Stefan Schulz, Martin Boeker, Elena Beisswanger, Holger Stenzhorn, Djamila Raufie, Daniel Schober, Udo Hahn 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 Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network (mapping files available) application/rdf+xml 20120424 http://purl.org/biotop/biotop.owl 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) http://creativecommons.org/licenses/by/3.0 An experimental top level ontology for biology and medicine. Biology, Medicine BioTop Last modification Apr 24, 2012 by Stefan Schulz 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. Example: a header is an abstract part of a jpg file. abstract part of Relation in which immaterial entities (information entities, roles, qualities) are involved. abstractlyRelatedTo is meant as an organizing parent. It should not be asserted. abstractly related to 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. agent in 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 attached to 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. bearer of 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 branch of Expresses a causal chain between material or processual entities. causallyRelatedTo is meant as an organizing parent. It should not be asserted. causally related to Causation of a process is here understood as the disjunction between agency (a continuant causes a process) and as the realization of a disposition, i.e. a disposition is considered the cause of a process. caused by Causation of a process is here understood as the disjunction between agency (a continuant causes a process) and as the realization of a disposition, i.e. a disposition is considered the cause of a process. causes 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. component part of ContiguousWith describes the connection between two material objects that abut and can transmit forces. contiguous with 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 continuous with The relation coocurring with relates two processes if their temporal extensions overlap. cooccurring with denotedBy (inverse: denotes) relates entities with symbols, which are information entities. In contrast to encoding, the denoted entity is completely independent on the denoting one. Example: The inflamation of a sinus is denoted by the word "Sinusitis", as well as by the ICD code "J10" denoted by denotedBy (inverse: denotes) relates entities with symbols, which are information entities. In contrast to encoding, the denoted entity is completely independent on the denoting one. Example: The inflamation of a sinus is denoted by the word "Sinusitis", as well as by the ICD code "J10" denotes 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 derived into 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 derives from 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) encodedBy 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) encodes feature of hasGranularPart (inverse: granularPartOf) relate Pluralities with their constituents. The constituents 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. Example: A cow is a granular part of a herd of cows. A water molecule is a granular part of some amount of water granular part of 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. has abstract part 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. has agent 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 has branch 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. has component part hasDuration relates a process with the time interval it covers. has duration has feature hasGranularPart (inverse: granularPartOf) relate Pluralities with their constituents. The constituents 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. Example: A cow is a granular part of a herd of cows. A water molecule is a granular part of some amount of water has granular part hasLocus (inverse: locusOf) 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 located where the process is located. Example: A heart pumping process is located in a heart. has locus has origin hasOriginalPart (inverse: originalPartOf). original parts of A are no longer parts of A but were parts of A when they came into existence. Example: Apples harvested from an apple tree, tissue samples in a lab. has original part originatingPhysicalPartOf (inverse: hasOriginatingPhysicalPart) An originating physical part is a proper physical part that has never ceased to be part of the object it is related to. Example: my brain is an originating physical part of my body has originating physical part 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. has outcome 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. has participant 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. has patient hasPhysicalPart (inverse: physicalPartOf) obtains between physical objects. The distinction between parthood and locatedness is complex and does not obey strict criteria. This relation is reflexive, i.e. every physical object has itself as a physical 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" has physical part 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. has point in time 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. has process quality processRoleOf (abstract: hasProcessRole) links a role attributed to a process to this process. Process roles are asserted where the process cannot sufficiently be described by the roles of its participants only. Example: The process of injuring has the process role "allowed" in case of a surgical intervention agreed by both the patient and the doctor. has process role hasProcessualPart (inverse: processualPartOf) relates a process with a subprocess (process part). Example: G1 phase is a processual part of the process mitosis. has processual part 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. has proper physical part Realization occurs if a disposition