]> Stefan Schulz, Martin Boeker, Elena Beisswanger, Holger Stenzhorn, Djamila Raufie, Daniel Schober, Udo Hahn http://creativecommons.org/licenses/by/3.0 20120129 An experimental top level ontology for biology and medicine. application/rdf+xml http://purl.org/biotop/biotop.owl Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network (mapping files available) BioTop Biology, Medicine 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 attached to 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 branch 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 contiguous with ContiguousWith describes the connection between two material objects that abut and can transmit forces. continuous 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 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 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 encodes 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) has branch 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 duration hasDuration relates a process with the time interval it covers. has origin has point in time 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 proper physical 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. cooccurring with The relation coocurring with relates two processes if their temporal extensions overlap. 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) physically connected to 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 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 disconnected from 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 originates from 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 physically adjacent to physicalAdjacentTo relates two physical objects that abut without physical overlap. Examples: see subrelations physically contains 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 interconnects physically surrounded by Partly or completely covering from outside (establishing boundaries, enclosing, confining, enclosing, circumscribing) physically surrounds Partly or completely covering from outside (establishing boundaries, enclosing, confining, enclosing, circumscribing) physically traverses crossing over and crossing through proper physical part of 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. touches 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 acquired abnormal structure biological structure that deviates from what is considered normal and that evolved during lifetime acquired pathological condition Ill-formed state of a biological entity,acquired after birth [steschu 20071010] acquired pathological static processual entity acquired pathological state pathological state acquired during lifetime action on biological system an action which externally acts upon a biological system adult organism organism in reproductive phase adult value region "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". affecting Producing a direct effect on age quality the quality of having a livespan alga alpha particle Positively charged particles composed of two protons and two neutrons, i.e. equivalent to Helium nuclei amino acid molecule or residue 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 amino acids as monomers and polymers amino acid sequence Chain of amino acids, joined by peptide bonds. Folded or unfolded. amino acid sequence information The information that describes the make-up of a (physical) amino acid sequence. amount of body substance 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) amphibian analyzing animal cell animal excluding human animal including human Multicellular organisms of the kingdom Animalia animal language language used in communication between animals animal population EXAMPLE OF POPULATION antibiotic role the role a chemical plays if used to combat a bacterial infection archaebacterial cell Archaebacterium artefact role The role an entity plays when it has been artificially produced. [steschu 20071010] arthropod one arthropod arthropod population EXAMPLE OF POPULATION bacteria population EXAMPLE OF POPULATION bacterial cell Bacterium bacterial colony Cluster of bacteria, usually cultured from a single cell. bakers yeast cell one saccharomyces cerevisiae cell bakers yeast population EXAMPLE OF POPULATION behavior An (often habitual) action of an organism that is the realization of some disposition bio molecular process Process occuring on molecular level. It has exclusivly subclasses of MolecularEntity as participants. bio molecular sequence information 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 structure chain (segment) of similar monomers such as proteins or nucleotides biological action Action that has some biological entity as agent biological boundary boundary in or of a biological entity biological colony Plurality of several individual organisms living closely together, usually for mutual benefit biological function a function that inheres in some structured biological entity. biological life The whole process from origin to death of an organism biological processual entity Process specific for biological systems. biological size quality of being visible with or without microscope biological size value region values that describe the size of biological entities biological space space that is located inside a biological entity biological system role A role specific to biological processes biomedical material role Role of Non-drug material used for therapeutic Purpose biomolecule Monomolecular entity that stems from some organism 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. FMAID:256135 Body body liquid Suspension and / or solution of biomolecules, ions, bigger particles in Water. body system Mereological sum of heterogeneous body components that constitute a functional unity candida albicans cell One candida albicans cell candida albicans population EXAMPLE OF POPULATION canonical processual entity a process that is considered normal canonical static processual entity a biological state that is considered "normal" canonical state carbohydrate molecule or residue carbohydrate monomer carbohydrate sequence information The information that describes the make-up of a (physical) carbohydrate sequence. catalytic role The role a substance plays in accelerating a chemical reaction