Term IRI Term label Parent term IRI Parent term label Alternative term Definition http://purl.obolibrary.org/obo/CHEBI_24636 proton http://purl.obolibrary.org/obo/CHEBI_36342 subatomic particle Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. http://purl.obolibrary.org/obo/PATO_0002193 electric charge http://purl.obolibrary.org/obo/COB_0000502 characteristic 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. http://purl.obolibrary.org/obo/PO_0025131 plant anatomical entity http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity An anatomical entity that is or was part of a plant. http://purl.obolibrary.org/obo/IAO_0000005 objective specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity 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. http://purl.obolibrary.org/obo/IAO_0000007 action specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity A directive information entity that describes an action the bearer will take. http://purl.obolibrary.org/obo/IAO_0000027 data item http://purl.obolibrary.org/obo/IAO_0000030 information content entity 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. http://purl.obolibrary.org/obo/IAO_0000033 directive information entity http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. http://purl.obolibrary.org/obo/IAO_0000104 plan specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity 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. http://purl.obolibrary.org/obo/IAO_0000109 measurement datum http://purl.obolibrary.org/obo/IAO_0000027 data item A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. http://purl.obolibrary.org/obo/OBI_0000066 investigation http://purl.obolibrary.org/obo/COB_0000035 completely executed planned process a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). http://purl.obolibrary.org/obo/OBI_0000070 assay http://purl.obolibrary.org/obo/COB_0000035 completely executed planned process A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. http://purl.obolibrary.org/obo/OBI_0000260 plan http://purl.obolibrary.org/obo/BFO_0000017 realizable entity A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a completely executed planned process. http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://purl.obolibrary.org/obo/COB_0000035 completely executed planned process A completely executed planned process that produces output data from input data. http://purl.obolibrary.org/obo/PATO_0000125 mass http://purl.obolibrary.org/obo/COB_0000502 characteristic A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. http://purl.obolibrary.org/obo/PR_000000001 protein http://purl.obolibrary.org/obo/PR_000018263 amino acid chain An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. http://purl.obolibrary.org/obo/CHEBI_33252 atomic nucleus http://purl.obolibrary.org/obo/CHEBI_36342 subatomic particle A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. http://purl.obolibrary.org/obo/CHEBI_30222 neutron http://purl.obolibrary.org/obo/CHEBI_36342 subatomic particle Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u. http://purl.obolibrary.org/obo/CL_0000000 cell http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity 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. http://purl.obolibrary.org/obo/CHEBI_36342 subatomic particle http://purl.obolibrary.org/obo/BFO_0000040 material entity A particle smaller than an atom. http://purl.obolibrary.org/obo/GO_0005575 cellular_component http://purl.obolibrary.org/obo/BFO_0000040 material entity 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). http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity http://purl.obolibrary.org/obo/UBERON_0001062 anatomical entity Anatomical entity that has mass. http://purl.obolibrary.org/obo/UBERON_0000466 immaterial anatomical entity http://purl.obolibrary.org/obo/UBERON_0001062 anatomical entity Anatomical entity that has no mass. http://purl.obolibrary.org/obo/CHEBI_10545 electron http://purl.obolibrary.org/obo/CHEBI_36342 subatomic particle 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. http://purl.obolibrary.org/obo/PCO_0000000 collection of organisms http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity that consists of two or more organisms, viruses, or viroids. http://purl.obolibrary.org/obo/COB_0000011 atom http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. http://purl.obolibrary.org/obo/COB_0000013 molecule http://purl.obolibrary.org/obo/BFO_0000040 material entity 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. http://purl.obolibrary.org/obo/COB_0000021 gross anatomical part http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. http://purl.obolibrary.org/obo/COB_0000022 organism http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome http://purl.obolibrary.org/obo/COB_0000026 processed material entity http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity processed by human activity with an intent to produce it. http://purl.obolibrary.org/obo/COB_0000049 nucleic acid chain http://purl.obolibrary.org/obo/COB_0000013 molecule A molecule that consists of nucleotides (unmodified nucleotide residues and/or modified nucleotide residues) linked by phosphodiester bonds or derivatives of such bonds. http://purl.obolibrary.org/obo/COB_0000080 complex of molecules http://purl.obolibrary.org/obo/BFO_0000040 material entity A complex of two or more molecules that are not covalently bound. http://purl.obolibrary.org/obo/COB_0000110 material processing http://purl.obolibrary.org/obo/COB_0000035 completely executed planned process A completely executed planned process that intends to output material entities from input material entities http://purl.obolibrary.org/obo/GO_0003674 gene product or complex activity http://purl.obolibrary.org/obo/BFO_0000015 process 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. http://purl.obolibrary.org/obo/GO_0008150 biological process http://purl.obolibrary.org/obo/BFO_0000015 process 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. http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex http://purl.obolibrary.org/obo/COB_0000080 complex of molecules 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. http://purl.obolibrary.org/obo/GO_0044423 virion component http://purl.obolibrary.org/obo/GO_0005575 cellular_component Any constituent part of a virion, a complete fully infectious extracellular virus particle. http://purl.obolibrary.org/obo/PR_000018263 amino acid chain http://purl.obolibrary.org/obo/COB_0000013 molecule 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. http://purl.obolibrary.org/obo/ENVO_01000813 geophysical entity