COB brings together key terms from a wide range of OBO projects to improve interoperability. Core Ontology for Biology and Biomedicine 2022-11-02 based on definition HumanCurated part of part of HumanCurated has part has part HumanCurated realized in realized in HumanCurated occurs in occurs in HumanCurated contains process contains process is concretized as HumanCurated is concretized as is concretized as executed by HumanCurated topObjectProperty executed by characteristic of HumanCurated inheres in characteristic of participates in HumanCurated participates in participates in is specified input of HumanCurated is_specified_input_of is specified input of is specified output of HumanCurated is_specified_output_of is specified output of realized in HumanCurated realized in realized in contains process HumanCurated contains process contains process has specified input HumanCurated has_specified_input has specified input has specified output HumanCurated has_specified_output has specified output has part HumanCurated has part has part has participant HumanCurated has participant has participant occurs in HumanCurated occurs in occurs in part of HumanCurated part of part of enabled by HumanCurated enabled by enabled by concretizes intended to realize has plan intended plan process type executes HumanCurated executes executes realizes has characteristic https://github.com/oborel/obo-relations/pull/284 HumanCurated bearer of has characteristic Anything can have a characteristic http://purl.obolibrary.org/obo/IAO_0000136 is about HumanCurated is about is about HumanCurated is about is about HumanCurated has_specified_input has specified input HumanCurated is_specified_input_of is specified input of HumanCurated has_specified_output has specified output HumanCurated is_specified_output_of is specified output of HumanCurated inheres in characteristic of HumanCurated bearer of has characteristic HumanCurated participates in participates in HumanCurated has participant has participant HumanCurated is concretized as is concretized as HumanCurated enabled by enabled by HumanCurated executes executes The range of this property should be a user-defined unit datatype, e.g 182^:cm has quantity https://github.com/OBOFoundry/COB/issues/35 HumanCurated topDataProperty has quantity Number of protons in an atomic nucleus We are undecided as to whether to ultimately model this as a data property of object property + cardinality, but for now we are using DPs as these are faster for reasoning has atomic number has number of atomic nuclei has inchi string HumanCurated process process HumanCurated disposition disposition HumanCurated realizable entity realizable HumanCurated specifically dependent continuant characteristic HumanCurated role role HumanCurated site site HumanCurated function function HumanCurated material entity material entity HumanCurated immaterial entity immaterial entity HumanCurated gross anatomical part gross anatomical part HumanCurated organism or virus or viroid organism HumanCurated cellular organism cellular organism HumanCurated electron electron HumanCurated nucleic acid nucleic acid polymer HumanCurated protein polypeptide chain protein HumanCurated proton proton HumanCurated monoatomic ion monoatomic ion HumanCurated neutron neutron HumanCurated atom uncharged atom HumanCurated atomic nucleus atomic nucleus HumanCurated subatomic particle subatomic particle HumanCurated characteristic role HumanCurated cell cell HumanCurated native cell native cell HumanCurated cell in vitro cell in vitro http://purl.obolibrary.org/obo/PATO_0000125 mass HumanCurated mass mass http://purl.obolibrary.org/obo/PATO_0002193 charge HumanCurated electric charge no longer needed obsolete_elementary charge true HumanCurated owl:Thing elementary charge http://purl.obolibrary.org/obo/BFO_0000040 material entity HumanCurated material entity material entity http://purl.obolibrary.org/obo/CHEBI_36342 subatomic particle HumanCurated subatomic particle subatomic particle http://purl.obolibrary.org/obo/CHEBI_24636 proton HumanCurated proton proton http://purl.obolibrary.org/obo/CHEBI_30222 neutron HumanCurated neutron neutron 0 http://purl.obolibrary.org/obo/CHEBI_10545 electron HumanCurated electron electron 1 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 HumanCurated atom atom http://purl.obolibrary.org/obo/CHEBI_33252 Some people may be uncomfortable calling every proton an atomic nucleus This is equivalent to CHEBI:33252 atomic nucleus HumanCurated atomic nucleus atomic nucleus 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. molecular entity HumanCurated molecular entity molecular entity HumanCurated molecule molecular entity A material entity consisting of multiple atoms that are completely connected by covalent bonds and structured in subunits, and where the most determinate class identity of the macromolecule is not necessarily changed when there is an addition or subtraction of atoms or bonds. Terms moved to 'molecular entity', see https://github.com/OBOFoundry/Experimental-OBO-Core/issues/33 obsolete macromolecular entity true http://purl.obolibrary.org/obo/CHEBI_16541 http://purl.obolibrary.org/obo/PR_000000001 protein HumanCurated protein polypeptide chain protein HumanCurated protein protein http://purl.obolibrary.org/obo/CL_0000000 A material entity that has a plasma membrane and results from cellular division. 