ABSTRACT: Background: Distinguishing bona fide (i.e. natural) and fiat (i.e. artificial) physical boundaries plays a key role for distinguishing natural from artificial material entities and is thus relevant to any scientific formal foundational top-level ontology, as for instance the Basic Formal Ontology (BFO). In BFO, the distinction is essential for demarcating two foundational categories of material entity: object and fiat object part. The commonly used basis for demarcating bona fide from fiat boundary refers to two criteria: (i) intrinsic qualities of the boundary bearers (i.e. spatial/physical discontinuity, qualitative heterogeneity) and (ii) mind-independent existence of the boundary. The resulting distinction of bona fide and fiat boundaries is considered to be categorial and exhaustive.
By referring to various examples from biology, we demonstrate that the hitherto used distinction of boundaries is not categorial: (i) spatial/physical discontinuity is a matter of scale and the differentiation of
bona fide and fiat boundaries is thus granularity-dependent, and (ii) this differentiation is not absolute, but comes in degrees. By reducing the demarcation criteria to mind-independence and by also considering dispositions and historical relations of the bearers of boundaries, instead of only considering their spatio-structural properties, we demonstrate with various examples that spatio-structurally fiat boundaries can nevertheless be mind-independent and in this sense bona fide.
We argue that the ontological status of a given boundary is perspective-dependent and that the strictly spatio-structural demarcation criteria follow a static perspective that is ignorant of causality and the dynamics of reality. Based on a distinction of several ontologically independent perspectives, we suggest different types of boundaries and corresponding material entities, including boundaries based on function (locomotion, physiology, ecology, development, reproduction) and common history (development, heredity, evolution). We argue that for each perspective one can differentiate respective bona fide from fiat boundaries.
PLoS ONE 12/2012; 7(12):e48603. · 4.09 Impact Factor
ABSTRACT: The Ecdysozoa-hypothesis on the origin of arthropods questions the homology of segmentation in arthropods, onychophorans,
and annelids. The implication of convergent gain of metamery in these groups seems to conflict particularly with the correspondence
in the development of serial coelomic cavities and metanephridia. Ultrastructural studies of the mesoderm development in Onychophora
revealed that main correspondence with the state in annelids concerns the involvement of epithelial lining cells of the embryonic
coelomic cavities in the formation of the visceral and somatic musculature. The significance of this correspondence, however,
remained unclear as comparable data on the state in arthropods were still missing. Developmental studies on selected representatives
covering all major arthropod subgroups aim to fill in this gap. Data were raised by a combination of transmission electron
microscopy and fluorescent stainings of the muscular system and nuclei for the anostracan crustacean Artemia salina. In this species, putative transitory coelomic cavities proved to be absent in all trunk segments. In the second antennal
and second maxillary segments small, compact nephridial anlagen develop into a sacculus and excretory duct. The sacculus originates
from the terminal cells of the nephridial duct, which is formed in advance. The lumen of the sacculus is inconspicuous in
its earliest functional stage and later enlarges to a bulb; it accordingly represents no remnant of any primarily large coelomic
cavity. The muscular system is entirely formed prior to and independent of coelomic or nephridial anlagen. Visceral and somatic
mesoderm already separate in the caudal body region. Transitory segmental clusters of mesodermal cells are composed of somatic
cells only and accordingly represent no “somites”. Our observations overall do not provide any support for the homology of
coelomic cavities in annelids and arthropods.
Zeitschrift für Morphologie der Tiere 04/2012; 128(3):247-262. · 1.28 Impact Factor
ABSTRACT: The Basic Formal Ontology (BFO) is a top-level formal foundational ontology for the biomedical domain. It has been developed with the purpose to serve as an ontologically consistent template for top-level categories of application oriented and domain reference ontologies within the Open Biological and Biomedical Ontologies Foundry (OBO). BFO is important for enabling OBO ontologies to facilitate in reliably communicating and managing data and metadata within and across biomedical databases. Following its intended single inheritance policy, BFO's three top-level categories of material entity (i.e. 'object', 'fiat object part', 'object aggregate') must be exhaustive and mutually disjoint. We have shown elsewhere that for accommodating all types of constitutively organized material entities, BFO must be extended by additional categories of material entity.
Unfortunately, most biomedical material entities are cumulative-constitutively organized. We show that even the extended BFO does not exhaustively cover cumulative-constitutively organized material entities. We provide examples from biology and everyday life that demonstrate the necessity for 'portion of matter' as another material building block. This implies the necessity for further extending BFO by 'portion of matter' as well as three additional categories that possess portions of matter as aggregate components. These extensions are necessary if the basic assumption that all parts that share the same granularity level exhaustively sum to the whole should also apply to cumulative-constitutively organized material entities. By suggesting a notion of granular representation we provide a way to maintain the single inheritance principle when dealing with cumulative-constitutively organized material entities.
We suggest to extend BFO to incorporate additional categories of material entity and to rearrange its top-level material entity taxonomy. With these additions and the notion of granular representation, BFO would exhaustively cover all top-level types of material entities that application oriented ontologies may use as templates, while still maintaining the single inheritance principle.
PLoS ONE 01/2012; 7(1):e30004. · 4.09 Impact Factor
ABSTRACT: Application oriented ontologies are important for reliably communicating and managing data in databases. Unfortunately, they often differ in the definitions they use and thus do not live up to their potential. This problem can be reduced when using a standardized and ontologically consistent template for the top-level categories from a top-level formal foundational ontology. This would support ontological consistency within application oriented ontologies and compatibility between them. The Basic Formal Ontology (BFO) is such a foundational ontology for the biomedical domain that has been developed following the single inheritance policy. It provides the top-level template within the Open Biological and Biomedical Ontologies Foundry. If it wants to live up to its expected role, its three top-level categories of material entity (i.e., 'object', 'fiat object part', 'object aggregate') must be exhaustive, i.e. every concrete material entity must instantiate exactly one of them.
By systematically evaluating all possible basic configurations of material building blocks we show that BFO's top-level categories of material entity are not exhaustive. We provide examples from biology and everyday life that demonstrate the necessity for two additional categories: 'fiat object part aggregate' and 'object with fiat object part aggregate'. By distinguishing topological coherence, topological adherence, and metric proximity we furthermore provide a differentiation of clusters and groups as two distinct subcategories for each of the three categories of material entity aggregates, resulting in six additional subcategories of material entity.
We suggest extending BFO to incorporate two additional categories of material entity as well as two subcategories for each of the three categories of material entity aggregates. With these additions, BFO would exhaustively cover all top-level types of material entity that application oriented ontologies may use as templates. Our result, however, depends on the premise that all material entities are organized according to a constitutive granularity.
PLoS ONE 01/2011; 6(4):e18794. · 4.09 Impact Factor