openminds.v5.sands

Metadata about brain atlases, as well as anatomical locations and relations of non-atlas data.

Brain Atlases

class AnatomicalAtlas(name=None, alias=None, abbreviation=None, comments=None, contributions=None, contributor_affiliations=None, description=None, digital_identifier=None, documentation=None, full_name=None, has_terminology=None, has_versions=None, homepage=None, how_to_cite=None, is_input_to=None, is_part_of=None, keywords=None, learning_resources=None, ontology_identifier=None, related_publications=None, short_name=None, support_channels=None, used_taxon=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• abbreviation (str) – no description available

• contributions (Contribution) – no description available

• contributor_affiliations (Affiliation) – no description available

• description (str) – Longer statement or account giving the characteristics of the anatomical atlas.

• digital_identifier (DOI, ISBN, RRID) – Digital handle to identify objects or legal persons.

• documentation (DOI, File, ISBN, WebResource) – no description available

• full_name (str) – Whole, non-abbreviated name of the anatomical atlas.

• has_terminology (ParcellationTerminology) – no description available

• homepage (IRI) – Main website of the anatomical atlas.

• how_to_cite (str) – Preferred format for citing a particular object or legal person.

• keywords (AccessChannel, AccessEligibilityType, AccessForm, AccessProcessType, ActionStatusType, AgeCategory, AgeReference, AnalysisTechnique, AnatomicalAxesOrientation, AnatomicalCavity, AnatomicalIdentificationType, AnatomicalPlane, AnnotationCriteriaType, AnnotationType, AtlasType, AuditoryStimulusType, BiologicalOrder, BiologicalProcess, BiologicalSex, BreedingType, CellCultureType, CellType, ChemicalMixtureType, Colormap, CommunicationInterfaceType, CommunicationProtocol, ContributionType, CranialWindowConstructionType, CranialWindowReinforcementType, CriteriaQualityType, DataType, DependencyImpact, DeploymentEnvironmentType, DeviceMountingType, DeviceType, DifferenceMeasure, Disease, DiseaseModel, EducationalLevel, ElectricalStimulusType, ExperimentalApproach, ExternalBodyRegion, FileBundleGrouping, FileRepositoryType, FileUsageRole, GeneticStrainType, GustatoryStimulusType, Handedness, Language, Laterality, LearningResourceType, MRIFatSuppressionTechnique, MRIParallelAcquisitionTechnique, MRIPulseSequence, MRISpoilingTechnique, MRIWeighting, MeasuredQuantity, MeasuredSignalType, MetaDataModelType, ModelAbstractionLevel, ModelScope, ModificationConsentRequirement, ModificationConstraint, ModificationForm, ModificationScope, MolecularEntity, MuscularStructure, NervousSystemStructure, OlfactoryStimulusType, OperatingDevice, OperatingSystem, OperationalApproach, OpticalStimulusType, Organ, OrganSystemStructure, OrganismSubstance, OrganismSystem, OrganizationType, PatchClampVariation, PaymentModelType, PreparationType, ProgrammingLanguage, ProjectType, PublicationStatus, PulseShape, QualitativeOverlap, SemanticDataType, SetupType, SignalDirectionality, SkeletalStructure, SoftwareApplicationCategory, SoftwareFeature, SovereignState, SpatialEncoding, Species, StimulationApproach, StimulationTechnique, SubcellularEntity, SubjectAttribute, SupranationalBody, TactileStimulusType, Technique, TermSuggestion, Terminology, TissueSampleAttribute, TissueSampleType, TissueStructure, TypeOfUncertainty, UnitOfMeasurement, VascularStructure, VisualStimulusType, WeightType) – Significant word or concept that are representative of the anatomical atlas.

• ontology_identifier (IRI) – Term or code used to identify the anatomical atlas registered within a particular ontology.

• related_publications (DOI, GenericIdentifier, HANDLE, ISBN, ISSN, Book, Chapter, ScholarlyArticle) – Reference to something that was made available for the general public to see or buy.

• short_name (str) – Shortened or fully abbreviated name of the anatomical atlas.

• support_channels (str) – Way of communication used to interact with users or customers.

