COB brings together key terms from a wide range of OBO projects to improve interoperability. Core Ontology for Biology and Biomedicine 2025-02-20 definition editor note term replaced by a core relation that holds between a part and its whole part of executed by intended to realize has plan intended plan process type is about The inverse property of is specified input of has specified input A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. is specified input of The inverse property of is specified output of has specified output a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. characteristic of Inverse of characteristic_of has characteristic a relation between a continuant and a process, in which the continuant is somehow involved in the process participates in A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity derives from a relation between two independent continuants, the location and the target, in which the target is entirely within the location location of a relation between two independent continuants, the target and the location, in which the target is entirely within the location located in x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x surrounded by inverse of surrounded by surrounds p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. has output inverse of enables enabled by has quantity Number of protons in an atomic nucleus has atomic number has number of atomic nuclei has inchi string BFO:0000015 process BFO:0000016 disposition BFO:0000017 realizable entity BFO:0000023 role BFO:0000029 site BFO:0000034 function BFO:0000040 Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity BFO:0000141 immaterial entity CHEBI:10545 Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. electron CHEBI:24636 Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. proton CHEBI:30222 Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u. neutron CHEBI:33252 A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. Some people may be uncomfortable calling every proton an atomic nucleus This is equivalent to CHEBI:33252 atomic nucleus CHEBI:36342 A particle smaller than an atom. subatomic particle CL:0000000 A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. cell COB:0000005 obsolete elementary charge true COB:0000011 A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. This atom is closely related to ChEBI's atom, but not exactly equivalent to. atom COB:0000013 A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. This molecular entity is different than ChEBI's 'molecular entity'. We would like to have cardinality restrictions on the logic, but there are some technical limitations. molecule COB:0000014 obsolete macromolecular entity true COB:0000020 obsolete subcellular structure true COB:0000021 A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. gross anatomical part COB:0000022 A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'. Includes virus - we will later have a class for cellular organisms. organism COB:0000026 A material entity processed by human activity with an intent to produce it. In the COB 2024 workshop there was much disagreement about this label. processed material entity COB:0000032 obsolete geographical location true COB:0000035 completely executed planned process COB:0000049 A molecule that consists of nucleotides (unmodified nucleotide residues and/or modified nucleotide residues) linked by phosphodiester bonds or derivatives of such bonds. nucleic acid chain COB:0000056 obsolete immaterial anatomical entity true COB:0000073 obsolete gene product true COB:0000077 obsolete action specification true COB:0000080 A complex of two or more molecular entities that are not covalently bound. complex of molecules COB:0000082 A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. planned process COB:0000083 failed planned process COB:0000110 A planned process that intends to output material entities from input material entities material processing COB:0000116 obsolete cellular membrane true COB:0000122 obsolete physical information carrier true COB:0000502 characteristic COB:0001000 A process during which an organism comes into contact with another entity. exposure of organism COB:0001300 A processed material entity which is designed to be capable of a process. device ENVO:01000813 A material part of an astronomical body. geophysical entity ENVO:01001110 An environmental system which includes both living and non-living components. ecosystem ENVO:02500000 A process in which includes the components of an environmental system as participants. environmental system process GO:0003674 A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. This is the same as GO molecular function gene product or complex activity GO:0005575 A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). cellular_component GO:0008150 A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. biological process GO:0032991 A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. This is not covalently bonded, which conflicts with changes to the parent definition. protein-containing complex GO:0044423 Any constituent part of a virion, a complete fully infectious extracellular virus particle. virion component GO:0110165 A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes. Overlaps with some cellular components from GO cellular anatomical entity IAO:0000005 A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. objective specification IAO:0000007 A directive information entity that describes an action the bearer will take. action specification IAO:0000027 An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. data item IAO:0000030 A generically dependent continuant that is about some thing. Pier: 'data, information or knowledge'. OR 'representation' information content entity IAO:0000033 An information content entity whose concretizations indicate to their bearer how to realize them in a process. directive information entity IAO:0000104 A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. plan specification IAO:0000109 A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. measurement datum MOP:0000543 A process in which at least one of the participants is a molecule. This is meant to capture processes that are more fundamental than macromolecular activities physico-chemical process NCBITaxon:131567 cellular organism OBI:0000066 a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). investigation OBI:0000070 A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. assay OBI:0000260 A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. plan OBI:0200000 A planned process that produces output data from input data. data transformation PATO:0000125 A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. mass PATO:0002193 A molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons. electric charge PCO:0000000 A material entity that consists of two or more organisms, viruses, or viroids. collection of organisms PO:0025131 An anatomical entity that is or was part of a plant. plant anatomical entity PR:000000001 An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. protein PR:000018263 An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. amino acid chain UBERON:0000465 Anatomical entity that has mass. material anatomical entity UBERON:0000466 Anatomical entity that has no mass. immaterial anatomical entity UBERON:0001062 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. anatomical entity 2025-02-20 a core relation that holds between a whole and its part has part Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. is specified output of a relation between a process and a continuant, in which the continuant is somehow involved in the process has participant A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. capable of COB brings together key terms from a wide range of OBO projects to improve interoperability. Core Ontology for Biology and Biomedicine 2025-02-20