or function manifests itself as a process. Example: the disposition of a bird to fly (which exists even when it does not fly) is realized by its process of flying. has realization 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. inheres in replaced by denotes is about hasLocus (inverse: locusOf) 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 located where the process is located. Example: A heart pumping process is located in a heart. locus of hasOriginalPart (inverse: originalPartOf). original parts of A are no longer parts of A but were parts of A when they came into existence. Example: Apples harvested from an apple tree, tissue samples in a lab. original part of 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 originates from originatingPhysicalPartOf (inverse: hasOriginatingPhysicalPart) An originating physical part is a proper physical part that has never ceased to be part of the object it is related to. Example: my brain is an originating physical part of my body originating physical part of 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. outcome of 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. participates in 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. patient in physicallylocatedIn (inverse: physical location of) relates two physical objects in terms of space. All point in space occupied by the first object are also occupied by the second object. Generally, this relation is further specificed in terms of parthood or containment Examples: my thumb is physically located in my hand, food is located in my stomach or also in the cavity of my stomach. A 10 Euro bill is located in my wallet. physical location of hasPhysicalPart (inverse: physicalPartOf) obtains between physical objects. The distinction between parthood and locatedness is complex and does not obey strict criteria. This relation is reflexive, i.e. every physical object has itself as a physical 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" physical part of physicalAdjacentTo relates two physical objects that abut without physical overlap. Examples: see subrelations physically adjacent to 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. physically bounded by 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. physically bounds 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. physically connected to 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 physically contained in 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 physically contains 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 physically disconnected from physically interconnects physicallylocatedIn (inverse: physical location of) relates two physical objects in terms of space. All point in space occupied by the first object are also occupied by the second object. Generally, this relation is further specificed in terms of parthood or containment Examples: my thumb is physically located in my hand, food is located in my stomach or also in the cavity of my stomach. A 10 Euro bill is located in my wallet. physically located in Partly or completely covering from outside (establishing boundaries, enclosing, confining, enclosing, circumscribing) physically surrounded by Partly or completely covering from outside (establishing boundaries, enclosing, confining, enclosing, circumscribing) physically surrounds crossing over and crossing through physically traverses precedes (inverse: precededBy) relates two processes, one of which ends or totally happens before the second one begins. Example: fecundation preceeds embryonic development. preceded by precedes (inverse: precededBy) relates two processes, one of which ends or totally happens before the second one begins. Example: fecundation preceeds embryonic development. precedes 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. process quality of processRoleOf (abstract: hasProcessRole) links a role attributed to a process to this process. Process roles are asserted where the process cannot sufficiently be described by the roles of its participants only. Example: The process of injuring has the process role "allowed" in case of a surgical intervention agreed by both the patient and the doctor. process role of hasProcessualPart (inverse: processualPartOf) relates a process with a subprocess (process part). Example: G1 phase is a processual part of the process mitosis. processual part of Relations that connect processes with other entities. processuallyRelatedTo is meant as an organizing parent. It should not be asserted. processually related to 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. proper physical part of qualityLocated (inverse: qualityLocationOf) 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 "quality located some RedColorRegion" quality located qualityLocated (inverse: qualityLocationOf) 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 "quality located some RedColorRegion" quality location of Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 ramification of Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 ramifies Realization occurs if a disposition or function manifests itself as a process. Example: the disposition of a bird to fly (which exists even when it does not fly) is realized by its process of flying. realization of Most general relation that relates entities in terms of physical location. spatiallyRelatedTo is meant as an organizing parent. It should not be asserted. spatially related to The temporal arrangement of processes, events, durations and temporal measurements. temporallyRelatedTo is meant as an organizing parent. It should not be asserted. temporally related to 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 touches AcquiredAbnormalStructure biological structure that deviates from what is considered normal and that evolved during lifetime acquired abnormal structure AcquiredPathologicalCondition Ill-formed state of a