Stefan Schulz, Martin Boeker, Elena Beisswanger, Holger Stenzhorn, Djamila Raufie, Daniel Schober, Udo Hahn
Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Stefan-Meier-Strasse 26, 79104 Freiburg, Germany
Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network (mapping files available)
Last modification May 24, 2011 by Stefan Schulz
An experimental top level ontology for biology and medicine.
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
This version contains inverse relation axioms. These may have an impact on the performance. To remove them use the perl script: #!/usr/bin/perl my $buffer;my @zeilen;my @rules; #! RemoveInverses.pl #! by Stefan Schulz, 2009/09/25 #! First argument: owl file open(DAT0, $ARGV[0]) || die " Please specify an owl file from which you want to remove the inverse relation axioms.\n"; while(<DAT0>){push(@zeilen,$_)}close(DAT0); #! Write text file into buffer for(my $i = 0;$i <
mereological relationship between immaterial entities, e.g. pieces of information
Relation in which immaterial entities (information entities, roles, qualities) are involved
A participant of a process, with the additional condition that the component instance is causally active in the relevant process. The latter is the reason that it has also the relation "causes" as an additional parent.
Contiguous with a clear bona fide boundary between the connected parts. Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
Inverse relation of inheresIn. Relates an independent continuant to a dependent one (e.g. quality, state, function, or disposition) Formerly "has inherence". Note that for processes there is a separate relation pair "hasProcessQuality" and "processQualityOf"
A is a branch of B if it is contiguous with B and if some flow of matter or energy of information flows form B to A. Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
Expresses a causal chain between material or processual entities
Causation of a process is here understood as the disjunction between agency (a continuant causes a process) or as the realization of a disposition, i.e. a disposition is considered the cause of a process. Note the property chain!
Causation of a process is here understood as the disjunction between agency (a continuant causes a process) or as the realization of a disposition, i.e. a disposition is considered the cause of a process.
Components are those (first-order) parts which partition a compound. The whole is exactly the mereological sum of its components. A loss of a component affects the sortality of the compound (e.g. a complete vs. a defective organism). In many cases, the choice of what is a component of a compound is arbitrary, because there are several ways to divide a whole into parts. 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.
Abutting with transmission of forces Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
Two events cooccur if their temporal extensions overlap.
Corresponds to the inverse of the RO relation "derives from" Derivation is a relation holding between non-identicals. More precisely, it holds between distinct material continuants 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 continuant is inherited by the later. Thus we will have axioms to the effect that from c derivesFrom c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.
Corresponds to the RO relation "derives from" Derivation is a relation holding between non-identicals. More precisely, it holds between distinct material continuants 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 continuant is inherited by the later. Thus we will have axioms to the effect that from c derivesFrom c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.
Some real world entity is referred to by a symbol (code)
Granular parts are the constitutent parts of Pluralities. They are of the same sort. Generally pluralities have a high number of grains. The loss of a grain has no effect on the sortality of the identity of the plurality.
A participant of a process, with the additional condition that the component instance is causally active in the relevant process. The latter is the reason that it has also the relation causedBy as an additional parent.
B hasBranch A if it is contiguous with B and if some flow of matter or energy of information flows form B to A. Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
Relating a process with the time interval it covers.
hasLocus 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.
relates a place with an entity which occurs, inheres, or is part of it
A is an original part of B iff A is not a proper part of B now but A was a proper part of B at the time A came into existence.
x is an originating physical part of y iff x is a proper physical part of Y and x has been a physical part of y up to now.
participant which either - a) comes into being during the process or - b) undergoes some change during the process and constitutes (one of) the main result(s) of the process
HasParticipant is a primitive instance-level relation between a process and a continuant which participates in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane hasParticipant this particular sample of hemoglobin.
Physical parthood obtains between material or immaterial objects. It is distinguished from locatedness by a series of criteria, see: Schulz S, Daumke P, Smith B, Hahn U. How to distinguish parthood from location in bioontologies. AMIA Annu Symp Proc. 2005:669-73. PMID: 16779124 Note that for abstract entities like information artefacts there is a separate relation pair "abstractPartOf" and "hasAbstractPart"
Relating a processual entity with some point in the interval it occupies. If there is no temporal extension (process boundary, event) it relates it to the time it occurs.
links a process to a quality that describes this process, e.g. normal, abnormal
relates a process to a role which qualifies this process
Relates a process with a subprocess (process part)
Something that occurs can be the realization of a function, a disposition, or a role.
inheresIn relates a dependent continuant (a state, quality, property, function, disposition) with the independent continuant it depends on. Note that for processes there is a separate relation pair "hasProcessQuality" and "processQualityOf"
locusOf is a very broad relation which relates the place at which an entity occurs, inheres, or is part of.
a relation which is more general than derivation (in the OBO RO sense) as it also includes actual parts (provided they were always parts), as well as original (historical) parts
outcomeOf 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
participatesIn is a primitive instance-level relation between a continuant and a process.
