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openMINDS pipeline
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‎README.md‎

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@@ -66,7 +66,7 @@ This work is licensed under the MIT License.
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## Getting help
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In case of questions about **openMINDS**, please contact us via https://ebrains.eu/support/.
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In case of questions about **openMINDS**, please contact us at support@openmetadatainitiative.org.
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If you find a bug in the Python library or would like to suggest an enhancement or new feature,
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please open a ticket in the [openMINDS Python library issue tracker](https://github.com/openMetadataInitiative/openMINDS_Python/issues).
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‎openminds/base.py‎

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@@ -171,6 +171,8 @@ class LinkedMetadata(Node):
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A Python representation of a metadata node that should have a unique identifier.
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"""
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_instance_lookup = None
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def __init__(self, id=None, **properties):
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self.id = id # todo: check this is a URI
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for name, value in properties.items():

‎openminds/latest/computation/__init__.py‎

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@@ -1,17 +1,17 @@
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from .workflow_recipe_version import WorkflowRecipeVersion
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from .validation_test import ValidationTest
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from .workflow_recipe import WorkflowRecipe
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from .simulation import Simulation
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from .optimization import Optimization
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from .model_validation import ModelValidation
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from .hardware_system import HardwareSystem
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from .launch_configuration import LaunchConfiguration
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from .data_copy import DataCopy
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from .software_agent import SoftwareAgent
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from .simulation import Simulation
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from .visualization import Visualization
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from .model_validation import ModelValidation
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from .workflow_recipe_version import WorkflowRecipeVersion
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from .local_file import LocalFile
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from .environment import Environment
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from .data_copy import DataCopy
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from .workflow_execution import WorkflowExecution
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from .environment import Environment
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from .generic_computation import GenericComputation
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from .validation_test_version import ValidationTestVersion
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from .hardware_system import HardwareSystem
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from .validation_test import ValidationTest
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from .data_analysis import DataAnalysis
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from .generic_computation import GenericComputation
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from .workflow_recipe import WorkflowRecipe
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from .launch_configuration import LaunchConfiguration

