COB brings together key terms from a wide range of OBO projects to improve interoperability. Core Ontology for Biology and Biomedicine 2023-11-16 definition is concretized as executed by characteristic of participates in is specified input of is specified output of realized in contains process has specified input has specified output has part has participant occurs in part of enabled by concretizes intended to realize has plan intended plan process type executes realizes has characteristic https://github.com/oborel/obo-relations/pull/284 Anything can have a characteristic http://purl.obolibrary.org/obo/IAO_0000136 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 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 mass charge no longer needed obsolete_elementary charge true material entity subatomic particle proton neutron 0 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 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 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 protein 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 native cell 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 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 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 Should revisit if we can place outside of material entity - a collection of roles. organization A material entity processed by human activity with an intent to produce processed material entity immaterial entity geographical location realizable process completely executed planned process 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 This is the same as GO molecular function gene product or complex activity monoatomic ion uncharged atom nucleic acid polymer collection of organisms immaterial anatomical entity site conclusion based on data Pier: 'data, information or knowledge'. OR 'representation information disease diagnosis phenotypic finding disease course environmental process This is meant to capture processes that are more fundamental than macromolecular activities physico-chemical process ecosystem geophysical entity directive information entity gene product This is not covalently bonded, which conflicts with changes to the parent definition. protein-containing macromolecular complex objective specification action specification plan specification A complex of two or more molecular entities that are not covalently bound. 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 A processed material entity created to be administered to an individual with the intent to improve health. drug product document data item cell nucleus assay data transformation investigation material processing disposition function plan role cellular membrane 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 A role realized by a participant in a process such that the participant causes the process. agent role characteristic https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 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