Stefan Schulz, Martin Boeker, Elena Beisswanger, Holger Stenzhorn, Djamila Raufie, Daniel Schober, Udo Hahn
An experimental top level ontology for biology and medicine.
Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network (mapping files available)
Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Stefan-Meier-Strasse 26, 79104 Freiburg, Germany Institute of Medical Informatics, Statistics and Documentation, Medical University of Graz, Auenbruggerplatz 2/V , 8036 Graz (Austria)
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
Last modification Apr 24, 2012 by Stefan Schulz
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
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
ContiguousWith describes the connection between two material objects that abut and can transmit forces.
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
EncodedBy (inverse: encodes) relates entities with symbols, which are information entities. In contrast to denotation, encoding entails that the makeup of the encoded entity is determined by the code. There is a dependence of the former on the latter. Note that the association of human-made codes with entities (e.g. for coding and classification systems like ICD-10) is nothing more than denotation and is therefore not in the scope of the encodedBy (encodes) relation. Example: A material gene sequence is related to a sequence of nucleotide symbols (like ACCGATTGA)
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
hasDuration relates a process with the time interval it covers.
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.
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.
The relation coocurring with relates two processes if their temporal extensions overlap.
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.
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
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
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
Partly or completely covering from outside (establishing boundaries, enclosing, confining, enclosing, circumscribing)
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
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 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
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 Acids molecules or residues (residues as in peptide bonds)
(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 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)
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]
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"
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.
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.
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.
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
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.
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
Amino Acid Polymer longer than 100 monomers.
(QCR) Peptide and hasComponent min 101 AminoAcidMonomer and not (ro:properPartOf some MolecularEntity)
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.
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
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"
TODO: Discuss whether all genes are DNA !
region of nucleic acid macromolecule that carry information
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
A process with non-material participants, e.g. legal or organizational entities or information objects
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
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
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.
not self-standing aggregation of atoms which are part of a bigger molecule
Particle that consists of entire molecules.
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"
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
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.
former name: "ill formed biological structure"
biological structure that is non-canonic
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.
process that only involves non-biological participants
Quality of being solid, liquid, gaseous, ... [steschu20080127]
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
all child classes of population are only meant as examples demonstrating how population classes can be postcoordinated
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")
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
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.
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.
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
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)
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.
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
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
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
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
abstract region in which the value "canonical" of canonicity is located
Components which only can be formed inside living cells but which may survive their host cell.
Physical spaces that have a threedimensional spatial dimension but no mass. Old name: immaterial anatomical entity
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).
abstract region in which the value "noncanonical" of canonicity is located
typically the boundary of a time interval
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.
The quality of one or more biological organisms, as well as of parts of organism of partaining to a biological taxon. [steschu20080127]