‎openminds/latest/controlled_terms/__init__.py‎

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@@ -1,78 +1,78 @@
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from .operating_system import OperatingSystem
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from .criteria_quality_type import CriteriaQualityType
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from .preparation_type import PreparationType
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from .software_feature import SoftwareFeature
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from .file_usage_role import FileUsageRole
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from .handedness import Handedness
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from .setup_type import SetupType
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from .action_status_type import ActionStatusType
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from .uberon_parcellation import UBERONParcellation
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from .stimulation_technique import StimulationTechnique
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from .visual_stimulus_type import VisualStimulusType
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from .anatomical_axes_orientation import AnatomicalAxesOrientation
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from .electrical_stimulus_type import ElectricalStimulusType
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from .tissue_sample_attribute import TissueSampleAttribute
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from .contribution_type import ContributionType
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from .terminology import Terminology
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from .qualitative_overlap import QualitativeOverlap
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from .anatomical_identification_type import AnatomicalIdentificationType
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from .organ import Organ
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from .gustatory_stimulus_type import GustatoryStimulusType
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from .molecular_entity import MolecularEntity
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from .terminology import Terminology
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from .annotation_criteria_type import AnnotationCriteriaType
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from .chemical_mixture_type import ChemicalMixtureType
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from .tissue_sample_type import TissueSampleType
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from .cranial_window_construction_type import CranialWindowConstructionType
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from .laterality import Laterality
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from .analysis_technique import AnalysisTechnique
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from .anatomical_axes_orientation import AnatomicalAxesOrientation
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from .optical_stimulus_type import OpticalStimulusType
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from .measured_quantity import MeasuredQuantity
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from .disease import Disease
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from .disease_model import DiseaseModel
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from .atlas_type import AtlasType
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from .software_application_category import SoftwareApplicationCategory
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from .auditory_stimulus_type import AuditoryStimulusType
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from .operating_device import OperatingDevice
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from .contribution_type import ContributionType
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from .colormap import Colormap
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from .type_of_uncertainty import TypeOfUncertainty
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from .stimulation_technique import StimulationTechnique
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from .unit_of_measurement import UnitOfMeasurement
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from .semantic_data_type import SemanticDataType
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from .anatomical_plane import AnatomicalPlane
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from .olfactory_stimulus_type import OlfactoryStimulusType
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from .operating_system import OperatingSystem
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from .species import Species
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from .language import Language
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from .service import Service
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from .difference_measure import DifferenceMeasure
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from .programming_language import ProgrammingLanguage
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from .age_category import AgeCategory
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from .patch_clamp_variation import PatchClampVariation
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from .technique import Technique
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from .measured_signal_type import MeasuredSignalType
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from .atlas_type import AtlasType
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from .molecular_entity import MolecularEntity
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from .measured_quantity import MeasuredQuantity
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from .experimental_approach import ExperimentalApproach
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from .file_repository_type import FileRepositoryType
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from .biological_order import BiologicalOrder
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from .data_type import DataType
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from .criteria_quality_type import CriteriaQualityType
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from .electrical_stimulus_type import ElectricalStimulusType
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from .anatomical_identification_type import AnatomicalIdentificationType
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from .learning_resource_type import LearningResourceType
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from .stimulation_approach import StimulationApproach
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from .difference_measure import DifferenceMeasure
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from .operating_device import OperatingDevice
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from .model_abstraction_level import ModelAbstractionLevel
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from .subcellular_entity import SubcellularEntity
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from .preparation_type import PreparationType
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from .visual_stimulus_type import VisualStimulusType
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from .file_usage_role import FileUsageRole
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from .anatomical_plane import AnatomicalPlane
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from .tissue_sample_type import TissueSampleType
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from .cell_culture_type import CellCultureType
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from .handedness import Handedness
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from .technique import Technique
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from .chemical_mixture_type import ChemicalMixtureType
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from .disease_model import DiseaseModel
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from .organism_substance import OrganismSubstance
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from .service import Service
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from .organism_system import OrganismSystem
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from .experimental_approach import ExperimentalApproach
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from .tactile_stimulus_type import TactileStimulusType
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from .organ import Organ
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from .learning_resource_type import LearningResourceType
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from .annotation_type import AnnotationType
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from .cell_type import CellType
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from .auditory_stimulus_type import AuditoryStimulusType
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from .unit_of_measurement import UnitOfMeasurement
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from .product_accessibility import ProductAccessibility
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from .model_scope import ModelScope
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from .disease import Disease
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from .analysis_technique import AnalysisTechnique
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from .biological_sex import BiologicalSex
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from .meta_data_model_type import MetaDataModelType
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from .subject_attribute import SubjectAttribute
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from .ethics_assessment import EthicsAssessment
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from .device_type import DeviceType
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from .cell_type import CellType
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from .meta_data_model_type import MetaDataModelType
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from .measured_signal_type import MeasuredSignalType
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from .biological_order import BiologicalOrder
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from .olfactory_stimulus_type import OlfactoryStimulusType
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from .software_feature import SoftwareFeature
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from .breeding_type import BreedingType
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from .species import Species
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from .tissue_sample_attribute import TissueSampleAttribute
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from .organism_substance import OrganismSubstance
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from .biological_process import BiologicalProcess
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from .annotation_type import AnnotationType
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from .model_abstraction_level import ModelAbstractionLevel
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from .file_repository_type import FileRepositoryType
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from .semantic_data_type import SemanticDataType
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from .file_bundle_grouping import FileBundleGrouping
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from .term_suggestion import TermSuggestion
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from .biological_sex import BiologicalSex
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from .educational_level import EducationalLevel
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from .ethics_assessment import EthicsAssessment
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from .annotation_criteria_type import AnnotationCriteriaType
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from .laterality import Laterality
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from .cranial_window_reinforcement_type import CranialWindowReinforcementType
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from .patch_clamp_variation import PatchClampVariation
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from .cell_culture_type import CellCultureType
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from .term_suggestion import TermSuggestion
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from .breeding_type import BreedingType
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from .model_scope import ModelScope
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from .software_application_category import SoftwareApplicationCategory
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from .optical_stimulus_type import OpticalStimulusType
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from .type_of_uncertainty import TypeOfUncertainty
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from .genetic_strain_type import GeneticStrainType
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from .age_category import AgeCategory
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from .uberon_parcellation import UBERONParcellation
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from .setup_type import SetupType
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from .stimulation_approach import StimulationApproach
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from .action_status_type import ActionStatusType
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from .programming_language import ProgrammingLanguage
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from .educational_level import EducationalLevel
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from .tactile_stimulus_type import TactileStimulusType