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 HumanCurated cell cell http://purl.obolibrary.org/obo/CL_0000003 native cell HumanCurated native cell native cell http://purl.obolibrary.org/obo/CL_0001034 cell in vitro HumanCurated cell in vitro cell in vitro A material entity consisting of at least two macromolecular entities derived from a cell as parts, and that has a function for the cell. 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 subcellular structure HumanCurated owl:Thing subcellular structure http://purl.obolibrary.org/obo/CARO_0001008 A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. Bodily fluids, such as urine, are currently defined as anatomical entities in UBERON. We should make sure there is a proper home for these here. gross anatomical part HumanCurated gross anatomical part gross anatomical part http://purl.obolibrary.org/obo/CARO_0001010 http://purl.obolibrary.org/obo/OBI_0100026 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 HumanCurated organism or virus or viroid organism HumanCurated organism organism http://purl.obolibrary.org/obo/OBI_0000245 Should revisit if we can place outside of material entity - a collection of roles. organization HumanCurated organization organization http://purl.obolibrary.org/obo/OBI_0000047 A material entity processed by human activity with an intent to produce processed material entity HumanCurated processed material processed material entity http://purl.obolibrary.org/obo/BFO_0000041 immaterial entity HumanCurated immaterial entity immaterial entity geographical location HumanCurated owl:Thing geographical location http://purl.obolibrary.org/obo/BFO_0000017 realizable HumanCurated realizable entity realizable http://purl.obolibrary.org/obo/BFO_0000015 process HumanCurated process process http://purl.obolibrary.org/obo/OBI_0000011 completely executed planned process HumanCurated planned process planned process http://purl.obolibrary.org/obo/GO_0008150 A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. A biological process is an evolved process biological process HumanCurated biological process biological process http://purl.obolibrary.org/obo/GO_0003674 This is the same as GO molecular function gene product or complex activity HumanCurated molecular function gene product or complex activity http://purl.obolibrary.org/obo/CHEBI_24867 monoatomic ion HumanCurated monoatomic ion monoatomic ion http://purl.obolibrary.org/obo/CHEBI_33250 uncharged atom HumanCurated atom uncharged atom http://purl.obolibrary.org/obo/CHEBI_10545 nucleic acid polymer HumanCurated nucleic acid nucleic acid polymer http://purl.obolibrary.org/obo/PCO_0000000 collection of organisms HumanCurated collection of organisms collection of organisms immaterial anatomical entity http://purl.obolibrary.org/obo/BFO_0000029 site HumanCurated site site http://purl.obolibrary.org/obo/OBI_0001909 conclusion based on data HumanCurated conclusion based on data conclusion based on data http://purl.obolibrary.org/obo/IAO_0000030 Pier: 'data, information or knowledge'. OR 'representation information HumanCurated information content entity information http://purl.obolibrary.org/obo/OGMS_0000073 disease diagnosis HumanCurated diagnosis disease diagnosis http://purl.obolibrary.org/obo/OGMS_0000014 phenotypic finding HumanCurated clinical finding phenotypic finding http://purl.obolibrary.org/obo/OGMS_0000063 disease course HumanCurated disease course disease course http://purl.obolibrary.org/obo/ENVO_02500000 environmental process HumanCurated environmental system process environmental process http://purl.obolibrary.org/obo/MOP_0000543 This is meant to capture processes that are more fundamental than macromolecular activities physico-chemical process HumanCurated molecular process physico-chemical process http://purl.obolibrary.org/obo/ENVO_01001110 ecosystem HumanCurated ecosystem ecosystem http://purl.obolibrary.org/obo/ENVO_01000813 geophysical entity HumanCurated astronomical body part geophysical entity http://purl.obolibrary.org/obo/IAO_0000033 directive information entity HumanCurated directive information entity directive information entity gene product HumanCurated owl:Thing gene product http://purl.obolibrary.org/obo/GO_0032991 This is not covalently bonded, which conflicts with changes to the parent definition. protein-containing macromolecular complex HumanCurated protein-containing complex protein-containing macromolecular complex http://purl.obolibrary.org/obo/IAO_0000005 objective specification HumanCurated objective specification objective specification action specification http://purl.obolibrary.org/obo/IAO_0000104 plan specification HumanCurated plan specification plan specification A complex of two or