Atlas Ontology Model
type: Ontology
description: An ontology model for anatomical atlases.
comment: Core OWL2 entities for describing anatomical atlases.
version info: 2023-04-27
contributor: Jan G. Bjaalie - https://orcid.org/0000-0001-7899-906X
contributor: Lyuba Zehl - https://orcid.org/0000-0002-5947-9939
contributor: Maryann Martone - https://orcid.org/0000-0002-8406-3871
contributor: Timo Dickscheid - https://orcid.org/0000-0002-9051-3701
creator: Heidi Kleven - https://orcid.org/0000-0002-3710-321X
creator: Tom Gillespie - https://orcid.org/0000-0002-7509-4801
creator: Trygve B. Leergaard - https://orcid.org/0000-0001-5965-8470
license: CC-BY-4.0
audience: researchers using or creating anatomical atlases
bug-database: issues
git respository: NIF-Ontology
axiom patterns: OWL restrictions are used, however there are no general patterns that are employed at scale.
competition: bspo.owl
dereferenceable iris: `atom:' and `ilxtr:' identifiers are not currently dereferenceable, but they are planned to be.
development community: NIF-Ontology
development environment: Protégé, FaCT++, ELK
entity deprecation strategy: Specific ontology ids are never deprecated.
entity metadata policy: `rdfs:label' should be present. Old iris that are equivalent classes may not contain a label.
entity naming convention: Entities are named in English according to the technical terminology used in the field.
evaluation: No formal external evaluation has been conducted, however external groups have applied the model to their atlases. See https://doi.org/10.1101/2023.01.22.525049
example of use: https://doi.org/10.1101/2023.01.22.525049
identifier generation policy: Identifiers should not be automatically generated. Human readable iris are created as needed.
knowledge acquisition methodology: https://doi.org/10.1101/2023.01.22.525049
knowledge representation language: owl
methodological framework: https://doi.org/10.1101/2023.01.22.525049
need: There is a need to establish a minimal model for anatomical atlases for use in information systems. There is also a need to establish a shared vocabulary to facilitate communication between groups that are creating anatomical atlases that use slightly different words to describe the same things. Finally there is a need for such a model to provide a foundation for documenting the criteria used in the creation and versioning of atlases.
scope and coverage: Scope: components of anatomical atlases, their parts, and metadata. Coverage: AtOM provides a core model for describing anatomical atlases.
source knowledge location: https://doi.org/10.1101/2023.01.22.525049
sustainability plan: AtOM is maintained as part of the NIF-Ontology.
testing: See https://doi.org/10.1101/2023.01.22.525049
versioning policy: Development versions of the ontology are released continuously and are identified by their git commit hashes. Stable versions are released periodically and can be accessed by their git tag.

annotates
type: ObjectProperty
synonym: isAnchoredTo
synonym: isCoordinatedTo
domain: parcellation annotation
range: anatomical space
has ilx id: ilx_0778137

hasResolution
type: ObjectProperty
domain: anatomical data
range: resolution
has ilx id: ilx_0778134

hasSpace
type: ObjectProperty
domain: anatomical data
range: anatomical space
has ilx id: ilx_0778135

hasUnit
type: ObjectProperty
has ilx id: ilx_0778136

isMeasurementOf
type: ObjectProperty
domain: anatomical data

names
type: ObjectProperty
domain: parcellation region
range: parcellation annotation
has ilx id: ilx_0778133

transforms
type: ObjectProperty
domain: transformation rule
range: anatomical space

labelPartOf
type: ObjectProperty
type: TransitiveProperty
sub property of: BFO_0000050

hasResolutionX
type: DatatypeProperty

hasResolutionY
type: DatatypeProperty

hasResolutionZ
type: DatatypeProperty

spatial alignment
type: Class
IAO_0000115: dataset -> dataset, rotation, translation
subclass of: process
subclass of: Restriction
  on property: BFO_0000051
  some values from: space preserving linear transformation
subclass of: Restriction
  on property: hasInformationOutput
  some values from: transformation rule
local name: alignment

anatomical axis
type: Class
IAO_0000115: an anatomical axis, e.g. rostral caudal, dorsal ventral, etc. is composed of two colinear and opposed anatomical directions
subclass of: axis

