Bodily Systems and the Modular Structure of the Human Body

Papakin, Igor; Munn, Katherine

doi:10.1007/978-3-540-39907-0_13

Cited by 10 publications

(21 citation statements)

References 4 publications

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“…But BFO makes no claim to completeness, and thus it leaves open whether there are entities properly to be conceived of as functions of processes which might form an additional category deserving to be recognized by BFO. Favored examples of functional processes -for example the cycle of green-red or of green-amber-red illuminations of traffic lights, or the process of blinking when exposed to bright lights, or the process of blood flowing through the body to bring oxygen to its cells -are all, as far as we have been able to ascertain, capable of being treated as examples of functions of material entities in the BFO sense (of traffic light installations, of the upper eyelid musculature, and of the circulatory system, respectively) (Smith et al, 2003). …”

Section: Bfo Functionmentioning

confidence: 99%

“…On biological systems -for instance the cardiovascular system -as parts of organisms see Smith et al (2003). Following the account of 'canonical anatomical structures' in Rosse and Mejino (2003), we may say that a biological function is a function which inheres in an entity that is (i) part of an organism and (ii) exists and has the physical structure it has as a result of the coordinated expression of that organism's structural genes.…”

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confidence: 99%

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Functions in Basic Formal Ontology

Spear

Ceusters

2016

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Abstract. The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO's account of function, provide some reasons for favoring it over competing views, and defend it against objections.

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Section: Bfo Functionmentioning

confidence: 99%

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confidence: 99%

Functions in Basic Formal Ontology

Spear

Ceusters

2016

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“…The high-level view of anatomical systems provides some additional challenges in terms of multiple inheritance or "fuzzy" definitions of specific systems (Smith et al, 2003). For example, the definition of the kidney as being part of genitourinary and renal systems entails functional associations with reproductive, blood gas and electrolyte regulation, and excretory systems.…”

Section: Birth Of Ai and Symbolic Programmingmentioning

confidence: 99%

Anatomical reasoning in the informatics age: Principles, ontologies, and agendas

Trelease

2006

Anat. Rec.

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Reasoning about anatomy shares historical scientific roots with formal logic and artificial intelligence. With advances in computer-based intelligent programming, high-level biological structural knowledge may be exploited directly for biomedical research, clinical tasks, and educational applications. We consider the special nature of anatomical domain knowledge, emphasizing the complex concepts and semantics that must be represented in the development of ontologies, formally structured databases of biological information. We review the evolution of the fundamental scientific principles of logic and artificial intelligence needed for building machines that can make use of anatomical knowledge. We look at methods for compiling ontologies and compare the structural designs of the Foundational Model of Anatomy and Open GALEN ontologies. We further consider issues related to mapping developing anatomy resources with other biological ontologies in genomics, proteomics, and physiology. Although early results are promising, considerable resources and continuing effort must be committed to completing and extending anatomical ontologies for the ultimate success of computer-based anatomical reasoning. Anat Rec (Part B: New Anat) 289B:72-84, 2006. (c) 2006 Wiley-Liss, Inc.

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“…The idea that a domain can be modeled by different granular perspectives is not new (e.g., Burger et al, 2004;Smith et al, 2004;Jagers Op Akkerhuis, 2008;Winther, 2006), but Keet (2008a) provides the first general formal theory of granularity that incorporates different granular perspectives within a single domain granularity framework. Keet's theory can therefore be understood as the attempt to accept descriptive pluralism about the idea of levels (Craver, 2015), but nevertheless integrates the resulting set of diverse hierarchies within an integrated strictly formalized framework, her general formal theory of granularity.…”

Section: Keet's Formal Theory Of Granularitymentioning

confidence: 99%

“…A granular partition can be represented as a granularity tree (Reitsma & Bittner, 2003;Kumar et al, 2004;Smith et al, 2004), because every finite granular partition can be represented as a rooted tree of finite length (Mark, 1978;Bittner & Smith, 2001b, 2003a, i.e. a rooted directed graph without cycles (Wilson & Watkins, 1990).…”

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confidence: 99%

Levels and building blocks—towards a domain granularity framework for the life sciences

Vogt

2017

Preprint

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The use of online data repositories and the establishment of new data standards that require data to be computer-parsable so that algorithms can reason over them have become increasingly important with the emergence of high-throughput technologies, Big Data and eScience. As a consequence, there is an increasing need for new approaches for organizing and structuring data from various sources into integrated hierarchies of levels of entities that facilitate algorithm-based approaches for data exploration, data comparison and analysis. In this paper I contrast various accounts of the level idea and resulting hierarchies published by philosophers and natural scientists with the more formal approaches of theories of granularity published by information scientists and ontology researchers. I discuss the shortcomings of the former and argue that the general theory of granularity proposed by Keet circumvents these problems and allows the integration of various different hierarchies into a domain granularity framework. I introduce the concept of general building blocks, which gives rise to a hierarchy of levels that can be formally characterized by Keet's theory. This hierarchy functions as an organizational backbone for integrating various other hierarchies that I briefly discuss, resulting in a general domain granularity framework for the life sciences. I also discuss the implicit consequences of this granularity framework for the structure of top-level categories of 'material entity' of the Basic Formal Ontology. The here suggested domain granularity framework is meant to provide the basis on which a more comprehensive information framework for the life sciences can be developed.PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.2429v2 | CC BY 4.0 Open Access |

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Bodily Systems and the Modular Structure of the Human Body

Cited by 10 publications

References 4 publications

Functions in Basic Formal Ontology

Functions in Basic Formal Ontology

Anatomical reasoning in the informatics age: Principles, ontologies, and agendas

Levels and building blocks—towards a domain granularity framework for the life sciences

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