A participant passively participating in a process.
Containment is location without parthood. E.g. Food is contained in the stomach. Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
Abutting without physical overlap. Cf. Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
No sharing of parts and no sharing of boundaries. Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
Partly or completely covering from outside (establishing boundaries, enclosing, confining, enclosing, circumscribing)
p precededBy p' if and only if: given any process p at a time t, there is some process p' at time t', and t' is earlier than t.
Process A precedes B if A ends at or totally happens before the beginning of B
links a quality to a process, e.g. normal, abnormal
Relates a subprocess with the process it is part of.
As for physical part of, with the additional constraint that part and whole are distinct (nothing can be proper physical part of itself)
relates a quality with an (abstract) value region, following DOLCE
relates a value region with a quality , following DOLCE
Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
most general relation that relates an entity with its physical location
The temporal arrangement of processes, events, durations and temporal measurements
Abutting without mechanical connection. Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118
This attribute specifies the process which the property describes, and on which the property (of this observable) depends. The process can be very general (e.g. "excretion").
Direct site represents the specific entity on which the observation is directly made, and is used when the observation is indirect, such as when a direct observation is not possible to be done on the entity in which the observable inheres.
This attribute is used to specify the continuant (such as a body structure or organism) that is causally active in the process on which the property depends. It appears to have the same meaning as 'has_agent' in the OBO Relations Ontology. It may specialize the meaning of the process named as the value of CHARACTERIZES, or it may simply recapitulate the meaning that is already there. The PROCESS AGENT can be left unspecified.
This attribute specifies the duration of the process characterized by the observable property type.
This attribute is used to specify the ingredient substance type of the independent continuant in which the property inheres.
This attribute is used to specify a body site or other location of the independent continuant in which the property inheres.
This attribute specifies the substance produced by the process characterized by the observable property type.
This attribute specifies the independent continuant in which the quality inheres, and on which the dependent quality (of this observable) depends.
This attribute specifies the independent continuant which the value of "relative to" is part of, if different from the independent continuant in which the property type inheres. Its main use is for relative substance concentrations, where the same substance has a concentration in two different fluids. In this case, TOWARDS and RELATIVE TO will have the same substance value, and the two fluids will be represented as values of INHERES IN and REL-TO PART OF.
This attribute is used to specify body state, timing, challenges, and other situations that must be true of the entity to be observed.
This attribute is used to specify the type of inherent quality or process that is to be observed. Its values are abstract types of quality (length, odor, concentration) or abstract types of process features (rate, speed), and do not include qualities that are located (length of arm, odor of urine), or given a value (elevated concentration).
This attribute is used to specify the denominator of a relational property type, such as a ratio or proportion.
This attribute refers to the scale of the result of an observation or a diagnostic test (i.e., quantitative, qualitative, semi-quantitative).
This attribute links concepts in the Observable entity hierarchy to their related Technique.
This attribute is used to specify the third element of a relational quality, the first two elements being the type of property and the entity in which the quality inheres.
This attribute represents the units used in assigning a value to an observation.
biological structure that deviates from what is considered normal and that evolved during lifetime
Ill-formed state of a biological entity,acquired after birth [steschu 20071010]
acquired pathological static processual entity
pathological state acquired during lifetime
An action is a processual entity that that is promoted by an agent, having a clear role distinction between agent and patient
an action which externally acts upon a biological system
"adult" as the value of a developmental stage. E.g. a 4 year old dog has a quality which has its value located in "adult value region".
Positively charged particles composed of two protons and two neutrons, i.e. equivalent to Helium nuclei
(QCR) ro:hasPart some CarbonHydrogenSubstructure and ((hasComponent myx 2 CarboxyGroup) and (hasComponent min 1 CarboxyGroup) and (hasComponent exactly 1 AminoGroup)) or ((hasComponent max 2 AminoGroup) and (hasComponent min 1 AminoGroup) and (hasComponent exactly 1 CarboxyGroup))
Amino Acids molecules or residues (residues as in peptide bonds)
In chemistry, an amino acid is any molecule that contains both amine and carboxyl functional groups. However, in biochemistry, this more general term is frequently used to refer to alpha amino acids (amino acids in which the amino and carboxylate functionalities are attached to the same carbon, called ?–carbon). Amino Acids have at least one amino and one carboxy group. Those having two carboxy groups have only one amino group and vice versa.
amino acid or peptide molecule or structure
Chain of amino acids, joined by peptide bonds. Folded or unfolded.