anatomical axis alignment vector
type: Class

cartesian anatomical axis alignment vector
type: Class
subclass of: anatomical axis alignment vector
subclass of: Restriction
  on property: hasDirectionMappedToPositiveX
  some values from: anatomical direction
subclass of: Restriction
  on property: hasDirectionMappedToPositiveY
  some values from: anatomical direction
subclass of: Restriction
  on property: hasDirectionMappedToPositiveZ
  some values from: anatomical direction
local name: anatomical axis alignment vector

anatomical dataset
type: Class
synonym: default image
synonym: raw image
synonym: template
synonym: uncoordinated dataset
synonym: unoriented dataset
subclass of: anatomical data
subclass of: Restriction
  on property: hasSpace
  some values from: anatomical image space
local name: anatomical dataset

anatomical direction
type: Class
subclass of: direction

anchoring
type: Class
synonym: RegistrationUsingAnnotationOnly
IAO_0000115: dataset -> annotation
subclass of: process
local name: anchoring

parcellation annotation
type: Class
synonym: atlas annotation
subclass of: parcellation artifact
subclass of: Restriction
  on property: annotates
  some values from: anatomical space
  cardinality: 1
local name: annotation

anatomical annotation criteria
type: Class
synonym: anatomical delineation criteria
synonym: delineation criteria
synonym: parcellation annotation criteria
subclass of: parcellation artifact
local name: annotation criteria

annotation criteria application
type: Class
subclass of: process
local name: annotation criteria application

anatomical annotation set
type: Class
synonym: annotation set
synonym: parcellation annotation set
IAO_0000115: A set of anatomical annotations that are anchored in the same space.
subclass of: parcellation artifact
subclass of: Restriction
  on property: RO_0002351
  some values from: parcellation annotation
IAO_0000116: It is probably the case that the hasMember Annotation restriction could be an equivalent class axiom.
has ilx id: ilx_0777108
local name: annotation set

anterior
type: Class
subclass of: anatomical direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: posterior

anterior posterior axis
type: Class
subclass of: anatomical axis
subclass of: Restriction
  on property: hasDirection
  some values from: anterior
subclass of: Restriction
  on property: hasDirection
  some values from: posterior

parcellation artifact
type: Class
equivalent class: parcellationArtifact
synonym: parcellation artifact
has ilx id: ilx_0777105
local name: artifact

parcellation atlas
type: Class
equivalent class: parcellationAtlas
synonym: anatomical reference atlas
IAO_0000115: An anatomical reference atlas is information content entity that contains minimally a notion of space and one of an annotation set or an unannotated but registered set of source data, the space may be explicit or implicit. An atlas is anything that is used to guide experiments or deal with some spatial relation between things or the location of things. For example a feature atlas may have only a boolean mask of stained/unstained for a given marker across the whole brain. On the other hand there may be purely schematic or conceptual atlases that show the relative positions of landmarks that are useful for guiding surgical procedures that have an intentionally distorted or schematic representation of space but that nonetheless capture real an critical spatial relations between regions. Reference atlases usually have additional parts that make them more useful in certain situations, such as a well defined coordinate system, delineations indicating the boundaries of various regions or cell populations, landmarks, and labels and names to make it easier to communicate about well known and useful locations.
subclass of: parcellation artifact
subclass of: Restriction
  on property: BFO_0000051
  some values from: anatomical annotation set
subclass of: Restriction
  on property: BFO_0000051
  some values from: anatomical space
subclass of: Restriction
  on property: BFO_0000051
  some values from: parcellation terminology
has ilx id: ilx_0777109
local name: atlas

axis
type: Class
subclass of: Restriction
  on property: hasDirection
  some values from: direction
  cardinality: 2

axis direction matrix
type: Class
subclass of: matrix

axis origin
type: Class
subclass of: vector

anatomical border
type: Class
IAO_0000115: A border is a spatial entities that when projected into two dimensions forms a line (line in 2d or plane in 3d). The border may be of finite length, and may occupy a subsegment of a longer closed boundary.
IAO_0000115: A border is topologically equivalent to a point. A finite point, line, or plane. It can be used to define notions of nearness and relative position in the context of another landmark. For example if there are two points you can talk about a third point being on one side of the border point relative to the landmark point.
subclass of: anatomical line
local name: border