biological entity,acquired after birth [steschu 20071010] acquired pathological condition AcquiredPathologicalStaticProcessualEntity pathological state acquired during lifetime acquired pathological static processual entity acquired pathological state Action An action is a processual entity that that is promoted by an agent, having a clear role distinction between agent and patient action ActionOnBiologicalSystem an action which externally acts upon a biological system action on biological system AdultOrganism organism in reproductive phase adult organism AdultValueRegion "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". adult value region Affecting Producing a direct effect on affecting AgeQuality the quality of having a livespan age quality Alga alga AlphaParticle Positively charged particles composed of two protons and two neutrons, i.e. equivalent to Helium nuclei alpha particle AminoAcidMoleculeOrResidue 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)) 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 molecule or residue AminoAcidOrPeptideMoleculeOrStructure amino acids as monomers and polymers amino acid or peptide molecule or structure AminoAcidSequence Chain of amino acids, joined by peptide bonds. Folded or unfolded. amino acid sequence AminoAcidSequenceInformation The information that describes the make-up of a (physical) amino acid sequence. amino acid sequence information AmountOfBodySubstance 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) amount of body substance AmountOfPureSubstance collection with molecules or atoms as granular parts of the same sort amount of pure substance Amphibian amphibian Analyzing analyzing AnimalCell animal cell AnimalExcludingHuman animal excluding human AnimalIncludingHuman Multicellular organisms of the kingdom Animalia animal including human AnimalLanguage language used in communication between animals animal language AnimalPopulation EXAMPLE OF POPULATION animal population AntibioticRole the role a chemical plays if used to combat a bacterial infection antibiotic role ArchaebacterialCell Archaebacterium archaebacterial cell ArtefactRole The role an entity plays when it has been artificially produced. [steschu 20071010] artefact role Arthropod one arthropod arthropod ArthropodPopulation EXAMPLE OF POPULATION arthropod population Atom 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. atom BacteriaPopulation EXAMPLE OF POPULATION bacteria population BacterialCell Bacterium bacterial cell BacterialColony Cluster of bacteria, usually cultured from a single cell. bacterial colony BakersYeastCell one saccharomyces cerevisiae cell bakers yeast cell BakersYeastPopulation EXAMPLE OF POPULATION bakers yeast population Behavior An (often habitual) action of an organism that is the realization of some disposition behavior BioMolecularProcess Process occuring on molecular level. It has exclusivly subclasses of MolecularEntity as participants. bio molecular process BioMolecularSequenceInformation 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. bio molecular sequence information BioMolecularSequenceStructure chain (segment) of similar monomers such as proteins or nucleotides bio molecular sequence structure BiologicalAction Action that has some biological entity as agent biological action BiologicalBoundary boundary in or of a biological entity biological boundary BiologicalColony Plurality of several individual organisms living closely together, usually for mutual benefit biological colony BiologicalFunction a function that inheres in some structured biological entity. biological function BiologicalLife The whole process from origin to death of an organism biological life BiologicalProcessualEntity Process specific for biological systems. biological processual entity BiologicalSize quality of being visible with or without microscope biological size BiologicalSizeValueRegion values that describe the size of biological entities biological size value region BiologicalSpace space that is located inside a biological entity biological space BiologicalSystemRole A role specific to biological processes biological system role BiomedicalMaterialRole Role of Non-drug material used for therapeutic Purpose biomedical material role Biomolecule Monomolecular entity that stems from some organism biomolecule Bird bird Body 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. body FMAID:256135 Body BodyLiquid Suspension and / or solution of biomolecules, ions, bigger particles in Water. body liquid BodySystem Mereological sum of heterogeneous body components that constitute a functional unity body system CandidaAlbicansCell One candida albicans cell candida albicans cell CandidaAlbicansPopulation EXAMPLE OF POPULATION candida albicans population CanonicalProcessualEntity a process that is considered normal canonical processual entity CanonicalStaticProcessualEntity a biological state that is considered "normal" canonical static processual entity canonical state CanonicalValueRegion abstract region in which the value "canonical" of canonicity is located canonical value region Canonicity The condition of an entity (state, process, function, object) in terms of being well or ill-formed or behaving canonicity CanonicityValueRegion abstract region in which values of canonicity are located canonicity value region CarbohydrateMoleculeOrResidue carbohydrate molecule or residue CarbohydrateMonomer carbohydrate monomer CarbohydrateSequenceInformation The information that describes the make-up of a (physical) carbohydrate sequence. carbohydrate sequence information CatalyticRole The role a substance plays in accelerating a chemical reaction catalytic role CategorizationSystem A categorization system is a human artifact that aims at partinioning object classes, denotations, or concepts of a given domain. categorization system Causing action that causes an effect causing Cell Constituting unit