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      Why functions are not special dispositions: an improved classification of realizables for top-level ontologies

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          Abstract

          Background

          The concept of function is central to both biology and technology, but neither in philosophy nor in formal ontology is there a generally accepted theory of functions. In particular, there is no consensus how to include functions into a top-level ontology or whether to include them at all.

          Methods

          We first review current conceptions of functions in philosophy and formal ontology and evaluate them against a set of criteria. These evaluation criteria are derived from a synopsis of theoretical and practical requirements that have been suggested for formal accounts of functions. In a second step, we elucidate in particular the relation between functions and dispositions.

          Results

          We argue that functions should not be taken as a subtype of dispositions. The strongest reason for this is that any view that identifies functions with certain dispositions cannot account for malfunctioning, which is having a function but lacking the matching disposition. As a result, we suggest a cross-classification of realizables with dispositions supervening on the physical structure of their bearer, whereas both functions and roles also have some external grounding. While bearers can survive the gain, loss and change of roles, functions are rigid properties that are essentially connected to their particular bearers. Therefore, Function should not be regarded as a subtype of Disposition; rather, the classes of functions and dispositions are disjoint siblings of Realizable.

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          Most cited references13

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          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Functions

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              A top-level ontology of functions and its application in the Open Biomedical Ontologies.

              A clear understanding of functions in biology is a key component in accurate modelling of molecular, cellular and organismal biology. Using the existing biomedical ontologies it has been impossible to capture the complexity of the community's knowledge about biological functions. We present here a top-level ontological framework for representing knowledge about biological functions. This framework lends greater accuracy, power and expressiveness to biomedical ontologies by providing a means to capture existing functional knowledge in a more formal manner. An initial major application of the ontology of functions is the provision of a principled way in which to curate functional knowledge and annotations in biomedical ontologies. Further potential applications include the facilitation of ontology interoperability and automated reasoning. A major advantage of the proposed implementation is that it is an extension to existing biomedical ontologies, and can be applied without substantial changes to these domain ontologies. The Ontology of Functions (OF) can be downloaded in OWL format from http://onto.eva.mpg.de/. Additionally, a UML profile and supplementary information and guides for using the OF can be accessed from the same website.
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                Author and article information

                Contributors
                Journal
                J Biomed Semantics
                J Biomed Semantics
                Journal of Biomedical Semantics
                BioMed Central
                2041-1480
                2014
                2 June 2014
                : 5
                : 27
                Affiliations
                [1 ]Institut für Philosophie, Universität Rostock, 18055 Rostock, Germany
                [2 ]Philosophisches Seminar, Universität Münster, 48143 Münster, Germany
                Article
                2041-1480-5-27
                10.1186/2041-1480-5-27
                4089563
                f66504ce-5e8e-49d7-bb1a-6a9faf736e4a
                Copyright © 2014 Röhl and Jansen; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 25 February 2014
                : 23 April 2014
                Categories
                Research

                Bioinformatics & Computational biology
                function,disposition,role,process,realizable,artefacts,top-level ontology,bfo

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