]> Holger Stenzhorn Elena Beisswanger Last modification March 31, 2009 Stefan Schulz / Elena Beiswanger Stefan Schulz Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network (mapping files available) Stefan Schulz, Elena Beisswanger, Udo Hahn, Joachim Wermter, Holger Stenzhorn and Anand Kumar: "From GENIA to BioTop - Towards a top-level Ontology for Biology" (in Proceedings of the American Medical Informatics Association Annual Conference (AMIA 2006), Washington, November 2006) Holger Stenzhorn, Stefan Schulz and Elena Beisswanger: "Towards a Top-Domain Ontology for Linking Biomedical Ontologies" (in Proceedings of the 12th World Congress on Health (Medical) Informatics (Medinfo 2007), Brisbane, Australia, August 2007) Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Stefan-Meier-Strasse 26, 79104 Freiburg, Germany BioTop Stefan Schulz, Elena Beisswanger, Joachim Wermter and Udo Hahn: "Towards an Upper Level Ontology for Molecular Biology" (in Proceedings of the International Conference on Formal Ontology in Information Systems (FOIS 2006), Baltimore, USA, November 2006) Biology, Medicine http://purl.org/biotop/1.0/biotop.owl en application/rdf+xml abstract part of physically adjacent to Cf. Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 agent in inverseOf hasAgent attached to Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 physically bounded by physically bounds branch of Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 component part of For performance reasons, inverse relations are not encoded as such in OWL. Components are those (first-order) parts which partition a compound. The whole is exactly the mereological sum of its components. A loss of a component affects the sortality of the compound (e.g. a complete vs. a defective organism). In many cases, the choice of what is a component of a compound is arbitrary, because there are several ways to divide a whole into parts. Components should be - at least - partly bona fide parts. The use of this relation also requires the commitment to an underlying granularity level. So could we consider the codons (base triples) as the components of a DNA molecule but also the single nucleotides. Note that components of a compound may also be portions of matter. inverse of hasComponent. physically connected to physically contained in inverse of physically contains 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 Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 inverse of physically contained in contiguous with 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 Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 cooccurring with derived into inverseOf derivesFrom derives from Derivation is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derivesFrom c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant. inverseOf derivedInto physically disconnected from Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 encodes feature of granular part of For performance reasons, inverse relations are not encoded as such in OWL. Inverse relation to hasGranularPart Granular parts are the constitutent parts of Pluralities. They are of the same sort. Generally pluralities have a high number of grains. The loss of a grain has no effect on the sortality of the identity of the plurality. has abstract part has agent inverseOf agentIn As for hasParticipant, but with the additional condition that the component instance is causally active in the relevant process has branch Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 has component part inverse of componentOf. has feature has granular part Previous label: hasGrain inverse of granularPartOf. bearer of For performance reasons, inverse relations are not encoded as such in OWL. Inverse relation of inheresIn. Relates an independent continuant to a dependent one (e.g. quality, state, function, or disposition) Formerly "has inherence". has locus where some processual entity takes place has member has original part A is a historical part of B iff A is not a proper part of B now but A was a proper part of B at the time A came into existence. has physical part inverseOf partOf Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 has participant HasParticipant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane hasParticipant this particular sample of hemoglobin at this particular time. inverseOf participatesIn has patient has processual part mereological relation between processes has proper physical part inverse of proper physical part of has realization inverser of realizationOf inheres in inverse of hasInherence For performance reasons, inverse relations are not encoded as such in OWL. inheresIn relates a dependent continuant (a state, quality, property, function, disposition) with the independent continuant it depends on. physically interconnects physically located in inverseOf locationOf Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 physical location of inverseOf locatedIn Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 relates a processual entity with the place it occurs locus of member of original part of A is a historical part of B iff A is not a proper part of B now but A was a proper part of B at the time A came into existence. physical part of Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 inverseOf hasPart participates in inverseOf hasParticipant patient in preceded by p precededBy p' if and only if: given any process p at a time t, there is some process p' at time t', and t' is earlier than t. inverseOf precedes precedes inverseOf precededBy processual part of mereological relation between processes proper physical part of As for partOf, with the additional constraint that subject and object are distinct inverse of has proper physical part quality located quality location of 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 Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 realization of Something that occurs can be the realization of a function spatially related to physically surrounds loosely defined relation: establishing boundaries, enclosing, confining, enclosing, circumscribing temporally related to touches Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 physically traverses crossing over and crossing through acquired abnormal structure acquired pathological condition Ill-formed state of a biological entity,acquired after birth [steschu 20071010] 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 adult organism adult region affecting Producing a direct effect on age quality alga amino acid monomer 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 amino acid sequence Chain of amino acids, joined by peptide bonds. Folded or unfolded. amino acid sequence information amount of substance amphibian analyzing animal cell animal excluding human animal including human Multicellular organisms of the kingdom Animalia animal language animal population antibiotic role archaebacterial cell Archaebacterium artefact role The role an entity plays when it has been artificially produced. [steschu 20071010] arthropod one arthropod 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. bacteria 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 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. 