The information that describes the make-up of a (physical) amino acid sequence.
collection with molecules or atoms as granular parts (but which may have also bigger granular parts) that is produced by a biological system (e.g. blood, urine, ivory)
collection with molecules or atoms as granular parts of the same sort
Multicellular organisms of the kingdom Animalia
language used in communication between animals
the role a chemical plays if used to combat a bacterial infection
The role an entity plays when it has been artificially produced. [steschu 20071010]
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.
Cluster of bacteria, usually cultured from a single cell.
An (often habitual) action of an organism that is the realization of some disposition
Process occuring on molecular level. It has exclusivly subclasses of MolecularEntity as participants.
Sequence as an entity of information. The same sequence can inhere in different biopolymers. Sequence information can be theoretical, therefore a "real" sequence is not implied.
chain (segment) of similar monomers such as proteins or nucleotides
Action that has some biological entity as agent
Plurality of several individual organisms living closely together, usually for mutual benefit
a function that inheres in some structured biological entity.
The whole process from origin to death of an organism
Process specific for biological systems.
quality of being visible with or without microscope
values that describe the size of biological entities
space that is located inside a biological entity
Role of Non-drug material used for therapeutic Purpose
Monomolecular entity that stems from some organism
Entire biological structure that constitutes a (living) organism. A body can be living or dead. Whether a living organism coincides with its body or hasPart its body, is controversial. We use "hasPhysicalPart" for relating organism to body. Being reflexive, this would not be incompatible with a view in which a living organism is a body.
Suspension and / or solution of biomolecules, ions, bigger particles in Water.
Mereological sum of heterogeneous body components that constitute a functional unity
a biological state that is considered "normal"
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
The information that describes the make-up of a (physical) carbohydrate sequence.
The role a substance plays in accelerating a chemical reaction
A categorization system is a human artifact that aims at partinioning object classes, denotations, or concepts of a given domain.
Constituting unit of an organism. The boundary between cell, syncytium and subcellular fragments such as platelets is problematic. Hence no full definition possible.
CellByLocusPartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint.
CellByTaxonPartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint.
CellByTypePartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint.
Living cell that is not removed from a living system
Semipermeable lipid bilayer found in all cells.[1] It contains a wide variety of biological molecules, primarily proteins and lipids, which are involved in a vast array of cellular processes, and also serves as the attachment point for both the intracellular cytoskeleton and, if present, the cell wall.
Components which only can be formed inside living cells but which may survive their host cell.
the central control unit of an organism. Constitutes the brain in higher organisms.
Any role performed by a chemical substance.
the role an organism plays in relation to its parent
Organized form of DNA in cells, containing one very long, continuous piece of DNA, which contains many genes, regulatory elements and other intervening nucleotide sequences. Includes also the DNA-bound proteins which serve to package and manage the DNA.
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.
The fuzzyness of this class is due to the "same sort" criterion.
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)
biological structure that deviates from what is considered normal and that already existed at birth
Ill-formed state of a biological entity, present from birth [steschu 20071010]
congenital pathological static processual entity
Gelatinous, semi-transparent fluid that fills most cells. E
Place for currently non maintained classes. It should be assured that they are not being referred to by application ontologies that import BioTop
A DNA is a complex, high-molecular-weight biochemical macromolecule composed of deoxyribonumcleotide chains that convey genetic information. Any kind of NucleicAcid that is composed of Deoxyribonucleotides is here defined as DNA.
body that is the transformation of a living body after death
abstract region in which the values of developmental stages are located
any kind of information that is fully expressible by a sequence of binary values.
A disposition is a realizable entity. Its manifestation is a process its bearer is involved in virtue of the bearer's physical make-up.
The role of a chemical of biological entity of being deliberately used in virtue of its expected positive impact on a dysfunctional biological system
The role a person plays that is occupied by educational activities
An oxygenated metabolite from polyunsaturated 20 carbon fatty acids including lipoxygenase and cyclooxygenase products and their synthetic analogs. This includes the prostaglandins and thromboxanes. (UMLS SN)
evolving organism before birth, with not yet fully formed organs
An embryo or any structure derived from it. There may be structures derived from an embryo that are no longer considered embryonic ones, hence no full definition.
