COB brings together key terms from a wide range of OBO projects to improve interoperability. Core Ontology for Biology and Biomedicine 2023-11-16 based on definition part of part of has part has part realized in realized in occurs in occurs in contains process contains process is concretized as is concretized as is concretized as executed by topObjectProperty executed by characteristic of inheres in characteristic of participates in participates in participates in is specified input of is_specified_input_of is specified input of is specified output of is_specified_output_of is specified output of realized in contains process has specified input has_specified_input has specified input has specified output has_specified_output has specified output has part has participant has participant has participant occurs in part of enabled by enabled by enabled by concretizes intended to realize has plan intended plan process type executes executes executes realizes has characteristic https://github.com/oborel/obo-relations/pull/284 bearer of has characteristic Anything can have a characteristic http://purl.obolibrary.org/obo/IAO_0000136 is about is about is about 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 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 process process disposition disposition realizable entity realizable specifically dependent continuant characteristic role role site site function function material entity material entity immaterial entity immaterial entity gross anatomical part gross anatomical part organism or virus or viroid organism cellular organism cellular organism electron electron protein polypeptide chain protein proton proton monoatomic ion monoatomic ion neutron neutron atom uncharged atom atomic nucleus atomic nucleus nucleic acid nucleic acid polymer subatomic particle subatomic particle characteristic role cell cell native cell native cell cell in vitro cell in vitro http://purl.obolibrary.org/obo/PATO_0000125 mass mass mass http://purl.obolibrary.org/obo/PATO_0002193 charge electric charge no longer needed obsolete_elementary charge true owl:Thing elementary charge http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/CHEBI_36342 subatomic particle http://purl.obolibrary.org/obo/CHEBI_24636 proton http://purl.obolibrary.org/obo/CHEBI_30222 neutron 0 http://purl.obolibrary.org/obo/CHEBI_10545 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 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 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 molecular entity molecular entity 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 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 http://purl.obolibrary.org/obo/CL_0000003 native cell http://purl.obolibrary.org/obo/CL_0001034 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 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 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 organism organism http://purl.obolibrary.org/obo/OBI_0000245 Should revisit if we can place outside of material entity - a collection of roles. organization organization organization http://purl.obolibrary.org/obo/OBI_0000047 A material entity processed by human activity with an intent to produce processed material entity processed material processed material entity http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity geographical location owl:Thing geographical location http://purl.obolibrary.org/obo/BFO_0000017 realizable http://purl.obolibrary.org/obo/BFO_0000015 process http://purl.obolibrary.org/obo/OBI_0000011 completely executed planned process 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 biological process biological process http://purl.obolibrary.org/obo/GO_0003674 This is the same as GO molecular function gene product or complex activity molecular function gene product or complex activity http://purl.obolibrary.org/obo/CHEBI_24867 monoatomic ion http://purl.obolibrary.org/obo/CHEBI_33250 uncharged atom http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid polymer http://purl.obolibrary.org/obo/PCO_0000000 collection of organisms collection of organisms collection of organisms immaterial anatomical entity http://purl.obolibrary.org/obo/BFO_0000029 site http://purl.obolibrary.org/obo/OBI_0001909 conclusion based on data conclusion based on data conclusion based on data http://purl.obolibrary.org/obo/IAO_0000030 Pier: 'data, information or knowledge'. OR 'representation information information content entity information http://purl.obolibrary.org/obo/OGMS_0000073 disease diagnosis diagnosis disease diagnosis http://purl.obolibrary.org/obo/OGMS_0000014 phenotypic finding clinical finding phenotypic finding http://purl.obolibrary.org/obo/OGMS_0000063 disease course disease course disease course http://purl.obolibrary.org/obo/ENVO_02500000 environmental process 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 molecular process physico-chemical process http://purl.obolibrary.org/obo/ENVO_01001110 ecosystem ecosystem ecosystem http://purl.obolibrary.org/obo/ENVO_01000813 geophysical entity astronomical body part geophysical entity http://purl.obolibrary.org/obo/IAO_0000033 directive information entity directive information entity directive information entity gene product 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 protein-containing complex protein-containing macromolecular complex http://purl.obolibrary.org/obo/IAO_0000005 objective specification objective specification objective specification action specification http://purl.obolibrary.org/obo/IAO_0000104 plan specification plan specification plan specification A complex of two or more molecular entities that are not covalently bound. complex of molecular entities 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 drug product drug product drug drug product http://purl.obolibrary.org/obo/IAO_0000310 document document document http://purl.obolibrary.org/obo/IAO_0000027 data item data item data item http://purl.obolibrary.org/obo/GO_0005634 cell nucleus nucleus cell nucleus http://purl.obolibrary.org/obo/OBI_0000070 assay assay assay http://purl.obolibrary.org/obo/OBI_0200000 data transformation data transformation data transformation http://purl.obolibrary.org/obo/OBI_0000066 investigation investigation investigation http://purl.obolibrary.org/obo/OBI_0000094 material processing material processing material processing http://purl.obolibrary.org/obo/BFO_0000016 disposition http://purl.obolibrary.org/obo/BFO_0000034 function http://purl.obolibrary.org/obo/OBI_0000260 plan plan plan http://purl.obolibrary.org/obo/BFO_0000023 role cellular membrane owl:Thing cellular membrane http://purl.obolibrary.org/obo/CARO_0010004 http://purl.obolibrary.org/obo/NCBITaxon_131567 cellular organism 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 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 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 A processed material entity which is designed to perform a function. 2023-03-24T16:04:27Z In this definition we assume devices are made of processed material, not natural artifacts, so we involve artifactual function rather than biological function, but align with a general BFO function sense where functions such as pumping, lifting can occur in both contexts. Thus we can compare a biological arm with a robotic arm device. We say "designed" to emphasize a device's primary function rather than all the other possible dispositions a device may have that may also be useful. E.g. one can use a hammer for a paper weight. Regarding usage then, we don't say a naturally formed rock is a hammering device - it wasn't designed to bear a hammering function per se. However, a given rock may still happen to have the disposition to bear a hammering function, and so we could say it is a hammering "tool", which does not necessarily convey intentional design. Example of use: A whole device like an engine; a component like a bolt is also a device. device geophysical entity geographical entity organism Viruses organism cellular organisms agent role investigation agent role cellular organism whole plant cell plant cell immaterial anatomical entity plant anatomical space native cell native plant cell material entity sequence_feature characteristic sequence_attribute material entity sequence_variant material entity sequence_collection immaterial anatomical entity immaterial anatomical entity cellular organism multicellular organism gross anatomical part multicellular anatomical structure native cell xenopus cell native cell zebrafish cell