• used_taxon (BiologicalOrder, Species) – no description available

• comments (Comment) – reverse of ‘about’

• has_versions (AnatomicalAtlasVersion) – reverse of ‘is_version_of’

• is_input_to (DatasetVersion) – reverse of ‘input_data’

• is_part_of (Project, ResearchProductGroup) – reverse of ‘has_parts’

• learning_resources (LearningResource) – reverse of ‘about’

class AnatomicalAtlasVersion(name=None, alias=None, abbreviation=None, accessibility=None, comments=None, contributions=None, contributor_affiliations=None, coordinate_framework=None, copyright=None, description=None, digital_identifier=None, documentation=None, full_name=None, funding=None, has_terminology=None, has_variants=None, homepage=None, how_to_cite=None, is_input_to=None, is_part_of=None, is_preceded_by=None, is_used_by=None, is_variant_of=None, is_version_of=None, keywords=None, learning_resources=None, major_version_identifier=None, ontology_identifier=None, publication_status=None, related_publications=None, release_date=None, repository=None, short_name=None, support_channels=None, type=None, usage_conditions=None, used_specimens=None, version_identifier=None, version_specification=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• abbreviation (str) – no description available

• accessibility (Accessibility) – Level to which something is accessible to the anatomical atlas version.

• contributions (Contribution) – no description available

• contributor_affiliations (Affiliation) – no description available

• coordinate_framework (CommonCoordinateFrameworkVersion) – no description available

• copyright (Copyright) – Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.

• description (str) – Longer statement or account giving the characteristics of the anatomical atlas version.

• digital_identifier (DOI, ISBN, RRID) – Digital handle to identify objects or legal persons.

• documentation (DOI, File, ISBN, WebResource) – no description available

• full_name (str) – Whole, non-abbreviated name of the anatomical atlas version.

• funding (Funding) – Money provided by a legal person for a particular purpose.

• has_terminology (ParcellationTerminologyVersion) – no description available

• homepage (IRI) – Main website of the anatomical atlas version.

• how_to_cite (str) – Preferred format for citing a particular object or legal person.

• is_preceded_by (AnatomicalAtlasVersion) – no description available

• is_variant_of (AnatomicalAtlasVersion) – no description available

• is_version_of (AnatomicalAtlas) – no description available

• keywords (AccessChannel, AccessEligibilityType, AccessForm, AccessProcessType, ActionStatusType, AgeCategory, AgeReference, AnalysisTechnique, AnatomicalAxesOrientation, AnatomicalCavity, AnatomicalIdentificationType, AnatomicalPlane, AnnotationCriteriaType, AnnotationType, AtlasType, AuditoryStimulusType, BiologicalOrder, BiologicalProcess, BiologicalSex, BreedingType, CellCultureType, CellType, ChemicalMixtureType, Colormap, CommunicationInterfaceType, CommunicationProtocol, ContributionType, CranialWindowConstructionType, CranialWindowReinforcementType, CriteriaQualityType, DataType, DependencyImpact, DeploymentEnvironmentType, DeviceMountingType, DeviceType, DifferenceMeasure, Disease, DiseaseModel, EducationalLevel, ElectricalStimulusType, ExperimentalApproach, ExternalBodyRegion, FileBundleGrouping, FileRepositoryType, FileUsageRole, GeneticStrainType, GustatoryStimulusType, Handedness, Language, Laterality, LearningResourceType, MRIFatSuppressionTechnique, MRIParallelAcquisitionTechnique, MRIPulseSequence, MRISpoilingTechnique, MRIWeighting, MeasuredQuantity, MeasuredSignalType, MetaDataModelType, ModelAbstractionLevel, ModelScope, ModificationConsentRequirement, ModificationConstraint, ModificationForm, ModificationScope, MolecularEntity, MuscularStructure, NervousSystemStructure, OlfactoryStimulusType, OperatingDevice, OperatingSystem, OperationalApproach, OpticalStimulusType, Organ, OrganSystemStructure, OrganismSubstance, OrganismSystem, OrganizationType, PatchClampVariation, PaymentModelType, PreparationType, ProgrammingLanguage, ProjectType, PublicationStatus, PulseShape, QualitativeOverlap, SemanticDataType, SetupType, SignalDirectionality, SkeletalStructure, SoftwareApplicationCategory, SoftwareFeature, SovereignState, SpatialEncoding, Species, StimulationApproach, StimulationTechnique, SubcellularEntity, SubjectAttribute, SupranationalBody, TactileStimulusType, Technique, TermSuggestion, Terminology, TissueSampleAttribute, TissueSampleType, TissueStructure, TypeOfUncertainty, UnitOfMeasurement, VascularStructure, VisualStimulusType, WeightType) – Significant word or concept that are representative of the anatomical atlas version.

• major_version_identifier (str) – no description available

• ontology_identifier (IRI) – Term or code used to identify the anatomical atlas version registered within a particular ontology.

• publication_status (PublicationStatus) – no description available

• related_publications (DOI, GenericIdentifier, HANDLE, ISBN, ISSN, Book, Chapter, ScholarlyArticle) – Reference to something that was made available for the general public to see or buy.