of an organism. The boundary between cell, syncytium and subcellular fragments such as platelets is problematic. Hence no full definition possible. cell CellByLocusPartition CellByLocusPartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. * CellByTaxonPartition CellByTaxonPartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. * CellByTypePartition CellByTypePartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. * CellInVivo Living cell that is not removed from a living system cell in vivo CellMembrane 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. cell membrane CellNucleus cell nucleus CellularComponent Components which only can be formed inside living cells but which may survive their host cell. cellular component CentralNervousSystem the central control unit of an organism. Constitutes the brain in higher organisms. central nervous system ChainOfCarbohydrateMonomers chain of carbohydrate monomers ChainOfNucleotideMonomers chain of nucleotide monomers ChemicalRole Any role performed by a chemical substance. chemical role ChildRole the role an organism plays in relation to its parent child role ChlamydiaCell chlamydia cell Chromosome 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. chromosome ClassGammaProteobacteriaValueRegion EXAMPLE OF TAXON REGION class gamma proteobacteria value region ClassInsectaValueRegion EXAMPLE OF TAXON REGION class insecta value region ClassMammaliaValueRegion EXAMPLE OF TAXON REGION class mammalia value region ClassSaccharomycetesValueRegion EXAMPLE OF TAXON REGION class saccharomycetes value region CollectiveMaterialEntity 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. collective material entity Complicating causes to become more severe complicating CompoundOfCollectiveMaterialEntities 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 compound of collective material entities Condition 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) condition CongenitalAbnormalStructure biological structure that deviates from what is considered normal and that already existed at birth congenital abnormal structure CongenitalPathologicalCondition Ill-formed state of a biological entity, present from birth [steschu 20071010] congenital pathological condition CongenitalPathologicalStaticProcessualEntity pathological state present at birth congenital pathological static processual entity congenital pathological state Cytoplasm Gelatinous, semi-transparent fluid that fills most cells. E cytoplasm DEPRECATED Place for currently non maintained classes. It should be assured that they are not being referred to by application ontologies that import BioTop DNAChain 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. DNA chain DeadBody body that is the transformation of a living body after death dead body Death End of live of a biological system death DevelopmentalQuality Ontogenetic stage developmental quality DevelopmentalValueRegion abstract region in which the values of developmental stages are located developmental value region DigitalEntity any kind of information that is fully expressible by a sequence of binary values. (OBI 306) digital entity Disposition A disposition is a realizable entity. Its manifestation is a process its bearer is involved in virtue of the bearer's physical make-up. disposition Disrupting Producing a negative effect on disrupting DrugRole The role of a chemical of biological entity of being deliberately used in virtue of its expected positive impact on a dysfunctional biological system drug role EducatorRole The role a person plays that is occupied by educational activities educator role Eicosanoid 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) eicosanoid Electron Negatively Charged Particle electron EmbryonicOrganism evolving organism before birth, with not yet fully formed organs embryonic organism EmbryonicStructure 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 structure EmbryonicValueRegion "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". embryonic value region EntireCarbohydrateMonomer entire carbohydrate monomer EntireMolecularEntity 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. entire molecular entity EntireNucleicAcidMolecule not (properPartOf some MonoMolecularEntity) REMOVED entire nucleic acid molecule EntireProteinMolecule Amino Acid Polymer longer than 100 monomers. (QCR) Peptide and hasComponent min 101 AminoAcidMonomer and not (ro:properPartOf some MolecularEntity) entire protein molecule EnzymeRole The role a peptide plays in accelerating a biochemical reaction enzyme role EpithelialCell epithelial cell EscherichiaColiCell escherichia coli cell EscherichiaColiPopulation EXAMPLE OF POPULATION escherichia coli population Eukaryote 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. eukaryote EukaryotePopulation EXAMPLE OF POPULATION eukaryote population Event ExaminationResultRole The role a measurement plays if it has been produced in the context of the quantitative assessment of a biological system examination result role FamilyDrosophilidaeValueRegion EXAMPLE OF TAXON REGION family drosophilidae value region FamilyEnterobacteriaceaeaValueRegion EXAMPLE OF TAXON REGION family enterobacteriaceaea value region FamilyHominidaeValueRegion EXAMPLE OF TAXON REGION family hominidae value region FamilyOfIndividualOrganisms unclear classe. to be revised family of individual organisms FamilyRole family role FamilySaccharomycetaceaeValueRegion EXAMPLE OF TAXON REGION family saccharomycetaceae value region FattyAcidMoleculeOrResidue Carboxylic acid often with a long unbranched aliphatic tail. fatty acid molecule or residue FindingRole The role that may inhere in any biological structure, state, or process that is of reportable interest in a diagnostic process. finding role Fish fish FoodRole The role of an entity components of which are used for supplying energy and vital substrates to a biological system food