]> Stefan Schulz, Martin Boeker, Elena Beisswanger, Holger Stenzhorn, Daniel Schober 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) Beisswanger E, Schulz S, Stenzhorn H, Hahn U: BioTop: An upper domain ontology for the life sciences. A description of its current structure, contents and interfaces to OBO ontologies. Applied Ontology, 2008; 3 (4): 205-212: http://dx.doi.org/10.3233/AO-2008-0057 Upper-Level ontology for Biology and Medicine. Compatible with BFO, DOLCE, and the UMLS Semantic Network (mapping files available) Last modification September 25, 2009 Stefan Schulz The new version has a number of modified class and relation IDs in order to restore consistency with labels (left: old, right: new). MolecularEntityByOrganicInorganic;MolecularEntityByOrganicInorganicPartition NucleicAcidNucleotideOrNucleoside;NucleicAcidNucleotideOrNucleosideMoleculeOrResidue FamilyEnterobacteriaceaeRegion;FamilyEnterobacteriaceaeaRegion StructuredNonbiologicalEntity;StructuredNonbiologicalCompound OrganismByDevelopmentalStage;OrganismByDevelopmentalStagePartition PathologicalCondition;PathologicalRegion AminoAcidOrPeptide;AminoAcidOrPeptideMoleculeOrStructure disconnectedFrom;physicallyDisconnectedFrom spatiallyRelated;spatiallyRelatedTo AminoAcidMonomer;AminoAcidMoleculeOrResidue HeterocyclicBase;HeterocyclicBaseMoleculeOrResidue EColiPopulation;EscherichiaColiPopulation Epithelial_Cell;EpithelialCell ProteinFunction;PeptideFunction coocurringWith;cooccurringWith TreatingPerson;TreatingOrganism bacterial_cell;BacterialCell length_quality;PhysicalLength hasProperPart;hasProperPhysicalPart interconnects;physicallyInterconnects BodySubstance;AmountOfBodySubstance hasInherence;bearerOf properPartOf;properPhysicalPartOf Carbohydrate;CarbohydrateMoleculeOrResidue connectedTo;physicallyConnectedTo containedIn;physicallyContainedIn NucleicAcid;NucleicAcidStructure adjacentTo;physicallyAdjacentTo locationOf;physicalLocationOf Nucleoside;NucleosideMolecule Nucleotide;NucleotideMolecule plant_cell;PlantCell boundedBy;physicallyBoundedBy locatedIn;physicallyLocatedIn surrounds;physicallySurrounds traverses;physicallyTraverses FattyAcid;FattyAcidMoleculeOrResidue Measuring;MeasuringAction contains;physicallyContains hasPart;hasPhysicalPart Peptide;PeptideStructure bounds;physicallyBounds partOf;physicalPartOf Lipid;LipidMoleculeOrResidue Using;UsingAction DNA;DNAChain RNA;RNAChain 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/biotop.owl http://creativecommons.org/licenses/by/3.0 application/rdf+xml This version contains inverse relation axioms. These may have an impact on the performance. To remove them use the perl script: #!/usr/bin/perl my $buffer;my @zeilen;my @rules; #! RemoveInverses.pl #! by Stefan Schulz, 2009/09/25 #! First argument: owl file open(DAT0, $ARGV[0]) || die "Please specify an owl file from which you want to remove the inverse relation axioms.\n"; while(<DAT0>){push(@zeilen,$_)}close(DAT0); #! Write text file into buffer for(my $i = 0;$i < @zeilen;$i++){$buffer = $buffer . $zeilen[$i]}; $buffer =~ s/<owl:inverseOf.*\/>//g; open(OUT, ">$ARGV[0]") or die "Writing error"; print OUT $buffer; close(OUT); abstract part of 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 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". 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. 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 encodedBy 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. 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 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 physical part Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 inverseOf partOf 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. locus of relates a processual entity with the place it occurs 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. participates in inverseOf hasParticipant patient in physical 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 inverseOf locatedIn 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 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 physically bounded by physically bounds physically connected to physically contained in 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 contains 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 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 physically interconnects physically located in Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 inverseOf locationOf physically surrounds loosely defined relation: establishing boundaries, enclosing, confining, enclosing, circumscribing physically traverses crossing over and crossing through 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 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 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 state pathological state acquired during lifetime 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 organism in reproductive phase adult region affecting Producing a direct effect on age quality the quality of having a livespan alga amino acid molecule or residue Amino Acids molecules or residues (residues as in peptide bonds) In chemistry, an amino acid is any molecule that contains both amine and carboxyl functional groups. However, in biochemistry, this more general term is frequently used to refer to alpha amino acids (amino acids in which the amino and carboxylate functionalities are attached to the same carbon, called ?–carbon). Amino Acids have at least one amino and one carboxy group. Those having two carboxy groups have only one amino group and vice versa. (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) amount of substance collection with molecules or atoms as granular parts (but which may have also bigger granular parts) 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 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 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. 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 processual entity Process specific for biological systems. 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 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 canonical processual entity a process that is considered normal canonical region abstract region in which the value "canonical" of canonicity is located canonical state a biological state that is considered "normal" canonicity The condition of an entity (state, process, function, object) in terms of being well or ill-formed or behaving canonicity region abstract region in which values of canonicity are located 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 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 Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. cell by taxon partition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. cell by type partition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. 