anatomical boundary
type: Class
IAO_0000115: A boundary is a closed curve or surface that is topologically equivalent to a circle, it defines an inside and an outside that are disconnected.
subclass of: anatomical closed curve
local name: boundary

caudal
type: Class
IAO_0000115: toward the tail
subclass of: anatomical direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: rostral

anatomical centroid
type: Class
IAO_0000115: a point surrounded by an indeterminate/unknown/probabilistic (but closed) boundary where the indeterminateness of said boundary is usually due to the fact that the context in which a label associated with the centroid is being used does not admit a single operational defintion, i.e. that there is not agreement on the exact definition of the term but there is some agreement that it exists
subclass of: anatomical point
local name: centroid

anatomical closed curve
type: Class
IAO_0000115: curves that are topologically equivalent to a circle
subclass of: parcellation annotation
local name: closed curve

coordinated dataset
type: Class
synonym: reconstructed brain
subclass of: anatomical data
subclass of: Restriction
  on property: hasSpace
  some values from: anatomical space
local name: coordinated dataset

coordinate system application
type: Class
subclass of: process
subclass of: Restriction
  on property: BFO_0000051
  some values from: spatial alignment
subclass of: Restriction
  on property: BFO_0000051
  some values from: spatial transformation
local name: coordinate system application

coordinate system definition
type: Class
synonym: coordination rule
subclass of: parcellation artifact
local name: coordinate system definition

anatomical data
type: Class
IAO_0000115: Some specialized data that is about some organism.
subclass of: parcellation artifact
subclass of: Restriction
  on property: hasResolution
  some values from: resolution
  cardinality: 1
subclass of: Restriction
  on property: hasSpace
  some values from: anatomical space
subclass of: Restriction
  on property: isMeasurementOf
  some values from: NCBITaxon 1
local name: data

anatomical delineation
type: Class
IAO_0000115: an annotation with criteria demarcating the border between two regions or the boundary of a single region
subclass of: parcellation annotation
local name: delineation

direction
type: Class

dorsal
type: Class
IAO_0000115: toward the back or toward the top of the skull in organisms where development has twisted things (humans)
subclass of: anatomical direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: ventral

dorsal ventral axis
type: Class
IAO_0000115: the anatomical axis from back to belly
subclass of: anatomical axis
subclass of: Restriction
  on property: hasDirection
  some values from: dorsal
subclass of: Restriction
  on property: hasDirection
  some values from: ventral

anatomical image space
type: Class
synonym: data space
synonym: dataset space
synonym: donor space
synonym: image space
synonym: individual space
synonym: intrinsic data space
synonym: intrinsic space
synonym: sample space
synonym: specimen space
IAO_0000115: an image space is the intrinsic or implicit space that is defined by an image, in digital images it is usually discretized as matrix, it usually euclidean and supports a cartesian distance metric, however in cases where there is a non-uniformly sampling sensor or if the image was collected in the frequency domain (e.g. for MRI images) then the image space has different dimensions which may non-spatial (FIXME need some clarity about data captured in the frequency domain)
subclass of: anatomical space
editor question: are specimen/individual space different from image/dataset space?
local name: image space

inferior
type: Class
subclass of: anatomical direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: superior

inferior superior axis
type: Class
subclass of: anatomical axis
subclass of: Restriction
  on property: hasDirection
  some values from: inferior
subclass of: Restriction
  on property: hasDirection
  some values from: superior

parcellation label
type: Class
synonym: Parcellation Label
synonym: parcellation term
synonym: term
definition: Parcellation labels are strings characthers sometimes associated with a unique identifier, such as an index number or an iri.
subclass of: UBERON_0001062
local name: label

anatomical landmark
type: Class
IAO_0000115: Any annotation that is not closed (topologically equivalent to a point).
subclass of: parcellation annotation
local name: landmark

lateral
type: Class
IAO_0000115: direction away from the midline
subclass of: anatomical direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: medial

left
type: Class
subclass of: anatomical direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: right

left right axis
type: Class
subclass of: anatomical axis
subclass of: Restriction
  on property: hasDirection
  some values from: left
subclass of: Restriction
  on property: hasDirection
  some values from: right

anatomical line
type: Class
subclass of: parcellation annotation
local name: line

linear registration
type: Class
subclass of: spatial registration
subclass of: Restriction
  on property: BFO_0000051
  some values from: linear transformation