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 structure as agent biological boundary biological colony Plurality of several individual organisms living closely together, usually for mutual benefit biological function biological processual entity Process specific for biological systems. biological space 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 FMAID:256135 Body body liquid Suspension and / or solution of biomolecules, ions, bigger particles in Water. body substance body system Mereological sum of heterogeneous body components that constitute a functional unity candida albicans cell One candida albicans cell candida albicans population canonical processual entity canonical region The condition of an entity considered well-formed. [steschu 20071126] canonical state canonicity The condition of an entity (state, process, function, object) in terms of being well or ill-formed or behaving canonicity region carbohydrate carbohydrate monomer carbohydrate sequence information catalytic role The role a substance plays in accelerating a chemical reaction categorization system 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 by locus partition disjoint partition: cell by locus cell by taxon partition disjoint partition: cell by taxon cell by type partition disjoint partition: by cell type 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 cellular component Components which only can be formed inside living cells but which may survive their host cell. chain of carbohydrate monomers chain of nucleotide monomers chemical role Any role performed by a chemical substance. child role 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 region class insecta region class mammalia region class saccharomycetes region collective material entity The fuzzyness of this class is due to the "same sort" criterion. Mereological Sum of multiple grains of the same sort without clear identity and unity criteria. complicating causes to become more severe compound of collective material entities Composition of different kinds of collections without clear unity and identity criteria. Old name: compound of collections congenital abnormal structure congenital pathological condition Ill-formed state of a biological entity, present from birth [steschu 20071010] congenital pathological state cytoplasm Gelatinous, semi-transparent fluid that fills most cells. E DNA 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. developmental quality Ontogenetic stage developmental region digital entity (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 dysfunction escherichia coli population 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 embryonic region 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. 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 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 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 region family enterobacteriaceaea region family hominidae region family of individual organisms family role family saccharomycetaceae region fatty acid 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 function A function is a realizable entity. The manifestation of a function is an essentialy end-directed activity of another entity in virtue of that entity being a specific kind of entity in the kind or kinds of contexts that it is made for or is supposed to have evolved to. fungus Heterotrophic organisms characterized by a chitinous cell wall. On fungus organisms fungus population gene TODO: Discuss whether all genes are DNA ! gene information Information that resides on a gene. gene region genome sum of genetic material in a cell genome information The totality of hereditary information of an organism genus candida region genus drosophila region genus escherichia region genus homo region genus saccharomyces region geographic entity government great ape one great ape great ape population group interaction growing process health professional role 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 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 human epithelial cell human language human population ill formed biological structure immaterial nonphysical entity Continuant entity that has neither a mass nor a volume and which do not inhere in other entities. immaterial physical entity Physical spaces that have a threedimensional spatial dimension but no mass. Old name: immaterial anatomical entity immaterial physical entity partition immaterial three dimensional physical entity immunologic role A role that is played by any biological entity in virtue of the defense of an organism against infective agents indicating indicator role A role a chemical plays for measuring or analyzing other chemical processes individual behavior Behavior of an individual organism information entity Piece of information (not necessarily human) , as it exists independently of any potential material carrier. 