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.
realized in
contains process
executed by
has specified input
is specified input of
has specified output
is specified output of
characteristic of
participates in
is concretized as
The range of this property should be a user-defined unit datatype, e.g 182^:cm
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
We should name the inverse in COB and avoid the confusing inverse(..) construct
role
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
electron
proton
neutron
Some people may be uncomfortable calling every proton an atomic nucleus
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
obsolete_elementary charge
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
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
A complex of two or more molecular entities that are not covalently bound.
>=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.
cellular membrane
This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc
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.
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.
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
data item
Pier: 'data, information or knowledge'. OR 'representation
document
This is meant to capture processes that are more fundamental than macromolecular activities
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
data transformation
mass
charge
protein
A role realized by a participant in a process such that the participant causes the process.