openminds.sands¶

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

Brain Atlases¶

class AtlasAnnotation(anchor_points=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)[source]¶

Parameters:

anchor_points (QuantitativeValue) – 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 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 BrainAtlas(name=None, alias=None, abbreviation=None, authors=None, comments=None, custodians=None, description=None, digital_identifier=None, full_name=None, has_terminology=None, has_versions=None, homepage=None, how_to_cite=None, is_input_to=None, is_part_of=None, learning_resources=None, ontology_identifier=None, short_name=None, used_species=None, versions=None, id=None, data=None, space=None, release_status=None)[source]¶

Parameters:

abbreviation (str) – no description available
authors (Consortium, Organization, Person) – Creator of a literary or creative work, as well as a dataset publication.
custodians (Consortium, Organization, Person) – The ‘custodian’ is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.
description (str) – Longer statement or account giving the characteristics of the brain atlas.
digital_identifier (DOI, ISBN, RRID) – Digital handle to identify objects or legal persons.
full_name (str) – Whole, non-abbreviated name of the brain atlas.
has_terminology (ParcellationTerminology) – no description available
has_versions (BrainAtlasVersion) – Reference to variants of an original.
homepage (IRI) – Main website of the brain atlas.
how_to_cite (str) – Preferred format for citing a particular object or legal person.
ontology_identifier (IRI) – Term or code used to identify the brain atlas registered within a particular ontology.
short_name (str) – Shortened or fully abbreviated name of the brain atlas.
used_species (Species) – no description available
comments (Comment) – reverse of ‘about’
is_input_to (DatasetVersion) – reverse of ‘input_data’
is_part_of (Project, ResearchProductGroup) – reverse of ‘has_parts’
learning_resources (LearningResource) – reverse of ‘about’

class BrainAtlasVersion(name=None, alias=None, abbreviation=None, accessibility=None, authors=None, comments=None, coordinate_space=None, copyright=None, custodians=None, description=None, digital_identifier=None, full_documentation=None, full_name=None, funding=None, has_terminology=None, homepage=None, how_to_cite=None, is_alternative_version_of=None, is_input_to=None, is_new_version_of=None, is_old_version_of=None, is_part_of=None, is_version_of=None, keywords=None, learning_resources=None, license=None, major_version_identifier=None, ontology_identifier=None, other_contributions=None, related_publications=None, release_date=None, repository=None, short_name=None, support_channels=None, type=None, used_specimens=None, version_identifier=None, version_innovation=None, id=None, data=None, space=None, release_status=None)[source]¶

Parameters:

abbreviation (str) – no description available
accessibility (ProductAccessibility) – Level to which something is accessible to the brain atlas version.
authors (Consortium, Organization, Person) – Creator of a literary or creative work, as well as a dataset publication.
coordinate_space (CommonCoordinateSpaceVersion) – Two or three dimensional geometric setting.
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.
custodians (Consortium, Organization, Person) – The ‘custodian’ is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.
description (str) – Longer statement or account giving the characteristics of the brain atlas version.
digital_identifier (DOI, ISBN, RRID) – Digital handle to identify objects or legal persons.
full_documentation (DOI, File, ISBN, WebResource) – Non-abridged instructions, comments, and information for using a particular product.
full_name (str) – Whole, non-abbreviated name of the brain 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 brain atlas version.
how_to_cite (str) – Preferred format for citing a particular object or legal person.
is_alternative_version_of (BrainAtlasVersion) – Reference to an original form where the essence was preserved, but presented in an alternative form.
is_new_version_of (BrainAtlasVersion) – Reference to a previous (potentially outdated) particular form of something.
keywords (ActionStatusType, AgeCategory, AnalysisTechnique, AnatomicalAxesOrientation, AnatomicalIdentificationType, AnatomicalPlane, AnnotationCriteriaType, AnnotationType, AtlasType, AuditoryStimulusType, BiologicalOrder, BiologicalProcess, BiologicalSex, BreedingType, CellCultureType, CellType, ChemicalMixtureType, Colormap, ContributionType, CranialWindowConstructionType, CranialWindowReinforcementType, CriteriaQualityType, DataType, DeviceType, DifferenceMeasure, Disease, DiseaseModel, EducationalLevel, ElectricalStimulusType, EthicsAssessment, ExperimentalApproach, FileBundleGrouping, FileRepositoryType, FileUsageRole, GeneticStrainType, GustatoryStimulusType, Handedness, Language, Laterality, LearningResourceType, MRIPulseSequence, MRIWeighting, MeasuredQuantity, MeasuredSignalType, MetaDataModelType, ModelAbstractionLevel, ModelScope, MolecularEntity, OlfactoryStimulusType, OperatingDevice, OperatingSystem, OpticalStimulusType, Organ, OrganismSubstance, OrganismSystem, PatchClampVariation, PreparationType, ProductAccessibility, ProgrammingLanguage, QualitativeOverlap, SemanticDataType, Service, SetupType, SoftwareApplicationCategory, SoftwareFeature, Species, StimulationApproach, StimulationTechnique, SubcellularEntity, SubjectAttribute, TactileStimulusType, Technique, TermSuggestion, Terminology, TissueSampleAttribute, TissueSampleType, TypeOfUncertainty, UBERONParcellation, UnitOfMeasurement, VisualStimulusType) – Significant word or concept that are representative of the brain atlas version.
license (License) – Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.
major_version_identifier (str) – no description available
ontology_identifier (IRI) – Term or code used to identify the brain atlas version registered within a particular ontology.
other_contributions (Contribution) – Giving or supplying of something (such as money or time) as a part or share other than what is covered elsewhere.
related_publications (DOI, 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 brain 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.
used_specimens (Subject, SubjectGroup, TissueSample, TissueSampleCollection) – 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.
comments (Comment) – reverse of ‘about’
is_input_to (DataAnalysis, DatasetVersion, ProtocolExecution) – reverse of input_data, inputs
is_old_version_of (BrainAtlasVersion) – reverse of ‘is_new_version_of’
is_part_of (Project, ResearchProductGroup, SoftwareVersion) – reverse of ‘has_parts’
is_version_of (BrainAtlas) – reverse of ‘has_versions’
learning_resources (LearningResource) – reverse of ‘about’