linear transformation
type: Class
subclass of: spatial transformation

matrix
type: Class
local name: matrix

medial
type: Class
IAO_0000115: toward the midline
subclass of: anatomical direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: lateral

medial lateral axis
type: Class
subclass of: anatomical axis
subclass of: Restriction
  on property: hasDirection
  some values from: lateral
subclass of: Restriction
  on property: hasDirection
  some values from: medial

negative x
type: Class
subclass of: spatial direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: positive x

negative y
type: Class
subclass of: spatial direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: positive y

negative z
type: Class
subclass of: spatial direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: positive z

nonlinear registration
type: Class
subclass of: spatial registration
subclass of: Restriction
  on property: BFO_0000051
  some values from: nonlinear transformation

nonlinear transformation
type: Class
subclass of: spatial transformation

spatial orienting
type: Class
synonym: orienting
IAO_0000115: axis -> axis
IAO_0000115: Orienting is the process of changing the relative position of two axes so that they become aligned for some definition of alignment.
subclass of: spatial alignment
local name: orienting

anatomical parcellation
type: Class
synonym: anatomical parcellation scheme
synonym: parcellation scheme
subclass of: anatomical annotation set
local name: parcellation

anatomical point
type: Class
IAO_0000115: a 1d point defined by a single vector having the same dimensions as the space in which it is defined
subclass of: parcellation annotation
local name: point

positive x
type: Class
subclass of: spatial direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: negative x

positive y
type: Class
subclass of: spatial direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: negative y

positive z
type: Class
subclass of: spatial direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: negative z

posterior
type: Class
IAO_0000115: toward the buttocks
subclass of: anatomical direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: anterior

process
type: Class
local name: process

parcellation region
type: Class
synonym: atlas region
synonym: Parcellation Region
definition: Parcellation regions are 'anatomical entities' that correspond to some part of a real biological system and are equivalent to an intersection between a parcellation label and a specific version of an atlas that defines or uses that label and that provides a definitive (0, 1, or probabilistic) way to determine whether a particular sample corresponds to any given region.
subclass of: parcellation label
subclass of: Restriction
  on property: names
  some values from: parcellation annotation
  cardinality: 1
local name: region

spatial registration
type: Class
IAO_0000115: dataset -> dataset, rotation, translation, scaling, or some nonlinear transformation
IAO_0000115: Registration is the process of changing the relative position and/or scaling of two datasets so that they become aligned for some definition of alignment.
subclass of: spatial alignment
subclass of: Restriction
  on property: BFO_0000051
  some values from: spatial transformation
local name: registration

resolution
type: Class
subclass of: vector
subclass of: Restriction
  on property: hasResolutionX
  some values from: real
subclass of: Restriction
  on property: hasResolutionY
  some values from: real
subclass of: Restriction
  on property: hasResolutionZ
  some values from: real
subclass of: Restriction
  on property: hasUnit
  some values from: spaceUnit
local name: resolution

right
type: Class
subclass of: anatomical direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: left

rostral
type: Class
IAO_0000115: toward the snount
subclass of: anatomical direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: caudal

rostral caudal axis
type: Class
IAO_0000115: The snout to tail axis.
subclass of: anatomical axis
subclass of: Restriction
  on property: hasDirection
  some values from: caudal
subclass of: Restriction
  on property: hasDirection
  some values from: rostral

rotation
type: Class
subclass of: space preserving linear transformation

rotation matrix
type: Class
subclass of: transformation matrix

scaling
type: Class
subclass of: linear transformation

anatomical segmentation
type: Class
IAO_0000115: an annotation set that may or may not have an explicit bounding region but that does break or separate the area or volume into distinct segments
subclass of: anatomical annotation set
IAO_0000116: This isn't really distinct from an annotation set.
local name: segmentation

