Semantic Integration of Cervical Cancer Data Repositories to Facilitate Multicenter Association Studies: The ASSIST Approach

The current work addresses the unifi cation of Electronic Health Records related to cervical cancer into a single medical knowledge source, in the context of the EU-funded ASSIST research project. The project aims to facilitate the research for cervical precancer and cancer through a system that virtually unifi es multiple patient record repositories, physically located in different medical centers/hospitals, thus, increasing fl exibility by allowing the formation of study groups “on demand” and by recycling patient records in new studies. To this end, ASSIST uses semantic technologies to translate all medical entities (such as patient examination results, history, habits, genetic profi le) and represent them in a common form, encoded in the ASSIST Cervical Cancer Ontology. The current paper presents the knowledge elicitation approach followed, towards the defi nition and representation of the disease’s medical concepts and rules that constitute the basis for the ASSIST Cervical Cancer Ontology. The proposed approach constitutes a paradigm for semantic integration of heterogeneous clinical data that may be applicable to other biomedical application domains

Digital Ecosystems: Ecosystem-Oriented Architectures

We view Digital Ecosystems to be the digital counterparts of biological ecosystems. Here, we are concerned with the creation of these Digital Ecosystems, exploiting the self-organising properties of biological ecosystems to evolve high-level software applications. Therefore, we created the Digital Ecosystem, a novel optimisation technique inspired by biological ecosystems, where the optimisation works at two levels: a first optimisation, migration of agents which are distributed in a decentralised peer-to-peer network, operating continuously in time; this process feeds a second optimisation based on evolutionary computing that operates locally on single peers and is aimed at finding solutions to satisfy locally relevant constraints. The Digital Ecosystem was then measured experimentally through simulations, with measures originating from theoretical ecology, evaluating its likeness to biological ecosystems. This included its responsiveness to requests for applications from the user base, as a measure of the ecological succession (ecosystem maturity). Overall, we have advanced the understanding of Digital Ecosystems, creating Ecosystem-Oriented Architectures where the word ecosystem is more than just a metaphor.Comment: 39 pages, 26 figures, journa

What can developmental disorders tell us about the neurocomputational constraints that shape development? the case of Williams syndrome

The uneven cognitive phenotype in the adult outcome of Williams syndrome has led some researchers to make strong claims about the modularity of the brain and the purported genetically determined, innate specification of cognitive modules. Such arguments have particularly been marshaled with respect to language. We challenge this direct generalization from adult phenotypic outcomes to genetic specification and consider instead how genetic disorders provide clues to the constraints on plasticity that shape the outcome of development. We specifically examine behavioral studies, brain imaging, and computational modeling of language in Williams syndrome but contend that our theoretical arguments apply equally to other cognitive domains and other developmental disorders. While acknowledging that selective deficits in normal adult patients might justify claims about cognitive modularity, we question whether similar, seemingly selective deficits found in genetic disorders can be used to argue that such cognitive modules are prespecified in infant brains. Cognitive modules are, in our view, the outcome of development, not its starting point. We note that most work on genetic disorders ignores one vital factor, the actual process of ontogenetic development, and argue that it is vital to view genetic disorders as proceeding under different neurocomputational constraints, not as demonstrations of static modularity

Tracing the Biological Roots of Knowledge

The essay is a critical review of three possible approaches in the theory of knowledge while tracing the biological roots of knowledge: empiricist, rationalist and developmentalist approaches. Piaget's genetic epistemology, a developmentalist approach, is one of the first comprehensive treatments on the question of tracing biological roots of knowledge. This developmental approach is currently opposed, without questioning the biological roots of knowledge, by the more popular rationalist approach, championed by Chomsky. Developmental approaches are generally coherent with cybernetic models, of which the theory of autopoiesis proposed by Maturana and Varela made a significant theoretical move in proposing an intimate connection between metabolism and knowledge. Modular architecture is currently considered more or less an undisputable model for both biology as well as cognitive science. By suggesting that modulation of modules is possible by motor coordination, a proposal is made to account for higher forms of conscious cognition within the four distinguishable layers of the human mind. Towards the end, the problem of life and cognition is discussed in the context of the evolution of complex cognitive systems, suggesting the unique access of phylogeny during the ontogeny of human beings as a very special case, and how the problem cannot be dealt with independent of the evolution of coding systems in nature

Providing a Realist Perspective on the eyeGENE Database System

One of the achievements of the eyeGENE Network is a repository of DNA samples of patients with inherited eye diseases and an associated database that tracks key elements of phenotype and genotype information for each patient. Although its database structure serves its direct research needs, eyeGENE has set a goal of enhancing this structure to become increasingly well integrated with medical information standards over time. This goal should be achieved by ensuring semantic interoperability with other information systems but without adopting the incoherencies and inconsistencies found in available biomedical standards. Therefore, eyeGENE’s current pragmatic perspective with focus on data and information, rather than what the information is about, should shift to a realism-based perspective that includes also the portion of reality described, and the competing opinions that clinicians may hold about it. An analysis of eyeGENE’s database structure and user interfaces suggests that such a transition is possible indeed

A Molecular Biology Database Digest

Computational Biology or Bioinformatics has been defined as the application of mathematical and Computer Science methods to solving problems in Molecular Biology that require large scale data, computation, and analysis [18]. As expected, Molecular Biology databases play an essential role in Computational Biology research and development. This paper introduces into current Molecular Biology databases, stressing data modeling, data acquisition, data retrieval, and the integration of Molecular Biology data from different sources. This paper is primarily intended for an audience of computer scientists with a limited background in Biology