Paper criticizes biomedical ontologies based purely on philosophical ideas

An article published in Methods of Information in Medicine discloses the scientific strictures of such ideas, prompting a sweeping epistemological debate

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.

These constraints, they explain, include issues like the inadequacy of Aristotelian approaches for dealing with diverse aspects of computational ontologies, the a priori acceptance of a supposed external ontological reality, the failure to consider aspects like organization and emergence in biology, the fundamental differences between ontologies with a classical philosophical groundwork and modern scientific theories, and the obstacles to addressing other questions, like volume and graphical pattern and structure representation.

Maojo et al. broach the problems that the use of such methodologies so strictly bound by philosophy can pose to biomedicine from the scientific viewpoint. This, the first article containing a critical analysis of these philosophical approaches to be published in the field of biomedicine and biomedical informatics, advocates the need to scientifically appraise Aristotelian-inspired ontologies.

For example, Maojo et al. analyse recent philosophical approaches for building 2D and 3D graphical or visual pattern and structure ontologies and conclude that they fail to properly account for the scientific knowledge amassed on these topics in the wake of Gauss, Euler, Riemann, as well as decades of research on image processing. In their paper, Maojo et al. include numerous scientific references (Monod, Lorenz or Feynman) that recall the recurrent and sterile endeavours to establish classical philosophical ideas in the scientific world.

Epistemological debate

The critique formulated in this article has not left the philosophical and scientific communities indifferent. In a counter published in the same issue of the journal, ten well-known researchers confront the article by Maojo et al.

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 so-called semantic web.

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

For example, a host of companies use ontologies in their web pages to organize information, and many other researchers, particularly in biomedicine, use them in their research work. Recent literature includes thousands of references to ontologies.

Years after their proposal, a group of philosophers proclaimed that computational ontologies should be based on classical (philosophical) ontological ideas and argued that this would improve their clarity, rigour and scientific groundwork. This led to the development of computational ontology formalization methodologies based on Aristotelian philosophy, which are now widely accepted and used in biomedicine and were the target of the critique formulated through the medium of the cited specialized journal.