http://purl.obolibrary.org/obo/BFO_0000040 material entity A material part of an astronomical body. http://purl.obolibrary.org/obo/ENVO_02500000 environmental system process http://purl.obolibrary.org/obo/BFO_0000015 process A process in which includes the components of an environmental system as participants. http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity http://purl.obolibrary.org/obo/UBERON_0000465 material anatomical entity 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. http://purl.obolibrary.org/obo/COB_0000082 planned process http://purl.obolibrary.org/obo/BFO_0000015 process 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. http://purl.obolibrary.org/obo/MOP_0000543 physico-chemical process http://purl.obolibrary.org/obo/BFO_0000015 process A process in which at least one of the participants is a molecule. http://purl.obolibrary.org/obo/COB_0001000 exposure of organism http://purl.obolibrary.org/obo/BFO_0000015 process A process during which an organism comes into contact with another entity. http://purl.obolibrary.org/obo/COB_0001300 device http://purl.obolibrary.org/obo/COB_0000026 processed material entity A processed material entity which is designed to be capable of a process. http://purl.obolibrary.org/obo/ENVO_01001110 ecosystem http://purl.obolibrary.org/obo/BFO_0000040 material entity An environmental system which includes both living and non-living components. http://purl.obolibrary.org/obo/BFO_0000034 function http://purl.obolibrary.org/obo/BFO_0000016 disposition http://purl.obolibrary.org/obo/BFO_0000016 disposition http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000023 role http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000029 site http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://purl.obolibrary.org/obo/NCBITaxon_10239 virus http://purl.obolibrary.org/obo/COB_0000022 organism http://purl.obolibrary.org/obo/NCBITaxon_131567 cellular organism http://purl.obolibrary.org/obo/COB_0000022 organism http://purl.obolibrary.org/obo/COB_0000035 completely executed planned process http://purl.obolibrary.org/obo/COB_0000082 planned process http://purl.obolibrary.org/obo/COB_0000083 failed planned process http://purl.obolibrary.org/obo/COB_0000082 planned process http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/COB_0000502 characteristic http://purl.obolibrary.org/obo/IAO_0000030 information content entity A generically dependent continuant that is about some thing. http://purl.obolibrary.org/obo/UBERON_0001062 anatomical entity 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. http://purl.obolibrary.org/obo/COB_0000122 obsolete physical information carrier http://purl.obolibrary.org/obo/BFO_0000015 process http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://purl.obolibrary.org/obo/COB_0000005 obsolete elementary charge http://purl.obolibrary.org/obo/COB_0000014 obsolete macromolecular entity http://purl.obolibrary.org/obo/COB_0000020 obsolete subcellular structure http://purl.obolibrary.org/obo/COB_0000032 obsolete geographical location http://purl.obolibrary.org/obo/COB_0000056 obsolete immaterial anatomical entity http://purl.obolibrary.org/obo/COB_0000073 obsolete gene product http://purl.obolibrary.org/obo/COB_0000116 obsolete cellular membrane http://purl.obolibrary.org/obo/COB_0000077 obsolete action specification http://purl.obolibrary.org/obo/COB_0000502 characteristic http://purl.obolibrary.org/obo/RO_0002234 has output 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. http://purl.obolibrary.org/obo/COB_0000800 has atomic number Number of protons in an atomic nucleus http://purl.obolibrary.org/obo/BFO_0000055 realizes 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 http://purl.obolibrary.org/obo/OBI_0000293 has specified input The inverse property of is specified input of http://purl.obolibrary.org/obo/OBI_0000295 is specified input of A relation between a completely executed 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. http://purl.obolibrary.org/obo/OBI_0000299 has specified output The inverse property of is specified output of http://purl.obolibrary.org/obo/OBI_0000312 is specified output of A relation between a completely executed 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. http://purl.obolibrary.org/obo/RO_0000052 characteristic of 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. http://purl.obolibrary.org/obo/RO_0000053 has characteristic Inverse of characteristic_of http://purl.obolibrary.org/obo/RO_0000056 participates in a relation between a continuant and a process, in which the continuant is somehow involved in the process http://purl.obolibrary.org/obo/RO_0000057 has participant a relation between a process and a continuant, in which the continuant is somehow involved in the process http://purl.obolibrary.org/obo/RO_0000058 is concretized as 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. http://purl.obolibrary.org/obo/RO_0000059 concretizes 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. http://purl.obolibrary.org/obo/RO_0001000 derives from 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 http://purl.obolibrary.org/obo/RO_0001015 location of a relation between two independent continuants, the location and the target, in which the target is entirely within the location http://purl.obolibrary.org/obo/RO_0002219 surrounded by 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 http://purl.obolibrary.org/obo/RO_0001025 located in a relation between two independent continuants, the target and the location, in which the target is entirely within the location http://purl.obolibrary.org/obo/BFO_0000051 has part a core relation that holds between a whole and its part http://purl.obolibrary.org/obo/RO_0002333 enabled by inverse of enables http://purl.obolibrary.org/obo/BFO_0000050 part of a core relation that holds between a part and its whole http://purl.obolibrary.org/obo/RO_0002233 has input 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. http://purl.obolibrary.org/obo/RO_0002215 capable of 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. http://purl.obolibrary.org/obo/RO_0002221 surrounds inverse of surrounded by http://purl.obolibrary.org/obo/COB_0000801 has number of atomic nuclei http://purl.obolibrary.org/obo/COB_0000803 has inchi string http://purl.obolibrary.org/obo/IAO_0000136 is about http://purl.obolibrary.org/obo/COB_0000081 intended to realize http://purl.obolibrary.org/obo/COB_0000084 has plan http://purl.obolibrary.org/obo/COB_0000085 intended plan process type http://purl.obolibrary.org/obo/COB_0000511 has quantity http://purl.obolibrary.org/obo/COB_0000016 executed by