BioTop Website: http://purl.org/biotop See related articles at: http://www.google.com/search?q=Schulz+BioTop+site:www.ncbi.nlm.nih.gov/pmc/articles+ontology+OR+ontologies
Institute fir Medical Informatics, Statistics and Documentation, Medical University of Graz, Austria
Stefan Schulz, Martin Boeker, Elena Beisswanger, Holger Stenzhorn, Djamila Raufie, Daniel Schober, Udo Hahn
An experimental top level ontology for biology and medicine. Lite Version
Last modification November 6, 2012 by Stefan Schulz
Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network (mapping files available)
agentIn (inverse: hasAgent) relates a participant with a process, with the condition that this participant is causally active in the relevant process. This is the reason why agentIn is subsumed by the relation causedBy. Example: A physician is the agent in a opeeration process; a solvent is the agent in a solving process.
abstractPartOf (inverse: hasAbstractPart) Relates parts and wholes of abstract entities. Abstract entities are neither processes, material objects, regions or spaces. Typical abstract entities are pieces of information. For instance, a header is an abstract part of a jpg file.
this relation relates a continuant (objects, qualities, dispositions...) to some of its TQCs (snapshot continuant).
Causation of a process is here understood as the disjunction between agency (a continuant causes a process) and as the realization of a disposition or a function, i.e. a disposition is considered the cause of a process.
DerivesFrom (inverse: derivedInto) holds between distinct material objects when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier object is included into the later. There is some instant of time t such that the first object exists only prior to and the second one only subsequent to t. These relations are borrowed from the OBO Relation Ontology Example: "Three simple kinds of instance-level derivation can then be distinguished (Figure 3): first, the succession of one single continuant by another single continuant across a temporal threshold (for example, this blastocyst derives from this zygote); second, the fusion of two or more continuants into one continuant (for example, this zygote derives from this sperm and from this ovum); and third, the fission of an earlier single continuant to create a plurality of later continuants (for example, these promyelocytes derive from this myeoloblast). " from http://genomebiology.com/2005/6/5/R46
physicallyBounds (inverse: physically boundedBy) relates a three-dimensional physical object with its two dimensional boundary. Example: the surface of my liver physically bounds my liver.
The non-transitive relation hasComponentPart (inverse: componentPartOf) relates components with a compound. Components strictly partition the compound, and the compound is the mereological sum of its components. A loss of some component affects the integrity of the compound, and possibly the type it instantiates, e.g. a complete vs. a defective organism. The choice of what is a component of a compound is somewhat arbitrary, because there are several ways to divide a whole into parts. Strictly spoken, this relation should refer to some partition. Components should be - at least - partly bona fide parts. The use of this relation also requires the commitment to an underlying granularity level. So could we consider the codons (base triples) as the components of a DNA molecule but also the single nucleotides. Note that components of a compound may also be portions of matter. Examples: my liver is a component of my organism, a carboxy group is a component of some organic acid molecule.
hasDuration relates a process with the time interval it covers.
outcomeOf (inverse: hasOutcome) relates a participant to a process. This participant either - a) comes into being during the process or - b) undergoes some change during the process, so that it instantiates a different class at the end of the process and it constitutes (one of) the main result(s) of the process Example: a Protein molecule is the outcome of a translation process.
HasParticipant (inverse: participatesIn) relates a process with a non processual entity which plays some role in the process. Process participants may exist during the whole process, remain unchanged or undergo changes; they may come into being or get out of being during the process. Process participation is distinguished from process location. Example: An urea molecule which is excreted in a renal filtration process is participant of this process. A person who undergoes an operation is participant of this process.
patientIn (inverse: hasPatient) relates a participant with a process, with the condition that that this participant is not causally active. Example: A prey is the patient in a hunting process; a solute is the patient in a solving process.
hasPointInTome relates a processual entity with some point in the interval it occupies. If there is no temporal extension (process boundary) it relates it to the time it occurs.
processQualityOf (abstract: hasProcessQuality) links a quality that further characterizes a process to this process. Process qualities are asserted where the process cannot sufficiently be described by the qualities of its participants only. Example: The process of heart beating has the process quality heart rate.
hasProcessualPart (inverse: processualPartOf) relates a process with a subprocess (process part). Example: G1 phase is a processual part of the process mitosis.
hasProperPhysicalPart (inverse: properPhysicalPartOf) obtains between physical objects. The distinction between parthood and locatedness is complex and does not obey strict criteria. This relation is irreflexive, i.e. a physical object cannot have itself as a physical proper part. Note that for abstract entities like information artefacts there is a separate relation pair "abstractPartOf" and "hasAbstractPart" For processes there are the relations "hasProcessualPart" and "processualPartOf" Examples: my thumb is a proper physical part of my hand, this keyboard is a proper physical part of my computer.