categorization system A categorization system is a human artifact that aims at partinioning object classes, denotations, or concepts of a given domain. causing action that causes an effect cell in vivo Living cell that is not removed from a living system cell membrane 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 nucleus central nervous system the central control unit of an organism. Constitutes the brain in higher organisms. chain of carbohydrate monomers chain of nucleotide monomers chemical role Any role performed by a chemical substance. child role the role an organism plays in relation to its parent 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. class gamma proteobacteria value region EXAMPLE OF TAXON REGION class insecta value region EXAMPLE OF TAXON REGION class mammalia value region EXAMPLE OF TAXON REGION class saccharomycetes value region EXAMPLE OF TAXON REGION complicating causes to become more severe congenital abnormal structure biological structure that deviates from what is considered normal and that already existed at birth congenital pathological condition Ill-formed state of a biological entity, present from birth [steschu 20071010] congenital pathological static processual entity congenital pathological state pathological state present at birth cytoplasm Gelatinous, semi-transparent fluid that fills most cells. E DNA chain 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. dead body body that is the transformation of a living body after death death End of live of a biological system developmental quality Ontogenetic stage developmental value region abstract region in which the values of developmental stages are located digital entity any kind of information that is fully expressible by a sequence of binary values. (OBI 306) disrupting Producing a negative effect on drug role The role of a chemical of biological entity of being deliberately used in virtue of its expected positive impact on a dysfunctional biological system educator role The role a person plays that is occupied by educational activities 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) electron Negatively Charged Particle embryonic organism evolving organism before birth, with not yet fully formed organs embryonic structure 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 value region "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". entire carbohydrate monomer entire molecular entity 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 nucleic acid molecule not (properPartOf some MonoMolecularEntity) REMOVED entire protein molecule Amino Acid Polymer longer than 100 monomers. (QCR) Peptide and hasComponent min 101 AminoAcidMonomer and not (ro:properPartOf some MolecularEntity) enzyme role The role a peptide plays in accelerating a biochemical reaction epithelial cell escherichia coli cell escherichia coli population EXAMPLE OF 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 population EXAMPLE OF POPULATION examination result role The role a measurement plays if it has been produced in the context of the quantitative assessment of a biological system family drosophilidae value region EXAMPLE OF TAXON REGION family enterobacteriaceaea value region EXAMPLE OF TAXON REGION family hominidae value region EXAMPLE OF TAXON REGION family role family saccharomycetaceae value region EXAMPLE OF TAXON REGION fatty acid molecule or residue Carboxylic acid often with a long unbranched aliphatic tail. finding role The role that may inhere in any biological structure, state, or process that is of reportable interest in a diagnostic process. fish food role The role of an entity components of which are used for supplying energy and vital substrates to a biological system fruit fly one drosophila melanogaster fruit fly population EXAMPLE OF POPULATION fungus On fungus organisms Heterotrophic organisms characterized by a chitinous cell wall. fungus population EXAMPLE OF POPULATION gaseous value region "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" gene TODO: Discuss whether all genes are DNA ! region of nucleic acid macromolecule that carry information gene information Information that resides on a gene. genetic information information that can be interpreted by a genetic code genome sum of genetic material in a cell genome information The totality of hereditary information of an organism genus candida value region EXAMPLE OF TAXON REGION genus drosophila value region EXAMPLE OF TAXON REGION genus escherichia value region EXAMPLE OF TAXON REGION genus homo value region EXAMPLE OF TAXON REGION genus saccharomyces value region EXAMPLE OF TAXON REGION geographic surface previous name "geographic entity" delineated surface of a large solid body in space (earth, moon, sun,...) government entity governing a defined group of people great ape one great ape great ape population EXAMPLE OF POPULATION group interaction action in which physical or legal groups interact growing process health professional role the role a human plays as active part in a health system health related role A role an entity plays as an actor or participant in processes that assess or influence the health status of an organism. heterocyclic base molecule or residue Organic compounds that contain a ring structure containing N as proton receptor. Important parts of DNA and RNA molecules. hormone role The role a biologically active substance plays when it participates in the transmission of messages across a certain distance in an organism. human human action Action that has some human as agent human epithelial cell human language language used in communication between non-human animals human population EXAMPLE OF POPULATION human reasoning Process in which a human creates an intellectual product hurting negatively affecting a biological system by using physical force immaterial processual entity A process with non-material participants, e.g. legal or organizational entities or information objects immunologic role A role that is played by any biological entity in virtue of the defense of an organism against infective agents indicating action that indicates something indicator role A role a chemical plays for measuring or analyzing other chemical processes individual behavior Behavior of an individual organism inorganic