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 intellectual product interacting intra cellular process Process occuring in a cell. invertebrate juvenile organism juvenile region kingdom animalia region kingdom archaea region kingdom bacteria region kingdom chromista region kingdom fungi region kingdom plantae region kingdom protozoa region kingdom viruses region language language partition legal entity lipid Fat-soluble (lipophilic), naturally-occurring molecule. machine action An action performed by a machine. A machine is here seen as a non-biological artifact. machine language mammal one mammal mammal population managing care material entity A material object that has exactly one mass and one volume at a time. Material objects may have Immaterial nonphysical entities as parts (e.g. Heart and Heart Ventricle). material entity by size partition disjoint partition: material entity by granularity measure measuring mind modified cell Cells that grow and replicate continuously outside the living organism. molecular entity by granularity partition disjoint partition: molecular entity by granularity molecular entity by organic inorganic disjoint partition: molecular entity according to the classical organic / inorganic distinction molecular function Inherent function of a molecule. molecular residue molecule complex Particle that consists of entire molecules. mono molecular entity A 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 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 noncanonical region The condition of an entity considered ill-formed. [steschu 20071010] noncanonical state nucleic acid A nucleic acid is a complex, high-molecular-weight biochemical macromolecule composed of nucleotide chains that convey genetic information. nucleic acid nucleotide or nucleoside nucleic acid region nucleoside nucleotide 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 'bt:bio molecular sequence information' and 'bt:inheres in' some 'bt:sequence of nucleotides' removed for performance and due to the fact that such information may exists independently of a biomolecule 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 A OligoOrPolymer 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 one dimensional physical entity order diptera region order enterobacteriales region order primates region order saccharomycetales 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. organic molecular entity partition disjoint partition: organic molecules divided by structural criteria 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 action organism by developmental stage disjoint partition: by developmental stage organism by taxon partition disjoint partition by taxon organism interaction 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. organization parent role pathological region state of an organism or an organism part requiring therapeutic or palliative intervention 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. peptide 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 region phylum ascomycota region phylum chordata region phylum proteobacteria region physical boundary 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 partition disjoint partition physical force physical mass Mass (gravity independent) - not weight. Measured in g, kg, ... physical state former name: StateOfAggregation Quality of being solid, liquid, gaseous, ... [steschu20080127] physical volume Volume of three-dimensional objects physician role The role a physician plays plan (OBI 344) plant Organism of the kingdom Plantae. plant population plurality of organisms The mereological sum of two or more organisms. Not constrained by any additional criterion. [steschu20080127] poison role The role of a substance of mixture of substance of a defined amount thereof to be toxic to (parts of) biological organisms poly molecular composite entity 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. 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") 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 portion of homogenous matter Composition of granular components of the same kind. 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 processual entity A process entity has temporal parts (i.e. there is no time in which all parts of a process are simultaneously present). Processes have physical entities as participants. producing 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 function Inherent Function of a protein or a part of it. 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 proton Positively Charged Particle quality A quality is a realizable entity that is exhibited if it inheres in some other entity or entities at all. quality region A quality region is an abstract region in which values of qualities are located. RNA any kind of NucleicAcid that is composed of Ribonucleotides which are not Deoxyribonucleotides 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 regulatory body reptile researcher role 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. sibling role 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 social behavior Behaviour of a group of organisms 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 region species drosophila melanogaster region species escherichia coli region species homo sapiens region species saccharomyces cerevisiae region state Static condition that inheres in a physical entity. Other than processes, state have no temporal parts. 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 compound by canonicity structured biological compound by granularity partition disjoint partition: structured biological compound by granularity 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. subatomic particle Parts of Atoms. subatomic particle by charge disjoint partition: subatomic particle by electric charge subfamily drosophilinae region subject of care role submolecular group A moiety is a group of covalently bound atoms that occurs only as part of a molecule subphylum saccharomycotina region subphylum vertebrata region substance interaction syncytium taxon quality removed for performance reasons: inheresIn some (rol:hasPart some NucleicAcid) inheresIn only (rol:hasPart some NucleicAcid) The quality of one or more biological organisms, as well as of parts of organism of partaining to a biological taxon. [steschu20080127] taxon region temporal entity Occurrent that is not a processual entity. It corresponds to the disjunction of span:TemporalRegion and span:SpatiotemporalRegion 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 treating treating condition treating person two dimensional biological entity two dimensional boundary two dimensional physical 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 vertebrate one vertebrate 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 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 well formed biological structure yeast cell Unicellular Fungi. yeast population