• release_date (date) – Fixed date on which a product is due to become or was made available for the general public to see or buy

• repository (FileRepository) – Place, room, or container where something is deposited or stored.

• short_name (str) – Shortened or fully abbreviated name of the anatomical atlas version.

• support_channels (str) – Way of communication used to interact with users or customers.

• type (AtlasType) – Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.

• usage_conditions (License, UsageAgreement) – no description available

• used_specimens (Subject, SubjectGroup, TissueSample, TissueSampleCollection) – no description available

• version_identifier (str) – Term or code used to identify the version of something.

• version_specification (str) – no description available

• comments (Comment) – reverse of ‘about’

• has_variants (AnatomicalAtlasVersion) – reverse of ‘is_variant_of’

• is_input_to (DataAnalysis, DatasetVersion, ProtocolExecution) – reverse of input_data, inputs

• is_part_of (Project, ResearchProductGroup) – reverse of ‘has_parts’

• is_used_by (ServiceDeployment) – reverse of ‘uses’

• learning_resources (LearningResource) – reverse of ‘about’

class AtlasAnnotation(criteria=None, criteria_quality_type=None, criteria_type=None, inspired_by=None, internal_identifier=None, lateralities=None, preferred_visualization=None, specification=None, type=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• criteria (ProtocolExecution) – Aspects or standards on which a judgement or decision is based.

• criteria_quality_type (CriteriaQualityType) – Distinct class that defines how the judgement or decision was made for a particular criteria.

• criteria_type (AnnotationCriteriaType) – no description available

• inspired_by (File) – Reference to an inspiring element.

• internal_identifier (str) – Term or code that identifies the atlas annotation within a particular product.

• lateralities (Laterality) – Differentiation between a pair of lateral homologous parts of the body.

• preferred_visualization (ViewerSpecification) – no description available

• specification (File) – Detailed and precise presentation of, or proposal for something.

• type (AnnotationType) – Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.

class CommonCoordinateFramework(name=None, alias=None, abbreviation=None, comments=None, contributions=None, contributor_affiliations=None, description=None, digital_identifier=None, documentation=None, full_name=None, has_versions=None, homepage=None, how_to_cite=None, is_input_to=None, is_part_of=None, is_used_to_group=None, keywords=None, learning_resources=None, ontology_identifiers=None, related_publications=None, short_name=None, support_channels=None, used_taxon=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• abbreviation (str) – no description available

• contributions (Contribution) – no description available

• contributor_affiliations (Affiliation) – no description available

• description (str) – Longer statement or account giving the characteristics of the common coordinate framework.

• digital_identifier (DOI, ISBN, RRID) – Digital handle to identify objects or legal persons.

• documentation (DOI, File, ISBN, WebResource) – no description available

• full_name (str) – Whole, non-abbreviated name of the common coordinate framework.

• homepage (IRI) – Main website of the common coordinate framework.

• how_to_cite (str) – Preferred format for citing a particular object or legal person.

• keywords (AccessChannel, AccessEligibilityType, AccessForm, AccessProcessType, ActionStatusType, AgeCategory, AgeReference, AnalysisTechnique, AnatomicalAxesOrientation, AnatomicalCavity, AnatomicalIdentificationType, AnatomicalPlane, AnnotationCriteriaType, AnnotationType, AtlasType, AuditoryStimulusType, BiologicalOrder, BiologicalProcess, BiologicalSex, BreedingType, CellCultureType, CellType, ChemicalMixtureType, Colormap, CommunicationInterfaceType, CommunicationProtocol, ContributionType, CranialWindowConstructionType, CranialWindowReinforcementType, CriteriaQualityType, DataType, DependencyImpact, DeploymentEnvironmentType, DeviceMountingType, DeviceType, DifferenceMeasure, Disease, DiseaseModel, EducationalLevel, ElectricalStimulusType, ExperimentalApproach, ExternalBodyRegion, FileBundleGrouping, FileRepositoryType, FileUsageRole, GeneticStrainType, GustatoryStimulusType, Handedness, Language, Laterality, LearningResourceType, MRIFatSuppressionTechnique, MRIParallelAcquisitionTechnique, MRIPulseSequence, MRISpoilingTechnique, MRIWeighting, MeasuredQuantity, MeasuredSignalType, MetaDataModelType, ModelAbstractionLevel, ModelScope, ModificationConsentRequirement, ModificationConstraint, ModificationForm, ModificationScope, MolecularEntity, MuscularStructure, NervousSystemStructure, OlfactoryStimulusType, OperatingDevice, OperatingSystem, OperationalApproach, OpticalStimulusType, Organ, OrganSystemStructure, OrganismSubstance, OrganismSystem, OrganizationType, PatchClampVariation, PaymentModelType, PreparationType, ProgrammingLanguage, ProjectType, PublicationStatus, PulseShape, QualitativeOverlap, SemanticDataType, SetupType, SignalDirectionality, SkeletalStructure, SoftwareApplicationCategory, SoftwareFeature, SovereignState, SpatialEncoding, Species, StimulationApproach, StimulationTechnique, SubcellularEntity, SubjectAttribute, SupranationalBody, TactileStimulusType, Technique, TermSuggestion, Terminology, TissueSampleAttribute, TissueSampleType, TissueStructure, TypeOfUncertainty, UnitOfMeasurement, VascularStructure, VisualStimulusType, WeightType) – Significant word or concept that are representative of the common coordinate framework.

