Research
A novel paradigm for cell and molecule interaction ontology: from the CMM model to IMGT-ONTOLOGY
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* Corresponding author: Francesco Pappalardo fp@francescopappalardo.net
1 Institute for Computing Applications 'M. Picone', National Research Council (CNR), Rome, Italy
2 Faculty of Pharmacy, University of Catania, Catania, Italy
3 IMGT, Laboratoire d'ImmunoGénétique Moléculaire, Institut de Génétique Humaine, UPR CNRS 1142, Montpellier, France
4 Dipartimento di Ematologia e Scienze Oncologiche, Università di Bologna, Bologna, Italy
Immunome Research 2010, 6:1 doi:10.1186/1745-7580-6-1
Published: 18 February 2010Abstract
Background
Biology is moving fast toward the virtuous circle of other disciplines: from data to quantitative modeling and back to data. Models are usually developed by mathematicians, physicists, and computer scientists to translate qualitative or semi-quantitative biological knowledge into a quantitative approach. To eliminate semantic confusion between biology and other disciplines, it is necessary to have a list of the most important and frequently used concepts coherently defined.
Results
We propose a novel paradigm for generating new concepts for an ontology, starting from model rather than developing a database. We apply that approach to generate concepts for cell and molecule interaction starting from an agent based model. This effort provides a solid infrastructure that is useful to overcome the semantic ambiguities that arise between biologists and mathematicians, physicists, and computer scientists, when they interact in a multidisciplinary field.
Conclusions
This effort represents the first attempt at linking molecule ontology with cell ontology, in IMGT-ONTOLOGY, the well established ontology in immunogenetics and immunoinformatics, and a paradigm for life science biology. With the increasing use of models in biology and medicine, the need to link different levels, from molecules to cells to tissues and organs, is increasingly important.