COB brings together key terms from a wide range of OBO projects to improve interoperability. Core Ontology for Biology and Biomedicine This version of COB includes native OBO URIs, only using COB IRIs where equivalent natives could not be found. To see the edition that includes native IRIs, consult cob-edit.owl. 2023-05-12 definition part of has part realized in occurs in contains process executed by concretizes intended to realize has plan intended plan process type realizes http://purl.obolibrary.org/obo/IAO_0000136 is about has specified input is specified input of has specified output is specified output of characteristic of has characteristic https://github.com/oborel/obo-relations/pull/284 Anything can have a characteristic participates in has participant is concretized as enabled by 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 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 disposition realizable 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 role site function material entity immaterial entity 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 cellular organism 0 electron nucleic acid polymer proton monoatomic ion neutron uncharged atom Some people may be uncomfortable calling every proton an atomic nucleus This is equivalent to CHEBI:33252 atomic nucleus subatomic particle 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 no longer needed obsolete_elementary charge true 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 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 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 geographical location immaterial anatomical entity gene product action 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 cellular membrane 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 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. 2023-03-24T16:04:27+00:00 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 A processed material entity created to be administered to an individual with the intent to improve health. drug product geophysical entity ecosystem environmental process This is the same as GO molecular function gene product or complex activity cell nucleus 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 not covalently bonded, which conflicts with changes to the parent definition. protein-containing macromolecular complex objective specification data item Pier: 'data, information or knowledge'. OR 'representation information directive information entity plan specification document This is meant to capture processes that are more fundamental than macromolecular activities physico-chemical process completely executed planned process A material entity processed by human activity with an intent to produce processed material entity investigation assay material processing Should revisit if we can place outside of material entity - a collection of roles. organization plan conclusion based on data data transformation phenotypic finding disease course disease diagnosis mass charge collection of organisms protein A role realized by a participant in a process such that the participant causes the process. agent role