Realization occurs if a disposition, a function, or a role manifests itself as a process. Certain information entities can also have realizations, e.g. plans that are realized in processes. Example: the disposition of a bird to fly (which exists even when it does not fly) is realized by its process of flying.
includedIn (inverse: includes) is a very broad relation which relates an entity with the place it occurs, inheres, or is part of. See property chains: a participant of a process at a given time is included in the region that includes the process. Example: A heart pumping process is included in a heart.
inheresIn (inverse: bearerOf) relates a quality, role, function, disposition, or information object with the physical entity it depends on. (Note that for processes there is a separate relation pair "hasProcessQuality" and "processQualityOf") Example: a color inheres in a paint, the ability to fly inheres in a bird, or a pdf file inheres in a USB stick.
isIncludedIn is a very broad relation which relates an entity with the place it occurs, inheres, or is part of. See property chain: a participant of a process at a given time is located where the process is located.
includedIn (inverse: includes) is a very broad relation which relates an entity with the place it occurs, inheres, or is part of. Example: A heart pumping process is included in a heart.
precedes (inverse: precededBy) relates two processes, one of which ends or totally happens before the second one begins. Example: fecundation preceeds embryonic development.
projectsOnto (inverse: isProjectionOf) relates a quality with an abstract value region. The underlying idea, borrowed from the DOLCE ontology, is that the attribute / value distinction - as ubiquitous in information systems - should at least be optionally expressible in ontologies. Value regions are abstract regions, in which qualitative just as quantitative "values" are located. Like in topographic regions, these entities can overlap or be disjoint. Example: "Color" as quality may be refined as "Red Color". It can be fully defined in by "projects onto some RedColorRegion"
is represented by (inverse: represents) relates entities with information entities. In contrast to encoding, the represented entity is completely independent on the denoting one. Example: The inflammation of a sinus is representd by the word 'Sinusitis';, as well as by the ICD code "J10"
originatesFrom relates two material objects one of which originates from the other in a very broad sense. It includes derivation (in the OBO RO sense), actual actual parts (provided they were always parts), as well as original (historical) parts. Examples: see Subrelations
physicalAdjacentTo relates two physical objects that abut without physical overlap. Examples: see subrelations
physicallyConnectedTo (a symmetric relation) relates two spatially relevant entities (material entities or spaces) which overlap at least one point in space. Example: France is connected to Germany, my optic nerve is connected to my eyeball.
projectsOnto (inverse: projectionOf) relates a quality with an abstract value region. The underlying idea, borrowed from the DOLCE ontology, is that the attribute / value distinction - as ubiquitous in information systems - should at least be optionally expressible in ontologies. Value regions are abstract regions, in which qualitative just as quantitative "values" are located. Like in topographic regions, these entities can overlap or be disjoint. Example: "Color" as quality may be refined as "Red Color". It can be fully defined in by "projects onto some RedColorRegion"
An action is a processual entity that that is promoted by an agent, having a clear role distinction between agent and patient
collection with molecules or atoms as granular parts of the same sort
Basic building block of molecules. Particle of discrete types. Biologically important atoms are C, N, H, O, P, S, Na, Ca, K, Mg, Cl, J, Fe, Co, Zn ,... Atoms may be electrically neutral or ionic.
abstract region in which the value "canonical" of canonicity is located
The condition of an entity (state, process, function, object) in terms of being well or ill-formed or behaving
abstract region in which values of canonicity are located
Constituting unit of an organism. The boundary between cell, syncytium and subcellular fragments such as platelets is problematic. Hence no full definition possible.
Components which only can be formed inside living cells but which may survive their host cell.
The fuzzyness of this class is due to the "same sort" criterion.
Mereological Sum of multiple grains of the same sort without clear identity and unity criteria. Whether or not the grains are considered of the same sort depends on the view. Therefore this class does not really make a clear categorial distinction, because all matter can be described as a collection of atoms. As a consequence, these classes are not fully defined.
compound of collective material entities
Composition of different kinds of collections without clear unity and identity criteria. Old name: compound of collections. Practically all naturally occurring substances are of this sort. The different compounds are also called fractions
Union of material entity, process, or disposition. The rationale of this class is to represent the ambiguous nature of what is commonly referred to by health-related condition (not necessarily pathologic)
A disposition is a realizable entity. Its manifestation is a process its bearer is involved in virtue of the bearer's physical make-up.
