An ontology model for anatomical atlases.
Core OWL2 entities for describing anatomical atlases.
Jan G. Bjaalie - https://orcid.org/0000-0001-7899-906X
Maryann Martone - https://orcid.org/0000-0002-8406-3871
Timo Dickscheid - https://orcid.org/0000-0002-9051-3701
Heidi Kleven - https://orcid.org/0000-0002-3710-321X
Tom Gillespie - https://orcid.org/0000-0002-7509-4801
Trygve B. Leergaard - https://orcid.org/0000-0001-5965-8470
researchers using or creating anatomical atlases
OWL restrictions are used, however there are no general patterns that are employed at scale.
`atom:' and `ilxtr:' identifiers are not currently dereferenceable, but they are planned to be.
Specific ontology ids are never deprecated.
`rdfs:label' should be present. Old iris that are equivalent classes may not contain a label.
Entities are named in English according to the technical terminology used in the field.
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
Identifiers should not be automatically generated. Human readable iris are created as needed.
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: components of anatomical atlases, their parts, and metadata. Coverage: AtOM provides a core model for describing anatomical atlases.
AtOM is maintained as part of the NIF-Ontology.
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.
dataset -> dataset, rotation, translation
an anatomical axis, e.g. rostral caudal, dorsal ventral, etc. is composed of two colinear and opposed anatomical directions
cartesian anatomical axis alignment vector
A set of anatomical annotations that are anchored in the same space.
It is probably the case that the hasMember Annotation restriction could be an equivalent class axiom.
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.
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.
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.
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.
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
curves that are topologically equivalent to a circle
Some specialized data that is about some organism.
an annotation with criteria demarcating the border between two regions or the boundary of a single region
toward the back or toward the top of the skull in organisms where development has twisted things (humans)
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)
are specimen/individual space different from image/dataset space?
Parcellation labels are strings characthers sometimes associated with a unique identifier, such as an index number or an iri.
Any annotation that is not closed (topologically equivalent to a point).
Orienting is the process of changing the relative position of two axes so that they become aligned for some definition of alignment.
a 1d point defined by a single vector having the same dimensions as the space in which it is defined
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.
dataset -> dataset, rotation, translation, scaling, or some nonlinear transformation
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.
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
This isn't really distinct from an annotation set.
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.
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
a collection of terms that can be used to name annotations in an atlas
an annotation set that forms a non-overlapping cover of a single bounding annotation
closure axioms related to the bounding annotation need to be considered
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.
Left Posterior Superior anatomical axis alignment
Posterior Ventral Right anatomical axis alignment
Right Anterior Dorsal anatomical axis alignment
Right Anterior Superior anatomical axis alignment