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