COB brings together key terms from a wide range of OBO projects to improve interoperability.
Core Ontology for Biology and Biomedicine
editor note
term replaced by
a core relation that holds between a part and its whole
part of
a core relation that holds between a whole and its part
has part
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
realizes
executed by
intended to realize
has plan
intended plan process type
is about
The inverse property of is specified input of
has specified input
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.
is specified input of
The inverse property of is specified output of
has specified output
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.
is specified output 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.
characteristic of
Inverse of characteristic_of
has characteristic
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates in
a relation between a process and a continuant, in which the continuant is somehow involved in the process
has participant
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.
is concretized as
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.
concretizes
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
derives from
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
location of
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
located in
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.
capable of
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
surrounded by
surrounds
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.
has input
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.
has output
enabled by
has quantity
Number of protons in an atomic nucleus
has atomic number
has number of atomic nuclei
has inchi string
process
disposition
realizable entity
role
site
function
Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
material entity
immaterial entity
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.
Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.
Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u.
A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.
Some people may be uncomfortable calling every proton an atomic nucleus
This is equivalent to CHEBI:33252
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.
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.
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.
molecule
A part of a multicellular organism that is a collection of cell components that are not all contained in one cell.
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
A material entity processed by human activity with an intent to produce it.
In the COB 2024 workshop there was much disagreement about this label.
processed material entity
completely executed planned process
A molecule that consists of nucleotides (unmodified nucleotide residues and/or modified nucleotide residues) linked by phosphodiester bonds or derivatives of such bonds.
nucleic acid chain
A complex of two or more molecules that are not covalently bound.
complex of molecules
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 completely executed planned process that intends to output material entities from input material entities
material processing
characteristic
A process during which an organism comes into contact with another entity.
exposure of organism
A processed material entity which is designed to be capable of a process.
device
A material part of an astronomical body.
geophysical entity
An environmental system which includes both living and non-living components.
ecosystem
A process in which includes the components of an environmental system as participants.
environmental system 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.
This is the same as GO molecular function
gene product or complex activity
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).
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.
biological process
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.
This is not covalently bonded, which conflicts with changes to the parent definition.
Any constituent part of a virion, a complete fully infectious extracellular virus particle.
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.
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
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.
objective specification
A directive information entity that describes an action the bearer will take.
action specification
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.
data item
A generically dependent continuant that is about some thing.
Pier: 'data, information or knowledge'. OR 'representation'
information content entity
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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.
plan specification
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
measurement datum
A process in which at least one of the participants is a molecule.
This is meant to capture processes that are more fundamental than macromolecular activities
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
investigation
A planned process that has the objective to produce information about a material entity (the evaluant) by examining it.
assay
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.
plan
A completely executed planned process that produces output data from input data.
data transformation
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
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.
A material entity that consists of two or more organisms, viruses, or viroids.
collection of organisms
An anatomical entity that is or was part of a plant.
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
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.
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.