class CommonCoordinateSpace(name=None, alias=None, abbreviation=None, authors=None, comments=None, custodians=None, description=None, digital_identifier=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, learning_resources=None, ontology_identifiers=None, short_name=None, used_species=None, versions=None, id=None, data=None, space=None, release_status=None)[source]¶

Parameters:

abbreviation (str) – no description available
authors (Consortium, Organization, Person) – Creator of a literary or creative work, as well as a dataset publication.
custodians (Consortium, Organization, Person) – The ‘custodian’ is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.
description (str) – Longer statement or account giving the characteristics of the common coordinate space.
digital_identifier (DOI, ISBN, RRID) – Digital handle to identify objects or legal persons.
full_name (str) – Whole, non-abbreviated name of the common coordinate space.
has_versions (CommonCoordinateSpaceVersion) – Reference to variants of an original.
homepage (IRI) – Main website of the common coordinate space.
how_to_cite (str) – Preferred format for citing a particular object or legal person.
ontology_identifiers (str) – Term or code used to identify the common coordinate space registered within a particular ontology.
short_name (str) – Shortened or fully abbreviated name of the common coordinate space.
used_species (Species) – no description available
comments (Comment) – reverse of ‘about’
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 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_uberon_term=None, studied_in=None, versions=None, id=None, data=None, space=None, release_status=None)[source]¶

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.
has_versions (ParcellationEntityVersion) – Reference to variants of an original.
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_uberon_term (Organ, UBERONParcellation) – no description available
has_children (ParcellationEntity, ParcellationEntityVersion) – reverse of ‘has_parents’
is_location_of (TissueSample, TissueSampleCollection, ElectrodeArrayUsage, ElectrodeUsage, PipetteUsage) – reverse of anatomical_location, anatomical_locations, anatomical_locations_of_electrodes
is_target_of (AnatomicalTargetPosition) – reverse of ‘anatomical_targets’
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_part_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)[source]¶

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.
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_part_of (ParcellationTerminologyVersion) – reverse of ‘has_entities’
is_target_of (AnatomicalTargetPosition) – reverse of ‘anatomical_targets’
is_used_to_group (FileBundle) – reverse of ‘grouped_by’
is_version_of (ParcellationEntity) – reverse of ‘has_versions’
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, has_entities=None, ontology_identifiers=None, id=None, data=None, space=None, release_status=None)[source]¶

Parameters:

data_locations (File) – no description available
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, has_entities=None, ontology_identifiers=None, id=None, data=None, space=None, release_status=None)[source]¶

Parameters:

data_locations (File) – no description available
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_uberon_term=None, relation_assessments=None, studied_in=None, id=None, data=None, space=None, release_status=None)[source]¶

Parameters:

has_annotations (CustomAnnotation) – no description available
name (str) – Word or phrase that constitutes the distinctive designation of the custom anatomical entity.
related_uberon_term (Organ, UBERONParcellation) – 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 (AnatomicalTargetPosition) – reverse of ‘anatomical_targets’
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(anchor_points=None, coordinate_space=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)[source]¶

Parameters:

anchor_points (QuantitativeValue) – no description available
coordinate_space (CommonCoordinateSpaceVersion, CustomCoordinateSpace) – Two or three dimensional geometric setting.
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 CustomCoordinateSpace(name=None, anatomical_axes_orientation=None, axes_origins=None, default_images=None, is_coordinate_space_of=None, is_used_to_group=None, native_unit=None, id=None, data=None, space=None, release_status=None)[source]¶

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 space.
native_unit (UnitOfMeasurement) – Determinate quantity used in the original measurement.
is_coordinate_space_of (CustomAnnotation) – reverse of ‘coordinate_space’
is_used_to_group (FileBundle) – reverse of ‘grouped_by’

Shapes¶

class Circle(radius=None, id=None, data=None, space=None, release_status=None)[source]¶

Parameters:: radius (QuantitativeValue) – no description available

class Ellipse(semi_major_axis=None, semi_minor_axis=None, id=None, data=None, space=None, release_status=None)[source]¶

Parameters:

semi_major_axis (QuantitativeValue) – no description available
semi_minor_axis (QuantitativeValue) – no description available

class Rectangle(length=None, width=None, id=None, data=None, space=None, release_status=None)[source]¶

Parameters:

length (QuantitativeValue) – no description available
width (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)[source]¶

Parameters:

additional_remarks (str) – Mention of what deserves additional attention or notice.
anatomical_targets (CellType, Organ, OrganismSubstance, SubcellularEntity, UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – no description available
spatial_locations (CoordinatePoint) – no description available
target_identification_type (AnatomicalIdentificationType) – no description available

class CoordinatePoint(coordinate_space=None, coordinates=None, id=None, data=None, space=None, release_status=None)[source]¶

Parameters:

coordinate_space (CommonCoordinateSpaceVersion, CustomCoordinateSpace) – Two or three dimensional geometric setting.
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)[source]¶

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)[source]¶

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.