• ontology_identifiers (str) – Term or code used to identify the common coordinate framework registered within a particular ontology.

• related_publications (DOI, GenericIdentifier, HANDLE, ISBN, ISSN, Book, Chapter, ScholarlyArticle) – Reference to something that was made available for the general public to see or buy.

• short_name (str) – Shortened or fully abbreviated name of the common coordinate framework.

• support_channels (str) – Way of communication used to interact with users or customers.

• used_taxon (BiologicalOrder, Species) – no description available

• comments (Comment) – reverse of ‘about’

• has_versions (CommonCoordinateFrameworkVersion) – reverse of ‘is_version_of’

• is_input_to (DatasetVersion) – reverse of ‘input_data’

• is_part_of (Project, ResearchProductGroup) – reverse of ‘has_parts’

• is_used_to_group (FileBundle) – reverse of ‘grouped_by’

• learning_resources (LearningResource) – reverse of ‘about’

class CommonCoordinateFrameworkVersion(name=None, alias=None, abbreviation=None, accessibility=None, anatomical_axes_orientation=None, axes_origins=None, comments=None, contributions=None, contributor_affiliations=None, copyright=None, default_images=None, description=None, digital_identifier=None, documentation=None, full_name=None, funding=None, has_variants=None, homepage=None, how_to_cite=None, is_coordinate_framework_of=None, is_input_to=None, is_part_of=None, is_preceded_by=None, is_used_by=None, is_used_to_group=None, is_variant_of=None, is_version_of=None, keywords=None, learning_resources=None, native_unit=None, ontology_identifiers=None, publication_status=None, related_publications=None, release_date=None, repository=None, short_name=None, support_channels=None, usage_conditions=None, used_specimens=None, version_identifier=None, version_specification=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• abbreviation (str) – no description available

• accessibility (Accessibility) – Level to which something is accessible to the common coordinate framework version.

• anatomical_axes_orientation (AnatomicalAxesOrientation) – Relation between reference planes used in anatomy and mathematics.

• axes_origins (QuantitativeValue) – Special point in a coordinate system used as a fixed point of reference for the geometry of the surrounding space.

• contributions (Contribution) – no description available

• contributor_affiliations (Affiliation) – no description available

• copyright (Copyright) – Exclusive and assignable legal right of an originator to reproduce, publish, sell, or distribute the matter and form of a creative work for a defined time period.

• default_images (File) – Two or three dimensional image that particluarly represents a specific coordinate space.

• description (str) – Longer statement or account giving the characteristics of the common coordinate framework version.

• digital_identifier (DOI, ISBN, RRID) – Digital handle to identify objects or legal persons.

• documentation (DOI, File, ISBN, WebResource) – no description available

• full_name (str) – Whole, non-abbreviated name of the common coordinate framework version.

• funding (Funding) – Money provided by a legal person for a particular purpose.

• homepage (IRI) – Main website of the common coordinate framework version.

• how_to_cite (str) – Preferred format for citing a particular object or legal person.