role FruitFly one drosophila melanogaster fruit fly FruitFlyPopulation EXAMPLE OF POPULATION fruit fly population Function 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. function Fungus Heterotrophic organisms characterized by a chitinous cell wall. On fungus organisms fungus FungusPopulation EXAMPLE OF POPULATION fungus population GaseousValueRegion "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" gaseous value region Gene region of nucleic acid macromolecule that carry information gene TODO: Discuss whether all genes are DNA ! GeneInformation Information that resides on a gene. gene information GeneRegion part of a gene gene region GeneticInformation information that can be interpreted by a genetic code genetic information Genome sum of genetic material in a cell genome GenomeInformation The totality of hereditary information of an organism genome information GenusCandidaValueRegion EXAMPLE OF TAXON REGION genus candida value region GenusDrosophilaValueRegion EXAMPLE OF TAXON REGION genus drosophila value region GenusEscherichiaValueRegion EXAMPLE OF TAXON REGION genus escherichia value region GenusHomoValueRegion EXAMPLE OF TAXON REGION genus homo value region GenusSaccharomycesValueRegion EXAMPLE OF TAXON REGION genus saccharomyces value region GeographicSurface delineated surface of a large solid body in space (earth, moon, sun,...) previous name "geographic entity" geographic surface Government entity governing a defined group of people government GreatApe one great ape great ape GreatApePopulation EXAMPLE OF POPULATION great ape population GroupInteraction action in which physical or legal groups interact group interaction GrowingProcess growing process HealthProfessionalRole the role a human plays as active part in a health system health professional role HealthRelatedRole A role an entity plays as an actor or participant in processes that assess or influence the health status of an organism. health related role HeterocyclicBaseMoleculeOrResidue Organic compounds that contain a ring structure containing N as proton receptor. Important parts of DNA and RNA molecules. heterocyclic base molecule or residue HormoneRole The role a biologically active substance plays when it participates in the transmission of messages across a certain distance in an organism. hormone role Human human HumanAction Action that has some human as agent human action HumanEpithelialCell human epithelial cell HumanLanguage language used in communication between non-human animals human language HumanPopulation EXAMPLE OF POPULATION human population HumanReasoning Process in which a human creates an intellectual product human reasoning Hurting negatively affecting a biological system by using physical force hurting ImmaterialNonphysicalEntity Continuant entity that has neither a mass nor a volume and which do not inhere in other entities. immaterial nonphysical entity ImmaterialObject Physical spaces that have a threedimensional spatial dimension but no mass. Old name: immaterial anatomical entity immaterial object immaterial physical entity ImmaterialPhysicalEntity ImmaterialProcessualEntity A process with non-material participants, e.g. legal or organizational entities or information objects immaterial processual entity ImmaterialThreeDimensionalPhysicalEntity three-dimensional space immaterial three dimensional physical entity ImmunologicRole A role that is played by any biological entity in virtue of the defense of an organism against infective agents immunologic role Indicating action that indicates something indicating IndicatorRole A role a chemical plays for measuring or analyzing other chemical processes indicator role IndividualBehavior Behavior of an individual organism individual behavior InformationEntity InformationObject Piece of information (not necessarily human) , as it exists independently of any potential material carrier. information object information entity InorganicMolecularEntity 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. inorganic molecular entity Insect one insect insect InsectPopulation EXAMPLE OF POPULATION insect population InstantaneousProcess What happens at one point in time, typically a process boundary. Name "event" deprecated instantaneous process IntellectualProduct An intellectual product is a piece of information that is the outcome of a human reasoning process intellectual product Interacting two or more interaction partners exerce a mutual effect that may lead to structural transformation. interacting IntraCellularProcess Process occuring in a cell. intra cellular process Invertebrate invertebrate JuvenileOrganism born organism, not yet in reproductive age juvenile organism JuvenileValueRegion juvenile value region KingdomAnimaliaValueRegion EXAMPLE OF TAXON REGION kingdom animalia value region KingdomArchaeaValueRegion EXAMPLE OF TAXON REGION kingdom archaea value region KingdomBacteriaValueRegion EXAMPLE OF TAXON REGION kingdom bacteria value region KingdomChromistaValueRegion EXAMPLE OF TAXON REGION kingdom chromista value region KingdomFungiValueRegion EXAMPLE OF TAXON REGION kingdom fungi value region KingdomPlantaeValueRegion EXAMPLE OF TAXON REGION kingdom plantae value region KingdomProtozoaValueRegion EXAMPLE OF TAXON REGION kingdom protozoa value region KingdomVirusesValueRegion EXAMPLE OF TAXON REGION kingdom viruses value region Language system of signs used for communication between biological and / or machine agents language LanguagePartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. LegalEntity nonmaterial entity that as an existence in a legal system legal entity LipidMoleculeOrResidue Fat-soluble (lipophilic), naturally-occurring molecule. lipid molecule or residue LiquidValueRegion "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" liquid value region LivingBody Entirety of the biological structure that constitutes a living organism living body LivingOrganism 