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Anatomical Structure Schema

The Anatomical Structure schema is designed to represent types and relationships of anatomical brain structures.

URI: https://identifiers.org/brain-bican/anatomical-structure-schema

Name: anatomical-structure-schema

Classes

Class Description
Annotation Biolink Model root class for entity annotations
        QuantityValue A value of an attribute that is quantitative and measurable, expressed as a c...
ChemicalEntityOrGeneOrGeneProduct A union of chemical entities and children, and gene or gene product
Entity Root Biolink Model class for all things and informational relationships, real...
        Checksum Checksum values associated with digital entities
        NamedThing a databased entity or concept/class
                Activity An activity is something that occurs over a period of time and acts upon or w...
                Attribute A property or characteristic of an entity
                BiologicalEntity
                        Gene A region (or regions) that includes all of the sequence elements necessary to...
                        Genome A genome is the sum of genetic material within a cell or virion
                InformationContentEntity a piece of information that typically describes some topic of discourse or is...
                        Dataset an item that refers to a collection of data from a data source
                        StudyResult A collection of data items from a study that are about a particular study sub...
                                RelativeFrequencyAnalysisResult A result of a relative frequency analysis
                OrganismTaxon A classification of a set of organisms
                PhysicalEntity An entity that has material reality (a
                        MaterialSample A sample is a limited quantity of something (e
                Procedure A series of actions conducted in a certain order or manner
                VersionedNamedThing An iteration of the biolink:NamedThing class that stores metadata about the o...
                        AnatomicalAnnotationSet An anatomical annotation set is a versioned release of a set of anatomical an...
                        AnatomicalSpace An anatomical space is versioned release of a mathematical space with a defin...
                        ImageDataset An image dataset is versioned release of a multidimensional regular grid of m...
                        ParcellationAtlas A parcellation atlas is a versioned release reference used to guide experimen...
                        ParcellationColorScheme A parcellation color scheme is a versioned release color palette that can be ...
                        ParcellationTerm A parcellation term is an individual term within a specific parcellation term...
                        ParcellationTerminology A parcellation terminology is a versioned release set of terms that can be us...
                        ParcellationTermSet A parcellation term set is the set of parcellation terms within a specific pa...
GenomicEntity
MacromolecularMachineMixin A union of gene locus, gene product, and macromolecular complex
        GeneOrGeneProduct A union of gene loci or gene products
OntologyClass a concept or class in an ontology, vocabulary or thesaurus
        TaxonomicRank A descriptor for the rank within a taxonomic classification
ParcellationAnnotation A parcellation annotation defines a specific segment of an anatomical space d...
ParcellationAnnotationTermMap The parcellation annotation term map table defines the relationship between p...
ParcellationColorAssignment The parcellation color assignment associates hex color value to a parcellatio...
PhysicalEssenceOrOccurrent Either a physical or processual entity
        Occurrent A processual entity
                ActivityAndBehavior Activity or behavior of any independent integral living, organization or mech...
        PhysicalEssence Semantic mixin concept
SubjectOfInvestigation An entity that has the role of being studied in an investigation, study, or e...
ThingWithTaxon A mixin that can be used on any entity that can be taxonomically classified