more molecular entities that are not covalently bound. complex of molecular entities HumanCurated owl:Thing complex of molecular entities >=2 parts (not we cannot use cardinality with transitive properties) 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 failed planned process http://purl.obolibrary.org/obo/DRON_0000005 A processed material entity created to be administered to an individual with the intent to improve health. drug product HumanCurated drug product drug product HumanCurated drug drug product http://purl.obolibrary.org/obo/IAO_0000310 document HumanCurated document document http://purl.obolibrary.org/obo/IAO_0000027 data item HumanCurated data item data item http://purl.obolibrary.org/obo/GO_0005634 cell nucleus HumanCurated nucleus cell nucleus http://purl.obolibrary.org/obo/OBI_0000070 assay HumanCurated assay assay http://purl.obolibrary.org/obo/OBI_0200000 data transformation HumanCurated data transformation data transformation http://purl.obolibrary.org/obo/OBI_0000066 investigation HumanCurated investigation investigation http://purl.obolibrary.org/obo/OBI_0000094 material processing HumanCurated material processing material processing http://purl.obolibrary.org/obo/BFO_0000016 disposition HumanCurated disposition disposition http://purl.obolibrary.org/obo/BFO_0000034 function HumanCurated function function http://purl.obolibrary.org/obo/OBI_0000260 plan HumanCurated plan plan http://purl.obolibrary.org/obo/BFO_0000023 role HumanCurated role role cellular membrane HumanCurated owl:Thing cellular membrane http://purl.obolibrary.org/obo/CARO_0010004 http://purl.obolibrary.org/obo/NCBITaxon_131567 cellular organism HumanCurated cellular organism cellular organism HumanCurated cellular organisms cellular organism OBI:0000067 evaluant role http://purl.obolibrary.org/obo/IAO_0000015 Pier 'representational entity' This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc information representation http://purl.obolibrary.org/obo/IAO_0000109 measurement datum physical information carrier http://purl.obolibrary.org/obo/SEPIO_0000048 A role realized by a participant in a process such that the participant causes the process. agent role HumanCurated agent role agent role http://purl.obolibrary.org/obo/BFO_0000020 http://purl.obolibrary.org/obo/PATO_0000001 characteristic https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 HumanCurated specifically dependent continuant characteristic HumanCurated quality characteristic We should name the inverse in COB and avoid the confusing inverse(..) construct A process during which an organism comes into contact with another entity. exposure of organism HumanCurated drug product drug product HumanCurated astronomical body part geophysical entity HumanCurated ecosystem ecosystem HumanCurated environmental system process environmental process HumanCurated geophysical entity geographical entity HumanCurated molecular function gene product or complex activity HumanCurated nucleus cell nucleus HumanCurated biological process biological process HumanCurated protein-containing complex protein-containing macromolecular complex HumanCurated objective specification objective specification HumanCurated data item data item HumanCurated information content entity information HumanCurated directive information entity directive information entity HumanCurated plan specification plan specification HumanCurated document document HumanCurated molecular process physico-chemical process HumanCurated organism Viruses HumanCurated cellular organisms cellular organism HumanCurated organism cellular organisms HumanCurated planned process planned process HumanCurated processed material processed material entity HumanCurated investigation investigation HumanCurated assay assay HumanCurated material processing material processing HumanCurated agent role investigation agent role HumanCurated organization organization HumanCurated plan plan HumanCurated conclusion based on data conclusion based on data HumanCurated organism organism HumanCurated data transformation data transformation HumanCurated clinical finding phenotypic finding HumanCurated disease course disease course HumanCurated diagnosis disease diagnosis HumanCurated quality characteristic HumanCurated mass mass HumanCurated electric charge HumanCurated collection of organisms collection of organisms HumanCurated cellular organism whole plant HumanCurated cell plant cell HumanCurated immaterial anatomical entity plant anatomical space HumanCurated native cell native plant cell HumanCurated protein protein HumanCurated agent role agent role HumanCurated material entity sequence_feature HumanCurated characteristic sequence_attribute HumanCurated material entity sequence_variant HumanCurated material entity sequence_collection HumanCurated immaterial anatomical entity immaterial anatomical entity HumanCurated cellular organism multicellular organism HumanCurated gross anatomical part multicellular anatomical structure HumanCurated native cell xenopus cell HumanCurated native cell zebrafish cell