molecular entity 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. insect one insect insect population EXAMPLE OF POPULATION intellectual product An intellectual product is a piece of information that is the outcome of a human reasoning process interacting two or more interaction partners exerce a mutual effect that may lead to structural transformation. intra cellular process Process occuring in a cell. invertebrate juvenile organism born organism, not yet in reproductive age juvenile value region kingdom animalia value region EXAMPLE OF TAXON REGION kingdom archaea value region EXAMPLE OF TAXON REGION kingdom bacteria value region EXAMPLE OF TAXON REGION kingdom chromista value region EXAMPLE OF TAXON REGION kingdom fungi value region EXAMPLE OF TAXON REGION kingdom plantae value region EXAMPLE OF TAXON REGION kingdom protozoa value region EXAMPLE OF TAXON REGION kingdom viruses value region EXAMPLE OF TAXON REGION language 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. legal entity nonmaterial entity that as an existence in a legal system lipid molecule or residue Fat-soluble (lipophilic), naturally-occurring molecule. liquid value region "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" living body Entirety of the biological structure that constitutes a living organism living organism 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. machine action An action performed by a machine. A machine is here seen as a non-biological artifact. machine language language used for processing by machines macroscopic value region size values of objects that are visible to the naked eye mammal one mammal mammal population EXAMPLE OF POPULATION managing care action in which a subject cares for the well-being of some biological entity measure Numeric quantity or cardinality, reference for measurement processes. Example kilogram, hour, ampere. measurement method Plan that is realized by a measurement process. measuring action an action that aims at producing a measurement membership Process that endures while something or some person is part of a legal entity mental function biological function ascribed to the behavioral manisfestations of the brain mental process process in an organism as a realization of a mental function microorganism organism that can be seen only through a microscope microscopic value region size values of objects that are too small to be seen without a microscope mind Difficult concept. Better to be expressed by the primitive "mental function" modified cell Cells that grow and replicate continuously outside the living organism. molecular function Inherent function of a single molecule. molecular residue not self-standing aggregation of atoms which are part of a bigger molecule molecule complex Particle that consists of entire molecules. monomer Monomers can be described as constituted by molecularl groups. They are not repetitive and can constitute the building blocks of Polymers. multicellular organism Organisms that are composed by more than one cell. neoplastic process neuroreactive role A role a molecule plays if it acts as a neurotransmitter neutron Neutral Particle non steroid lipid Lipids that have aliphatic chains and no steroid rings noncanonical processual entity a process that is considered abnormal noncanonical static processual entity a biological state that is considered "abnormal" noncanonical state nucleic acid nucleotide or nucleoside molecule or residue nucleic acid structure A nucleic acid is a complex, high-molecular-weight biochemical macromolecule composed of nucleotide chains that convey genetic information. nucleoside molecule nucleotide molecule 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 sequence information The information that describes the make-up of a (physical) nucleotide sequence. nurse role The role a nurse plays occupational role The role that determines the occupation that characterizes the daily life of a human being or animal. oligo or polymer 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. one dimensional boundary line bounding a two-dimensional biological entity order diptera value region EXAMPLE OF TAXON REGION order enterobacteriales value region EXAMPLE OF TAXON REGION order primates value region EXAMPLE OF TAXON REGION order saccharomycetales value region EXAMPLE OF TAXON REGION organ Macroscopic, well delimited, functionally and structurally characterized part of an organism. Exact criteria of what an organ is do not exist. organ part FMAID:82472 Cardinal organ part organ system FMAID:7149 Organ system organ system part FMAID:67509 Organ system subdivistion organic molecular entity 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. Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. organism action Action that has some organism as agent Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. organism interaction action in which single biological organisms interact organism part 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 process any biological process that involves a whole organism organization collection of human or legal entities parent role the role an organism plays in relation to its children pathological condition 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 disposition 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. prior label "dysfunction" pathological process a biological process which is non-canonic pathological static processual entity pathological state 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 structure former name: "ill formed biological structure" biological structure that is non-canonic pathological value region state of an organism or an organism part requiring therapeutic or palliative intervention peptide function Inherent Function of a protein or a part of it. peptide structure Comment: We here use the term peptide in the most general sense, viz. a oligo or polymer made out of amino acids. phosphate Phosphate is a salt of phosphoric acid or a functional group on organic compounds. phylum arthropoda value region EXAMPLE OF TAXON REGION phylum ascomycota value region EXAMPLE OF TAXON REGION phylum chordata value region EXAMPLE OF TAXON REGION phylum proteobacteria value region EXAMPLE OF TAXON REGION physical processual entity process that only involves