‎openminds/latest/controlled_terms/action_status_type.py‎

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@@ -102,3 +102,66 @@ def __init__(
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preferred_ontology_identifier=preferred_ontology_identifier,
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synonyms=synonyms,
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)
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@classmethod
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def instances(cls):
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return [value for value in cls.__dict__.values() if isinstance(value, cls)]
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@classmethod
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def by_name(cls, name):
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if cls._instance_lookup is None:
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cls._instance_lookup = {}
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for instance in cls.instances():
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cls._instance_lookup[instance.name] = instance
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if instance.synonyms:
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for synonym in instance.synonyms:
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cls._instance_lookup[synonym] = instance
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return cls._instance_lookup[name]
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ActionStatusType.active = ActionStatusType(
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id="https://openminds.ebrains.eu/instances/actionStatusType/active",
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definition="An in-progress action.",
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name="active",
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preferred_ontology_identifier="https://schema.org/ActiveActionStatus",
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synonyms=["active action status", "active action"],
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)
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ActionStatusType.completed = ActionStatusType(
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id="https://openminds.ebrains.eu/instances/actionStatusType/completed",
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definition="An action that has already taken place with a successful outcome.",
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name="completed",
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preferred_ontology_identifier="https://schema.org/CompletedActionStatus",
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synonyms=["completed action status", "completed action", "finished successfully"],
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)
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ActionStatusType.failed = ActionStatusType(
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id="https://openminds.ebrains.eu/instances/actionStatusType/failed",
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definition="An action that failed to complete or completed but produced an error.",
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name="failed",
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preferred_ontology_identifier="https://schema.org/FailedActionStatus",
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synonyms=["failed action status", "failed action", "finished unsuccessfully", "error"],
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)
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ActionStatusType.inactive = ActionStatusType(
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id="https://openminds.ebrains.eu/instances/actionStatusType/inactive",
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definition="A pending or suspended action.",
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name="inactive",
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synonyms=["inactive action status", "inactive action"],
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)
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ActionStatusType.paused = ActionStatusType(
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id="https://openminds.ebrains.eu/instances/actionStatusType/paused",
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definition="A temporarily stopped action that can be resumed at a later point in time.",
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name="paused",
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synonyms=["paused action type", "paused action", "suspended"],
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)
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ActionStatusType.pending = ActionStatusType(
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id="https://openminds.ebrains.eu/instances/actionStatusType/pending",
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definition="An action which is awaiting execution.",
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name="pending",
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synonyms=["queued", "pending action type", "pending action"],
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)
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ActionStatusType.potential = ActionStatusType(
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id="https://openminds.ebrains.eu/instances/actionStatusType/potential",
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definition="A description of an action that is supported.",
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name="potential",
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preferred_ontology_identifier="https://schema.org/PotentialActionStatus",
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synonyms=["potential action type", "potential action"],
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)