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. living organism organism MachineAction An action performed by a machine. A machine is here seen as a non-biological artifact. machine action MachineLanguage language used for processing by machines machine language MacroscopicValueRegion size values of objects that are visible to the naked eye macroscopic value region Mammal one mammal mammal MammalPopulation EXAMPLE OF POPULATION mammal population ManagingCare action in which a subject cares for the well-being of some biological entity managing care MaterialEntity MaterialEntityBySizePartition MaterialEntityBySizePartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. * MaterialObject 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). material object material entity Measure Numeric quantity or cardinality, reference for measurement processes. Example kilogram, hour, ampere. measure MeasurementMethod Plan that is realized by a measurement process. measurement method MeasuringAction an action that aims at producing a measurement measuring action Membership Process that endures while something or some person is part of a legal entity membership MentalFunction biological function ascribed to the behavioral manisfestations of the brain mental function MentalProcess process in an organism as a realization of a mental function mental process Microorganism organism that can be seen only through a microscope microorganism MicroscopicValueRegion size values of objects that are too small to be seen without a microscope microscopic value region Mind Difficult concept. Better to be expressed by the primitive "mental function" mind ModifiedCell Cells that grow and replicate continuously outside the living organism. modified cell MolecularEntityByEntiretyPartition MolecularEntityByEntiretyPartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. * MolecularEntityByGranularityPartition MolecularEntityByGranularityPartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. * MolecularEntityByOrganicInorganicPartition MolecularEntityByOrganicInorganicPartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. * MolecularFunction Inherent function of a single molecule. molecular function MolecularResidue not self-standing aggregation of atoms which are part of a bigger molecule molecular residue MoleculeComplex Particle that consists of entire molecules. molecule complex MonoMolecularEntity 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. mono molecular entity Monomer Monomers can be described as constituted by molecularl groups. They are not repetitive and can constitute the building blocks of Polymers. monomer MulticellularOrganism Organisms that are composed by more than one cell. multicellular organism NeoplasticProcess neoplastic process NeuroreactiveRole A role a molecule plays if it acts as a neurotransmitter neuroreactive role Neutron Neutral Particle neutron NonSteroidLipid Lipids that have aliphatic chains and no steroid rings non steroid lipid NoncanonicalProcessualEntity a process that is considered abnormal noncanonical processual entity NoncanonicalStaticProcessualEntity a biological state that is considered "abnormal" noncanonical static processual entity noncanonical state NoncanonicalValueRegion abstract region in which the value "noncanonical" of canonicity is located noncanonical value region NucleicAcidNucleotideOrNucleosideMoleculeOrResidue nucleic acid nucleotide or nucleoside molecule or residue NucleicAcidRegion nucleic acid region NucleicAcidStructure A nucleic acid is a complex, high-molecular-weight biochemical macromolecule composed of nucleotide chains that convey genetic information. nucleic acid structure NucleosideMolecule nucleoside molecule NucleotideMolecule Comment: (QCR) hasComponent exactly 1 HeterocyclicBase and hasComponent exactly 1 Phosphate and hasComponent only (Phosphate or Ribose or HeterocyclicBase) and hasComponent exactly 1 Pentose nucleotide molecule NucleotideSequenceInformation The information that describes the make-up of a (physical) nucleotide sequence. nucleotide sequence information NurseRole The role a nurse plays nurse role ObjectQuality A quality that inheres in some material or immaterial physical object. object quality ObservingAction OccupationalRole The role that determines the occupation that characterizes the daily life of a human being or animal. occupational role OligoOrPolymer 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. oligo or polymer OneDimensionalBoundary line bounding a two-dimensional biological entity one dimensional boundary OneDimensionalPhysicalEntity line or curve one dimensional physical entity OrderDipteraValueRegion EXAMPLE OF TAXON REGION order diptera value region OrderEnterobacterialesValueRegion EXAMPLE OF TAXON REGION order enterobacteriales value region OrderPrimatesValueRegion EXAMPLE OF TAXON REGION order primates value region OrderSaccharomycetalesValueRegion EXAMPLE OF TAXON REGION order saccharomycetales value region Organ Macroscopic, well delimited, functionally and structurally characterized part of an organism. Exact criteria of what an organ is do not exist. organ OrganPart organ part FMAID:82472 Cardinal organ part OrganSystem organ system FMAID:7149 Organ system OrganSystemPart organ system part FMAID:67509 Organ system subdivistion OrganicMolecularEntity 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. organic molecular entity OrganicMolecularEntityPartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. OrganismAction Action that has some organism as agent organism action OrganismByDevelopmentalStagePartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. OrganismByTaxonPartition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. OrganismInteraction action in which single biological organisms interact organism interaction OrganismPart 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. organism part