• is_preceded_by (CommonCoordinateFrameworkVersion) – no description available

• is_variant_of (CommonCoordinateFrameworkVersion) – no description available

• is_version_of (CommonCoordinateFramework) – no description available

• keywords (AccessChannel, AccessEligibilityType, AccessForm, AccessProcessType, ActionStatusType, AgeCategory, AgeReference, AnalysisTechnique, AnatomicalAxesOrientation, AnatomicalCavity, AnatomicalIdentificationType, AnatomicalPlane, AnnotationCriteriaType, AnnotationType, AtlasType, AuditoryStimulusType, BiologicalOrder, BiologicalProcess, BiologicalSex, BreedingType, CellCultureType, CellType, ChemicalMixtureType, Colormap, CommunicationInterfaceType, CommunicationProtocol, ContributionType, CranialWindowConstructionType, CranialWindowReinforcementType, CriteriaQualityType, DataType, DependencyImpact, DeploymentEnvironmentType, DeviceMountingType, DeviceType, DifferenceMeasure, Disease, DiseaseModel, EducationalLevel, ElectricalStimulusType, ExperimentalApproach, ExternalBodyRegion, FileBundleGrouping, FileRepositoryType, FileUsageRole, GeneticStrainType, GustatoryStimulusType, Handedness, Language, Laterality, LearningResourceType, MRIFatSuppressionTechnique, MRIParallelAcquisitionTechnique, MRIPulseSequence, MRISpoilingTechnique, MRIWeighting, MeasuredQuantity, MeasuredSignalType, MetaDataModelType, ModelAbstractionLevel, ModelScope, ModificationConsentRequirement, ModificationConstraint, ModificationForm, ModificationScope, MolecularEntity, MuscularStructure, NervousSystemStructure, OlfactoryStimulusType, OperatingDevice, OperatingSystem, OperationalApproach, OpticalStimulusType, Organ, OrganSystemStructure, OrganismSubstance, OrganismSystem, OrganizationType, PatchClampVariation, PaymentModelType, PreparationType, ProgrammingLanguage, ProjectType, PublicationStatus, PulseShape, QualitativeOverlap, SemanticDataType, SetupType, SignalDirectionality, SkeletalStructure, SoftwareApplicationCategory, SoftwareFeature, SovereignState, SpatialEncoding, Species, StimulationApproach, StimulationTechnique, SubcellularEntity, SubjectAttribute, SupranationalBody, TactileStimulusType, Technique, TermSuggestion, Terminology, TissueSampleAttribute, TissueSampleType, TissueStructure, TypeOfUncertainty, UnitOfMeasurement, VascularStructure, VisualStimulusType, WeightType) – Significant word or concept that are representative of the common coordinate framework version.

• native_unit (UnitOfMeasurement) – Determinate quantity used in the original measurement.

• ontology_identifiers (str) – Term or code used to identify the common coordinate framework version registered within a particular ontology.

• publication_status (PublicationStatus) – no description available

• related_publications (DOI, GenericIdentifier, HANDLE, ISBN, ISSN, Book, Chapter, ScholarlyArticle) – Reference to something that was made available for the general public to see or buy.

• release_date (date) – Fixed date on which a product is due to become or was made available for the general public to see or buy

• repository (FileRepository) – Place, room, or container where something is deposited or stored.

• short_name (str) – Shortened or fully abbreviated name of the common coordinate framework version.

• support_channels (str) – Way of communication used to interact with users or customers.

• usage_conditions (License, UsageAgreement) – no description available

• used_specimens (Subject, SubjectGroup, TissueSample, TissueSampleCollection) – no description available

• version_identifier (str) – Term or code used to identify the version of something.

• version_specification (str) – no description available

• comments (Comment) – reverse of ‘about’

• has_variants (CommonCoordinateFrameworkVersion) – reverse of ‘is_variant_of’

• is_coordinate_framework_of (GridImage, GridImageSequence, GridImageStack, GridVolume, GridVolumeSequence, AnatomicalAtlasVersion, CustomAnnotation) – reverse of ‘coordinate_framework’

• is_input_to (DataAnalysis, DatasetVersion, ProtocolExecution) – reverse of input_data, inputs

• is_part_of (Project, ResearchProductGroup) – reverse of ‘has_parts’

• is_used_by (ServiceDeployment) – reverse of ‘uses’

• is_used_to_group (FileBundle) – reverse of ‘grouped_by’

• learning_resources (LearningResource) – reverse of ‘about’

class ParcellationEntity(name=None, lookup_label=None, abbreviation=None, alternate_names=None, definition=None, has_children=None, has_parents=None, has_versions=None, is_location_of=None, is_target_of=None, is_used_to_group=None, ontology_identifiers=None, related_interspecies_anatomy=None, studied_in=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• abbreviation (str) – no description available

• alternate_names (str) – no description available

• definition (str) – Short, but precise statement of the meaning of a word, word group, sign or a symbol.

• has_parents (ParcellationEntity) – Reference to a parent object or legal person.

• lookup_label (str) – no description available

• name (str) – Word or phrase that constitutes the distinctive designation of the parcellation entity.

• ontology_identifiers (str) – Term or code used to identify the parcellation entity registered within a particular ontology.

