diff --git a/schema/Makefile b/schema/Makefile index ff245da58..5d5ede786 100644 --- a/schema/Makefile +++ b/schema/Makefile @@ -41,9 +41,14 @@ clean-docs: .PHONY: build build: clean - python schema.py materialize $(METADATA_YAML) $(COMMON_YAML) $(METADATA_MATERIALIZED_YAML) - python schema.py materialize $(API_MODELS_YAML) $(COMMON_YAML) $(API_MODELS_MATERIALIZED_YAML) - python schema.py materialize $(INGESTION_CONFIG_MODELS_YAML) $(COMMON_YAML) $(INGESTION_CONFIG_MODELS_MATERIALIZED_YAML) + python3 schema.py materialize $(METADATA_YAML) $(COMMON_YAML) $(METADATA_MATERIALIZED_YAML) + python3 schema.py materialize $(API_MODELS_YAML) $(COMMON_YAML) $(API_MODELS_MATERIALIZED_YAML) + python3 schema.py materialize $(INGESTION_CONFIG_MODELS_YAML) $(COMMON_YAML) $(INGESTION_CONFIG_MODELS_MATERIALIZED_YAML) + + # Hardcoding these while we wait for an upstream LinkML bug to be fixed: https://github.com/linkml/linkml-runtime/pull/330 + python3 schema.py materialize core/v2.0.0/metadata.yaml core/v2.0.0/common.yaml core/v2.0.0/codegen/metadata_materialized.yaml + python3 schema.py materialize api/v2.0.0/api_models.yaml core/v2.0.0/common.yaml api/v2.0.0/codegen/api_models_materialized.yaml + linkml generate pydantic --black $(METADATA_MATERIALIZED_YAML) > $(METADATA_MODELS_PY) linkml generate pydantic $(INGESTION_CONFIG_MODELS_MATERIALIZED_YAML) > $(INGESTION_CONFIG_MODELS_PY) linkml generate json-schema $(INGESTION_CONFIG_MODELS_MATERIALIZED_YAML) > $(INGESTION_CONFIG_JSON_SCHEMA) diff --git a/schema/api/v2.0.0/api_models.yaml b/schema/api/v2.0.0/api_models.yaml new file mode 100644 index 000000000..37f2d913d --- /dev/null +++ b/schema/api/v2.0.0/api_models.yaml @@ -0,0 +1,865 @@ +name: cdp-api +id: cdp-api +version: 2.0.0 +description: Schema for CryoET API +imports: +- linkml:types +- ../../core/v2.0.0/common +prefixes: + linkml: + prefix_prefix: linkml + prefix_reference: https://w3id.org/linkml/ + +classes: + # ============================================================================ + # Mixins + # ============================================================================ + IDMixin: + mixin: true + attributes: + id: + identifier: true + exact_mappings: + - cdp-common:api_sequential_identifier + annotations: + auto_increment: true + S3PrefixedEntityMixin: + description: An entity with s3/https prefixes + mixin: true + attributes: + s3_prefix: + exact_mappings: + - cdp-common:api_s3_prefix + https_prefix: + exact_mappings: + - cdp-common:api_https_prefix + AuthorEntityMixin: + description: An entity with author data + mixin: true + mixins: + - AuthorMixin + attributes: + author_list_order: + exact_mappings: + - cdp-common:api_author_list_order + orcid: + exact_mappings: + - cdp-common:author_orcid + APIDateStampedEntityMixin: + description: A set of dates at which a data item was deposited, published and last modified. + mixin: true + attributes: + deposition_date: + exact_mappings: + - cdp-common:deposition_date + range: date + release_date: + exact_mappings: + - cdp-common:release_date + range: date + last_modified_date: + exact_mappings: + - cdp-common:last_modified_date + range: date + # ============================================================================ + + # ============================================================================ + # Entities + # ============================================================================ + Alignment: + mixins: + - IDMixin + description: Tiltseries Alignment + attributes: + annotation_files: + range: AnnotationFile + inverse: AnnotationFile.alignment + multivalued: true + per_section_alignments: + range: PerSectionAlignmentParameters + inverse: PerSectionAlignmentParameters.alignment + multivalued: true + deposition: + range: Deposition + inverse: Deposition.alignments + tiltseries: + range: Tiltseries + inverse: Tiltseries.alignments + tomograms: + range: Tomogram + inverse: Tomogram.alignment + multivalued: true + run: + range: Run + inverse: Run.alignments + alignment: + exact_mappings: + - cdp-common:api_alignment + alignment_type: + exact_mappings: + - cdp-common:alignment_alignment_type + volume_x_dimension: + exact_mappings: + - cdp-common:alignment_volume_x_dimension + volume_y_dimension: + exact_mappings: + - cdp-common:alignment_volume_y_dimension + volume_z_dimension: + exact_mappings: + - cdp-common:alignment_volume_z_dimension + volume_x_offset: + exact_mappings: + - cdp-common:alignment_volume_x_offset + volume_y_offset: + exact_mappings: + - cdp-common:alignment_volume_y_offset + volume_z_offset: + exact_mappings: + - cdp-common:alignment_volume_z_offset + volume_x_rotation: + exact_mappings: + - cdp-common:alignment_volume_x_rotation + tilt_offset: + exact_mappings: + - cdp-common:alignment_tilt_offset + local_alignment_file: + exact_mappings: + - cdp-common:alignment_local_alignment_file + annotations: + plural: Alignments + AnnotationAuthor: + mixins: + - IDMixin + - AuthorEntityMixin + description: Author of an annotation + attributes: + annotation: + range: Annotation + inverse: Annotation.authors + annotations: + plural: AnnotationAuthors + AnnotationFile: + mixins: + - IDMixin + description: Files associated with an annotation + attributes: + alignment: + range: Alignment + inverse: Alignment.annotation_files + annotation_shape: + range: AnnotationShape + inverse: AnnotationShape.annotation_files + tomogram_voxel_spacing: + range: TomogramVoxelSpacing + inverse: TomogramVoxelSpacing.annotation_files + format: + exact_mappings: + - cdp-common:api_file_format + s3_path: + exact_mappings: + - cdp-common:api_s3_path + https_path: + exact_mappings: + - cdp-common:api_https_path + is_visualization_default: + exact_mappings: + - cdp-common:annotation_source_file_is_visualization_default + source: + exact_mappings: + - cdp-common:api_annotation_file_source + annotations: + plural: AnnotationFiles + AnnotationShape: + mixins: + - IDMixin + description: Shapes associated with an annotation + attributes: + annotation: + range: Annotation + inverse: Annotation.annotation_shapes + annotation_files: + range: AnnotationFile + description: Files associated with an annotation + inverse: AnnotationFile.annotation_shape + multivalued: true + shape_type: + range: annotation_file_shape_type_enum + annotations: + plural: AnnotationShapes + Annotation: + mixins: + - IDMixin + - APIDateStampedEntityMixin + description: Metadata about an annotation for a run + attributes: + run: + range: Run + inverse: Run.annotations + annotation_shapes: + range: AnnotationShape + inverse: AnnotationShape.annotation + multivalued: true + authors: + range: AnnotationAuthor + inverse: AnnotationAuthor.annotation + multivalued: true + deposition: + range: Deposition + inverse: Deposition.annotations + s3_metadata_path: + exact_mappings: + - cdp-common:api_s3_path + https_metadata_path: + exact_mappings: + - cdp-common:api_https_path + annotation_publication: + exact_mappings: + - cdp-common:annotation_publications + annotation_method: + exact_mappings: + - cdp-common:annotation_method + ground_truth_status: + exact_mappings: + - cdp-common:annotation_ground_truth_status + object_id: + exact_mappings: + - cdp-common:annotation_object_id + object_name: + exact_mappings: + - cdp-common:annotation_object_name + object_description: + exact_mappings: + - cdp-common:annotation_object_description + object_state: + exact_mappings: + - cdp-common:annotation_object_state + object_count: + exact_mappings: + - cdp-common:annotation_object_count + confidence_precision: + exact_mappings: + - cdp-common:annotation_confidence_precision + confidence_recall: + exact_mappings: + - cdp-common:annotation_confidence_recall + ground_truth_used: + exact_mappings: + - cdp-common:annotation_ground_truth_used + annotation_software: + exact_mappings: + - cdp-common:annotation_software + is_curator_recommended: + exact_mappings: + - cdp-common:annotation_is_curator_recommended + method_type: + exact_mappings: + - cdp-common:annotation_method_type + annotations: + plural: Annotations + DatasetAuthor: + mixins: + - IDMixin + - AuthorEntityMixin + description: An author of a dataset + attributes: + dataset: + range: Dataset + inverse: Dataset.authors + annotations: + plural: DatasetAuthors + DatasetFunding: + mixins: + - IDMixin + description: Information about how a dataset was funded + attributes: + dataset: + range: Dataset + inverse: Dataset.funding_sources + funding_agency_name: + exact_mappings: + - cdp-common:funding_agency_name + grant_id: + exact_mappings: + - cdp-common:funding_grant_id + annotations: + plural: DatasetFunding + Dataset: + mixins: + - IDMixin + - APIDateStampedEntityMixin + - CrossReferencesMixin + - S3PrefixedEntityMixin + description: An author of a dataset + attributes: + deposition: + range: Deposition + inverse: Deposition.datasets + funding_sources: + range: DatasetFunding + inverse: DatasetFunding.dataset + multivalued: true + authors: + range: DatasetAuthor + inverse: DatasetAuthor.dataset + multivalued: true + runs: + range: Run + inverse: Run.dataset + multivalued: true + title: + exact_mappings: + - cdp-common:dataset_title + description: + exact_mappings: + - cdp-common:dataset_description + organism_name: + exact_mappings: + - cdp-common:organism_name + organism_taxid: + exact_mappings: + - cdp-common:organism_taxid + tissue_name: + exact_mappings: + - cdp-common:tissue_name + # TODO THIS SHOULD BE REQUIRED + required: False + # NOTE this doesn't expand to an explicit range. + tissue_id: + exact_mappings: + - cdp-common:tissue_id + cell_name: + exact_mappings: + - cdp-common:cell_name + # TODO THIS SHOULD BE REQUIRED + required: False + cell_type_id: + exact_mappings: + - cdp-common:cell_type_id + cell_strain_name: + exact_mappings: + - cdp-common:cell_strain_name + range: string + required: False + cell_strain_id: + exact_mappings: + - cdp-common:cell_strain_id + range: string + sample_type: + exact_mappings: + - cdp-common:preparation_sample_type + required: true + sample_preparation: + exact_mappings: + - cdp-common:sample_preparation + grid_preparation: + exact_mappings: + - cdp-common:grid_preparation + other_setup: + exact_mappings: + - cdp-common:preparation_other_setup + key_photo_url: + exact_mappings: + - cdp-common:dataset_key_photo_url + key_photo_thumbnail_url: + exact_mappings: + - cdp-common:dataset_key_photo_thumbnail_url + cell_component_name: + exact_mappings: + - cdp-common:cell_component_name + # TODO THIS SHOULD BE REQUIRED + required: False + cell_component_id: + exact_mappings: + - cdp-common:cell_component_id + annotations: + plural: Datasets + DepositionAuthor: + mixins: + - IDMixin + - AuthorEntityMixin + description: Author of a deposition + attributes: + deposition: + range: Deposition + inverse: Deposition.authors + annotations: + plural: DepositionAuthors + + Deposition: + mixins: + - IDMixin + - CrossReferencesMixin + - APIDateStampedEntityMixin + attributes: + authors: + range: DepositionAuthor + inverse: DepositionAuthor.deposition + multivalued: true + alignments: + range: Alignment + inverse: Alignment.deposition + multivalued: true + annotations: + range: Annotation + inverse: Annotation.deposition + multivalued: true + datasets: + range: Dataset + inverse: Dataset.deposition + multivalued: true + frames: + range: Frame + inverse: Frame.deposition + multivalued: true + tiltseries: + range: Tiltseries + inverse: Tiltseries.deposition + multivalued: true + tomograms: + range: Tomograms + inverse: Tomogram.deposition + multivalued: true + deposition_title: + exact_mappings: + - cdp-common:deposition_title + deposition_description: + exact_mappings: + - cdp-common:deposition_description + deposition_types: + range: DepositionType + inverse: DepositionType.deposition + multivalued: true + annotations: + plural: Depositions + DepositionType: + mixins: + - IDMixin + attributes: + deposition: + range: Deposition + inverse: Deposition.deposition_types + type: + range: cdp-common:deposition_types_enum + annotations: + plural: DepositionTypes + Frame: + mixins: + - IDMixin + - S3PrefixedEntityMixin + attributes: + deposition: + range: Deposition + inverse: Deposition.frames + per_section_parameters: + inverse: PerSectionParameters.frame + range: PerSectionParameters + multivalued: true + run: + range: Run + inverse: Run.frames + raw_angle: + exact_mappings: + - cdp-common:api_frame_raw_angle + acquisition_order: + exact_mappings: + - cdp-common:api_frame_acquisition_order + dose: + exact_mappings: + - cdp-common:api_frame_dose + is_gain_corrected: + exact_mappings: + - cdp-common:api_frame_is_gain_corrected + s3_gain_file: + exact_mappings: + - cdp-common:api_frame_s3_gain_file + https_gain_file: + exact_mappings: + - cdp-common:api_frame_https_gain_file + annotations: + plural: Frames + PerSectionParameters: + mixins: + - IDMixin + description: Record how frames get mapped to TiltSeries + attributes: + frame: + range: Frame + inverse: Frame.per_section_parameters + required: True + tiltseries: + range: Tiltseries + inverse: Tiltseries.per_section_parameters + required: True + z_index: + exact_mappings: + - cdp-common:per_section_z_index + defocus: + exact_mappings: + - cdp-common:per_section_defocus + astigmatism: + exact_mappings: + - cdp-common:per_section_astigmatism + astigmatic_angle: + exact_mappings: + - cdp-common:per_section_astigmatic_angle + annotations: + plural: PerSectionParameters + + PerSectionAlignmentParameters: + mixins: + - IDMixin + description: Map alignment parameters to tilt series frames + attributes: + alignment: + range: Alignment + inverse: Alignment.per_section_alignments + required: True + z_index: + exact_mappings: + - cdp-common:per_section_z_index + x_offset: + exact_mappings: + - cdp-common:per_section_alignment_x_offset + y_offset: + exact_mappings: + - cdp-common:per_section_alignment_y_offset + in_plane_rotation: + exact_mappings: + - cdp-common:per_section_alignment_in_plane_rotation + beam_tilt: + exact_mappings: + - cdp-common:per_section_alignment_beam_tilt + tilt_angle: + exact_mappings: + - cdp-common:per_section_alignment_tilt_angle + annotations: + plural: PerSectionAlignmentParameters + + Run: + mixins: + - IDMixin + - S3PrefixedEntityMixin + attributes: + alignments: + range: Alignment + inverse: Alignment.run + multivalued: true + annotations: + range: Annotation + inverse: Annotation.run + multivalued: true + dataset: + range: Dataset + required: true + inverse: Dataset.runs + frames: + range: Frame + inverse: Frame.run + multivalued: true + tiltseries: + range: Tiltseries + multivalued: true + inverse: Tiltseries.run + tomogram_voxel_spacings: + range: TomogramVoxelSpacing + multivalued: true + inverse: TomogramVoxelSpacing.run + tomograms: + range: Tomogram + multivalued: true + inverse: Tomogram.run + name: + exact_mappings: + - cdp-common:api_run_name + annotations: + plural: Runs + Tiltseries: + mixins: + - IDMixin + attributes: + alignments: + range: Alignment + multivalued: true + inverse: Alignment.tiltseries + per_section_parameters: + range: PerSectionParameters + inverse: PerSectionParameters.tiltseries + multivalued: true + run: + range: Run + required: true + inverse: Run.tiltseries + deposition: + range: Deposition + required: False + inverse: Deposition.tiltseries + s3_omezarr_dir: + exact_mappings: + - cdp-common:tiltseries_s3_omezarr_dir + s3_mrc_bin1: + exact_mappings: + - cdp-common:tiltseries_s3_mrc_bin1 + https_omezarr_dir: + exact_mappings: + - cdp-common:tiltseries_https_omezarr_dir + https_mrc_bin1: + exact_mappings: + - cdp-common:tiltseries_https_mrc_bin1 + s3_collection_metadata: + exact_mappings: + - cdp-common:tiltseries_s3_collection_metadata + https_collection_metadata: + exact_mappings: + - cdp-common:tiltseries_https_collection_metadata + s3_angle_list: + exact_mappings: + - cdp-common:tiltseries_s3_angle_list + https_angle_list: + exact_mappings: + - cdp-common:tiltseries_https_angle_list + s3_gain_file: + exact_mappings: + - cdp-common:tiltseries_s3_gain_file + https_gain_file: + exact_mappings: + - cdp-common:tiltseries_https_gain_file + acceleration_voltage: + exact_mappings: + - cdp-common:tiltseries_acceleration_voltage + spherical_abberation_constant: + exact_mappings: + - cdp-common:tiltseries_spherical_aberration_constant + microscope_manufacturer: + exact_mappings: + - cdp-common:tiltseries_microscope_manufacturer + microscope_model: + exact_mappings: + - cdp-common:tiltseries_microscope_model + microscope_energy_filter: + exact_mappings: + - cdp-common:tiltseries_microscope_energy_filter + microscope_phase_plate: + exact_mappings: + - cdp-common:tiltseries_microscope_phase_plate + microscope_image_corrector: + exact_mappings: + - cdp-common:tiltseries_microscope_image_corrector + microscope_additional_info: + exact_mappings: + - cdp-common:tiltseries_microscope_additional_info + camera_manufacturer: + exact_mappings: + - cdp-common:tiltseries_camera_manufacturer + camera_model: + exact_mappings: + - cdp-common:tiltseries_camera_model + tilt_min: + exact_mappings: + - cdp-common:tiltseries_tilt_min + tilt_max: + exact_mappings: + - cdp-common:tiltseries_tilt_max + tilt_range: + exact_mappings: + - cdp-common:api_tiltseries_tilt_range + tilt_step: + exact_mappings: + - cdp-common:tiltseries_tilt_step + tilting_scheme: + exact_mappings: + - cdp-common:tiltseries_tilting_scheme + tilt_axis: + exact_mappings: + - cdp-common:tiltseries_tilt_axis + total_flux: + exact_mappings: + - cdp-common:tiltseries_total_flux + data_acquisition_software: + exact_mappings: + - cdp-common:tiltseries_data_acquisition_software + related_empiar_entry: + exact_mappings: + - cdp-common:tiltseries_related_empiar_entry + binning_from_frames: + exact_mappings: + - cdp-common:tiltseries_binning_from_frames + tilt_series_quality: + exact_mappings: + - cdp-common:tiltseries_tilt_series_quality + is_aligned: + exact_mappings: + - cdp-common:tiltseries_is_aligned + pixel_spacing: + exact_mappings: + - cdp-common:tiltseries_pixel_spacing + aligned_tiltseries_binning: + exact_mappings: + - cdp-common:tiltseries_aligned_tiltseries_binning + tiltseries_frames_count: + exact_mappings: + - cdp-common:tiltseries_frames_count + annotations: + plural: Tiltseries + TomogramAuthor: + mixins: + - IDMixin + - AuthorEntityMixin + description: Author of a tomogram + attributes: + tomogram: + range: Tomogram + inverse: Tomogram.authors + annotations: + plural: TomogramAuthors + TomogramVoxelSpacing: + mixins: + - IDMixin + - S3PrefixedEntityMixin + description: Voxel spacings for a run + attributes: + annotation_files: + range: AnnotationFile + inverse: AnnotationFile.tomogram_voxel_spacing + multivalued: true + run: + range: Run + inverse: run.tomogram_voxel_spacings + tomograms: + range: Tomogram + inverse: Tomogram.tomogram_voxel_spacing + multivalued: true + voxel_spacing: + exact_mappings: + - cdp-common:tomogram_voxel_spacing + annotations: + plural: TomogramVoxelSpacings + Tomogram: + mixins: + - IDMixin + - S3PrefixedEntityMixin + description: Metadata describing a tomogram. + attributes: + alignment: + range: Alignment + inverse: Alignment.tomograms + authors: + range: TomogramAuthor + inverse: TomogramAuthor.tomogram + multivalued: true + deposition: + range: Deposition + inverse: Deposition.tomograms + run: + range: Run + inverse: Run.tomograms + tomogram_voxel_spacing: + range: TomogramVoxelSpacing + inverse: tomogram_voxel_spacing.tomograms + name: + exact_mappings: + - cdp-common:tomogram_name + size_x: + exact_mappings: + - cdp-common:api_tomogram_size_x + size_y: + exact_mappings: + - cdp-common:api_tomogram_size_y + size_z: + exact_mappings: + - cdp-common:api_tomogram_size_z + voxel_spacing: + exact_mappings: + - cdp-common:tomogram_voxel_spacing + fiducial_alignment_status: + exact_mappings: + - cdp-common:tomogram_fiducial_alignment_status + reconstruction_method: + exact_mappings: + - cdp-common:tomogram_reconstruction_method + processing: + exact_mappings: + - cdp-common:tomogram_processing + tomogram_version: + exact_mappings: + - cdp-common:tomogram_version + required: false + range: float + processing_software: + exact_mappings: + - cdp-common:tomogram_processing_software + reconstruction_software: + exact_mappings: + - cdp-common:tomogram_reconstruction_software + is_canonical: + range: boolean + description: whether this tomogram is canonical for the run + s3_omezarr_dir: + exact_mappings: + - cdp-common:tomogram_s3_omezarr_dir + https_omezarr_dir: + exact_mappings: + - cdp-common:tomogram_https_omezarr_dir + s3_mrc_scale0: + exact_mappings: + - cdp-common:tomogram_s3_mrc_scale0 + https_mrc_scale0: + exact_mappings: + - cdp-common:tomogram_https_mrc_scale0 + scale0_dimensions: + exact_mappings: + - cdp-common:tomogram_scale0_dimensions + scale1_dimensions: + exact_mappings: + - cdp-common:tomogram_scale1_dimensions + scale2_dimensions: + exact_mappings: + - cdp-common:tomogram_scale2_dimensions + ctf_corrected: + exact_mappings: + - cdp-common:tomogram_ctf_corrected + offset_x: + range: integer + required: true + description: x offset data relative to the canonical tomogram in pixels + unit: + descriptive_name: pixels + symbol: px + offset_y: + range: integer + required: true + description: y offset data relative to the canonical tomogram in pixels + unit: + descriptive_name: pixels + symbol: px + offset_z: + range: integer + required: true + description: z offset data relative to the canonical tomogram in pixels + unit: + descriptive_name: pixels + symbol: px + affine_transformation_matrix: + description: The flip or rotation transformation of this author submitted tomogram is indicated here + range: Any + array: + exact_number_dimensions: 2 + dimensions: + - exact_cardinality: 4 + - exact_cardinality: 4 + key_photo_url: + exact_mappings: + - cdp-common:tomogram_key_photo_url + key_photo_thumbnail_url: + exact_mappings: + - cdp-common:tomogram_key_photo_thumbnail_url + neuroglancer_config: + exact_mappings: + - cdp-common:tomogram_neuroglancer_config + tomogram_type: + range: tomogram_type_enum + is_standardized: + exact_mappings: + - cdp-common:api_tomogram_is_standardized + annotations: + plural: Tomograms + # ============================================================================ diff --git a/schema/api/v2.0.0/codegen/api_models_materialized.yaml b/schema/api/v2.0.0/codegen/api_models_materialized.yaml new file mode 100644 index 000000000..634848f5e --- /dev/null +++ b/schema/api/v2.0.0/codegen/api_models_materialized.yaml @@ -0,0 +1,5232 @@ +name: cdp-api +description: Schema for CryoET API +id: cdp-api +version: 2.0.0 +imports: +- linkml:types +- ../../../core/v2.0.0/common +prefixes: + linkml: + prefix_prefix: linkml + prefix_reference: https://w3id.org/linkml/ +default_prefix: cdp-api/ +types: + string: + name: string + description: A character string + notes: + - In RDF serializations, a slot with range of string is treated as a literal or + type xsd:string. If you are authoring schemas in LinkML YAML, the type is + referenced with the lower case "string". + from_schema: cdp-api + exact_mappings: + - schema:Text + base: str + uri: xsd:string + integer: + name: integer + description: An integer + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "integer". + from_schema: cdp-api + exact_mappings: + - schema:Integer + base: int + uri: xsd:integer + boolean: + name: boolean + description: A binary (true or false) value + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "boolean". + from_schema: cdp-api + exact_mappings: + - schema:Boolean + base: Bool + uri: xsd:boolean + repr: bool + float: + name: float + description: A real number that conforms to the xsd:float specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "float". + from_schema: cdp-api + exact_mappings: + - schema:Float + base: float + uri: xsd:float + double: + name: double + description: A real number that conforms to the xsd:double specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "double". + from_schema: cdp-api + close_mappings: + - schema:Float + base: float + uri: xsd:double + decimal: + name: decimal + description: A real number with arbitrary precision that conforms to the xsd:decimal + specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "decimal". + from_schema: cdp-api + broad_mappings: + - schema:Number + base: Decimal + uri: xsd:decimal + time: + name: time + description: A time object represents a (local) time of day, independent of any + particular day + notes: + - URI is dateTime because OWL reasoners do not work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "time". + from_schema: cdp-api + exact_mappings: + - schema:Time + base: XSDTime + uri: xsd:time + repr: str + date: + name: date + description: a date (year, month and day) in an idealized calendar + notes: + - URI is dateTime because OWL reasoners don't work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date". + from_schema: cdp-api + exact_mappings: + - schema:Date + base: XSDDate + uri: xsd:date + repr: str + datetime: + name: datetime + description: The combination of a date and time + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "datetime". + from_schema: cdp-api + exact_mappings: + - schema:DateTime + base: XSDDateTime + uri: xsd:dateTime + repr: str + date_or_datetime: + name: date_or_datetime + description: Either a date or a datetime + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date_or_datetime". + from_schema: cdp-api + base: str + uri: linkml:DateOrDatetime + repr: str + uriorcurie: + name: uriorcurie + description: a URI or a CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uriorcurie". + from_schema: cdp-api + base: URIorCURIE + uri: xsd:anyURI + repr: str + curie: + name: curie + conforms_to: https://www.w3.org/TR/curie/ + description: a compact URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "curie". + comments: + - in RDF serializations this MUST be expanded to a URI + - in non-RDF serializations MAY be serialized as the compact representation + from_schema: cdp-api + base: Curie + uri: xsd:string + repr: str + uri: + name: uri + conforms_to: https://www.ietf.org/rfc/rfc3987.txt + description: a complete URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uri". + comments: + - in RDF serializations a slot with range of uri is treated as a literal or type + xsd:anyURI unless it is an identifier or a reference to an identifier, in which + case it is translated directly to a node + from_schema: cdp-api + close_mappings: + - schema:URL + base: URI + uri: xsd:anyURI + repr: str + ncname: + name: ncname + description: Prefix part of CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "ncname". + from_schema: cdp-api + base: NCName + uri: xsd:string + repr: str + objectidentifier: + name: objectidentifier + description: A URI or CURIE that represents an object in the model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "objectidentifier". + comments: + - Used for inheritance and type checking + from_schema: cdp-api + base: ElementIdentifier + uri: shex:iri + repr: str + nodeidentifier: + name: nodeidentifier + description: A URI, CURIE or BNODE that represents a node in a model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "nodeidentifier". + from_schema: cdp-api + base: NodeIdentifier + uri: shex:nonLiteral + repr: str + jsonpointer: + name: jsonpointer + conforms_to: https://datatracker.ietf.org/doc/html/rfc6901 + description: A string encoding a JSON Pointer. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to a valid object within the current + instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpointer". + from_schema: cdp-api + base: str + uri: xsd:string + repr: str + jsonpath: + name: jsonpath + conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html + description: A string encoding a JSON Path. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to zero or more valid objects within + the current instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpath". + from_schema: cdp-api + base: str + uri: xsd:string + repr: str + sparqlpath: + name: sparqlpath + conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths + description: A string encoding a SPARQL Property Path. The value of the string + MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects + within the current instance document when encoded as RDF. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "sparqlpath". + from_schema: cdp-api + base: str + uri: xsd:string + repr: str + StringFormattedString: + name: StringFormattedString + description: A formatted string (variable) that represents a string. + from_schema: cdp-api + base: string + pattern: ^[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + FloatFormattedString: + name: FloatFormattedString + description: A formatted string that represents a floating point number. + from_schema: cdp-api + base: string + pattern: ^float[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + IntegerFormattedString: + name: IntegerFormattedString + description: A formatted string that represents an integer. + from_schema: cdp-api + base: string + pattern: ^int[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + VersionString: + name: VersionString + description: A version number (only major, minor versions) + from_schema: cdp-api + base: float + minimum_value: 0 + URLorS3URI: + name: URLorS3URI + description: A URL or S3 URI + from_schema: cdp-api + base: string + pattern: ^(((https?|s3)://)|cryoetportal-rawdatasets-dev).*$ + ORCID: + name: ORCID + description: A unique, persistent identifier for researchers, provided by ORCID. + from_schema: cdp-api + base: string + pattern: '[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$' + BTO_ID: + name: BTO_ID + description: A BRENDA Tissue Ontology identifier + from_schema: cdp-api + base: string + pattern: ^BTO:[0-9]{7}$ + CL_ID: + name: CL_ID + description: A Cell Ontology identifier + from_schema: cdp-api + base: string + pattern: ^CL:[0-9]{7}$ + GO_ID: + name: GO_ID + description: A Gene Ontology identifier + from_schema: cdp-api + base: string + pattern: ^GO:[0-9]{7}$ + WORMBASE_ID: + name: WORMBASE_ID + description: A WormBase identifier + from_schema: cdp-api + base: string + pattern: WBStrain[0-9]{8}$ + ONTOLOGY_ID: + name: ONTOLOGY_ID + description: An ontology identifier + from_schema: cdp-api + base: string + pattern: ^[a-zA-Z]+:[0-9]+$ + DOI: + name: DOI + description: A Digital Object Identifier + from_schema: cdp-api + base: string + pattern: ^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+$ + DOI_LIST: + name: DOI_LIST + description: A list of Digital Object Identifiers + from_schema: cdp-api + base: string + pattern: ^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+(\s*,\s*(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+)*$ + EMPIAR_ID: + name: EMPIAR_ID + description: An Electron Microscopy Public Image Archive identifier + from_schema: cdp-api + base: string + pattern: ^EMPIAR-[0-9]+$ + EMDB_ID: + name: EMDB_ID + description: An Electron Microscopy Data Bank identifier + from_schema: cdp-api + base: string + pattern: ^EMD-[0-9]{4,5}$ + PDB_ID: + name: PDB_ID + description: A Protein Data Bank identifier + from_schema: cdp-api + base: string + pattern: ^pdb[0-9a-zA-Z]{4,8}$ + EMPIAR_EMDB_PDB_LIST: + name: EMPIAR_EMDB_PDB_LIST + description: A list of EMPIAR, EMDB, and PDB identifiers + from_schema: cdp-api + base: string + pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$ + EMPIAR_EMDB_DOI_PDB_LIST: + name: EMPIAR_EMDB_DOI_PDB_LIST + description: A list of EMPIAR, EMDB, DOI, and PDB identifiers + from_schema: cdp-api + base: string + pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$ +enums: + annotation_file_source_enum: + name: annotation_file_source_enum + description: How the annotation file was acquired + from_schema: cdp-api + permissible_values: + dataset_author: + text: dataset_author + description: Annotation submitted by dataset author + community: + text: community + description: Annotation submitted by community member + portal_standard: + text: portal_standard + description: Annotation submitted by portal standardization + annotation_method_type_enum: + name: annotation_method_type_enum + description: Describes how the annotations were generated. + from_schema: cdp-api + permissible_values: + manual: + text: manual + description: Annotations were generated manually. + automated: + text: automated + description: Annotations were generated automatically. + hybrid: + text: hybrid + description: Annotations were generated semi-automatically. + annotation_file_shape_type_enum: + name: annotation_file_shape_type_enum + description: Describes the shape of the annotation + from_schema: cdp-api + permissible_values: + SegmentationMask: + text: SegmentationMask + description: A binary mask volume + OrientedPoint: + text: OrientedPoint + description: A series of coordinates and an orientation + Point: + text: Point + description: A series of coordinates + InstanceSegmentation: + text: InstanceSegmentation + description: A volume with labels for multiple instances + annotation_method_link_type_enum: + name: annotation_method_link_type_enum + description: Describes the type of link associated to the annotation method. + from_schema: cdp-api + permissible_values: + documentation: + text: documentation + description: Links to the documentation related to the method. + models_weights: + text: models_weights + description: Links to the weights that the models used for generating annotations + were trained with. + other: + text: other + description: Link to resources that does not fit in the other categories. + source_code: + text: source_code + description: Links to the source code of the method. + website: + text: website + description: Links to a website of the method or tool used to generate the + annotation. + deposition_types_enum: + name: deposition_types_enum + description: Types of data a deposition has + from_schema: cdp-api + permissible_values: + annotation: + text: annotation + description: The deposition comprises of new annotations for existing datasets + dataset: + text: dataset + description: The deposition comprises of new dataset(s). + tomogram: + text: tomogram + description: The deposition comprises of new tomograms for existing datasets + sample_type_enum: + name: sample_type_enum + description: Type of sample imaged in a CryoET study. + from_schema: cdp-api + permissible_values: + cell: + text: cell + description: Tomographic data of whole cells or cell sections. + tissue: + text: tissue + description: Tomographic data of tissue sections. + organism: + text: organism + description: Tomographic data of sections through multicellular organisms. + organelle: + text: organelle + description: Tomographic data of purified organelles. + virus: + text: virus + description: Tomographic data of purified viruses or VLPs. + in_vitro: + text: in_vitro + description: Tomographic data of in vitro reconstituted systems or mixtures + of proteins. + in_silico: + text: in_silico + description: Simulated tomographic data. + other: + text: other + description: Other type of sample. + tiltseries_camera_acquire_mode_enum: + name: tiltseries_camera_acquire_mode_enum + description: Camera acquisition mode + from_schema: cdp-api + permissible_values: + counting: + text: counting + description: Counting mode + superresolution: + text: superresolution + description: Super-resolution mode + linear: + text: linear + description: Linear mode + cds: + text: cds + description: Correlated double sampling mode + tiltseries_microscope_manufacturer_enum: + name: tiltseries_microscope_manufacturer_enum + description: Microscope manufacturer + from_schema: cdp-api + permissible_values: + FEI: + text: FEI + description: FEI Company + TFS: + text: TFS + description: Thermo Fisher Scientific + JEOL: + text: JEOL + description: JEOL Ltd. + fiducial_alignment_status_enum: + name: fiducial_alignment_status_enum + description: Fiducial Alignment method + from_schema: cdp-api + permissible_values: + FIDUCIAL: + text: FIDUCIAL + description: Alignment computed based on fiducial markers + NON_FIDUCIAL: + text: NON_FIDUCIAL + description: Alignment computed without fiducial markers + tomogram_processing_enum: + name: tomogram_processing_enum + description: Tomogram processing method + from_schema: cdp-api + permissible_values: + denoised: + text: denoised + description: Tomogram was denoised + filtered: + text: filtered + description: Tomogram was filtered + raw: + text: raw + description: Tomogram was not processed + tomogram_reconstruction_method_enum: + name: tomogram_reconstruction_method_enum + description: Tomogram reconstruction method + from_schema: cdp-api + permissible_values: + SART: + text: SART + description: Simultaneous Algebraic Reconstruction Technique + Fourier Space: + text: Fourier Space + description: Fourier space