‎openminds/latest/controlled_terms/age_category.py‎

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@@ -102,3 +102,96 @@ def __init__(
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preferred_ontology_identifier=preferred_ontology_identifier,
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synonyms=synonyms,
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)
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@classmethod
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def instances(cls):
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return [value for value in cls.__dict__.values() if isinstance(value, cls)]
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@classmethod
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def by_name(cls, name):
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if cls._instance_lookup is None:
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cls._instance_lookup = {}
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for instance in cls.instances():
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cls._instance_lookup[instance.name] = instance
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if instance.synonyms:
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for synonym in instance.synonyms:
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cls._instance_lookup[synonym] = instance
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return cls._instance_lookup[name]
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AgeCategory.adolescent = AgeCategory(
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id="https://openminds.ebrains.eu/instances/ageCategory/adolescent",
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definition="'Adolescent' categorizes a transitional life cycle stage of growth and development between childhood and adulthood, often described as 'puberty'.",
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name="adolescent",
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synonyms=["puberty"],
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)
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AgeCategory.adult = AgeCategory(
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id="https://openminds.ebrains.eu/instances/ageCategory/adult",
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definition="'Adult' categorizes the life cycle stage of an animal or human that reached sexual maturity.",
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interlex_identifier="http://uri.interlex.org/base/ilx_0729043",
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name="adult",
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preferred_ontology_identifier="http://purl.obolibrary.org/obo/UBERON_0000113",
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synonyms=["adult stage", "post-juvenile adult", "post-juvenile adult stage"],
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)
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AgeCategory.embryo = AgeCategory(
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id="https://openminds.ebrains.eu/instances/ageCategory/embryo",
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definition="'Embryo' categorizes the life cycle stage of an animal or human that starts with fertilitzation and ends with the fully formed embryo.",
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interlex_identifier="http://uri.interlex.org/base/ilx_0735599",
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name="embryo",
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preferred_ontology_identifier="http://purl.obolibrary.org/obo/UBERON_0000068",
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synonyms=["embryo stage", "embryonic stage"],
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)
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AgeCategory.infant = AgeCategory(
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id="https://openminds.ebrains.eu/instances/ageCategory/infant",
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definition="'Infant' categorizes the life cycle stage of mammals (animal or human) that follows the neonate stage and ends at weaning.",
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interlex_identifier="http://uri.interlex.org/base/ilx_0735063",
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name="infant",
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preferred_ontology_identifier="http://purl.obolibrary.org/obo/UBERON_0034920",
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synonyms=["infant stage"],
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)
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AgeCategory.juvenile = AgeCategory(
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id="https://openminds.ebrains.eu/instances/ageCategory/juvenile",
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definition="'Juvenile' categorizes the life cycle stage of an animal or human that starts with the independence of the nest and/or caregivers and ends with sexual maturity.",
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interlex_identifier="http://uri.interlex.org/base/ilx_0730395",
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name="juvenile",
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preferred_ontology_identifier="http://purl.obolibrary.org/obo/UBERON_0034919",
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synonyms=["juvenile stage"],
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)
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AgeCategory.late_adult = AgeCategory(
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id="https://openminds.ebrains.eu/instances/ageCategory/lateAdult",
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definition="'Late adult' categorizes the life cycle stage of an animal or human that follows the prime adult stage.",
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interlex_identifier="http://uri.interlex.org/base/ilx_0725713",
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name="late adult",
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preferred_ontology_identifier="http://purl.obolibrary.org/obo/UBERON_0007222",
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synonyms=["elderly", "elderly stage", "geriatric", "geriatric stage", "late adult stage"],
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)
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AgeCategory.neonate = AgeCategory(
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id="https://openminds.ebrains.eu/instances/ageCategory/neonate",
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definition="'Neonate' categorizes the life cycle stage of an animal or human that immediately follows birth.",
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interlex_identifier="http://uri.interlex.org/base/ilx_0732178",
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name="neonate",
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preferred_ontology_identifier="http://purl.obolibrary.org/obo/UBERON_0007221",
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synonyms=["neonatal stage", "neonate stage"],
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)
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AgeCategory.perinatal = AgeCategory(
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id="https://openminds.ebrains.eu/instances/ageCategory/perinatal",
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definition="'Perinatal' categorizes the life cycle stage of an animal or human that starts right before birth and ends right after birth.",
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interlex_identifier="http://uri.interlex.org/base/ilx_0724163",
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name="perinatal",
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preferred_ontology_identifier="http://purl.obolibrary.org/obo/UBERON_0012101",
182+
synonyms=["perinatal stage"],
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)
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AgeCategory.prime_adult = AgeCategory(
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id="https://openminds.ebrains.eu/instances/ageCategory/primeAdult",
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definition="'Prime adult' categorizes the life cycle stage of an animal or human that starts at the onset of sexual maturity or the cessation of growth, whichever comes last, and ends before senescence.",
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interlex_identifier="http://uri.interlex.org/base/ilx_0733125",
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name="prime adult",
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preferred_ontology_identifier="http://purl.obolibrary.org/obo/UBERON_0018241",
190+
synonyms=["adulthood stage", "prime adult stage"],
191+
)
192+
AgeCategory.young_adult = AgeCategory(
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id="https://openminds.ebrains.eu/instances/ageCategory/youngAdult",
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definition="'Young adult' categorizes the early adult stage of an animal or human when sexual maturity has been reached, but not the cessation of growth.",
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name="young adult",
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synonyms=["early adult", "early adult stage", "young adult stage"],
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)

‎openminds/latest/controlled_terms/analysis_technique.py‎

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@@ -102,3 +102,25 @@ def __init__(
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preferred_ontology_identifier=preferred_ontology_identifier,
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synonyms=synonyms,
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)
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@classmethod
107+
def instances(cls):
108+
return [value for value in cls.__dict__.values() if isinstance(value, cls)]
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@classmethod
111+
def by_name(cls, name):
112+
if cls._instance_lookup is None:
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cls._instance_lookup = {}
114+
for instance in cls.instances():
115+
cls._instance_lookup[instance.name] = instance
116+
if instance.synonyms:
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for synonym in instance.synonyms:
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cls._instance_lookup[synonym] = instance
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return cls._instance_lookup[name]
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AnalysisTechnique.ward_clustering = AnalysisTechnique(
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id="https://openminds.ebrains.eu/instances/technique/WardClustering",
124+
definition="'Ward clustering' is a general agglomerative hierarchical clustering procedure, where the criterion for choosing the pair of clusters to merge at each step is based on the optimal value of an objective function (typically aiming to minimize the total within-cluster variance). [adapted from [Wikipedia](https://en.wikipedia.org/wiki/Ward%27s_method)]",
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name="Ward clustering",
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)

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