anatomical space
type: Class
synonym: anatomical coordinate space
synonym: atlas space
synonym: common coordinate space
synonym: parameterized coordinate space
synonym: physical space
IAO_0000115: An anatomical space is a combination of a mathematical space with an anatomical space such that there is a defined mapping between the anatomical axes and the mathematical axes. A mathematical coordinate space by itself is NOT an anatomical space because it admits all possible orientations and reflections of the anatomical space, so for example a brain can be rotated in all directions and still be in that mathematical coordinate space. Such spaces are called unoriented spaces and are a source of significant pain when dealing with anatomical datasets.
subclass of: parcellation artifact
subclass of: Restriction
  on property: hasUnit
  some values from: spaceUnit
subclass of: Restriction
  on property: BFO_0000051
  some values from: anatomical axis alignment vector
subclass of: Restriction
  on property: BFO_0000051
  some values from: axis direction matrix
subclass of: Restriction
  on property: BFO_0000051
  some values from: axis origin
IAO_0000116: To avoid problems like those encountered by nifti an anatomical reference space MUST define an anatomical axis alignment vector which states, for example, [X, Y, Z] -> [R, A, D] (left hand rule). This immediately indicates the three annotations required on any unoriented dataset as opposed to someone trying to apply the anatomical directions directly to the unoriented dataset
has ilx id: ilx_0777106
local name: space

space preserving linear transformation
type: Class
subclass of: linear transformation

spatial axis
type: Class
subclass of: axis

spatial direction
type: Class
subclass of: direction

superior
type: Class
subclass of: anatomical direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: inferior

parcellation terminology
type: Class
equivalent class: parcellationTerminology
synonym: controlled vocabulary
IAO_0000115: a collection of terms that can be used to name annotations in an atlas
subclass of: parcellation artifact
has ilx id: ilx_0777107
local name: terminology

anatomical tiling parcellation
type: Class
synonym: tiling annotation set
synonym: tiling parcellation
IAO_0000115: an annotation set that forms a non-overlapping cover of a single bounding annotation
subclass of: anatomical annotation set
IAO_0000116: closure axioms related to the bounding annotation need to be considered
local name: tiling

spatial transformation
type: Class
IAO_0000115: space -> space
subclass of: process
subclass of: Restriction
  on property: hasInformationInput
  some values from: anatomical space
subclass of: Restriction
  on property: hasInformationOutput
  some values from: anatomical space
local name: transformation

transformation matrix
type: Class
subclass of: matrix
subclass of: transformation rule
local name: transformation matrix

transformation rule
type: Class
subclass of: parcellation artifact
subclass of: Restriction
  on property: transforms
  some values from: anatomical space
local name: transformation rule

translation
type: Class
subclass of: space preserving linear transformation

unoriented space
type: Class
IAO_0000115: A mathematical space that is not equipped with an explicit mapping between spatial and anatomical axes. In such spaces it is not possible to determine whether an anatomical dataset is correctly oriented even if that dataset has been annotated with landmarks that can be used to determine the anatomical axes.
local name: unoriented space

vector
type: Class
local name: vector

ventral
type: Class
IAO_0000115: toward the belly
subclass of: anatomical direction
subclass of: Restriction
  on property: hasOppositeDirection
  some values from: dorsal

x axis
type: Class
subclass of: spatial axis
subclass of: Restriction
  on property: hasDirection
  some values from: negative x
subclass of: Restriction
  on property: hasDirection
  some values from: positive x

y axis
type: Class
subclass of: spatial axis
subclass of: Restriction
  on property: hasDirection
  some values from: negative y
subclass of: Restriction
  on property: hasDirection
  some values from: positive y

z axis
type: Class
subclass of: spatial axis
subclass of: Restriction
  on property: hasDirection
  some values from: negative z
subclass of: Restriction
  on property: hasDirection
  some values from: positive z

Left Posterior Superior anatomical axis alignment
type: cartesian anatomical axis alignment vector
type: NamedIndividual
has direction mapped to positive x: left
has direction mapped to positive y: posterior
has direction mapped to positive z: superior

Posterior Ventral Right anatomical axis alignment
type: cartesian anatomical axis alignment vector
type: NamedIndividual
has direction mapped to positive x: posterior
has direction mapped to positive y: ventral
has direction mapped to positive z: right

Right Anterior Dorsal anatomical axis alignment
type: cartesian anatomical axis alignment vector
type: NamedIndividual
has direction mapped to positive x: right
has direction mapped to positive y: anterior
has direction mapped to positive z: dorsal

Right Anterior Superior anatomical axis alignment
type: cartesian anatomical axis alignment vector
type: NamedIndividual
has direction mapped to positive x: right
has direction mapped to positive y: anterior
has direction mapped to positive z: superior