]> en 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) http://purl.org/biotop/dev Martin Boeker Elena Beisswanger Stefan Schulz 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) application/rdf+xml dev Institute for Medical Biometry and Medical Informatics, University Medical Center Freiburg, Stefan-Meier-Strasse 26, 79104 Freiburg, Germany 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) last modification 29 Dec 2009 by Stefan Schulz Holger Stenzhorn abstract part of adjacent to 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 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 cooccurring with component part of inverse of hasComponent. 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. connected to contained in inverseOf contains Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 contains inverseOf containedIn 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 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 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 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 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 As for hasParticipant, but with the additional condition that the component instance is causally active in the relevant process inverseOf agentIn 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 granular part Previous label: hasGrain inverse of granularPartOf. bearer of Inverse relation of inheresIn. Relates an independent continuant to a dependent one (e.g. quality, state, function, or disposition) Formerly "has inherence". For performance reasons, inverse relations are not encoded as such in OWL. has locus 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 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 inverseOf participatesIn 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. has patient has processual part mereological relation between processes has proper part inverseOf properPartOf has realization has realization 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. interconnects 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 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 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. part of inverseOf hasPart Schulz S, Hahn U. Towards the ontological foundations of symbolic biological theories. Artif Intell Med. 2007 Mar;39(3):237-50. PMID: 17321118 participates in inverseOf hasParticipant patient in preceded by inverseOf precedes 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. precedes inverseOf precededBy processual part of mereological relation between processes proper part of As for partOf, with the additional constraint that subject and object are distinct inverseOf hasProperPart 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 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 traverses crossing over and crossing through acquired pathological state Ill-formed state of a biological entity,acquired after birth [steschu 20071010] AcquiredPathologicalState 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 quality affecting Producing a direct effect on age quality alga amino acid monomer 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 α–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 sequence Chain of amino acids, joined by peptide bonds. Folded or unfolded. AminoAcidSequence amino acid sequence information amphibian analyzing animal cell animal excluding human animal 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. BakersYeastCell one saccharomyces cerevisiae cell bakers yeast population behavior An (often habitual) action of an organism that is the realization of some disposition 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 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 process 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 fluid Suspension and / or solution of biomolecules, ions, bigger particles in Water. body system Mereological sum of heterogeneous body components that constitute a functional unity CandidaAlbicansCell One candida albicans cell candida albicans population canonical condition The condition of an entity considered well-formed. [steschu 20071126] canonical processual entity canonical state canonicity The condition of an entity (state, process, function, object) in terms of being well or ill-formed or behaving carbohydrate 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 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. amino acid sequence Chain of amino acids, joined by peptide bonds. Folded or unfolded. AminoAcidSequence 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 quality class insecta quality class mammalia quality class saccharomycetes quality collective material entity Mereological Sum of multiple grains of the same sort without clear identity and unity criteria. The fuzzyness of this class is due to the "same sort" criterion. 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 pathological state Ill-formed state of a biological entity, present from birth [steschu 20071010] CongenitalPathologicalState 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 diagnostic role 1. The role of a continuant participating in a process that provides insight into the functioning of a biological system. 2 The role of a process that provides insight into the functioning of a biological system. 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 quality 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 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 EscherichiaColiCell 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 eukaryotic cell Cell with membrane enclosed organells 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 quality family enterobacteriaceaea quality family hominidae quality family of individual organisms family role family saccharomycetaceae quality 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 realizable entity the manifestation of which is an essentialy end-directed activity of a continuant entity in virtue of that continuant entity being a specific kind of entity in the kind or kinds of contexts that it is made for. 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 quality genus drosophila quality genus escherichia quality genus homo quality genus saccharomyces quality two dimensional geographic region government great ape one great ape great ape population group interaction growing process health professional role