• related_interspecies_anatomy (AnatomicalCavity, ExternalBodyRegion, MuscularStructure, NervousSystemStructure, Organ, OrganSystemStructure, OrganismSubstance, OrganismSystem, SkeletalStructure, TissueStructure, VascularStructure) – no description available

• has_children (ParcellationEntity) – reverse of ‘has_parents’

• has_versions (ParcellationEntityVersion) – reverse of ‘is_version_of’

• is_location_of (TissueSample, TissueSampleCollection, ElectrodeArrayUsage, ElectrodeUsage, PipetteUsage) – reverse of anatomical_location, anatomical_locations, anatomical_locations_of_electrodes

• is_target_of (DynamicMRIAcquisition, StaticMRIAcquisition, AnatomicalTargetPosition) – reverse of anatomical_targets, target_anatomy

• is_used_to_group (FileBundle) – reverse of ‘grouped_by’

• studied_in (DataAnalysis, DataCopy, GenericComputation, ModelValidation, Optimization, Simulation, ValidationTest, Visualization, DatasetVersion, Model, ProtocolExecution, CellPatching, ElectrodePlacement, RecordingActivity, CranialWindowPreparation, TissueCulturePreparation, TissueSampleSlicing, StimulationActivity) – reverse of ‘study_targets’

class ParcellationEntityVersion(name=None, lookup_label=None, abbreviation=None, additional_remarks=None, alternate_names=None, corrected_name=None, has_annotations=None, has_children=None, has_parents=None, is_location_of=None, is_target_of=None, is_used_to_group=None, is_version_of=None, ontology_identifiers=None, relation_assessments=None, studied_in=None, version_identifier=None, version_innovation=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• abbreviation (str) – no description available

• additional_remarks (str) – Mention of what deserves additional attention or notice.

• alternate_names (str) – no description available

• corrected_name (str) – no description available

• has_annotations (AtlasAnnotation) – no description available

• has_parents (ParcellationEntity, ParcellationEntityVersion) – Reference to a parent object or legal person.

• is_version_of (ParcellationEntity) – no description available

• lookup_label (str) – no description available

• name (str) – Word or phrase that constitutes the distinctive designation of the parcellation entity version.

• ontology_identifiers (str) – Term or code used to identify the parcellation entity version registered within a particular ontology.

• relation_assessments (QualitativeRelationAssessment, QuantitativeRelationAssessment) – no description available

• version_identifier (str) – Term or code used to identify the version of something.

• version_innovation (str) – Documentation on what changed in comparison to a previously published form of something.

• has_children (ParcellationEntityVersion) – reverse of ‘has_parents’

• is_location_of (ServiceLink, TissueSample, TissueSampleCollection, ElectrodeArrayUsage, ElectrodeUsage, PipetteUsage) – reverse of anatomical_location, anatomical_locations, anatomical_locations_of_electrodes, data_location

• is_target_of (DynamicMRIAcquisition, StaticMRIAcquisition, AnatomicalTargetPosition) – reverse of anatomical_targets, target_anatomy

• is_used_to_group (FileBundle) – reverse of ‘grouped_by’

• studied_in (DataAnalysis, DataCopy, GenericComputation, ModelValidation, Optimization, Simulation, ValidationTest, Visualization, DatasetVersion, Model, ProtocolExecution, CellPatching, ElectrodePlacement, RecordingActivity, CranialWindowPreparation, TissueCulturePreparation, TissueSampleSlicing, StimulationActivity) – reverse of ‘study_targets’

class ParcellationTerminology(data_locations=None, digital_identifier=None, has_entities=None, ontology_identifiers=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• data_locations (File, WebResource) – no description available

• digital_identifier (DOI, ISBN, RRID) – Digital handle to identify objects or legal persons.

• has_entities (ParcellationEntity) – no description available

• ontology_identifiers (str) – Term or code used to identify the parcellation terminology registered within a particular ontology.

class ParcellationTerminologyVersion(data_locations=None, digital_identifier=None, has_entities=None, ontology_identifiers=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• data_locations (File, WebResource) – no description available

• digital_identifier (DOI, ISBN, RRID) – Digital handle to identify objects or legal persons.

• has_entities (ParcellationEntityVersion) – no description available

• ontology_identifiers (str) – Term or code used to identify the parcellation terminology version registered within a particular ontology.

Non-atlas-related

class CustomAnatomicalEntity(name=None, has_annotations=None, is_location_of=None, is_target_of=None, is_used_to_group=None, related_interspecies_anatomy=None, relation_assessments=None, studied_in=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• has_annotations (CustomAnnotation) – no description available

• name (str) – Word or phrase that constitutes the distinctive designation of the custom anatomical entity.