"embryonic" as the value of a developmental stage. E.g. a 3 days old mouse embryo has a quality which has its value located in "embryonic value region".
Separately distinguishable molecular structure, neither part of nor attached to any other molecular structure. Atoms are not considered molecular structures. The hierarchy of entire entities mirrors the hierarchy of structures.
not (properPartOf some MonoMolecularEntity) REMOVED
(QCR) Peptide and hasComponent min 101 AminoAcidMonomer and not (ro:properPartOf some MolecularEntity)
Amino Acid Polymer longer than 100 monomers.
The role a peptide plays in accelerating a biochemical reaction
An eukaryote is an organism with a complex cell or cells, in which the genetic material is organized into a membrane-bound nucleus or nuclei. Most Eukaryots are multicellular, haowever, there are some which are always unicellular (protists, some fungi) but there are also unicellular developmental stages (zygotes) of plants and animals.
What happens at one point in time, typically a process boundary
The role a measurement plays if it has been produced in the context of the quantitative assessment of a biological system
Carboxylic acid often with a long unbranched aliphatic tail.
The role that may inhere in any biological structure, state, or process that is of reportable interest in a diagnostic process.
The role of an entity components of which are used for supplying energy and vital substrates to a biological system
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.
Heterotrophic organisms characterized by a chitinous cell wall.
"gaseous" as the value of a states of matter. E.g. a portion of air has a quality which has its value located in "gaseous value region"
region of nucleic acid macromolecule that carry information
TODO: Discuss whether all genes are DNA !
information that can be interpreted by a genetic code
The totality of hereditary information of an organism
delineated surface of a large solid body in space (earth, moon, sun,...)
entity governing a defined group of people
action in which physical or legal groups interact
the role a human plays as active part in a health system
A role an entity plays as an actor or participant in processes that assess or influence the health status of an organism.
Organic compounds that contain a ring structure containing N as proton receptor. Important parts of DNA and RNA molecules.
The role a biologically active substance plays when it participates in the transmission of messages across a certain distance in an organism.
language used in communication between non-human animals
Process in which a human creates an intellectual product
negatively affecting a biological system by using physical force
Continuant entity that has neither a mass nor a volume and which do not inhere in other entities.
Physical spaces that have a threedimensional spatial dimension but no mass. Old name: immaterial anatomical entity
A process with non-material participants, e.g. legal or organizational entities or information objects
immaterial three dimensional physical entity
A role that is played by any biological entity in virtue of the defense of an organism against infective agents
A role a chemical plays for measuring or analyzing other chemical processes
Piece of information (not necessarily human) , as it exists independently of any potential material carrier.
Substances which do not include carbon and its derivatives as their principal elements. However, carbides, carbonates, cyanides, cyanates and carbon disulfide are included in this class.
An intellectual product is a piece of information that is the outcome of a human reasoning process
two or more interaction partners exerce a mutual effect that may lead to structural transformation.
born organism, not yet in reproductive age
system of signs used for communication between biological and / or machine agents
Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint.
nonmaterial entity that as an existence in a legal system
Fat-soluble (lipophilic), naturally-occurring molecule.
"liquid" as the value of a states of matter. E.g. a portion of water has a quality which has its value located in "liquid value region"
Entirety of the biological structure that constitutes a living organism
Living complex biological system which functions as a stable whole. In contrast to colonial organisms their components generally cannot survive on their own. We conceive organisms in a material sense. Therefore we do not assume any ontological difference between a unicellular organism and the cell it is made of. "Colonial Organism" are not considered Organisms. We here include viruses into the category of organisms. Organism in an inactive form which are not dead are considered living organisms. Whether a living organism coincides with its body or hasPart its body, is controversial. We use "hasPhysicalPart" for relating organism to body. Being reflexive, this would not be incompatible with a view in which a living organism is a body.
An action performed by a machine. A machine is here seen as a non-biological artifact.
language used for processing by machines
size values of objects that are visible to the naked eye
action in which a subject cares for the well-being of some biological entity
MaterialEntityBySizePartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint.
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).
Numeric quantity or cardinality, reference for measurement processes. Example kilogram, hour, ampere.
Plan that is realized by a measurement process.
an action that aims at producing a measurement
Process that endures while something or some person is part of a legal entity
biological function ascribed to the behavioral manisfestations of the brain
process in an organism as a realization of a mental function
organism that can be seen only through a microscope
size values of objects that are too small to be seen without a microscope
Difficult concept. Better to be expressed by the primitive "mental function"
Cells that grow and replicate continuously outside the living organism.
MolecularEntityByEntiretyPartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint.
MolecularEntityByGranularityPartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint.
MolecularEntityByOrganicInorganicPartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint.
not self-standing aggregation of atoms which are part of a bigger molecule
Particle that consists of entire molecules.
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.
Monomers can be described as constituted by molecularl groups. They are not repetitive and can constitute the building blocks of Polymers.
Organisms that are composed by more than one cell.
A role a molecule plays if it acts as a neurotransmitter
Lipids that have aliphatic chains and no steroid rings
a biological state that is considered "abnormal"
abstract region in which the value "noncanonical" of canonicity is located
nucleic acid nucleotide or nucleoside molecule or residue
A nucleic acid is a complex, high-molecular-weight biochemical macromolecule composed of nucleotide chains that convey genetic information.
Comment: (QCR) hasComponent exactly 1 HeterocyclicBase and hasComponent exactly 1 Phosphate and hasComponent only (Phosphate or Ribose or HeterocyclicBase) and hasComponent exactly 1 Pentose
The information that describes the make-up of a (physical) nucleotide sequence.
The role that determines the occupation that characterizes the daily life of a human being or animal.
An oligo or polymer macromolecular structure is a molecule of moderate to high relative molecular mass, the structure of which essentially comprises the multiple repetition (n >= 2) of units derived from molecules of low relative molecular mass.
line bounding a two-dimensional biological entity
Macroscopic, well delimited, functionally and structurally characterized part of an organism. Exact criteria of what an organ is do not exist.
Substances containing carbon and its derivatives as their prinicipal elements, usually combined with itself and with atoms of one or more other element such as hydrogen, oxygen, nitrogen, sulfur, phosphorus, chlorine or fluorine. They exist in either carbon chain or carbon ring form. Excludes carbides, carbonates and carbon oxides.
action in which single biological organisms interact
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.
any biological process that involves a whole organism
the role an organism plays in relation to its children
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.
pathological structure, disposition, or process. This disjoint category helps properly represent diseases becauses it is often left open whether they are meant as pathological structure, disposition, or process. In case this is to be left open, the relation has_locus should be used to connect them to anatomical entities
any kind of disposition considered non-canonical. The criteria of canonicity are not further specified. The classification of certain dispositions as dysfunctional or pathological is dependent on a historic and cultural context. Dysfunction or disease therefore hasn't the status of a universal.
a biological process which is non-canonic
Condition of an organism that deviates from what is considered normal. Often referred to by the terms "disorder", "disease", "syndrome", "sign", or "symptom". None of these denote clearly delineated ontological categories. See disease role etc.
biological structure that is non-canonic
former name: "ill formed biological structure"
state of an organism or an organism part requiring therapeutic or palliative intervention
Inherent Function of a protein or a part of it.
Comment: We here use the term peptide in the most general sense, viz. a oligo or polymer made out of amino acids.
Phosphate is a salt of phosphoric acid or a functional group on organic compounds.
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, ...
process that only involves non-biological participants
Quality of being solid, liquid, gaseous, ... [steschu20080127]
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
plurality of identical polymolecular entities
collection of identical things of the same sort
Collection of two or more organisms of the same sort.
typically the boundary of a time interval
The role of a substance of mixture of substance of a defined amount thereof to be toxic to (parts of) biological organisms
negatively affecting the integrity of a biologival system caused by one or more chemical substances
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.
Collection of Organisms of a defined taxon living in a given geographic area. In contrast to the "official" definition ("same species") this definition is broader and corresponds better to the use of the term in some contexts (e.g. "mixed population of 2 species")
all child classes of population are only meant as examples demonstrating how population classes can be postcoordinated
Liquid constituted by different kinds of collectives, e.g. aqueous NaCl solution
Solid constituted by different kinds of collectives, e.g. a NaCl crystal, granite
Composition of granular components of the same kind.
Hinders a process or the realization of a function. As the second argument represents sth non-existent, it cannot be expressed in FOL. Hence the special status of this class. (Cf. Condovardi et al. "Preventing Existence, FOIS 2001)
The role an action plays if it is intended to protect an organism against negative external influences.