A temporally qualified continuant is the temporal snapshot of a temporally extended object
A classical definition of function according to Wright is that the function F of X is Z means that X is there because it Zs, and Z is a consequence of X being there. For artefacts, functions are distinguished from dispositions by the purpose they have been built. For example, a hammer has the function to drive in nails, but not to be used as a weapon. However, it has the disposition to be used as a weapon under certain circumstances. For biological objects, which developed by evolution, the definition of function is still subject to controversy (e.g. Barry Smith's view of function as pertaining to a canonical life plan, cf. http://www.slideserve.com/presentation/103450/The-Canonical-Life). In BFO "Disposition" and "Function" are siblings, in BioTop Function is more specific.
Physical spaces that have a threedimensional spatial dimension but no mass. Old name: immaterial anatomical entity
immaterial three dimensional physical entity
Piece of information (not necessarily human) , as it exists independently of any potential material carrier.
What happens at one point in time, typically a process boundary
The whole process which is characterized by the existence of a physical entity. E.g. the life process of an orgamism perdures as long as this entity exists. The life lx of the continuant entity x does not have any process segment which does not x as participant.
A material object that has exactly one mass and one volume at a time. Material objects may have Immaterial nonphysical entities as parts (e.g. Heart and Heart Ventricle).
A mono-molecular entity is a self connected compound of two atoms or more which exhibit at least one covalent bound. Molecular entities can be isolated molecules or parts of molecules (groups, residue). They may be electrically neutral or not. In biological systems molecular entities generally occur in very high quantities. In text, references to chemicals are often ambiguous. When we state "water has a molecular weight of 18" we refer to single water molecules. However, saying that "water has a density of 1kg/dm³" under certain conditions then we make a statement about pluralities of water molecules each of which has water molecules as "grains" Old name: molecular entity The upper bound of monomolecular entities is shallow. Strictly even a diamond crystal would be a monomolecular entity. One argument against this idea is that a diamond crystal is still a diamond crystal if you take away some portions. This is not the case with a classical molecule.
abstract region in which the value "noncanonical" of canonicity is located
line bounding a two-dimensional biological entity
A well defined and circumscribed subdivision of an organism, not any arbitrary part. Macroscopic organism parts may be delimited mainly by natural boundaries but always exhibit at least small regions of fiat boundaries. An organism part may derive from an organism, i.e. it may continue to exist even when the organism does not exist any longer.
From an universalist point of view most BioTop classes can be considered the extension of universals. However, BioTop does not claim that all of its classes are the extension of universals and is agnostic with regard to the existence of universals and the delineation between universals and non-universals.
A independent physical entity that bounds or demarcates some other physical entity. Commonly viewed as a lower-dimensional part, the the notion of physical boundary here also encompasses ill-delimited spaces that fulfill the same function, e.g. biological joints.
force as defined by physics (mass + acceleration)
Mass (gravity independent) - not weight. Measured in g, kg, ...
Volume of three-dimensional objects - third potency of length
A plan is a series of steps to be carried out in order to achiev a goal. Plans can only be realized by processes
Collection of two or more organisms of the same sort.
typically the boundary of a time interval
An object which contains several molecules, has direct parts (components) of different types and which changes its ontological nature if subdivided. It must have clear unity and identity criteria.
Process is in BioTop the generic subsumer of anything that "occurs". Processes can span across time and have temporal parts (i.e. there is no time in which all parts of a process are simultaneously present). A special kind of process is the event, which has no temporal extension. It can be regarded as Process Boundary (BFO). Processes have physical or informational entities as participants.
A quality is a dependent entity that is exhibited if it inheres in some other entity or entities at all.
A role is a realizable entity the manifestation of which brings about some result or end that is not essential to its bearer in virtue of the kind of thing that it is, but that can be served or participated in by that kind of continuant entity in some kinds of natural, social or institutional contexts.
Corresponds to FMA anatomical structure but extends to any kind of orgnaism: Material anatomical entity which is generated by coordinated expression of the organism's own genes that guide its morphogenesis; has inherent 3D shape; its parts are connected and spatially related to one another in patterns determined by coordinated gene expression. Examples: heart, right ventricle, mitral valve, myocardium, endothelium, lymphocyte, fibroblast, thorax, cardiovascular system, hemoglobin, T cell receptor. Old name: anatomical structure
The quality of one or more biological organisms, as well as of parts of organism of partaining to a biological taxon. [steschu20080127]
abstract region in which the values of biological taxa are located (cf. Schulz et.al ISMB 2008). Biological taxa can be ascribed not only to organisms but also to ogranism parts, derivates, as well as populations.
A value region is an abstract region in which (non quantitative) values of qualities are located.
(wikipedia) disturbance that propagates through space and time, usually with transference of energy