• related_interspecies_anatomy (AnatomicalCavity, ExternalBodyRegion, MuscularStructure, NervousSystemStructure, Organ, OrganSystemStructure, OrganismSubstance, OrganismSystem, SkeletalStructure, TissueStructure, VascularStructure) – no description available

• relation_assessments (QualitativeRelationAssessment, QuantitativeRelationAssessment) – no description available

• is_location_of (TissueSample, TissueSampleCollection, ElectrodeArrayUsage, ElectrodeUsage, PipetteUsage) – reverse of anatomical_location, anatomical_locations, anatomical_locations_of_electrodes

• is_target_of (DynamicMRIAcquisition, StaticMRIAcquisition, AnatomicalTargetPosition) – reverse of anatomical_targets, target_anatomy

• is_used_to_group (FileBundle) – reverse of ‘grouped_by’

• studied_in (DataAnalysis, DataCopy, GenericComputation, ModelValidation, Optimization, Simulation, ValidationTest, Visualization, DatasetVersion, Model, ProtocolExecution, CellPatching, ElectrodePlacement, RecordingActivity, CranialWindowPreparation, TissueCulturePreparation, TissueSampleSlicing, StimulationActivity) – reverse of ‘study_targets’

class CustomAnnotation(coordinate_framework=None, criteria=None, criteria_quality_type=None, criteria_type=None, inspired_by=None, internal_identifier=None, lateralities=None, preferred_visualization=None, specification=None, type=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• coordinate_framework (CommonCoordinateFrameworkVersion, CustomCoordinateFramework) – no description available

• criteria (ProtocolExecution) – Aspects or standards on which a judgement or decision is based.

• criteria_quality_type (CriteriaQualityType) – Distinct class that defines how the judgement or decision was made for a particular criteria.

• criteria_type (AnnotationCriteriaType) – no description available

• inspired_by (File) – Reference to an inspiring element.

• internal_identifier (str) – Term or code that identifies the custom annotation within a particular product.

• lateralities (Laterality) – Differentiation between a pair of lateral homologous parts of the body.

• preferred_visualization (ViewerSpecification) – no description available

• specification (File, PropertyValueList) – Detailed and precise presentation of, or proposal for something.

• type (AnnotationType) – Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.

class CustomCoordinateFramework(name=None, anatomical_axes_orientation=None, axes_origins=None, default_images=None, is_coordinate_framework_of=None, is_used_to_group=None, native_unit=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• anatomical_axes_orientation (AnatomicalAxesOrientation) – Relation between reference planes used in anatomy and mathematics.

• axes_origins (QuantitativeValue) – Special point in a coordinate system used as a fixed point of reference for the geometry of the surrounding space.

• default_images (File) – Two or three dimensional image that particluarly represents a specific coordinate space.

• name (str) – Word or phrase that constitutes the distinctive designation of the custom coordinate framework.

• native_unit (UnitOfMeasurement) – Determinate quantity used in the original measurement.

• is_coordinate_framework_of (GridImage, GridImageSequence, GridImageStack, GridVolume, GridVolumeSequence, CustomAnnotation) – reverse of ‘coordinate_framework’

• is_used_to_group (FileBundle) – reverse of ‘grouped_by’

Mathematical Shapes

class CentroidalPyramid(apex_base_distance=None, base_shape=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• apex_base_distance (QuantitativeValue) – no description available

• base_shape (EquilateralTriangle, IsoscelesTriangle, Kite, Parallelogram, Rectangle, RegularPolygon, Rhombus, RightTriangle, Square, Trapezoid, Triangle) – no description available

class Circle(radius=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

radius (QuantitativeValue) – no description available

class CircularSector(central_angle=None, radius=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• central_angle (QuantitativeValue) – no description available

• radius (QuantitativeValue) – no description available

class Cube(side_length=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

side_length (QuantitativeValue) – no description available

class Ellipse(diameters=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

diameters (QuantitativeValue) – no description available

class Ellipsoid(intermediate_diameter=None, major_diameter=None, minor_diameter=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• intermediate_diameter (QuantitativeValue) – no description available

• major_diameter (QuantitativeValue) – no description available

• minor_diameter (QuantitativeValue) – no description available

class EquilateralTriangle(side_length=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

side_length (QuantitativeValue) – no description available

class Frustum(base_distance=None, major_base_shape=None, minor_base_scale=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• base_distance (QuantitativeValue) – no description available

• major_base_shape (Circle, CircularSector, Ellipse, EquilateralTriangle, IsoscelesTriangle, Kite, Parallelogram, Rectangle, RegularPolygon, Rhombus, RightTriangle, Square, Trapezoid, Triangle) – no description available