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.
action in which a new physical or informational entity comes into being
Cell lacking membrane enclosed organells
Mostly only proteins but composition with other molecules possible (e.g. Fe -> Hemoglobin) or also lipoproteins
Structural domain is the smallest element of protein tertiary structure that is self-stabilizing and often folds independently of the rest of the amino acid chain. It may contain one or more structural motives (ProteinSubstructure). A protein domain typically has its own function, the overall function of the protein results from the composition of the functions of all of its structural domains.
A secondary substructure of a protein (protein Motif)
A protein molecule that assembles with other protein molecules to form a protein complex. May have its own function. However, most proteinsubunits do not gain functionality until associated with the other subunits.
A quality is a realizable entity that is exhibited if it inheres in some other entity or entities at all.
any kind of NucleicAcid that is composed of Ribonucleotides which are not Deoxyribonucleotides
process in which energy-rich particles or electromagnetic waves participate
A role a chemical plays as participant in a chemical reation
The role a (membrane) protein or protein complex plays in acting as a receptor.
set of rules governing a particular kind of activity (WordNet)
organization that has the function of issuing regulations or laws
the role a human plays if he / she is involved in research activities
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.
the role an organism plays in relation to another organism that has the same parents
A role that can inhere in states, processes, or even in certain independent continuants (e.g. in a deformity). This a role is ascribed to an entity in a diagnostic process where the symptom is suspected to indicate a second state or process)
The role of a biological entity that participates in a biological signalling process.
"solid" as the value of a states of matter. E.g. a stone has a quality which has its value located in "solid value region"
The role attributed to a - mainly fiat - part of an object that is the site of some process or the location of some object of interest.
An independent continuant entity that is neither a bearer of qualities nor inheres in any other entity (snap:SpatialRegion)
species drosophila melanogaster value region
species saccharomyces cerevisiae value region
States of matter are the distinct forms that different phases of matter take on.
Values that a states of matter can have, e.g. liquid, solid.
Static condition as a special case of process in which temporal parts are neglected.
One of a group of polycyclic, 17-carbon-atom, fused-ring compounds occurring both in natural and synthetic forms. Included here are naturally occurring and synthetic steroids, bufanolides, cardanolides, homosteroids, norsteroids, and secosteroids. (UMLS SN)
StructuredBiologicalCompoundByCanonicityPartition ontologically irrelevant partition node
StructuredBiologicalCompoundByGranularityPartition ontologically irrelevant disjoint partition: structured biological compound by granularity
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
All those things that are not identified by belonging to any biological species Borderline cases are artifacts that use biological substance (a table, a cloth, a house, a meal ...) A criterion to draw the boundary is whether or not the species affiliation has some structural or functional implication.
SubatomicEntityByChargePartition ontologically irrelevant node: disjoint partition: subatomic entity by charge
the role an animal or human plays as receiver of health care
A submolecular group or moiety is a group of covalently bound atoms that occurs only as part of a molecule
action in which molecular entities interact
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.
1. The role of a continuant participating in a process with an expected positive impact on a dysfunctional biological system. 2. The role of a process with an expected positive impact on a dysfunctional biological system.
Aggregate of an arbitrary number of congeneric cells (cells with identical specialized characteristics), embedded into an amount of matter (matrix) that work together to perform a specific function.
action with the intention to produce a positive effect on a biological organism or in which a malfunctioning is relieved or disrupted.
action with the intention to relieve or disrupt a malfunctioning of a biological entity
action with the intention to produce a positive effect on a biological organism
plane bounding a three-dimensional biological entity
Organisms that (always or in certain initial stages) consist of a single cell. We conceive organisms in a material sense. Therefore we do not assume any ontological difference between a monocellular organism and the cell it is made of.
action that relates a user with an object he/she uses
A value region is an abstract region in which (non quantitative) values of qualities are located.
Sub-microscopic agent that requires a host cell to grow and reproduce. Viruses resemble other organisms in that they possess genes, and can evolve in infected cells by natural selection. We therefore classify viruses as organisms, although there is an open debate.
The role a certain substance can play in an organism. Vitamins are organic compounds that are essential to an organism for metabolic reactions. They are not food. Vitamin does not include essential fatty acids or essential amino acids
A water molecule is composed by one oxygen molecule and two hydrogen molecules
(wikipedia) disturbance that propagates through space and time, usually with transference of energy
Mass concentration is reported in mg/dL, while substance concentration is reported in mmol/L. If it is unclear how it will be reported, it is impossible to specify the detailed property, and a "quantity concentration" property type would have to be chosen as the value of PROPERTY TYPE.
Problem mapping to BioTop, only LivingOrganism (or Body) exists. Possibly stemming from the problem of demarcating substance and structure