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 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 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 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 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. developmental quality Ontogenetic stage developmental region abstract region in which the values of developmental stages are located digital entity (OBI 306) any kind of information that is fully expressible by a sequence of binary values. 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. 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 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. 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 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 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 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 unclear classe. to be revised family role family saccharomycetaceae 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 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 it had 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) fungus Heterotrophic organisms characterized by a chitinous cell wall. On fungus organisms fungus population gene TODO: Discuss whether all genes are DNA ! region of nucleic acid macromolecule that carry information gene information Information that resides on a gene. gene region part of a gene 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 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 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 ill formed biological structure biological structure that deviates from what is considered normal 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 Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. immaterial three dimensional physical entity three-dimensional space 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 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 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 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 system of signs used for communication between biological and / or machine agents language partition 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. 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 mammal one mammal mammal population managing care action in which a subject cares for the well-being of some biological entity 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 Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. measure numeric quantity or cardinality, reference for measurement processes. Example kilogram, hour, ampere measuring action an action that aims at producing a measurement mind what characterizes intelligent beings modified cell Cells that grow and replicate continuously outside the living organism. molecular entity by entirety partition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. molecular entity by granularity partition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. molecular entity by organic inorganic partition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. 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. 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 a process that is considered abnormal noncanonical region abstract region in which the value "noncanonical" of canonicity is located noncanonical state a biological state that is considered "abnormal" nucleic acid nucleotide or nucleoside molecule or residue nucleic acid region 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 one dimensional physical entity line or curve 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 Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. 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 Action that has some organism as agent organism by developmental stage partition Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. organism by taxon partition 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. organization collection of human or legal entities parent role the role an organism plays in relation to its children 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 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 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 Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. physical force force as defined by physics (mass + acceleration) physical length physical length (e.g. in meters) 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 - third potency of length physician role The role a physician plays plan A plan is a series of steps to be carried out in order to achiev a goal. Plans can only be realized by processes (OBI 344) plant Organism of the kingdom Plantae. plant cell 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") all child classes of population are only meant as examples demonstrating how population classes can be postcoordinated 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 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 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 chain 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 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 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 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 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 Ontologically irrelevant partitioning node. Used for improving ontology housekeeping. Its purpose is to express that all subclasses are mutually disjoint. subfamily drosophilinae 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 region subphylum vertebrata region substance interaction action in which molecular entities interact syncytium taxon quality The quality of one or more biological organisms, as well as of parts of organism of partaining to a biological taxon. [steschu20080127] taxon region abstract region in which the values of biological taxa are located (cf. Schulz et.al ISMB 2008) 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 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 two dimensional boundary plane bounding a three-dimensional biological entity two dimensional physical entity plane 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 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 A water molecule is composed by one oxygen molecule and two hydrogen molecules well formed biological structure yeast cell Unicellular Fungi. yeast population