• minor_base_scale (Real) – no description available

class IsoscelesTriangle(apex_angle=None, leg_length=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• apex_angle (QuantitativeValue) – no description available

• leg_length (QuantitativeValue) – no description available

class Kite(leg_lengths=None, symmetry_diagonal_length=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• leg_lengths (QuantitativeValue) – no description available

• symmetry_diagonal_length (QuantitativeValue) – no description available

class Parallelogram(base_distance=None, base_length=None, interior_angle=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• base_distance (QuantitativeValue) – no description available

• base_length (QuantitativeValue) – no description available

• interior_angle (QuantitativeValue) – no description available

class Rectangle(major_side_length=None, minor_side_length=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• major_side_length (QuantitativeValue) – no description available

• minor_side_length (QuantitativeValue) – no description available

class RegularPolygon(circumradius=None, number_of_sides=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• circumradius (QuantitativeValue) – no description available

• number_of_sides (int) – no description available

class Rhombus(diagonal_lengths=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

diagonal_lengths (QuantitativeValue) – no description available

class RightCone(apex_base_distance=None, base_shape=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• apex_base_distance (QuantitativeValue) – no description available

• base_shape (Circle, Ellipse) – no description available

class RightCylinder(base_distance=None, base_shape=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• base_distance (QuantitativeValue) – no description available

• base_shape (Circle, Ellipse) – no description available

class RightPrism(base_distance=None, base_shape=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• base_distance (QuantitativeValue) – no description available

• base_shape (EquilateralTriangle, IsoscelesTriangle, Kite, Parallelogram, Rectangle, RegularPolygon, Rhombus, RightTriangle, Square, Trapezoid, Triangle) – no description available

class RightTriangle(perpendicular_leg_lengths=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

perpendicular_leg_lengths (QuantitativeValue) – no description available

class Sphere(radius=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

radius (QuantitativeValue) – no description available

class Spheroid(equatorial_diameter=None, polar_diameter=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• equatorial_diameter (QuantitativeValue) – no description available

• polar_diameter (QuantitativeValue) – no description available

class Square(side_length=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

side_length (QuantitativeValue) – no description available

class Trapezoid(base_distance=None, base_lengths=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• base_distance (QuantitativeValue) – no description available

• base_lengths (QuantitativeValue) – no description available

class Triangle(apex_angle=None, leg_lengths=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• apex_angle (QuantitativeValue) – no description available

• leg_lengths (QuantitativeValue) – no description available

Miscellaneous

class AnatomicalTargetPosition(additional_remarks=None, anatomical_targets=None, spatial_locations=None, target_identification_type=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• additional_remarks (str) – Mention of what deserves additional attention or notice.

• anatomical_targets (AnatomicalCavity, CellType, ExternalBodyRegion, MuscularStructure, NervousSystemStructure, Organ, OrganSystemStructure, OrganismSubstance, OrganismSystem, SkeletalStructure, SubcellularEntity, TissueStructure, VascularStructure, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – no description available

• spatial_locations (CoordinatePoint) – no description available

• target_identification_type (AnatomicalIdentificationType) – no description available

class CoordinatePoint(coordinate_framework=None, coordinates=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• coordinate_framework (CommonCoordinateFrameworkVersion, CustomCoordinateFramework) – no description available

• coordinates (QuantitativeValue) – Pair or triplet of numbers defining a location in a given coordinate space.

class QualitativeRelationAssessment(criteria=None, in_relation_to=None, qualitative_overlap=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• criteria (ProtocolExecution) – Aspects or standards on which a judgement or decision is based.

• in_relation_to (CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Reference to a related element.

• qualitative_overlap (QualitativeOverlap) – Semantic characterization of how much two things occupy the same space.

class QuantitativeRelationAssessment(criteria=None, in_relation_to=None, quantitative_overlap=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• criteria (ProtocolExecution) – Aspects or standards on which a judgement or decision is based.

• in_relation_to (ParcellationEntityVersion) – Reference to a related element.

• quantitative_overlap (QuantitativeValue, QuantitativeValueRange) – Numerical characterization of how much two things occupy the same space.

class SingleColor(value=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

value (str) – Entry for a property.

class ViewerSpecification(additional_remarks=None, anchor_points=None, camera_position=None, preferred_display_color=None, id=None, data=None, space=None, release_status=None)

<description not available>

Parameters:

• additional_remarks (str) – Mention of what deserves additional attention or notice.

• anchor_points (QuantitativeValue) – no description available

• camera_position (CoordinatePoint) – no description available

• preferred_display_color (Colormap, SingleColor) – no description available