example, many companies use ontologies to organize information in their websites, as well as many other researchers use them in their work, particularly in biomedicine. Recent literature has thousands of references to them.

After a period of time, a group of philosophers proclaimed that computational ontologies should be based on classical ontological philosophical thoughts, saying that would give greater clarity, rigor and scientific basis. This idea has led to develop methods of formalization, based on the Aristotelian philosophy of computational ontologies. This formalization has been widely accepted and currently used in biomedicine, and have been the subject of the criticism made by the journal.