OrganismProcess any biological process that involves a whole organism organism process Organization collection of human or legal entities organization ParentRole the role an organism plays in relation to its children parent role Particular 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. particular entity ParticularEntity PathologicalCondition 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 pathological condition PathologicalDisposition 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. pathological disposition prior label "dysfunction" PathologicalProcess a biological process which is non-canonic pathological process PathologicalStaticProcessualEntity 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. pathological static processual entity pathological state PathologicalStructure biological structure that is non-canonic pathological structure former name: "ill formed biological structure" PathologicalValueRegion state of an organism or an organism part requiring therapeutic or palliative intervention pathological value region PeptideFunction Inherent Function of a protein or a part of it. peptide function PeptideStructure Comment: We here use the term peptide in the most general sense, viz. a oligo or polymer made out of amino acids. peptide structure Phosphate Phosphate is a salt of phosphoric acid or a functional group on organic compounds. phosphate PhylumArthropodaValueRegion EXAMPLE OF TAXON REGION phylum arthropoda value region PhylumAscomycotaValueRegion EXAMPLE OF TAXON REGION phylum ascomycota value region PhylumChordataValueRegion EXAMPLE OF TAXON REGION phylum chordata value region PhylumProteobacteriaValueRegion EXAMPLE OF TAXON REGION phylum proteobacteria value region PhysicalBoundary 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. physical boundary PhysicalForce force as defined by physics (mass + acceleration) physical force PhysicalLength physical length (e.g. in meters) physical length PhysicalMass Mass (gravity independent) - not weight. Measured in g, kg, ... physical mass PhysicalProcessualEntity process that only involves non-biological participants physical processual entity PhysicalState Quality of being solid, liquid, gaseous, ... [steschu20080127] former name: StateOfAggregation physical state PhysicalVolume Volume of three-dimensional objects - third potency of length physical volume PhysicianRole The role a physician plays physician role Plan A plan is an information entity that describes a series of steps to be carried out in order to achiev a goal. Plans can only be realized by processes. (OBI 344) plan Plant Organism of the kingdom Plantae. plant PlantCell plant cell PlantPopulation EXAMPLE OF POPULATION plant population PluralityOfIdenticalPolymolecularEntities collection of identical things of the same sort plurality of identical polymolecular entities PluralityOfOrganisms Collection of two or more organisms of the same sort. plurality of organisms PointInTime typically the boundary of a time interval point in time PoisonRole The role of a substance of mixture of substance of a defined amount thereof to be toxic to (parts of) biological organisms poison role Poisoning negatively affecting the integrity of a biologival system caused by one or more chemical substances poisoning PolyMolecularCompositeEntity 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. poly molecular composite entity Population 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 population PortionOfHeterogenousLiquid Liquid constituted by different kinds of collectives, e.g. aqueous NaCl solution portion of heterogenous liquid PortionOfHeterogenousSolid Solid constituted by different kinds of collectives, e.g. a NaCl crystal, granite portion of heterogenous solid PortionOfHomogenousMatter Composition of granular components of the same kind. portion of homogenous matter PreventionAction 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) prevention action PreventiveRole The role an action plays if it is intended to protect an organism against negative external influences. preventive role Primate one primate primate PrimatePopulation EXAMPLE OF POPULATION primate population Process 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. process processual entity ProcessQuality A quality that inheres in some process process quality Producing action in which a new physical or informational entity comes into being producing Prokaryote Cell lacking membrane enclosed organells prokaryote ProteinComplex Mostly only proteins but composition with other molecules possible (e.g. Fe -> Hemoglobin) or also lipoproteins protein complex ProteinDomain 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. protein domain ProteinSubstructure A secondary substructure of a protein (protein Motif) protein substructure ProteinSubunit 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. protein subunit Protist Organisms of the kingdom Protista protist ProtistPopulation EXAMPLE OF POPULATION protist population Proton Positively Charged Particle proton Quality Quality RNAChain any kind of NucleicAcid that is composed of Ribonucleotides which are not Deoxyribonucleotides RNA chain Radiation process in which energy-rich particles or electromagnetic waves participate radiation ReagentRole A role a chemical plays as participant in a chemical reation reagent role ReceptorRole The role a (membrane) protein or protein complex plays in acting as a receptor. receptor role RegulationOrLaw set of rules governing a particular kind of activity (WordNet) regulation or law RegulatoryBody organization that has the function of issuing regulations or laws regulatory body Reptile reptile ResearcherRole the role a human plays if he / she is involved in research activities researcher role RickettsiaCell rickettsia cell Role 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. role SiblingRole the role an organism plays in relation to another