non-biological participants physical state Quality of being solid, liquid, gaseous, ... [steschu20080127] former name: StateOfAggregation physician role The role a physician plays plant Organism of the kingdom Plantae. plant cell plant population EXAMPLE OF POPULATION poison role The role of a substance of mixture of substance of a defined amount thereof to be toxic to (parts of) biological organisms poisoning negatively affecting the integrity of a biologival system caused by one or more chemical substances population 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") portion of heterogenous liquid Liquid constituted by different kinds of collectives, e.g. aqueous NaCl solution portion of heterogenous solid Solid constituted by different kinds of collectives, e.g. a NaCl crystal, granite prevention action 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) preventive role The role an action plays if it is intended to protect an organism against negative external influences. primate one primate primate population EXAMPLE OF POPULATION producing action in which a new physical or informational entity comes into being prokaryote Cell lacking membrane enclosed organells protein complex Mostly only proteins but composition with other molecules possible (e.g. Fe -> Hemoglobin) or also lipoproteins protein domain 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 substructure A secondary substructure of a protein (protein Motif) protein subunit 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. protist Organisms of the kingdom Protista protist population EXAMPLE OF POPULATION proton Positively Charged Particle RNA chain any kind of NucleicAcid that is composed of Ribonucleotides which are not Deoxyribonucleotides radiation process in which energy-rich particles or electromagnetic waves participate reagent role A role a chemical plays as participant in a chemical reation receptor role The role a (membrane) protein or protein complex plays in acting as a receptor. regulation or law set of rules governing a particular kind of activity (WordNet) regulatory body organization that has the function of issuing regulations or laws reptile researcher role the role a human plays if he / she is involved in research activities rickettsia cell sibling role the role an organism plays in relation to another organism that has the same parents sign or symptom role 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) signalling role The role of a biological entity that participates in a biological signalling process. social action action that targets a population social behavior Behaviour of a group of organisms solid value region "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" spatial reference role 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 region An independent continuant entity that is neither a bearer of qualities nor inheres in any other entity (snap:SpatialRegion) species candida albicans value region EXAMPLE OF TAXON REGION species drosophila melanogaster value region EXAMPLE OF TAXON REGION species escherichia coli value region EXAMPLE OF TAXON REGION species homo sapiens value region EXAMPLE OF TAXON REGION species saccharomyces cerevisiae value region EXAMPLE OF TAXON REGION state of matter States of matter are the distinct forms that different phases of matter take on. state of matter value region Values that a states of matter can have, e.g. liquid, solid. static processual entity State Static condition as a special case of process in which temporal parts are neglected. 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) structured biological entity 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 nonbiological compound 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. subfamily drosophilinae value region EXAMPLE OF TAXON REGION subject of care role the role an animal or human plays as receiver of health care submolecular group A submolecular group or moiety is a group of covalently bound atoms that occurs only as part of a molecule subphylum saccharomycotina value region EXAMPLE OF TAXON REGION subphylum vertebrata value region EXAMPLE OF TAXON REGION substance interaction action in which molecular entities interact syncytium Fusion of cells therapeutic role 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. 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 process process occurring in a tissue treating action with the intention to produce a positive effect on a biological organism or in which a malfunctioning is relieved or disrupted. treating condition action with the intention to relieve or disrupt a malfunctioning of a biological entity treating organism action with the intention to produce a positive effect on a biological organism two dimensional biological entity surface or plane in a biological entity unicellular 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. using action action that relates a user with an object he/she uses vertebrate one vertebrate vertebrate population EXAMPLE OF 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 population EXAMPLE OF POPULATION vitamin role 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 water molecule A water molecule is composed by one oxygen molecule and two hydrogen molecules well formed biological structure yeast cell Unicellular Fungi. yeast population EXAMPLE OF POPULATION canonical value region abstract region in which the value "canonical" of canonicity is located cellular component Components which only can be formed inside living cells but which may survive their host cell. immaterial object immaterial physical entity Physical spaces that have a threedimensional spatial dimension but no mass. Old name: immaterial anatomical entity material object 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 entity noncanonical value region abstract region in which the value "noncanonical" of canonicity is located point in time typically the boundary of a time interval 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. processual entity process quality A quality that inheres in some process taxon quality The quality of one or more biological organisms, as well as of parts of organism of partaining to a biological taxon. [steschu20080127] time interval the interval between two time points