Slots

Slot Description
attribute_name The human-readable 'attribute name' can be set to a string which reflects its...
category Name of the high level ontology class in which this entity is categorized
checksum_algorithm The type of cryptographic hash function used to calculate the checksum value
chembl_chirality Tern indicating the chirality of the chemical entity
chembl_drug_warning Text describing warnings for use of chemicals as therapeutics
chembl_prodrug Flag indicating if a drug is a prodrug that is active only after being metabo...
color A string representing to hex triplet code of a color
content_url
creation_date date on which an entity was created
deprecated A boolean flag indicating that an entity is no longer considered current or v...
description a human-readable description of an entity
digest Stores checksum information
equivalent_identifiers A set of identifiers that are considered equivalent to the primary identifier...
format
full_name a long-form human readable name for a thing
has_attribute connects any entity to an attribute
has_attribute_type connects an attribute to a class that describes it
has_biological_sequence connects a genomic feature to its sequence
has_numeric_value connects a quantity value to a number
has_qualitative_value connects an attribute to a value
has_quantitative_value connects an attribute to a value
has_taxonomic_rank
has_unit connects a quantity value to a unit
has_anatomical_annotation_set Reference to the anatomical annotation set component of the parcellation atla...
has_anatomical_space Reference to the anatomical space component of the parcellation atlas
has_parcellation_terminology Reference to the parcellation terminology component of the parcellation atlas
has_parent_parcellation_term Reference to the parent parcellation term for which the parcellation term is ...
has_parent_parcellation_term_set Reference to the parent parcellation term set for which the parcellation term...
id A unique identifier for an entity
in_taxon connects an entity to its taxonomic classification
in_taxon_label The human readable scientific name for the taxon of the entity
information_content Information content (IC) value for a term, primarily from Automats
internal_identifier An identifier that uniquely denotes a specific parcellation annotation within...
iri An IRI for an entity
license
macromolecular_machine_mixin_name genes are typically designated by a short symbol and a full name
measures Reference to the specific image dataset used to define the anatomical space
name A human-readable name for an attribute or entity
named_thing_category Name of the high level ontology class in which this entity is categorized
node_property A grouping for any property that holds between a node and a value
ordinal
organism_taxon_has_taxonomic_rank
parameterizes Reference to the anatomical space for which the anatomical annotation set is ...
part_of_anatomical_annotation_set
part_of_parcellation_color_scheme Reference to the parcellation color scheme for which the color assignment is ...
part_of_parcellation_term_set Reference to the parcellation term set for which the parcellation term is par...
part_of_parcellation_terminology Reference to the parcellation terminology for which the parcellation term set...
provided_by The value in this node property represents the knowledge provider that create...
related_to A relationship that is asserted between two named things
related_to_at_instance_level Represents a relationship held between two instances of a data classes
revision_of
rights
specialization_of Reference to the general (non versioned) parcellation atlas for which the par...
subject_parcellation_annotation Reference to the parcellation annotation that is the subject of the associati...
subject_parcellation_term Reference to the parcellation term that is the subject of the association
subject_parcellation_terminology Reference to the parcellation terminology for which the parcellation color sc...
symbol Symbol for a particular thing
synonym Alternate human-readable names for a thing
type
unit A controlled vocabulary attribute defining the length unit of the x, y, and z...
value The checksum value obtained from a specific cryotographic hash function
version
voxel_count The number of voxels (3D pixels) spanned by the parcellation annotation (opti...
x_direction A controlled vocabulary attribute defining the x axis direction in terms of a...
x_resolution The resolution (length / pixel) in along the x axis (numerical value part)
x_size The number of pixels/voxels (size) along the x axis
xref A database cross reference or alternative identifier for a NamedThing or edge...
y_direction A controlled vocabulary attribute defining the y axis direction in terms of a...
y_resolution The resolution (length / pixel) in along the y axis (numerical value part)
y_size The number of pixels/voxels (size) along the y axis
z_direction A controlled vocabulary attribute defining the z axis direction in terms of a...
z_resolution The resolution (length / pixel) in along the z axis (numerical value part)
z_size The number of pixels/voxels (size) along the y axis

Enumerations

Enumeration Description
ANATOMICALDIRECTION A controlled vocabulary term defining axis direction in terms of anatomical d...
DigestType
DISTANCEUNIT

Types

Type Description
BiologicalSequence
Boolean A binary (true or false) value
Curie a compact URI
Date a date (year, month and day) in an idealized calendar
DateOrDatetime Either a date or a datetime
Datetime The combination of a date and time
Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci...
Double A real number that conforms to the xsd:double specification
Float A real number that conforms to the xsd:float specification
Integer An integer
IriType An IRI
Jsonpath A string encoding a JSON Path
Jsonpointer A string encoding a JSON Pointer
LabelType A string that provides a human-readable name for an entity
NarrativeText A string that provides a human-readable description of something
Ncname Prefix part of CURIE
Nodeidentifier A URI, CURIE or BNODE that represents a node in a model
Objectidentifier A URI or CURIE that represents an object in the model
Sparqlpath A string encoding a SPARQL Property Path
String A character string
SymbolType
Time A time object represents a (local) time of day, independent of any particular...
Unit
Uri a complete URI
Uriorcurie a URI or a CURIE

Subsets

Subset Description
ModelOrganismDatabase Subset that is relevant for a typical Model Organism Database (MOD)
Samples Sample/biosample datamodel
Testing TBD
TranslatorMinimal Minimum subset of translator work