organism that has the same parents sibling role SignOrSymptomRole 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) sign or symptom role SignallingRole The role of a biological entity that participates in a biological signalling process. signalling role SocialAction action that targets a population social action SocialBehavior Behaviour of a group of organisms social behavior SolidValueRegion "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" solid value region SpatialReferenceRole 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. spatial reference role SpatialRegion An independent continuant entity that is neither a bearer of qualities nor inheres in any other entity (snap:SpatialRegion) spatial region SpeciesCandidaAlbicansValueRegion EXAMPLE OF TAXON REGION species candida albicans value region SpeciesDrosophilaMelanogasterValueRegion EXAMPLE OF TAXON REGION species drosophila melanogaster value region SpeciesEscherichiaColiValueRegion EXAMPLE OF TAXON REGION species escherichia coli value region SpeciesHomoSapiensValueRegion EXAMPLE OF TAXON REGION species homo sapiens value region SpeciesSaccharomycesCerevisiaeValueRegion EXAMPLE OF TAXON REGION species saccharomyces cerevisiae value region StateOfMatter States of matter are the distinct forms that different phases of matter take on. state of matter StateOfMatterValueRegion Values that a states of matter can have, e.g. liquid, solid. state of matter value region StaticProcessualEntity Static condition as a special case of process in which temporal parts are neglected. static processual entity State Steroid 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) steroid StructuredBiologicalCompoundByCanonicityPartition StructuredBiologicalCompoundByCanonicityPartition ontologically irrelevant partition node * StructuredBiologicalCompoundByGranularityPartition StructuredBiologicalCompoundByGranularityPartition ontologically irrelevant disjoint partition: structured biological compound by granularity * StructuredBiologicalEntity 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 structured biological entity StructuredNonbiologicalCompound 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. structured nonbiological compound SubatomicEntityByChargePartition SubatomicEntityByChargePartition ontologically irrelevant node: disjoint partition: subatomic entity by charge * SubatomicParticle Parts of Atoms. subatomic particle SubfamilyDrosophilinaeValueRegion EXAMPLE OF TAXON REGION subfamily drosophilinae value region SubjectOfCareRole the role an animal or human plays as receiver of health care subject of care role SubmolecularGroup A submolecular group or moiety is a group of covalently bound atoms that occurs only as part of a molecule submolecular group SubphylumSaccharomycotinaValueRegion EXAMPLE OF TAXON REGION subphylum saccharomycotina value region SubphylumVertebrataValueRegion EXAMPLE OF TAXON REGION subphylum vertebrata value region SubstanceInteraction action in which molecular entities interact substance interaction Syncytium Fusion of cells syncytium TaxonQuality The quality of one or more biological organisms, as well as of parts of organism of partaining to a biological taxon. [steschu20080127] taxon quality TaxonValueRegion 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. taxon value region TemporalEntity TherapeuticRole 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. therapeutic role Time Point or interval on the time axis time temporal entity TimeInterval the interval between two time points time interval Tissue 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. tissue TissueProcess process occurring in a tissue tissue process Treating action with the intention to produce a positive effect on a biological organism or in which a malfunctioning is relieved or disrupted. treating TreatingCondition action with the intention to relieve or disrupt a malfunctioning of a biological entity treating condition TreatingOrganism action with the intention to produce a positive effect on a biological organism treating organism TwoDimensionalBiologicalEntity surface or plane in a biological entity two dimensional biological entity TwoDimensionalBoundary plane bounding a three-dimensional biological entity two dimensional boundary TwoDimensionalPhysicalEntity plane two dimensional physical entity UnicellularOrganism 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. unicellular organism UsingAction action that relates a user with an object he/she uses using action ValueRegion A value region is an abstract region in which (non quantitative) values of qualities are located. value region Vertebrate one vertebrate vertebrate VertebratePopulation EXAMPLE OF POPULATION vertebrate population Virus 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. virus VirusPopulation EXAMPLE OF POPULATION virus population VitaminRole 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 vitamin role WaterMolecule A water molecule is composed by one oxygen molecule and two hydrogen molecules water molecule Wave (wikipedia) disturbance that propagates through space and time, usually with transference of energy wave WellFormedBiologicalStructure well formed biological structure YeastCell Unicellular Fungi. yeast cell YeastPopulation EXAMPLE OF POPULATION yeast population owl:Thing Last modification Apr 24, 2012 by Stefan Schulz Stefan Schulz, Martin Boeker, Elena Beisswanger, Holger Stenzhorn, Djamila Raufie, Daniel Schober, Udo Hahn 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 Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network (mapping files available) application/rdf+xml 20120424 http://purl.org/biotop/biotop.owl 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) http://creativecommons.org/licenses/by/3.0 An experimental top level ontology for biology and medicine. Biology, Medicine BioTop Last modification Apr 24, 2012 by Stefan Schulz