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BKE Taxonomy Schema

The BKE Taxonomy Schema represents the structure of classifications of cell types and their hierarchical relationships in the mammalian brain.

URI: https://w3id.org/brain-bican/bke-taxonomy

Name: BKETaxonomy

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...
AnnotationCollection
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
                Abbreviation Maps an abbreviation string to its decoded meaning
                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...
                                GeneAnnotation Represents a single gene
                        Genome A genome is the sum of genetic material within a cell or virion
                                GenomeAnnotation Represents a genome annotation
                CellSpecimen ( defined as in BERS)
                CellTypeSet A grouping of cell type taxons
                CellTypeTaxon A cell type taxon is a node in a taxonomy
                CellTypeTaxonomy A cell type taxonomy is a systematic classification of cell types and their h...
                Cluster One specific cluster from the set of clusters determined by a clustering proc...
                ClusterSet The output of a clustering process where input observations are organized or ...
                ColorPalette A schematic set of display colors that can be applied to individual component...
                DisplayColor One element of a color palette representing the association between a color a...
                GenomeAssembly Represents a genome assembly
                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
                                        SpatialProportions Spatial distribution of expression, labeling, or anatomical density of a give...
                MatrixFile A digital file containing the representation of full or partial data matrix
                ObservationMatrix A matrix (potentially virtual) of observations
                ObservationRow One specific row of the observation matrix representing a set of measurements...
                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
                        CellTypeTaxonomyCreationProcess The process of organizing cells or clusters into a systematic classification ...
                        ClusteringProcess The process of organizing and classifying observations into groups or cluster...
                        ObservationMatrixCreationProcess The process of aggregating data to create an observation matrix (potentially ...
                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
ProvActivity An activity is something that occurs over a period of time and acts upon or w...
ProvEntity An entity is a physical, digital, conceptual, or other kind of thing with som...
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
accession_id A provider assigned accession identifier for a given entity
adj Proportion of composition found in Adjacent Regions
annotations
attribute_name The human-readable 'attribute name' can be set to a string which reflects its...
authority The organization responsible for publishing the data
category Name of the high level ontology class in which this entity is categorized
cell_type_set_type A tag denoting the type or purpose of the cell type set
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
color_hex_triplet A hex string representing the display color for an associated entity
contains_cluster One of potentially cell clusters which together defines the cell type taxon
contains_observation One of potentially many input observations which together define the cluster
contains_sample One of potentially many sample which together define the cluster
contains_taxon One of potentially many cell types taxons which together defines the cell typ...
content_url
creation_date date on which an entity was created
curated_markers_to_mouse Marker genes in the mouse species that are related to the respective cell typ...
curated_markers_to_primates Marker genes in the primate species that are related to the respective cell t...
denotes_cell_type One of potentially many cell type terms which the abbreviation denotes
denotes_gene_annotation One of potentially many gene annotation terms to which the abbreviation denot...
denotes_parcellation_term One of potentially many parcellation terms (anatomical structures) which the ...
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
entity_type The entity type which the abbreviation term denotes
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
genome_annotations
genome_assemblies
gpe Proportion of composition found in External Globus Pallidus
gpi Proportion of composition found in Internal Globus Pallidus
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_abbreviation
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
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...
has_variable One of set of genes which together forms the variable set of an observation m...
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
is_color_for_set The associated cell type set of the specified display color
is_color_for_taxon The associated cell type taxon for the specified display color
is_palette_for The cell types taxonomy for which the palette provides display color properti...
is_revision_of
label
license
macromolecular_machine_mixin_name genes are typically designated by a short symbol and a full name
meaning The meaning of an abbreviation term
measures Reference to the specific image dataset used to define the anatomical space
molecular_type
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
number_of_cells The aggregated number of cells that defines the cell type taxon
number_of_observations The number of observations in the cluster
order The priority or display order of an entity among all other entiites of the sa...
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_matrix The observation matrix for which is observation row is part of
part_of_palette The color palette for which the display color map is part of
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...
part_of_set The cluster set from which the cluster is part of
part_of_taxonomy
provided_by The value in this node property represents the knowledge provider that create...
reference_assembly The reference genome assembly that this genome annotation was created from
referenced_in The genome annotation that this gene was referenced from
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
represented_by One of potentially matrix files which together represents the entire observat...
represented_in The specific file where this observation row is represented
revision_of
rights
sn Proportion of composition found in Substantia Nigra
source_id The authority specific identifier
spatial_proportions_human Quantification of regional composition (how much of something is found in eac...
spatial_proportions_macaque Quantification of regional composition (how much of something is found in eac...
spatial_proportions_marmoset Quantification of regional composition (how much of something is found in eac...
spatial_regional_proportions Species-independent quantification of regional composition (how much of somet...
specialization_of Reference to the general (non versioned) parcellation atlas for which the par...
sth Proportion of composition found in Subthalamic Nucleus
str Proportion of composition found in Striatum
strain The genetic variant or subtype of a species or organism
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
term An abbreviation term
type
unit A controlled vocabulary attribute defining the length unit of the x, y, and z...
used Usage is the beginning of utilizing an entity by an activity
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...
was_derived_from A derivation is a transformation of an entity into another, an update of an e...
was_generated_by Generation is the completion of production of a new entity by an activity
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
AbbreviationEntityType
ANATOMICALDIRECTION A controlled vocabulary term defining axis direction in terms of anatomical d...
AuthorityType
BioType
CellTypeSetType
DigestType
DISTANCEUNIT
Region

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