reconstruction + SIRT: + text: SIRT + description: Simultaneous Iterative Reconstruction Technique + WBP: + text: WBP + description: Weighted Back-Projection + Unknown: + text: Unknown + description: Unknown reconstruction method + tomogram_type_enum: + name: tomogram_type_enum + description: Tomogram type + from_schema: cdp-api + permissible_values: + CANONICAL: + text: CANONICAL + description: Canonical tomogram (basis geometry for all annotations) + UNKNOWN: + text: UNKNOWN + description: Tomogram's was not submitted by the dataset author + alignment_type_enum: + name: alignment_type_enum + description: Type of alignment + from_schema: cdp-api + permissible_values: + LOCAL: + text: LOCAL + description: per-section non-rigid alignment available + GLOBAL: + text: GLOBAL + description: only per-section rigid alignment available +classes: + IDMixin: + name: IDMixin + annotations: + auto_increment: + tag: auto_increment + value: true + from_schema: cdp-api + mixin: true + attributes: + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: IDMixin + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + S3PrefixedEntityMixin: + name: S3PrefixedEntityMixin + description: An entity with s3/https prefixes + from_schema: cdp-api + mixin: true + attributes: + s3_prefix: + name: s3_prefix + description: Path to a directory containing data for this entity as an S3 + url + from_schema: cdp-api + exact_mappings: + - cdp-common:api_s3_prefix + alias: s3_prefix + owner: S3PrefixedEntityMixin + domain_of: + - S3PrefixedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + https_prefix: + name: https_prefix + description: Path to a directory containing data for this entity as an HTTPS + url + from_schema: cdp-api + exact_mappings: + - cdp-common:api_https_prefix + alias: https_prefix + owner: S3PrefixedEntityMixin + domain_of: + - S3PrefixedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + AuthorEntityMixin: + name: AuthorEntityMixin + description: An entity with author data + from_schema: cdp-api + mixin: true + mixins: + - AuthorMixin + attributes: + author_list_order: + name: author_list_order + description: The order that the author is listed as in the associated publication + from_schema: cdp-api + exact_mappings: + - cdp-common:api_author_list_order + alias: author_list_order + owner: AuthorEntityMixin + domain_of: + - AuthorEntityMixin + range: integer + required: true + inlined: true + inlined_as_list: true + orcid: + name: orcid + description: The ORCID identifier for the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_orcid + alias: orcid + owner: AuthorEntityMixin + domain_of: + - AuthorEntityMixin + range: ORCID + recommended: true + inlined: true + inlined_as_list: true + pattern: '[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$' + name: + name: name + description: The full name of the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_name + alias: name + owner: AuthorEntityMixin + domain_of: + - AuthorMixin + - Run + - Tomogram + range: string + required: true + inlined: true + inlined_as_list: true + email: + name: email + description: The email address of the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_email + alias: email + owner: AuthorEntityMixin + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_name: + name: affiliation_name + description: The name of the author's affiliation. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_name + alias: affiliation_name + owner: AuthorEntityMixin + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_address: + name: affiliation_address + description: The address of the author's affiliation. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_address + alias: affiliation_address + owner: AuthorEntityMixin + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_identifier: + name: affiliation_identifier + description: A Research Organization Registry (ROR) identifier. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_identifier + alias: affiliation_identifier + owner: AuthorEntityMixin + domain_of: + - AuthorMixin + range: string + recommended: true + inlined: true + inlined_as_list: true + corresponding_author_status: + name: corresponding_author_status + description: Whether the author is a corresponding author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_corresponding_author_status + ifabsent: 'False' + alias: corresponding_author_status + owner: AuthorEntityMixin + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + primary_author_status: + name: primary_author_status + description: Whether the author is a primary author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_primary_author_status + ifabsent: 'False' + alias: primary_author_status + owner: AuthorEntityMixin + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + APIDateStampedEntityMixin: + name: APIDateStampedEntityMixin + description: A set of dates at which a data item was deposited, published and + last modified. + from_schema: cdp-api + mixin: true + attributes: + deposition_date: + name: deposition_date + description: The date a data item was received by the cryoET data portal. + from_schema: cdp-api + exact_mappings: + - cdp-common:deposition_date + alias: deposition_date + owner: APIDateStampedEntityMixin + domain_of: + - DateStampedEntityMixin + - APIDateStampedEntityMixin + range: date + required: true + inlined: true + inlined_as_list: true + release_date: + name: release_date + description: The date a data item was received by the cryoET data portal. + from_schema: cdp-api + exact_mappings: + - cdp-common:release_date + alias: release_date + owner: APIDateStampedEntityMixin + domain_of: + - DateStampedEntityMixin + - APIDateStampedEntityMixin + range: date + required: true + inlined: true + inlined_as_list: true + last_modified_date: + name: last_modified_date + description: The date a piece of data was last modified on the cryoET data + portal. + from_schema: cdp-api + exact_mappings: + - cdp-common:last_modified_date + alias: last_modified_date + owner: APIDateStampedEntityMixin + domain_of: + - DateStampedEntityMixin + - APIDateStampedEntityMixin + range: date + required: true + inlined: true + inlined_as_list: true + Alignment: + name: Alignment + annotations: + plural: + tag: plural + value: Alignments + description: Tiltseries Alignment + from_schema: cdp-api + mixins: + - IDMixin + attributes: + annotation_files: + name: annotation_files + description: Files associated with an annotation + from_schema: cdp-api + alias: annotation_files + owner: Alignment + domain_of: + - Alignment + - AnnotationShape + - TomogramVoxelSpacing + inverse: AnnotationFile.alignment + range: AnnotationFile + multivalued: true + per_section_alignments: + name: per_section_alignments + description: Map alignment parameters to tilt series frames + from_schema: cdp-api + alias: per_section_alignments + owner: Alignment + domain_of: + - Alignment + inverse: PerSectionAlignmentParameters.alignment + range: PerSectionAlignmentParameters + multivalued: true + deposition: + name: deposition + from_schema: cdp-api + alias: deposition + owner: Alignment + domain_of: + - Alignment + - Annotation + - Dataset + - DepositionAuthor + - DepositionType + - Frame + - Tiltseries + - Tomogram + inverse: Deposition.alignments + range: Deposition + tiltseries: + name: tiltseries + from_schema: cdp-api + alias: tiltseries + owner: Alignment + domain_of: + - Alignment + - Deposition + - PerSectionParameters + - Run + inverse: Tiltseries.alignments + range: Tiltseries + tomograms: + name: tomograms + description: Metadata describing a tomogram. + from_schema: cdp-api + alias: tomograms + owner: Alignment + domain_of: + - Alignment + - Deposition + - Run + - TomogramVoxelSpacing + inverse: Tomogram.alignment + range: Tomogram + multivalued: true + run: + name: run + from_schema: cdp-api + alias: run + owner: Alignment + domain_of: + - Alignment + - Annotation + - Frame + - Tiltseries + - TomogramVoxelSpacing + - Tomogram + inverse: Run.alignments + range: Run + alignment: + name: alignment + description: Describe a tiltseries alignment + from_schema: cdp-api + exact_mappings: + - cdp-common:api_alignment + alias: alignment + owner: Alignment + domain_of: + - Alignment + - AnnotationFile + - PerSectionAlignmentParameters + - Tomogram + range: string + required: true + inlined: true + inlined_as_list: true + alignment_type: + name: alignment_type + description: Type of alignment included, i.e. is a non-rigid alignment included? + from_schema: cdp-api + exact_mappings: + - cdp-common:alignment_alignment_type + alias: alignment_type + owner: Alignment + domain_of: + - Alignment + range: alignment_type_enum + inlined: true + inlined_as_list: true + pattern: (^LOCAL$)|(^GLOBAL$) + volume_x_dimension: + name: volume_x_dimension + description: X dimension of the reconstruction volume in angstrom + from_schema: cdp-api + exact_mappings: + - cdp-common:alignment_volume_x_dimension + alias: volume_x_dimension + owner: Alignment + domain_of: + - Alignment + range: float + inlined: true + inlined_as_list: true + unit: + symbol: Å + descriptive_name: Angstrom + volume_y_dimension: + name: volume_y_dimension + description: Y dimension of the reconstruction volume in angstrom + from_schema: cdp-api + exact_mappings: + - cdp-common:alignment_volume_y_dimension + alias: volume_y_dimension + owner: Alignment + domain_of: + - Alignment + range: float + inlined: true + inlined_as_list: true + unit: + symbol: Å + descriptive_name: Angstrom + volume_z_dimension: + name: volume_z_dimension + description: Z dimension of the reconstruction volume in angstrom + from_schema: cdp-api + exact_mappings: + - cdp-common:alignment_volume_z_dimension + alias: volume_z_dimension + owner: Alignment + domain_of: + - Alignment + range: float + inlined: true + inlined_as_list: true + unit: + symbol: Å + descriptive_name: Angstrom + volume_x_offset: + name: volume_x_offset + description: X shift of the reconstruction volume in angstrom + from_schema: cdp-api + exact_mappings: + - cdp-common:alignment_volume_x_offset + alias: volume_x_offset + owner: Alignment + domain_of: + - Alignment + range: float + inlined: true + inlined_as_list: true + unit: + symbol: Å + descriptive_name: Angstrom + volume_y_offset: + name: volume_y_offset + description: Y shift of the reconstruction volume in angstrom + from_schema: cdp-api + exact_mappings: + - cdp-common:alignment_volume_y_offset + alias: volume_y_offset + owner: Alignment + domain_of: + - Alignment + range: float + inlined: true + inlined_as_list: true + unit: + symbol: Å + descriptive_name: Angstrom + volume_z_offset: + name: volume_z_offset + description: Z shift of the reconstruction volume in angstrom + from_schema: cdp-api + exact_mappings: + - cdp-common:alignment_volume_z_offset + alias: volume_z_offset + owner: Alignment + domain_of: + - Alignment + range: float + inlined: true + inlined_as_list: true + unit: + symbol: Å + descriptive_name: Angstrom + volume_x_rotation: + name: volume_x_rotation + description: Additional X rotation of the reconstruction volume in degrees + from_schema: cdp-api + exact_mappings: + - cdp-common:alignment_volume_x_rotation + alias: volume_x_rotation + owner: Alignment + domain_of: + - Alignment + range: float + inlined: true + inlined_as_list: true + unit: + symbol: ° + descriptive_name: degrees + tilt_offset: + name: tilt_offset + description: Additional tilt offset in degrees + from_schema: cdp-api + exact_mappings: + - cdp-common:alignment_tilt_offset + alias: tilt_offset + owner: Alignment + domain_of: + - Alignment + range: float + inlined: true + inlined_as_list: true + unit: + symbol: ° + descriptive_name: degrees + local_alignment_file: + name: local_alignment_file + description: Path to the local alignment file + from_schema: cdp-api + exact_mappings: + - cdp-common:alignment_local_alignment_file + alias: local_alignment_file + owner: Alignment + domain_of: + - Alignment + range: string + inlined: true + inlined_as_list: true + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: Alignment + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + AnnotationAuthor: + name: AnnotationAuthor + annotations: + plural: + tag: plural + value: AnnotationAuthors + description: Author of an annotation + from_schema: cdp-api + mixins: + - IDMixin + - AuthorEntityMixin + attributes: + annotation: + name: annotation + description: Metadata about an annotation for a run + from_schema: cdp-api + alias: annotation + owner: AnnotationAuthor + domain_of: + - AnnotationAuthor + - AnnotationShape + inverse: Annotation.authors + range: Annotation + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: AnnotationAuthor + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + author_list_order: + name: author_list_order + description: The order that the author is listed as in the associated publication + from_schema: cdp-api + exact_mappings: + - cdp-common:api_author_list_order + alias: author_list_order + owner: AnnotationAuthor + domain_of: + - AuthorEntityMixin + range: integer + required: true + inlined: true + inlined_as_list: true + orcid: + name: orcid + description: The ORCID identifier for the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_orcid + alias: orcid + owner: AnnotationAuthor + domain_of: + - AuthorEntityMixin + range: ORCID + recommended: true + inlined: true + inlined_as_list: true + pattern: '[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$' + name: + name: name + description: The full name of the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_name + alias: name + owner: AnnotationAuthor + domain_of: + - AuthorMixin + - Run + - Tomogram + range: string + required: true + inlined: true + inlined_as_list: true + email: + name: email + description: The email address of the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_email + alias: email + owner: AnnotationAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_name: + name: affiliation_name + description: The name of the author's affiliation. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_name + alias: affiliation_name + owner: AnnotationAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_address: + name: affiliation_address + description: The address of the author's affiliation. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_address + alias: affiliation_address + owner: AnnotationAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_identifier: + name: affiliation_identifier + description: A Research Organization Registry (ROR) identifier. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_identifier + alias: affiliation_identifier + owner: AnnotationAuthor + domain_of: + - AuthorMixin + range: string + recommended: true + inlined: true + inlined_as_list: true + corresponding_author_status: + name: corresponding_author_status + description: Whether the author is a corresponding author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_corresponding_author_status + ifabsent: 'False' + alias: corresponding_author_status + owner: AnnotationAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + primary_author_status: + name: primary_author_status + description: Whether the author is a primary author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_primary_author_status + ifabsent: 'False' + alias: primary_author_status + owner: AnnotationAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + AnnotationFile: + name: AnnotationFile + annotations: + plural: + tag: plural + value: AnnotationFiles + description: Files associated with an annotation + from_schema: cdp-api + mixins: + - IDMixin + attributes: + alignment: + name: alignment + description: Tiltseries Alignment + from_schema: cdp-api + alias: alignment + owner: AnnotationFile + domain_of: + - Alignment + - AnnotationFile + - PerSectionAlignmentParameters + - Tomogram + inverse: Alignment.annotation_files + range: Alignment + annotation_shape: + name: annotation_shape + description: Shapes associated with an annotation + from_schema: cdp-api + alias: annotation_shape + owner: AnnotationFile + domain_of: + - AnnotationFile + inverse: AnnotationShape.annotation_files + range: AnnotationShape + tomogram_voxel_spacing: + name: tomogram_voxel_spacing + description: Voxel spacings for a run + from_schema: cdp-api + alias: tomogram_voxel_spacing + owner: AnnotationFile + domain_of: + - AnnotationFile + - Tomogram + inverse: TomogramVoxelSpacing.annotation_files + range: TomogramVoxelSpacing + format: + name: format + description: File format label + from_schema: cdp-api + exact_mappings: + - cdp-common:api_file_format + alias: format + owner: AnnotationFile + domain_of: + - AnnotationFile + range: string + required: true + inlined: true + inlined_as_list: true + s3_path: + name: s3_path + description: Path to the file in s3 + from_schema: cdp-api + exact_mappings: + - cdp-common:api_s3_path + alias: s3_path + owner: AnnotationFile + domain_of: + - AnnotationFile + range: string + required: true + inlined: true + inlined_as_list: true + https_path: + name: https_path + description: Path to the file as an https url + from_schema: cdp-api + exact_mappings: + - cdp-common:api_https_path + alias: https_path + owner: AnnotationFile + domain_of: + - AnnotationFile + range: string + required: true + inlined: true + inlined_as_list: true + is_visualization_default: + name: is_visualization_default + description: This annotation will be rendered in neuroglancer by default. + from_schema: cdp-api + exact_mappings: + - cdp-common:annotation_source_file_is_visualization_default + ifabsent: 'False' + alias: is_visualization_default + owner: AnnotationFile + domain_of: + - AnnotationFile + range: boolean + inlined: true + inlined_as_list: true + source: + name: source + description: The source type for the annotation file + from_schema: cdp-api + exact_mappings: + - cdp-common:api_annotation_file_source + alias: source + owner: AnnotationFile + domain_of: + - AnnotationFile + range: annotation_file_source_enum + inlined: true + inlined_as_list: true + pattern: (^dataset_author$)|(^community$)|(^portal_standard$) + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: AnnotationFile + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + AnnotationShape: + name: AnnotationShape + annotations: + plural: + tag: plural + value: AnnotationShapes + description: Shapes associated with an annotation + from_schema: cdp-api + mixins: + - IDMixin + attributes: + annotation: + name: annotation + description: Metadata about an annotation for a run + from_schema: cdp-api + alias: annotation + owner: AnnotationShape + domain_of: + - AnnotationAuthor + - AnnotationShape + inverse: Annotation.annotation_shapes + range: Annotation + annotation_files: + name: annotation_files + description: Files associated with an annotation + from_schema: cdp-api + alias: annotation_files + owner: AnnotationShape + domain_of: + - Alignment + - AnnotationShape + - TomogramVoxelSpacing + inverse: AnnotationFile.annotation_shape + range: AnnotationFile + multivalued: true + shape_type: + name: shape_type + from_schema: cdp-api + alias: shape_type + owner: AnnotationShape + domain_of: + - AnnotationShape + range: annotation_file_shape_type_enum + inlined: true + inlined_as_list: true + pattern: (^SegmentationMask$)|(^OrientedPoint$)|(^Point$)|(^InstanceSegmentation$) + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: AnnotationShape + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + Annotation: + name: Annotation + annotations: + plural: + tag: plural + value: Annotations + description: Metadata about an annotation for a run + from_schema: cdp-api + mixins: + - IDMixin + - APIDateStampedEntityMixin + attributes: + run: + name: run + from_schema: cdp-api + alias: run + owner: Annotation + domain_of: + - Alignment + - Annotation + - Frame + - Tiltseries + - TomogramVoxelSpacing + - Tomogram + inverse: Run.annotations + range: Run + annotation_shapes: + name: annotation_shapes + description: Shapes associated with an annotation + from_schema: cdp-api + alias: annotation_shapes + owner: Annotation + domain_of: + - Annotation + inverse: AnnotationShape.annotation + range: AnnotationShape + multivalued: true + authors: + name: authors + description: Author of an annotation + from_schema: cdp-api + alias: authors + owner: Annotation + domain_of: + - Annotation + - Dataset + - Deposition + - Tomogram + inverse: AnnotationAuthor.annotation + range: AnnotationAuthor + multivalued: true + deposition: + name: deposition + from_schema: cdp-api + alias: deposition + owner: Annotation + domain_of: + - Alignment + - Annotation + - Dataset + - DepositionAuthor + - DepositionType + - Frame + - Tiltseries + - Tomogram + inverse: Deposition.annotations + range: Deposition + s3_metadata_path: + name: s3_metadata_path + description: Path to the file in s3 + from_schema: cdp-api + exact_mappings: + - cdp-common:api_s3_path + alias: s3_metadata_path + owner: Annotation + domain_of: + - Annotation + range: string + required: true + inlined: true + inlined_as_list: true + https_metadata_path: + name: https_metadata_path + description: Path to the file as an https url + from_schema: cdp-api + exact_mappings: + - cdp-common:api_https_path + alias: https_metadata_path + owner: Annotation + domain_of: + - Annotation + range: string + required: true + inlined: true + inlined_as_list: true + annotation_publication: + name: annotation_publication + description: List of publication IDs (EMPIAR, EMDB, DOI) that describe this + annotation method. Comma separated. + from_schema: cdp-api + exact_mappings: + - cdp-common:annotation_publications + alias: annotation_publication + owner: Annotation + domain_of: + - Annotation + range: EMPIAR_EMDB_DOI_PDB_LIST + inlined: true + inlined_as_list: true + pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$ + annotation_method: + name: annotation_method + description: Describe how the annotation is made (e.g. Manual, crYoLO, Positive + Unlabeled Learning, template matching) + from_schema: cdp-api + exact_mappings: + - cdp-common:annotation_method + alias: annotation_method + owner: Annotation + domain_of: + - Annotation + range: string + required: true + inlined: true + inlined_as_list: true + ground_truth_status: + name: ground_truth_status + description: Whether an annotation is considered ground truth, as determined + by the annotator. + from_schema: cdp-api + exact_mappings: + - cdp-common:annotation_ground_truth_status + ifabsent: 'False' + alias: ground_truth_status + owner: Annotation + domain_of: + - Annotation + range: boolean + recommended: true + inlined: true + inlined_as_list: true + object_id: + name: object_id + description: Gene Ontology Cellular Component identifier for the annotation + object + from_schema: cdp-api + exact_mappings: + - cdp-common:annotation_object_id + alias: object_id + owner: Annotation + domain_of: + - Annotation + range: GO_ID + required: true + inlined: true + inlined_as_list: true + pattern: ^GO:[0-9]{7}$ + object_name: + name: object_name + description: Name of the object being annotated (e.g. ribosome, nuclear pore + complex, actin filament, membrane) + from_schema: cdp-api + exact_mappings: + - cdp-common:annotation_object_name + alias: object_name + owner: Annotation + domain_of: + - Annotation + range: string + required: true + inlined: true + inlined_as_list: true + object_description: + name: object_description + description: A textual description of the annotation object, can be a longer + description to include additional information not covered by the Annotation + object name and state. + from_schema: cdp-api + exact_mappings: + - cdp-common:annotation_object_description + alias: object_description + owner: Annotation + domain_of: + - Annotation + range: string + inlined: true + inlined_as_list: true + object_state: + name: object_state + description: Molecule state annotated (e.g. open, closed) + from_schema: cdp-api + exact_mappings: + - cdp-common:annotation_object_state + alias: object_state + owner: Annotation + domain_of: + - Annotation + range: string + inlined: true + inlined_as_list: true + object_count: + name: object_count + description: Number of objects identified + from_schema: cdp-api + exact_mappings: + - cdp-common:annotation_object_count + alias: object_count + owner: Annotation + domain_of: + - Annotation + range: integer + inlined: true + inlined_as_list: true + confidence_precision: + name: confidence_precision + description: Describe the confidence level of the annotation. Precision is + defined as the % of annotation objects being true positive + from_schema: cdp-api + exact_mappings: + - cdp-common:annotation_confidence_precision + alias: confidence_precision + owner: Annotation + domain_of: + - Annotation + range: float + inlined: true + inlined_as_list: true + minimum_value: 0 + maximum_value: 100 + unit: + symbol: '%' + descriptive_name: percentage + confidence_recall: + name: confidence_recall + description: Describe the confidence level of the annotation. Recall is defined + as the % of true positives being annotated correctly + from_schema: cdp-api + exact_mappings: + - cdp-common:annotation_confidence_recall + alias: confidence_recall + owner: Annotation + domain_of: + - Annotation + range: float + inlined: true + inlined_as_list: true + minimum_value: 0 + maximum_value: 100 + unit: + symbol: '%' + descriptive_name: percentage + ground_truth_used: + name: ground_truth_used + description: Annotation filename used as ground truth for precision and recall + from_schema: cdp-api + exact_mappings: + - cdp-common:annotation_ground_truth_used + alias: ground_truth_used + owner: Annotation + domain_of: + - Annotation + range: string + inlined: true + inlined_as_list: true + annotation_software: + name: annotation_software + description: Software used for generating this annotation + from_schema: cdp-api + exact_mappings: + - cdp-common:annotation_software + alias: annotation_software + owner: Annotation + domain_of: + - Annotation + range: string + recommended: true + inlined: true + inlined_as_list: true + is_curator_recommended: + name: is_curator_recommended + description: This annotation is recommended by the curator to be preferred + for this object type. + from_schema: cdp-api + exact_mappings: + - cdp-common:annotation_is_curator_recommended + ifabsent: 'False' + alias: is_curator_recommended + owner: Annotation + domain_of: + - Annotation + range: boolean + inlined: true + inlined_as_list: true + method_type: + name: method_type + description: Classification of the annotation method based on supervision. + from_schema: cdp-api + exact_mappings: + - cdp-common:annotation_method_type + alias: method_type + owner: Annotation + domain_of: + - Annotation + range: annotation_method_type_enum + required: true + inlined: true + inlined_as_list: true + pattern: (^manual$)|(^automated$)|(^hybrid$) + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: Annotation + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + deposition_date: + name: deposition_date + description: The date a data item was received by the cryoET data portal. + from_schema: cdp-api + exact_mappings: + - cdp-common:deposition_date + alias: deposition_date + owner: Annotation + domain_of: + - DateStampedEntityMixin + - APIDateStampedEntityMixin + range: date + required: true + inlined: true + inlined_as_list: true + release_date: + name: release_date + description: The date a data item was received by the cryoET data portal. + from_schema: cdp-api + exact_mappings: + - cdp-common:release_date + alias: release_date + owner: Annotation + domain_of: + - DateStampedEntityMixin + - APIDateStampedEntityMixin + range: date + required: true + inlined: true + inlined_as_list: true + last_modified_date: + name: last_modified_date + description: The date a piece of data was last modified on the cryoET data + portal. + from_schema: cdp-api + exact_mappings: + - cdp-common:last_modified_date + alias: last_modified_date + owner: Annotation + domain_of: + - DateStampedEntityMixin + - APIDateStampedEntityMixin + range: date + required: true + inlined: true + inlined_as_list: true + DatasetAuthor: + name: DatasetAuthor + annotations: + plural: + tag: plural + value: DatasetAuthors + description: An author of a dataset + from_schema: cdp-api + mixins: + - IDMixin + - AuthorEntityMixin + attributes: + dataset: + name: dataset + description: An author of a dataset + from_schema: cdp-api + alias: dataset + owner: DatasetAuthor + domain_of: + - DatasetAuthor + - DatasetFunding + - Run + inverse: Dataset.authors + range: Dataset + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: DatasetAuthor + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + author_list_order: + name: author_list_order + description: The order that the author is listed as in the associated publication + from_schema: cdp-api + exact_mappings: + - cdp-common:api_author_list_order + alias: author_list_order + owner: DatasetAuthor + domain_of: + - AuthorEntityMixin + range: integer + required: true + inlined: true + inlined_as_list: true + orcid: + name: orcid + description: The ORCID identifier for the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_orcid + alias: orcid + owner: DatasetAuthor + domain_of: + - AuthorEntityMixin + range: ORCID + recommended: true + inlined: true + inlined_as_list: true + pattern: '[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$' + name: + name: name + description: The full name of the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_name + alias: name + owner: DatasetAuthor + domain_of: + - AuthorMixin + - Run + - Tomogram + range: string + required: true + inlined: true + inlined_as_list: true + email: + name: email + description: The email address of the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_email + alias: email + owner: DatasetAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_name: + name: affiliation_name + description: The name of the author's affiliation. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_name + alias: affiliation_name + owner: DatasetAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_address: + name: affiliation_address + description: The address of the author's affiliation. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_address + alias: affiliation_address + owner: DatasetAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_identifier: + name: affiliation_identifier + description: A Research Organization Registry (ROR) identifier. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_identifier + alias: affiliation_identifier + owner: DatasetAuthor + domain_of: + - AuthorMixin + range: string + recommended: true + inlined: true + inlined_as_list: true + corresponding_author_status: + name: corresponding_author_status + description: Whether the author is a corresponding author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_corresponding_author_status + ifabsent: 'False' + alias: corresponding_author_status + owner: DatasetAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + primary_author_status: + name: primary_author_status + description: Whether the author is a primary author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_primary_author_status + ifabsent: 'False' + alias: primary_author_status + owner: DatasetAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + DatasetFunding: + name: DatasetFunding + annotations: + plural: + tag: plural + value: DatasetFunding + description: Information about how a dataset was funded + from_schema: cdp-api + mixins: + - IDMixin + attributes: + dataset: + name: dataset + description: An author of a dataset + from_schema: cdp-api + alias: dataset + owner: DatasetFunding + domain_of: + - DatasetAuthor + - DatasetFunding + - Run + inverse: Dataset.funding_sources + range: Dataset + funding_agency_name: + name: funding_agency_name + description: The name of the funding source. + from_schema: cdp-api + exact_mappings: + - cdp-common:funding_agency_name + alias: funding_agency_name + owner: DatasetFunding + domain_of: + - DatasetFunding + range: string + recommended: true + inlined: true + inlined_as_list: true + grant_id: + name: grant_id + description: Grant identifier provided by the funding agency + from_schema: cdp-api + exact_mappings: + - cdp-common:funding_grant_id + alias: grant_id + owner: DatasetFunding + domain_of: + - DatasetFunding + range: string + recommended: true + inlined: true + inlined_as_list: true + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: DatasetFunding + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + Dataset: + name: Dataset + annotations: + plural: + tag: plural + value: Datasets + description: An author of a dataset + from_schema: cdp-api + mixins: + - IDMixin + - APIDateStampedEntityMixin + - CrossReferencesMixin + - S3PrefixedEntityMixin + attributes: + deposition: + name: deposition + from_schema: cdp-api + alias: deposition + owner: Dataset + domain_of: + - Alignment + - Annotation + - Dataset + - DepositionAuthor + - DepositionType + - Frame + - Tiltseries + - Tomogram + inverse: Deposition.datasets + range: Deposition + funding_sources: + name: funding_sources + description: Information about how a dataset was funded + from_schema: cdp-api + alias: funding_sources + owner: Dataset + domain_of: + - Dataset + inverse: DatasetFunding.dataset + range: DatasetFunding + multivalued: true + authors: + name: authors + description: An author of a dataset + from_schema: cdp-api + alias: authors + owner: Dataset + domain_of: + - Annotation + - Dataset + - Deposition + - Tomogram + inverse: DatasetAuthor.dataset + range: DatasetAuthor + multivalued: true + runs: + name: runs + from_schema: cdp-api + alias: runs + owner: Dataset + domain_of: + - Dataset + inverse: Run.dataset + range: Run + multivalued: true + title: + name: title + description: Title of a CryoET dataset. + from_schema: cdp-api + exact_mappings: + - cdp-common:dataset_title + alias: title + owner: Dataset + domain_of: + - Dataset + range: string + required: true + inlined: true + inlined_as_list: true + description: + name: description + description: A short description of a CryoET dataset, similar to an abstract + for a journal article or dataset. + from_schema: cdp-api + exact_mappings: + - cdp-common:dataset_description + alias: description + owner: Dataset + domain_of: + - Dataset + range: string + required: true + inlined: true + inlined_as_list: true + organism_name: + name: organism_name + description: Name of the organism from which a biological sample used in a + CryoET study is derived from, e.g. homo sapiens. + from_schema: cdp-api + exact_mappings: + - cdp-common:organism_name + alias: organism_name + owner: Dataset + domain_of: + - Dataset + range: string + required: true + inlined: true + inlined_as_list: true + organism_taxid: + name: organism_taxid + description: NCBI taxonomy identifier for the organism, e.g. 9606 + from_schema: cdp-api + exact_mappings: + - cdp-common:organism_taxid + alias: organism_taxid + owner: Dataset + domain_of: + - Dataset + range: integer + recommended: true + inlined: true + inlined_as_list: true + minimum_value: 1 + tissue_name: + name: tissue_name + description: Name of the tissue from which a biological sample used in a CryoET + study is derived from. + from_schema: cdp-api + exact_mappings: + - cdp-common:tissue_name + alias: tissue_name + owner: Dataset + domain_of: + - Dataset + range: string + required: false + inlined: true + inlined_as_list: true + tissue_id: + name: tissue_id + description: The UBERON identifier for the tissue. + from_schema: cdp-api + exact_mappings: + - cdp-common:tissue_id + alias: tissue_id + owner: Dataset + domain_of: + - Dataset + range: BTO_ID + recommended: true + inlined: true + inlined_as_list: true + pattern: ^BTO:[0-9]{7}$ + cell_name: + name: cell_name + description: Name of the cell type from which a biological sample used in + a CryoET study is derived from. + from_schema: cdp-api + exact_mappings: + - cdp-common:cell_name + alias: cell_name + owner: Dataset + domain_of: + - Dataset + range: string + required: false + inlined: true + inlined_as_list: true + cell_type_id: + name: cell_type_id + description: Cell Ontology identifier for the cell type + from_schema: cdp-api + exact_mappings: + - cdp-common:cell_type_id + alias: cell_type_id + owner: Dataset + domain_of: + - Dataset + range: CL_ID + recommended: true + inlined: true + inlined_as_list: true + pattern: ^CL:[0-9]{7}$ + cell_strain_name: + name: cell_strain_name + description: Cell line or strain for the sample. + from_schema: cdp-api + exact_mappings: + - cdp-common:cell_strain_name + alias: cell_strain_name + owner: Dataset + domain_of: + - Dataset + range: string + required: false + inlined: true + inlined_as_list: true + cell_strain_id: + name: cell_strain_id + description: Link to more information about the cell strain. + from_schema: cdp-api + exact_mappings: + - cdp-common:cell_strain_id + alias: cell_strain_id + owner: Dataset + domain_of: + - Dataset + range: string + recommended: true + inlined: true + inlined_as_list: true + pattern: (WBStrain[0-9]{8}$)|(^[a-zA-Z]+:[0-9]+$) + any_of: + - range: WORMBASE_ID + - range: ONTOLOGY_ID + sample_type: + name: sample_type + description: Type of sample imaged in a CryoET study. + from_schema: cdp-api + exact_mappings: + - cdp-common:preparation_sample_type + alias: sample_type + owner: Dataset + domain_of: + - Dataset + range: sample_type_enum + required: true + inlined: true + inlined_as_list: true + pattern: (^cell$)|(^tissue$)|(^organism$)|(^organelle$)|(^virus$)|(^in_vitro$)|(^in_silico$)|(^other$) + sample_preparation: + name: sample_preparation + description: Describes how the sample was prepared. + from_schema: cdp-api + exact_mappings: + - cdp-common:sample_preparation + alias: sample_preparation + owner: Dataset + domain_of: + - Dataset + range: string + recommended: true + inlined: true + inlined_as_list: true + grid_preparation: + name: grid_preparation + description: Describes Cryo-ET grid preparation. + from_schema: cdp-api + exact_mappings: + - cdp-common:grid_preparation + alias: grid_preparation + owner: Dataset + domain_of: + - Dataset + range: string + recommended: true + inlined: true + inlined_as_list: true + other_setup: + name: other_setup + description: Describes other setup not covered by sample preparation or grid + preparation that may make this dataset unique in the same publication. + from_schema: cdp-api + exact_mappings: + - cdp-common:preparation_other_setup + alias: other_setup + owner: Dataset + domain_of: + - Dataset + range: string + recommended: true + inlined: true + inlined_as_list: true + key_photo_url: + name: key_photo_url + description: URL for the dataset preview image. + from_schema: cdp-api + exact_mappings: + - cdp-common:dataset_key_photo_url + alias: key_photo_url + owner: Dataset + domain_of: + - Dataset + - Tomogram + range: string + inlined: true + inlined_as_list: true + key_photo_thumbnail_url: + name: key_photo_thumbnail_url + description: URL for the thumbnail of preview image. + from_schema: cdp-api + exact_mappings: + - cdp-common:dataset_key_photo_thumbnail_url + alias: key_photo_thumbnail_url + owner: Dataset + domain_of: + - Dataset + - Tomogram + range: string + inlined: true + inlined_as_list: true + cell_component_name: + name: cell_component_name + description: Name of the cellular component. + from_schema: cdp-api + exact_mappings: + - cdp-common:cell_component_name + alias: cell_component_name + owner: Dataset + domain_of: + - Dataset + range: string + required: false + inlined: true + inlined_as_list: true + cell_component_id: + name: cell_component_id + description: The GO identifier for the cellular component. + from_schema: cdp-api + exact_mappings: + - cdp-common:cell_component_id + alias: cell_component_id + owner: Dataset + domain_of: + - Dataset + range: GO_ID + recommended: true + inlined: true + inlined_as_list: true + pattern: ^GO:[0-9]{7}$ + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: Dataset + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + deposition_date: + name: deposition_date + description: The date a data item was received by the cryoET data portal. + from_schema: cdp-api + exact_mappings: + - cdp-common:deposition_date + alias: deposition_date + owner: Dataset + domain_of: + - DateStampedEntityMixin + - APIDateStampedEntityMixin + range: date + required: true + inlined: true + inlined_as_list: true + release_date: + name: release_date + description: The date a data item was received by the cryoET data portal. + from_schema: cdp-api + exact_mappings: + - cdp-common:release_date + alias: release_date + owner: Dataset + domain_of: + - DateStampedEntityMixin + - APIDateStampedEntityMixin + range: date + required: true + inlined: true + inlined_as_list: true + last_modified_date: + name: last_modified_date + description: The date a piece of data was last modified on the cryoET data + portal. + from_schema: cdp-api + exact_mappings: + - cdp-common:last_modified_date + alias: last_modified_date + owner: Dataset + domain_of: + - DateStampedEntityMixin + - APIDateStampedEntityMixin + range: date + required: true + inlined: true + inlined_as_list: true + publications: + name: publications + description: Comma-separated list of DOIs for publications associated with + the dataset. + from_schema: cdp-api + alias: publications + owner: Dataset + domain_of: + - CrossReferencesMixin + range: DOI_LIST + recommended: true + inlined: true + inlined_as_list: true + pattern: (^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+(\s*,\s*(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+)*$)|(^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+(\s*,\s*(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+)*$) + related_database_entries: + name: related_database_entries + description: Comma-separated list of related database entries for the dataset. + from_schema: cdp-api + alias: related_database_entries + owner: Dataset + domain_of: + - CrossReferencesMixin + range: EMPIAR_EMDB_PDB_LIST + recommended: true + inlined: true + inlined_as_list: true + pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$) + related_database_links: + name: related_database_links + description: Comma-separated list of related database links for the dataset. + from_schema: cdp-api + alias: related_database_links + owner: Dataset + domain_of: + - CrossReferencesMixin + range: string + inlined: true + inlined_as_list: true + dataset_citations: + name: dataset_citations + description: Comma-separated list of DOIs for publications citing the dataset. + from_schema: cdp-api + alias: dataset_citations + owner: Dataset + domain_of: + - CrossReferencesMixin + range: string + inlined: true + inlined_as_list: true + s3_prefix: + name: s3_prefix + description: Path to a directory containing data for this entity as an S3 + url + from_schema: cdp-api + exact_mappings: + - cdp-common:api_s3_prefix + alias: s3_prefix + owner: Dataset + domain_of: + - S3PrefixedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + https_prefix: + name: https_prefix + description: Path to a directory containing data for this entity as an HTTPS + url + from_schema: cdp-api + exact_mappings: + - cdp-common:api_https_prefix + alias: https_prefix + owner: Dataset + domain_of: + - S3PrefixedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + DepositionAuthor: + name: DepositionAuthor + annotations: + plural: + tag: plural + value: DepositionAuthors + description: Author of a deposition + from_schema: cdp-api + mixins: + - IDMixin + - AuthorEntityMixin + attributes: + deposition: + name: deposition + from_schema: cdp-api + alias: deposition + owner: DepositionAuthor + domain_of: + - Alignment + - Annotation + - Dataset + - DepositionAuthor + - DepositionType + - Frame + - Tiltseries + - Tomogram + inverse: Deposition.authors + range: Deposition + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: DepositionAuthor + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + author_list_order: + name: author_list_order + description: The order that the author is listed as in the associated publication + from_schema: cdp-api + exact_mappings: + - cdp-common:api_author_list_order + alias: author_list_order + owner: DepositionAuthor + domain_of: + - AuthorEntityMixin + range: integer + required: true + inlined: true + inlined_as_list: true + orcid: + name: orcid + description: The ORCID identifier for the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_orcid + alias: orcid + owner: DepositionAuthor + domain_of: + - AuthorEntityMixin + range: ORCID + recommended: true + inlined: true + inlined_as_list: true + pattern: '[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$' + name: + name: name + description: The full name of the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_name + alias: name + owner: DepositionAuthor + domain_of: + - AuthorMixin + - Run + - Tomogram + range: string + required: true + inlined: true + inlined_as_list: true + email: + name: email + description: The email address of the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_email + alias: email + owner: DepositionAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_name: + name: affiliation_name + description: The name of the author's affiliation. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_name + alias: affiliation_name + owner: DepositionAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_address: + name: affiliation_address + description: The address of the author's affiliation. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_address + alias: affiliation_address + owner: DepositionAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_identifier: + name: affiliation_identifier + description: A Research Organization Registry (ROR) identifier. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_identifier + alias: affiliation_identifier + owner: DepositionAuthor + domain_of: + - AuthorMixin + range: string + recommended: true + inlined: true + inlined_as_list: true + corresponding_author_status: + name: corresponding_author_status + description: Whether the author is a corresponding author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_corresponding_author_status + ifabsent: 'False' + alias: corresponding_author_status + owner: DepositionAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + primary_author_status: + name: primary_author_status + description: Whether the author is a primary author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_primary_author_status + ifabsent: 'False' + alias: primary_author_status + owner: DepositionAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + Deposition: + name: Deposition + annotations: + plural: + tag: plural + value: Depositions + from_schema: cdp-api + mixins: + - IDMixin + - CrossReferencesMixin + - APIDateStampedEntityMixin + attributes: + authors: + name: authors + description: Author of a deposition + from_schema: cdp-api + alias: authors + owner: Deposition + domain_of: + - Annotation + - Dataset + - Deposition + - Tomogram + inverse: DepositionAuthor.deposition + range: DepositionAuthor + multivalued: true + alignments: + name: alignments + description: Tiltseries Alignment + from_schema: cdp-api + alias: alignments + owner: Deposition + domain_of: + - Deposition + - Run + - Tiltseries + inverse: Alignment.deposition + range: Alignment + multivalued: true + annotations: + name: annotations + description: Metadata about an annotation for a run + from_schema: cdp-api + alias: annotations + owner: Deposition + domain_of: + - Deposition + - Run + inverse: Annotation.deposition + range: Annotation + multivalued: true + datasets: + name: datasets + description: An author of a dataset + from_schema: cdp-api + alias: datasets + owner: Deposition + domain_of: + - Deposition + inverse: Dataset.deposition + range: Dataset + multivalued: true + frames: + name: frames + from_schema: cdp-api + alias: frames + owner: Deposition + domain_of: + - Deposition + - Run + inverse: Frame.deposition + range: Frame + multivalued: true + tiltseries: + name: tiltseries + from_schema: cdp-api + alias: tiltseries + owner: Deposition + domain_of: + - Alignment + - Deposition + - PerSectionParameters + - Run + inverse: Tiltseries.deposition + range: Tiltseries + multivalued: true + tomograms: + name: tomograms + from_schema: cdp-api + alias: tomograms + owner: Deposition + domain_of: + - Alignment + - Deposition + - Run + - TomogramVoxelSpacing + inverse: Tomogram.deposition + range: Tomograms + multivalued: true + inlined: true + inlined_as_list: true + deposition_title: + name: deposition_title + description: Title of a CryoET deposition. + from_schema: cdp-api + exact_mappings: + - cdp-common:deposition_title + alias: deposition_title + owner: Deposition + domain_of: + - Deposition + range: string + required: true + inlined: true + inlined_as_list: true + deposition_description: + name: deposition_description + description: A short description of the deposition, similar to an abstract + for a journal article or dataset. + from_schema: cdp-api + exact_mappings: + - cdp-common:deposition_description + alias: deposition_description + owner: Deposition + domain_of: + - Deposition + range: string + required: true + inlined: true + inlined_as_list: true + deposition_types: + name: deposition_types + from_schema: cdp-api + alias: deposition_types + owner: Deposition + domain_of: + - Deposition + inverse: DepositionType.deposition + range: DepositionType + multivalued: true + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: Deposition + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + publications: + name: publications + description: Comma-separated list of DOIs for publications associated with + the dataset. + from_schema: cdp-api + alias: publications + owner: Deposition + domain_of: + - CrossReferencesMixin + range: DOI_LIST + recommended: true + inlined: true + inlined_as_list: true + pattern: (^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+(\s*,\s*(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+)*$)|(^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+(\s*,\s*(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+)*$) + related_database_entries: + name: related_database_entries + description: Comma-separated list of related database entries for the dataset. + from_schema: cdp-api + alias: related_database_entries + owner: Deposition + domain_of: + - CrossReferencesMixin + range: EMPIAR_EMDB_PDB_LIST + recommended: true + inlined: true + inlined_as_list: true + pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$) + related_database_links: + name: related_database_links + description: Comma-separated list of related database links for the dataset. + from_schema: cdp-api + alias: related_database_links + owner: Deposition + domain_of: + - CrossReferencesMixin + range: string + inlined: true + inlined_as_list: true + dataset_citations: + name: dataset_citations + description: Comma-separated list of DOIs for publications citing the dataset. + from_schema: cdp-api + alias: dataset_citations + owner: Deposition + domain_of: + - CrossReferencesMixin + range: string + inlined: true + inlined_as_list: true + deposition_date: + name: deposition_date + description: The date a data item was received by the cryoET data portal. + from_schema: cdp-api + exact_mappings: + - cdp-common:deposition_date + alias: deposition_date + owner: Deposition + domain_of: + - DateStampedEntityMixin + - APIDateStampedEntityMixin + range: date + required: true + inlined: true + inlined_as_list: true + release_date: + name: release_date + description: The date a data item was received by the cryoET data portal. + from_schema: cdp-api + exact_mappings: + - cdp-common:release_date + alias: release_date + owner: Deposition + domain_of: + - DateStampedEntityMixin + - APIDateStampedEntityMixin + range: date + required: true + inlined: true + inlined_as_list: true + last_modified_date: + name: last_modified_date + description: The date a piece of data was last modified on the cryoET data + portal. + from_schema: cdp-api + exact_mappings: + - cdp-common:last_modified_date + alias: last_modified_date + owner: Deposition + domain_of: + - DateStampedEntityMixin + - APIDateStampedEntityMixin + range: date + required: true + inlined: true + inlined_as_list: true + DepositionType: + name: DepositionType + annotations: + plural: + tag: plural + value: DepositionTypes + from_schema: cdp-api + mixins: + - IDMixin + attributes: + deposition: + name: deposition + from_schema: cdp-api + alias: deposition + owner: DepositionType + domain_of: + - Alignment + - Annotation + - Dataset + - DepositionAuthor + - DepositionType + - Frame + - Tiltseries + - Tomogram + inverse: Deposition.deposition_types + range: Deposition + type: + name: type + from_schema: cdp-api + alias: type + owner: DepositionType + domain_of: + - DepositionType + range: deposition_types_enum + inlined: true + inlined_as_list: true + pattern: (^annotation$)|(^dataset$)|(^tomogram$) + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: DepositionType + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + Frame: + name: Frame + annotations: + plural: + tag: plural + value: Frames + from_schema: cdp-api + mixins: + - IDMixin + - S3PrefixedEntityMixin + attributes: + deposition: + name: deposition + from_schema: cdp-api + alias: deposition + owner: Frame + domain_of: + - Alignment + - Annotation + - Dataset + - DepositionAuthor + - DepositionType + - Frame + - Tiltseries + - Tomogram + inverse: Deposition.frames + range: Deposition + per_section_parameters: + name: per_section_parameters + description: Record how frames get mapped to TiltSeries + from_schema: cdp-api + alias: per_section_parameters + owner: Frame + domain_of: + - Frame + - Tiltseries + inverse: PerSectionParameters.frame + range: PerSectionParameters + multivalued: true + run: + name: run + from_schema: cdp-api + alias: run + owner: Frame + domain_of: + - Alignment + - Annotation + - Frame + - Tiltseries + - TomogramVoxelSpacing + - Tomogram + inverse: Run.frames + range: Run + raw_angle: + name: raw_angle + description: Camera angle for a frame + from_schema: cdp-api + exact_mappings: + - cdp-common:api_frame_raw_angle + alias: raw_angle + owner: Frame + domain_of: + - Frame + range: float + required: true + inlined: true + inlined_as_list: true + minimum_value: -90 + maximum_value: 90 + acquisition_order: + name: acquisition_order + description: Frame's acquistion order within a tilt experiment + from_schema: cdp-api + exact_mappings: + - cdp-common:api_frame_acquisition_order + alias: acquisition_order + owner: Frame + domain_of: + - Frame + range: integer + required: false + inlined: true + inlined_as_list: true + dose: + name: dose + description: The raw camera angle for a frame + from_schema: cdp-api + exact_mappings: + - cdp-common:api_frame_dose + alias: dose + owner: Frame + domain_of: + - Frame + range: float + required: true + inlined: true + inlined_as_list: true + unit: + symbol: e-/Å2 + descriptive_name: electrons per square angstrom + is_gain_corrected: + name: is_gain_corrected + description: Whether this frame has been gain corrected + from_schema: cdp-api + exact_mappings: + - cdp-common:api_frame_is_gain_corrected + alias: is_gain_corrected + owner: Frame + domain_of: + - Frame + range: boolean + inlined: true + inlined_as_list: true + s3_gain_file: + name: s3_gain_file + description: S3 path to the gain file for this frame + from_schema: cdp-api + exact_mappings: + - cdp-common:api_frame_s3_gain_file + alias: s3_gain_file + owner: Frame + domain_of: + - Frame + - Tiltseries + range: string + inlined: true + inlined_as_list: true + https_gain_file: + name: https_gain_file + description: HTTPS path to the gain file for this frame + from_schema: cdp-api + exact_mappings: + - cdp-common:api_frame_https_gain_file + alias: https_gain_file + owner: Frame + domain_of: + - Frame + - Tiltseries + range: string + inlined: true + inlined_as_list: true + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: Frame + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + s3_prefix: + name: s3_prefix + description: Path to a directory containing data for this entity as an S3 + url + from_schema: cdp-api + exact_mappings: + - cdp-common:api_s3_prefix + alias: s3_prefix + owner: Frame + domain_of: + - S3PrefixedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + https_prefix: + name: https_prefix + description: Path to a directory containing data for this entity as an HTTPS + url + from_schema: cdp-api + exact_mappings: + - cdp-common:api_https_prefix + alias: https_prefix + owner: Frame + domain_of: + - S3PrefixedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + PerSectionParameters: + name: PerSectionParameters + annotations: + plural: + tag: plural + value: PerSectionParameters + description: Record how frames get mapped to TiltSeries + from_schema: cdp-api + mixins: + - IDMixin + attributes: + frame: + name: frame + from_schema: cdp-api + alias: frame + owner: PerSectionParameters + domain_of: + - PerSectionParameters + inverse: Frame.per_section_parameters + range: Frame + required: true + tiltseries: + name: tiltseries + from_schema: cdp-api + alias: tiltseries + owner: PerSectionParameters + domain_of: + - Alignment + - Deposition + - PerSectionParameters + - Run + inverse: Tiltseries.per_section_parameters + range: Tiltseries + required: true + z_index: + name: z_index + description: z-index of the frame in the tiltseries + from_schema: cdp-api + exact_mappings: + - cdp-common:per_section_z_index + alias: z_index + owner: PerSectionParameters + domain_of: + - PerSectionParameters + - PerSectionAlignmentParameters + range: integer + required: true + inlined: true + inlined_as_list: true + minimum_value: 0 + defocus: + name: defocus + description: defocus amount + from_schema: cdp-api + exact_mappings: + - cdp-common:per_section_defocus + alias: defocus + owner: PerSectionParameters + domain_of: + - PerSectionParameters + range: float + inlined: true + inlined_as_list: true + minimum_value: 100 + maximum_value: 100 + unit: + symbol: µm + descriptive_name: microns + astigmatism: + name: astigmatism + description: Astigmatism amount for this frame + from_schema: cdp-api + exact_mappings: + - cdp-common:per_section_astigmatism + alias: astigmatism + owner: PerSectionParameters + domain_of: + - PerSectionParameters + range: float + inlined: true + inlined_as_list: true + astigmatic_angle: + name: astigmatic_angle + description: Angle of ast + from_schema: cdp-api + exact_mappings: + - cdp-common:per_section_astigmatic_angle + alias: astigmatic_angle + owner: PerSectionParameters + domain_of: + - PerSectionParameters + range: float + inlined: true + inlined_as_list: true + minimum_value: -180 + maximum_value: 180 + unit: + symbol: ° + descriptive_name: degrees + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: PerSectionParameters + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + PerSectionAlignmentParameters: + name: PerSectionAlignmentParameters + annotations: + plural: + tag: plural + value: PerSectionAlignmentParameters + description: Map alignment parameters to tilt series frames + from_schema: cdp-api + mixins: + - IDMixin + attributes: + alignment: + name: alignment + description: Tiltseries Alignment + from_schema: cdp-api + alias: alignment + owner: PerSectionAlignmentParameters + domain_of: + - Alignment + - AnnotationFile + - PerSectionAlignmentParameters + - Tomogram + inverse: Alignment.per_section_alignments + range: Alignment + required: true + z_index: + name: z_index + description: z-index of the frame in the tiltseries + from_schema: cdp-api + exact_mappings: + - cdp-common:per_section_z_index + alias: z_index + owner: PerSectionAlignmentParameters + domain_of: + - PerSectionParameters + - PerSectionAlignmentParameters + range: integer + required: true + inlined: true + inlined_as_list: true + minimum_value: 0 + x_offset: + name: x_offset + description: In-plane X-shift of the projection in angstrom + from_schema: cdp-api + exact_mappings: + - cdp-common:per_section_alignment_x_offset + alias: x_offset + owner: PerSectionAlignmentParameters + domain_of: + - PerSectionAlignmentParameters + range: float + inlined: true + inlined_as_list: true + unit: + symbol: Å + descriptive_name: Angstrom + y_offset: + name: y_offset + description: In-plane Y-shift of the projection in angstrom + from_schema: cdp-api + exact_mappings: + - cdp-common:per_section_alignment_y_offset + alias: y_offset + owner: PerSectionAlignmentParameters + domain_of: + - PerSectionAlignmentParameters + range: float + inlined: true + inlined_as_list: true + unit: + symbol: Å + descriptive_name: Angstrom + in_plane_rotation: + name: in_plane_rotation + description: In-plane rotation of the projection in degrees + from_schema: cdp-api + exact_mappings: + - cdp-common:per_section_alignment_in_plane_rotation + alias: in_plane_rotation + owner: PerSectionAlignmentParameters + domain_of: + - PerSectionAlignmentParameters + range: float + inlined: true + inlined_as_list: true + unit: + symbol: ° + descriptive_name: degrees + beam_tilt: + name: beam_tilt + description: Beam tilt during projection in degrees + from_schema: cdp-api + exact_mappings: + - cdp-common:per_section_alignment_beam_tilt + alias: beam_tilt + owner: PerSectionAlignmentParameters + domain_of: + - PerSectionAlignmentParameters + range: float + inlined: true + inlined_as_list: true + unit: + symbol: ° + descriptive_name: degrees + tilt_angle: + name: tilt_angle + description: Tilt angle of the projection in degrees + from_schema: cdp-api + exact_mappings: + - cdp-common:per_section_alignment_tilt_angle + alias: tilt_angle + owner: PerSectionAlignmentParameters + domain_of: + - PerSectionAlignmentParameters + range: float + inlined: true + inlined_as_list: true + unit: + symbol: ° + descriptive_name: degrees + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: PerSectionAlignmentParameters + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + Run: + name: Run + annotations: + plural: + tag: plural + value: Runs + from_schema: cdp-api + mixins: + - IDMixin + - S3PrefixedEntityMixin + attributes: + alignments: + name: alignments + description: Tiltseries Alignment + from_schema: cdp-api + alias: alignments + owner: Run + domain_of: + - Deposition + - Run + - Tiltseries + inverse: Alignment.run + range: Alignment + multivalued: true + annotations: + name: annotations + description: Metadata about an annotation for a run + from_schema: cdp-api + alias: annotations + owner: Run + domain_of: + - Deposition + - Run + inverse: Annotation.run + range: Annotation + multivalued: true + dataset: + name: dataset + description: An author of a dataset + from_schema: cdp-api + alias: dataset + owner: Run + domain_of: + - DatasetAuthor + - DatasetFunding + - Run + inverse: Dataset.runs + range: Dataset + required: true + frames: + name: frames + from_schema: cdp-api + alias: frames + owner: Run + domain_of: + - Deposition + - Run + inverse: Frame.run + range: Frame + multivalued: true + tiltseries: + name: tiltseries + from_schema: cdp-api + alias: tiltseries + owner: Run + domain_of: + - Alignment + - Deposition + - PerSectionParameters + - Run + inverse: Tiltseries.run + range: Tiltseries + multivalued: true + tomogram_voxel_spacings: + name: tomogram_voxel_spacings + description: Voxel spacings for a run + from_schema: cdp-api + alias: tomogram_voxel_spacings + owner: Run + domain_of: + - Run + inverse: TomogramVoxelSpacing.run + range: TomogramVoxelSpacing + multivalued: true + tomograms: + name: tomograms + description: Metadata describing a tomogram. + from_schema: cdp-api + alias: tomograms + owner: Run + domain_of: + - Alignment + - Deposition + - Run + - TomogramVoxelSpacing + inverse: Tomogram.run + range: Tomogram + multivalued: true + name: + name: name + description: Name of a run + from_schema: cdp-api + exact_mappings: + - cdp-common:api_run_name + alias: name + owner: Run + domain_of: + - AuthorMixin + - Run + - Tomogram + range: string + required: true + inlined: true + inlined_as_list: true + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: Run + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + s3_prefix: + name: s3_prefix + description: Path to a directory containing data for this entity as an S3 + url + from_schema: cdp-api + exact_mappings: + - cdp-common:api_s3_prefix + alias: s3_prefix + owner: Run + domain_of: + - S3PrefixedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + https_prefix: + name: https_prefix + description: Path to a directory containing data for this entity as an HTTPS + url + from_schema: cdp-api + exact_mappings: + - cdp-common:api_https_prefix + alias: https_prefix + owner: Run + domain_of: + - S3PrefixedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + Tiltseries: + name: Tiltseries + annotations: + plural: + tag: plural + value: Tiltseries + from_schema: cdp-api + mixins: + - IDMixin + attributes: + alignments: + name: alignments + description: Tiltseries Alignment + from_schema: cdp-api + alias: alignments + owner: Tiltseries + domain_of: + - Deposition + - Run + - Tiltseries + inverse: Alignment.tiltseries + range: Alignment + multivalued: true + per_section_parameters: + name: per_section_parameters + description: Record how frames get mapped to TiltSeries + from_schema: cdp-api + alias: per_section_parameters + owner: Tiltseries + domain_of: + - Frame + - Tiltseries + inverse: PerSectionParameters.tiltseries + range: PerSectionParameters + multivalued: true + run: + name: run + from_schema: cdp-api + alias: run + owner: Tiltseries + domain_of: + - Alignment + - Annotation + - Frame + - Tiltseries + - TomogramVoxelSpacing + - Tomogram + inverse: Run.tiltseries + range: Run + required: true + deposition: + name: deposition + from_schema: cdp-api + alias: deposition + owner: Tiltseries + domain_of: + - Alignment + - Annotation + - Dataset + - DepositionAuthor + - DepositionType + - Frame + - Tiltseries + - Tomogram + inverse: Deposition.tiltseries + range: Deposition + required: false + s3_omezarr_dir: + name: s3_omezarr_dir + description: S3 path to this tiltseries in multiscale OME-Zarr format + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_s3_omezarr_dir + alias: s3_omezarr_dir + owner: Tiltseries + domain_of: + - Tiltseries + - Tomogram + range: string + inlined: true + inlined_as_list: true + s3_mrc_bin1: + name: s3_mrc_bin1 + description: S3 path to this tiltseries in MRC format (no scaling) + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_s3_mrc_bin1 + alias: s3_mrc_bin1 + owner: Tiltseries + domain_of: + - Tiltseries + range: string + inlined: true + inlined_as_list: true + https_omezarr_dir: + name: https_omezarr_dir + description: HTTPS path to this tiltseries in multiscale OME-Zarr format + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_https_omezarr_dir + alias: https_omezarr_dir + owner: Tiltseries + domain_of: + - Tiltseries + - Tomogram + range: string + inlined: true + inlined_as_list: true + https_mrc_bin1: + name: https_mrc_bin1 + description: HTTPS path to this tiltseries in MRC format (no scaling) + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_https_mrc_bin1 + alias: https_mrc_bin1 + owner: Tiltseries + domain_of: + - Tiltseries + range: string + inlined: true + inlined_as_list: true + s3_collection_metadata: + name: s3_collection_metadata + description: S3 path to the collection metadata file for this tiltseries + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_s3_collection_metadata + alias: s3_collection_metadata + owner: Tiltseries + domain_of: + - Tiltseries + range: string + inlined: true + inlined_as_list: true + https_collection_metadata: + name: https_collection_metadata + description: HTTPS path to the collection metadata file for this tiltseries + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_https_collection_metadata + alias: https_collection_metadata + owner: Tiltseries + domain_of: + - Tiltseries + range: string + inlined: true + inlined_as_list: true + s3_angle_list: + name: s3_angle_list + description: S3 path to the angle list file for this tiltseries + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_s3_angle_list + alias: s3_angle_list + owner: Tiltseries + domain_of: + - Tiltseries + range: string + inlined: true + inlined_as_list: true + https_angle_list: + name: https_angle_list + description: HTTPS path to the angle list file for this tiltseries + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_https_angle_list + alias: https_angle_list + owner: Tiltseries + domain_of: + - Tiltseries + range: string + inlined: true + inlined_as_list: true + s3_gain_file: + name: s3_gain_file + description: S3 path to the gain file for this tiltseries + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_s3_gain_file + alias: s3_gain_file + owner: Tiltseries + domain_of: + - Frame + - Tiltseries + range: string + inlined: true + inlined_as_list: true + https_gain_file: + name: https_gain_file + description: HTTPS path to the gain file for this tiltseries + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_https_gain_file + alias: https_gain_file + owner: Tiltseries + domain_of: + - Frame + - Tiltseries + range: string + inlined: true + inlined_as_list: true + acceleration_voltage: + name: acceleration_voltage + description: Electron Microscope Accelerator voltage in volts + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_acceleration_voltage + alias: acceleration_voltage + owner: Tiltseries + domain_of: + - Tiltseries + range: float + required: true + inlined: true + inlined_as_list: true + minimum_value: 20000 + unit: + symbol: V + descriptive_name: volts + spherical_abberation_constant: + name: spherical_abberation_constant + description: Spherical Aberration Constant of the objective lens in millimeters + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_spherical_aberration_constant + alias: spherical_abberation_constant + owner: Tiltseries + domain_of: + - Tiltseries + range: float + required: true + inlined: true + inlined_as_list: true + minimum_value: 0 + unit: + symbol: mm + descriptive_name: millimeters + microscope_manufacturer: + name: microscope_manufacturer + description: Name of the microscope manufacturer + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_microscope_manufacturer + alias: microscope_manufacturer + owner: Tiltseries + domain_of: + - Tiltseries + range: tiltseries_microscope_manufacturer_enum + required: true + inlined: true + inlined_as_list: true + pattern: (^FEI$)|(^TFS$)|(^JEOL$) + microscope_model: + name: microscope_model + description: Microscope model name + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_microscope_model + alias: microscope_model + owner: Tiltseries + domain_of: + - Tiltseries + range: string + required: true + inlined: true + inlined_as_list: true + microscope_energy_filter: + name: microscope_energy_filter + description: Energy filter setup used + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_microscope_energy_filter + alias: microscope_energy_filter + owner: Tiltseries + domain_of: + - Tiltseries + range: string + required: true + inlined: true + inlined_as_list: true + microscope_phase_plate: + name: microscope_phase_plate + description: Phase plate configuration + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_microscope_phase_plate + alias: microscope_phase_plate + owner: Tiltseries + domain_of: + - Tiltseries + range: string + inlined: true + inlined_as_list: true + microscope_image_corrector: + name: microscope_image_corrector + description: Image corrector setup + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_microscope_image_corrector + alias: microscope_image_corrector + owner: Tiltseries + domain_of: + - Tiltseries + range: string + inlined: true + inlined_as_list: true + microscope_additional_info: + name: microscope_additional_info + description: Other microscope optical setup information, in addition to energy + filter, phase plate and image corrector + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_microscope_additional_info + alias: microscope_additional_info + owner: Tiltseries + domain_of: + - Tiltseries + range: string + inlined: true + inlined_as_list: true + camera_manufacturer: + name: camera_manufacturer + description: Name of the camera manufacturer + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_camera_manufacturer + alias: camera_manufacturer + owner: Tiltseries + domain_of: + - Tiltseries + range: string + required: true + inlined: true + inlined_as_list: true + camera_model: + name: camera_model + description: Camera model name + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_camera_model + alias: camera_model + owner: Tiltseries + domain_of: + - Tiltseries + range: string + required: true + inlined: true + inlined_as_list: true + tilt_min: + name: tilt_min + description: Minimal tilt angle in degrees + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_tilt_min + alias: tilt_min + owner: Tiltseries + domain_of: + - Tiltseries + range: float + required: true + inlined: true + inlined_as_list: true + minimum_value: -90 + maximum_value: 90 + unit: + symbol: ° + descriptive_name: degrees + tilt_max: + name: tilt_max + description: Maximal tilt angle in degrees + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_tilt_max + alias: tilt_max + owner: Tiltseries + domain_of: + - Tiltseries + range: float + required: true + inlined: true + inlined_as_list: true + minimum_value: -90 + maximum_value: 90 + unit: + symbol: ° + descriptive_name: degrees + tilt_range: + name: tilt_range + description: Total tilt range from min to max in degrees + from_schema: cdp-api + exact_mappings: + - cdp-common:api_tiltseries_tilt_range + alias: tilt_range + owner: Tiltseries + domain_of: + - Tiltseries + range: float + required: true + inlined: true + inlined_as_list: true + minimum_value: 0 + maximum_value: 180 + unit: + symbol: ° + descriptive_name: degrees + tilt_step: + name: tilt_step + description: Tilt step in degrees + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_tilt_step + alias: tilt_step + owner: Tiltseries + domain_of: + - Tiltseries + range: float + required: true + inlined: true + inlined_as_list: true + minimum_value: 0 + maximum_value: 90 + unit: + symbol: ° + descriptive_name: degrees + tilting_scheme: + name: tilting_scheme + description: The order of stage tilting during acquisition of the data + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_tilting_scheme + alias: tilting_scheme + owner: Tiltseries + domain_of: + - Tiltseries + range: string + required: true + inlined: true + inlined_as_list: true + tilt_axis: + name: tilt_axis + description: Rotation angle in degrees + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_tilt_axis + alias: tilt_axis + owner: Tiltseries + domain_of: + - Tiltseries + range: float + required: true + inlined: true + inlined_as_list: true + minimum_value: -360 + maximum_value: 360 + unit: + symbol: ° + descriptive_name: degrees + total_flux: + name: total_flux + description: Number of Electrons reaching the specimen in a square Angstrom + area for the entire tilt series + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_total_flux + alias: total_flux + owner: Tiltseries + domain_of: + - Tiltseries + range: float + required: true + inlined: true + inlined_as_list: true + minimum_value: 0 + unit: + symbol: e^-/Å^2 + descriptive_name: electrons per square Angstrom + data_acquisition_software: + name: data_acquisition_software + description: Software used to collect data + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_data_acquisition_software + alias: data_acquisition_software + owner: Tiltseries + domain_of: + - Tiltseries + range: string + required: true + inlined: true + inlined_as_list: true + related_empiar_entry: + name: related_empiar_entry + description: If a tilt series is deposited into EMPIAR, enter the EMPIAR dataset + identifier + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_related_empiar_entry + alias: related_empiar_entry + owner: Tiltseries + domain_of: + - Tiltseries + range: EMPIAR_ID + inlined: true + inlined_as_list: true + pattern: ^EMPIAR-[0-9]+$ + binning_from_frames: + name: binning_from_frames + description: Describes the binning factor from frames to tilt series file + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_binning_from_frames + alias: binning_from_frames + owner: Tiltseries + domain_of: + - Tiltseries + range: float + inlined: true + inlined_as_list: true + minimum_value: 0 + tilt_series_quality: + name: tilt_series_quality + description: Author assessment of tilt series quality within the dataset (1-5, + 5 is best) + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_tilt_series_quality + alias: tilt_series_quality + owner: Tiltseries + domain_of: + - Tiltseries + range: integer + required: true + inlined: true + inlined_as_list: true + minimum_value: 1 + maximum_value: 5 + is_aligned: + name: is_aligned + description: Whether this tilt series is aligned + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_is_aligned + alias: is_aligned + owner: Tiltseries + domain_of: + - Tiltseries + range: boolean + required: true + inlined: true + inlined_as_list: true + pixel_spacing: + name: pixel_spacing + description: Pixel spacing for the tilt series + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_pixel_spacing + alias: pixel_spacing + owner: Tiltseries + domain_of: + - Tiltseries + range: float + required: true + inlined: true + inlined_as_list: true + minimum_value: 0.001 + unit: + symbol: Å/px + descriptive_name: Angstroms per pixel + aligned_tiltseries_binning: + name: aligned_tiltseries_binning + description: Binning factor of the aligned tilt series + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_aligned_tiltseries_binning + alias: aligned_tiltseries_binning + owner: Tiltseries + domain_of: + - Tiltseries + range: float + inlined: true + inlined_as_list: true + minimum_value: 0 + tiltseries_frames_count: + name: tiltseries_frames_count + description: Number of frames associated with this tiltseries + from_schema: cdp-api + exact_mappings: + - cdp-common:tiltseries_frames_count + alias: tiltseries_frames_count + owner: Tiltseries + domain_of: + - Tiltseries + range: integer + inlined: true + inlined_as_list: true + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: Tiltseries + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + TomogramAuthor: + name: TomogramAuthor + annotations: + plural: + tag: plural + value: TomogramAuthors + description: Author of a tomogram + from_schema: cdp-api + mixins: + - IDMixin + - AuthorEntityMixin + attributes: + tomogram: + name: tomogram + description: Metadata describing a tomogram. + from_schema: cdp-api + alias: tomogram + owner: TomogramAuthor + domain_of: + - TomogramAuthor + inverse: Tomogram.authors + range: Tomogram + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: TomogramAuthor + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + author_list_order: + name: author_list_order + description: The order that the author is listed as in the associated publication + from_schema: cdp-api + exact_mappings: + - cdp-common:api_author_list_order + alias: author_list_order + owner: TomogramAuthor + domain_of: + - AuthorEntityMixin + range: integer + required: true + inlined: true + inlined_as_list: true + orcid: + name: orcid + description: The ORCID identifier for the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_orcid + alias: orcid + owner: TomogramAuthor + domain_of: + - AuthorEntityMixin + range: ORCID + recommended: true + inlined: true + inlined_as_list: true + pattern: '[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$' + name: + name: name + description: The full name of the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_name + alias: name + owner: TomogramAuthor + domain_of: + - AuthorMixin + - Run + - Tomogram + range: string + required: true + inlined: true + inlined_as_list: true + email: + name: email + description: The email address of the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_email + alias: email + owner: TomogramAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_name: + name: affiliation_name + description: The name of the author's affiliation. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_name + alias: affiliation_name + owner: TomogramAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_address: + name: affiliation_address + description: The address of the author's affiliation. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_address + alias: affiliation_address + owner: TomogramAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_identifier: + name: affiliation_identifier + description: A Research Organization Registry (ROR) identifier. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_identifier + alias: affiliation_identifier + owner: TomogramAuthor + domain_of: + - AuthorMixin + range: string + recommended: true + inlined: true + inlined_as_list: true + corresponding_author_status: + name: corresponding_author_status + description: Whether the author is a corresponding author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_corresponding_author_status + ifabsent: 'False' + alias: corresponding_author_status + owner: TomogramAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + primary_author_status: + name: primary_author_status + description: Whether the author is a primary author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_primary_author_status + ifabsent: 'False' + alias: primary_author_status + owner: TomogramAuthor + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + TomogramVoxelSpacing: + name: TomogramVoxelSpacing + annotations: + plural: + tag: plural + value: TomogramVoxelSpacings + description: Voxel spacings for a run + from_schema: cdp-api + mixins: + - IDMixin + - S3PrefixedEntityMixin + attributes: + annotation_files: + name: annotation_files + description: Files associated with an annotation + from_schema: cdp-api + alias: annotation_files + owner: TomogramVoxelSpacing + domain_of: + - Alignment + - AnnotationShape + - TomogramVoxelSpacing + inverse: AnnotationFile.tomogram_voxel_spacing + range: AnnotationFile + multivalued: true + run: + name: run + from_schema: cdp-api + alias: run + owner: TomogramVoxelSpacing + domain_of: + - Alignment + - Annotation + - Frame + - Tiltseries + - TomogramVoxelSpacing + - Tomogram + inverse: run.tomogram_voxel_spacings + range: Run + tomograms: + name: tomograms + description: Metadata describing a tomogram. + from_schema: cdp-api + alias: tomograms + owner: TomogramVoxelSpacing + domain_of: + - Alignment + - Deposition + - Run + - TomogramVoxelSpacing + inverse: Tomogram.tomogram_voxel_spacing + range: Tomogram + multivalued: true + voxel_spacing: + name: voxel_spacing + description: Voxel spacing equal in all three axes in angstroms + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_voxel_spacing + alias: voxel_spacing + owner: TomogramVoxelSpacing + domain_of: + - TomogramVoxelSpacing + - Tomogram + range: float + required: true + inlined: true + inlined_as_list: true + minimum_value: 0.001 + unit: + symbol: Å/voxel + descriptive_name: Angstroms per voxel + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: TomogramVoxelSpacing + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + s3_prefix: + name: s3_prefix + description: Path to a directory containing data for this entity as an S3 + url + from_schema: cdp-api + exact_mappings: + - cdp-common:api_s3_prefix + alias: s3_prefix + owner: TomogramVoxelSpacing + domain_of: + - S3PrefixedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + https_prefix: + name: https_prefix + description: Path to a directory containing data for this entity as an HTTPS + url + from_schema: cdp-api + exact_mappings: + - cdp-common:api_https_prefix + alias: https_prefix + owner: TomogramVoxelSpacing + domain_of: + - S3PrefixedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + Tomogram: + name: Tomogram + annotations: + plural: + tag: plural + value: Tomograms + description: Metadata describing a tomogram. + from_schema: cdp-api + mixins: + - IDMixin + - S3PrefixedEntityMixin + attributes: + alignment: + name: alignment + description: Tiltseries Alignment + from_schema: cdp-api + alias: alignment + owner: Tomogram + domain_of: + - Alignment + - AnnotationFile + - PerSectionAlignmentParameters + - Tomogram + inverse: Alignment.tomograms + range: Alignment + authors: + name: authors + description: Author of a tomogram + from_schema: cdp-api + alias: authors + owner: Tomogram + domain_of: + - Annotation + - Dataset + - Deposition + - Tomogram + inverse: TomogramAuthor.tomogram + range: TomogramAuthor + multivalued: true + deposition: + name: deposition + from_schema: cdp-api + alias: deposition + owner: Tomogram + domain_of: + - Alignment + - Annotation + - Dataset + - DepositionAuthor + - DepositionType + - Frame + - Tiltseries + - Tomogram + inverse: Deposition.tomograms + range: Deposition + run: + name: run + from_schema: cdp-api + alias: run + owner: Tomogram + domain_of: + - Alignment + - Annotation + - Frame + - Tiltseries + - TomogramVoxelSpacing + - Tomogram + inverse: Run.tomograms + range: Run + tomogram_voxel_spacing: + name: tomogram_voxel_spacing + description: Voxel spacings for a run + from_schema: cdp-api + alias: tomogram_voxel_spacing + owner: Tomogram + domain_of: + - AnnotationFile + - Tomogram + inverse: tomogram_voxel_spacing.tomograms + range: TomogramVoxelSpacing + name: + name: name + description: Short name for this tomogram + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_name + alias: name + owner: Tomogram + domain_of: + - AuthorMixin + - Run + - Tomogram + range: string + inlined: true + inlined_as_list: true + size_x: + name: size_x + description: Tomogram voxels in the x dimension + from_schema: cdp-api + exact_mappings: + - cdp-common:api_tomogram_size_x + alias: size_x + owner: Tomogram + domain_of: + - Tomogram + range: float + required: true + inlined: true + inlined_as_list: true + minimum_value: 0 + unit: + symbol: voxel + descriptive_name: voxels + size_y: + name: size_y + description: Tomogram voxels in the y dimension + from_schema: cdp-api + exact_mappings: + - cdp-common:api_tomogram_size_y + alias: size_y + owner: Tomogram + domain_of: + - Tomogram + range: float + required: true + inlined: true + inlined_as_list: true + minimum_value: 0 + unit: + symbol: voxel + descriptive_name: voxels + size_z: + name: size_z + description: Tomogram voxels in the z dimension + from_schema: cdp-api + exact_mappings: + - cdp-common:api_tomogram_size_z + alias: size_z + owner: Tomogram + domain_of: + - Tomogram + range: float + required: true + inlined: true + inlined_as_list: true + minimum_value: 0 + unit: + symbol: voxel + descriptive_name: voxels + voxel_spacing: + name: voxel_spacing + description: Voxel spacing equal in all three axes in angstroms + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_voxel_spacing + alias: voxel_spacing + owner: Tomogram + domain_of: + - TomogramVoxelSpacing + - Tomogram + range: float + required: true + inlined: true + inlined_as_list: true + minimum_value: 0.001 + unit: + symbol: Å/voxel + descriptive_name: Angstroms per voxel + fiducial_alignment_status: + name: fiducial_alignment_status + description: Whether the tomographic alignment was computed based on fiducial + markers. + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_fiducial_alignment_status + alias: fiducial_alignment_status + owner: Tomogram + domain_of: + - Tomogram + range: fiducial_alignment_status_enum + required: true + inlined: true + inlined_as_list: true + pattern: (^FIDUCIAL$)|(^NON_FIDUCIAL$) + reconstruction_method: + name: reconstruction_method + description: Describe reconstruction method (WBP, SART, SIRT) + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_reconstruction_method + alias: reconstruction_method + owner: Tomogram + domain_of: + - Tomogram + range: tomogram_reconstruction_method_enum + required: true + inlined: true + inlined_as_list: true + pattern: (^SART$)|(^Fourier Space$)|(^SIRT$)|(^WBP$)|(^Unknown$) + processing: + name: processing + description: Describe additional processing used to derive the tomogram + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_processing + alias: processing + owner: Tomogram + domain_of: + - Tomogram + range: tomogram_processing_enum + required: true + inlined: true + inlined_as_list: true + pattern: (^denoised$)|(^filtered$)|(^raw$) + tomogram_version: + name: tomogram_version + description: Version of tomogram + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_version + alias: tomogram_version + owner: Tomogram + domain_of: + - Tomogram + range: float + required: false + inlined: true + inlined_as_list: true + processing_software: + name: processing_software + description: Processing software used to derive the tomogram + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_processing_software + alias: processing_software + owner: Tomogram + domain_of: + - Tomogram + range: string + recommended: true + inlined: true + inlined_as_list: true + reconstruction_software: + name: reconstruction_software + description: Name of software used for reconstruction + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_reconstruction_software + alias: reconstruction_software + owner: Tomogram + domain_of: + - Tomogram + range: string + required: true + inlined: true + inlined_as_list: true + is_canonical: + name: is_canonical + description: whether this tomogram is canonical for the run + from_schema: cdp-api + alias: is_canonical + owner: Tomogram + domain_of: + - Tomogram + range: boolean + inlined: true + inlined_as_list: true + s3_omezarr_dir: + name: s3_omezarr_dir + description: S3 path to this tomogram in multiscale OME-Zarr format + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_s3_omezarr_dir + alias: s3_omezarr_dir + owner: Tomogram + domain_of: + - Tiltseries + - Tomogram + range: string + inlined: true + inlined_as_list: true + https_omezarr_dir: + name: https_omezarr_dir + description: HTTPS path to this tomogram in multiscale OME-Zarr format + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_https_omezarr_dir + alias: https_omezarr_dir + owner: Tomogram + domain_of: + - Tiltseries + - Tomogram + range: string + inlined: true + inlined_as_list: true + s3_mrc_scale0: + name: s3_mrc_scale0 + description: S3 path to this tomogram in MRC format (no scaling) + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_s3_mrc_scale0 + alias: s3_mrc_scale0 + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + https_mrc_scale0: + name: https_mrc_scale0 + description: HTTPS path to this tomogram in MRC format (no scaling) + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_https_mrc_scale0 + alias: https_mrc_scale0 + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + scale0_dimensions: + name: scale0_dimensions + description: comma separated x,y,z dimensions of the unscaled tomogram + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_scale0_dimensions + alias: scale0_dimensions + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + scale1_dimensions: + name: scale1_dimensions + description: comma separated x,y,z dimensions of the scale1 tomogram + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_scale1_dimensions + alias: scale1_dimensions + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + scale2_dimensions: + name: scale2_dimensions + description: comma separated x,y,z dimensions of the scale2 tomogram + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_scale2_dimensions + alias: scale2_dimensions + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + ctf_corrected: + name: ctf_corrected + description: Whether this tomogram is CTF corrected + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_ctf_corrected + alias: ctf_corrected + owner: Tomogram + domain_of: + - Tomogram + range: boolean + recommended: true + inlined: true + inlined_as_list: true + offset_x: + name: offset_x + description: x offset data relative to the canonical tomogram in pixels + from_schema: cdp-api + alias: offset_x + owner: Tomogram + domain_of: + - Tomogram + range: integer + required: true + inlined: true + inlined_as_list: true + unit: + symbol: px + descriptive_name: pixels + offset_y: + name: offset_y + description: y offset data relative to the canonical tomogram in pixels + from_schema: cdp-api + alias: offset_y + owner: Tomogram + domain_of: + - Tomogram + range: integer + required: true + inlined: true + inlined_as_list: true + unit: + symbol: px + descriptive_name: pixels + offset_z: + name: offset_z + description: z offset data relative to the canonical tomogram in pixels + from_schema: cdp-api + alias: offset_z + owner: Tomogram + domain_of: + - Tomogram + range: integer + required: true + inlined: true + inlined_as_list: true + unit: + symbol: px + descriptive_name: pixels + affine_transformation_matrix: + name: affine_transformation_matrix + description: A placeholder for any type of data. + from_schema: cdp-api + array: + exact_number_dimensions: 2 + dimensions: + - exact_cardinality: 4 + - exact_cardinality: 4 + alias: affine_transformation_matrix + owner: Tomogram + domain_of: + - Tomogram + range: Any + inlined: true + inlined_as_list: true + key_photo_url: + name: key_photo_url + description: URL for the key photo + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_key_photo_url + alias: key_photo_url + owner: Tomogram + domain_of: + - Dataset + - Tomogram + range: string + inlined: true + inlined_as_list: true + key_photo_thumbnail_url: + name: key_photo_thumbnail_url + description: URL for the thumbnail of key photo + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_key_photo_thumbnail_url + alias: key_photo_thumbnail_url + owner: Tomogram + domain_of: + - Dataset + - Tomogram + range: string + inlined: true + inlined_as_list: true + neuroglancer_config: + name: neuroglancer_config + description: the compact json of neuroglancer config + from_schema: cdp-api + exact_mappings: + - cdp-common:tomogram_neuroglancer_config + alias: neuroglancer_config + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + tomogram_type: + name: tomogram_type + from_schema: cdp-api + alias: tomogram_type + owner: Tomogram + domain_of: + - Tomogram + range: tomogram_type_enum + inlined: true + inlined_as_list: true + pattern: (^CANONICAL$)|(^UNKNOWN$) + is_standardized: + name: is_standardized + description: Whether this tomogram was generated per the portal's standards + from_schema: cdp-api + exact_mappings: + - cdp-common:api_tomogram_is_standardized + alias: is_standardized + owner: Tomogram + domain_of: + - Tomogram + range: boolean + required: true + inlined: true + inlined_as_list: true + id: + name: id + description: An identifier to refer to a specific instance of this type + from_schema: cdp-api + exact_mappings: + - cdp-common:api_sequential_identifier + identifier: true + alias: id + owner: Tomogram + domain_of: + - IDMixin + range: integer + required: true + inlined: true + inlined_as_list: true + s3_prefix: + name: s3_prefix + description: Path to a directory containing data for this entity as an S3 + url + from_schema: cdp-api + exact_mappings: + - cdp-common:api_s3_prefix + alias: s3_prefix + owner: Tomogram + domain_of: + - S3PrefixedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + https_prefix: + name: https_prefix + description: Path to a directory containing data for this entity as an HTTPS + url + from_schema: cdp-api + exact_mappings: + - cdp-common:api_https_prefix + alias: https_prefix + owner: Tomogram + domain_of: + - S3PrefixedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + Any: + name: Any + description: A placeholder for any type of data. + from_schema: cdp-api + class_uri: linkml:Any + DateStampedEntityMixin: + name: DateStampedEntityMixin + description: A set of dates at which a data item was deposited, published and + last modified. + from_schema: cdp-api + mixin: true + attributes: + deposition_date: + name: deposition_date + description: The date a data item was received by the cryoET data portal. + from_schema: cdp-api + exact_mappings: + - cdp-common:deposition_date + alias: deposition_date + owner: DateStampedEntityMixin + domain_of: + - DateStampedEntityMixin + - APIDateStampedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + release_date: + name: release_date + description: The date a data item was received by the cryoET data portal. + from_schema: cdp-api + exact_mappings: + - cdp-common:release_date + alias: release_date + owner: DateStampedEntityMixin + domain_of: + - DateStampedEntityMixin + - APIDateStampedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + last_modified_date: + name: last_modified_date + description: The date a piece of data was last modified on the cryoET data + portal. + from_schema: cdp-api + exact_mappings: + - cdp-common:last_modified_date + alias: last_modified_date + owner: DateStampedEntityMixin + domain_of: + - DateStampedEntityMixin + - APIDateStampedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + CrossReferencesMixin: + name: CrossReferencesMixin + description: A set of cross-references to other databases and publications. + from_schema: cdp-api + mixin: true + attributes: + publications: + name: publications + description: Comma-separated list of DOIs for publications associated with + the dataset. + from_schema: cdp-api + alias: publications + owner: CrossReferencesMixin + domain_of: + - CrossReferencesMixin + range: DOI_LIST + recommended: true + inlined: true + inlined_as_list: true + pattern: (^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+(\s*,\s*(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+)*$)|(^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+(\s*,\s*(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+)*$) + related_database_entries: + name: related_database_entries + description: Comma-separated list of related database entries for the dataset. + from_schema: cdp-api + alias: related_database_entries + owner: CrossReferencesMixin + domain_of: + - CrossReferencesMixin + range: EMPIAR_EMDB_PDB_LIST + recommended: true + inlined: true + inlined_as_list: true + pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$) + related_database_links: + name: related_database_links + description: Comma-separated list of related database links for the dataset. + from_schema: cdp-api + alias: related_database_links + owner: CrossReferencesMixin + domain_of: + - CrossReferencesMixin + range: string + inlined: true + inlined_as_list: true + dataset_citations: + name: dataset_citations + description: Comma-separated list of DOIs for publications citing the dataset. + from_schema: cdp-api + alias: dataset_citations + owner: CrossReferencesMixin + domain_of: + - CrossReferencesMixin + range: string + inlined: true + inlined_as_list: true + AuthorMixin: + name: AuthorMixin + description: An entity with author data + from_schema: cdp-api + mixin: true + attributes: + name: + name: name + description: The full name of the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_name + alias: name + owner: AuthorMixin + domain_of: + - AuthorMixin + - Run + - Tomogram + range: string + required: true + inlined: true + inlined_as_list: true + email: + name: email + description: The email address of the author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_email + alias: email + owner: AuthorMixin + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_name: + name: affiliation_name + description: The name of the author's affiliation. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_name + alias: affiliation_name + owner: AuthorMixin + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_address: + name: affiliation_address + description: The address of the author's affiliation. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_address + alias: affiliation_address + owner: AuthorMixin + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_identifier: + name: affiliation_identifier + description: A Research Organization Registry (ROR) identifier. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_affiliation_identifier + alias: affiliation_identifier + owner: AuthorMixin + domain_of: + - AuthorMixin + range: string + recommended: true + inlined: true + inlined_as_list: true + corresponding_author_status: + name: corresponding_author_status + description: Whether the author is a corresponding author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_corresponding_author_status + ifabsent: 'False' + alias: corresponding_author_status + owner: AuthorMixin + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + primary_author_status: + name: primary_author_status + description: Whether the author is a primary author. + from_schema: cdp-api + exact_mappings: + - cdp-common:author_primary_author_status + ifabsent: 'False' + alias: primary_author_status + owner: AuthorMixin + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true +source_file: api/v2.0.0/api_models.yaml diff --git a/schema/core/v2.0.0/codegen/metadata_materialized.yaml b/schema/core/v2.0.0/codegen/metadata_materialized.yaml new file mode 100644 index 000000000..2ca196933 --- /dev/null +++ b/schema/core/v2.0.0/codegen/metadata_materialized.yaml @@ -0,0 +1,3500 @@ +name: cdp-meta +id: metadata +version: 1.1.0 +imports: +- linkml:types +prefixes: + linkml: + prefix_prefix: linkml + prefix_reference: https://w3id.org/linkml/ + cdp-meta: + prefix_prefix: cdp-meta + prefix_reference: metadata + ORCID: + prefix_prefix: ORCID + prefix_reference: https://orcid.org/ + ROR: + prefix_prefix: ROR + prefix_reference: https://ror.org/ + UBERON: + prefix_prefix: UBERON + prefix_reference: http://purl.obolibrary.org/obo/UBERON_ + CL: + prefix_prefix: CL + prefix_reference: http://purl.obolibrary.org/obo/CL_ + GO: + prefix_prefix: GO + prefix_reference: http://purl.obolibrary.org/obo/GO_ +default_prefix: cdp-meta +default_range: Any +types: + string: + name: string + description: A character string + notes: + - In RDF serializations, a slot with range of string is treated as a literal or + type xsd:string. If you are authoring schemas in LinkML YAML, the type is + referenced with the lower case "string". + from_schema: metadata + exact_mappings: + - schema:Text + base: str + uri: xsd:string + integer: + name: integer + description: An integer + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "integer". + from_schema: metadata + exact_mappings: + - schema:Integer + base: int + uri: xsd:integer + boolean: + name: boolean + description: A binary (true or false) value + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "boolean". + from_schema: metadata + exact_mappings: + - schema:Boolean + base: Bool + uri: xsd:boolean + repr: bool + float: + name: float + description: A real number that conforms to the xsd:float specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "float". + from_schema: metadata + exact_mappings: + - schema:Float + base: float + uri: xsd:float + double: + name: double + description: A real number that conforms to the xsd:double specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "double". + from_schema: metadata + close_mappings: + - schema:Float + base: float + uri: xsd:double + decimal: + name: decimal + description: A real number with arbitrary precision that conforms to the xsd:decimal + specification + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "decimal". + from_schema: metadata + broad_mappings: + - schema:Number + base: Decimal + uri: xsd:decimal + time: + name: time + description: A time object represents a (local) time of day, independent of any + particular day + notes: + - URI is dateTime because OWL reasoners do not work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "time". + from_schema: metadata + exact_mappings: + - schema:Time + base: XSDTime + uri: xsd:time + repr: str + date: + name: date + description: a date (year, month and day) in an idealized calendar + notes: + - URI is dateTime because OWL reasoners don't work with straight date or time + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date". + from_schema: metadata + exact_mappings: + - schema:Date + base: XSDDate + uri: xsd:date + repr: str + datetime: + name: datetime + description: The combination of a date and time + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "datetime". + from_schema: metadata + exact_mappings: + - schema:DateTime + base: XSDDateTime + uri: xsd:dateTime + repr: str + date_or_datetime: + name: date_or_datetime + description: Either a date or a datetime + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "date_or_datetime". + from_schema: metadata + base: str + uri: linkml:DateOrDatetime + repr: str + uriorcurie: + name: uriorcurie + description: a URI or a CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uriorcurie". + from_schema: metadata + base: URIorCURIE + uri: xsd:anyURI + repr: str + curie: + name: curie + conforms_to: https://www.w3.org/TR/curie/ + description: a compact URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "curie". + comments: + - in RDF serializations this MUST be expanded to a URI + - in non-RDF serializations MAY be serialized as the compact representation + from_schema: metadata + base: Curie + uri: xsd:string + repr: str + uri: + name: uri + conforms_to: https://www.ietf.org/rfc/rfc3987.txt + description: a complete URI + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "uri". + comments: + - in RDF serializations a slot with range of uri is treated as a literal or type + xsd:anyURI unless it is an identifier or a reference to an identifier, in which + case it is translated directly to a node + from_schema: metadata + close_mappings: + - schema:URL + base: URI + uri: xsd:anyURI + repr: str + ncname: + name: ncname + description: Prefix part of CURIE + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "ncname". + from_schema: metadata + base: NCName + uri: xsd:string + repr: str + objectidentifier: + name: objectidentifier + description: A URI or CURIE that represents an object in the model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "objectidentifier". + comments: + - Used for inheritance and type checking + from_schema: metadata + base: ElementIdentifier + uri: shex:iri + repr: str + nodeidentifier: + name: nodeidentifier + description: A URI, CURIE or BNODE that represents a node in a model. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "nodeidentifier". + from_schema: metadata + base: NodeIdentifier + uri: shex:nonLiteral + repr: str + jsonpointer: + name: jsonpointer + conforms_to: https://datatracker.ietf.org/doc/html/rfc6901 + description: A string encoding a JSON Pointer. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to a valid object within the current + instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpointer". + from_schema: metadata + base: str + uri: xsd:string + repr: str + jsonpath: + name: jsonpath + conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html + description: A string encoding a JSON Path. The value of the string MUST conform + to JSON Point syntax and SHOULD dereference to zero or more valid objects within + the current instance document when encoded in tree form. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "jsonpath". + from_schema: metadata + base: str + uri: xsd:string + repr: str + sparqlpath: + name: sparqlpath + conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths + description: A string encoding a SPARQL Property Path. The value of the string + MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects + within the current instance document when encoded as RDF. + notes: + - If you are authoring schemas in LinkML YAML, the type is referenced with the + lower case "sparqlpath". + from_schema: metadata + base: str + uri: xsd:string + repr: str + StringFormattedString: + name: StringFormattedString + description: A formatted string (variable) that represents a string. + from_schema: metadata + base: string + pattern: ^[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + FloatFormattedString: + name: FloatFormattedString + description: A formatted string that represents a floating point number. + from_schema: metadata + base: string + pattern: ^float[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + IntegerFormattedString: + name: IntegerFormattedString + description: A formatted string that represents an integer. + from_schema: metadata + base: string + pattern: ^int[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + VersionString: + name: VersionString + description: A version number (only major, minor versions) + from_schema: metadata + base: float + minimum_value: 0 + URLorS3URI: + name: URLorS3URI + description: A URL or S3 URI + from_schema: metadata + base: string + pattern: ^(((https?|s3)://)|cryoetportal-rawdatasets-dev).*$ + ORCID: + name: ORCID + description: A unique, persistent identifier for researchers, provided by ORCID. + from_schema: metadata + base: string + pattern: '[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$' + BTO_ID: + name: BTO_ID + description: A BRENDA Tissue Ontology identifier + from_schema: metadata + base: string + pattern: ^BTO:[0-9]{7}$ + CL_ID: + name: CL_ID + description: A Cell Ontology identifier + from_schema: metadata + base: string + pattern: ^CL:[0-9]{7}$ + GO_ID: + name: GO_ID + description: A Gene Ontology identifier + from_schema: metadata + base: string + pattern: ^GO:[0-9]{7}$ + WORMBASE_ID: + name: WORMBASE_ID + description: A WormBase identifier + from_schema: metadata + base: string + pattern: WBStrain[0-9]{8}$ + ONTOLOGY_ID: + name: ONTOLOGY_ID + description: An ontology identifier + from_schema: metadata + base: string + pattern: ^[a-zA-Z]+:[0-9]+$ + DOI: + name: DOI + description: A Digital Object Identifier + from_schema: metadata + base: string + pattern: ^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+$ + DOI_LIST: + name: DOI_LIST + description: A list of Digital Object Identifiers + from_schema: metadata + base: string + pattern: ^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+(\s*,\s*(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+)*$ + EMPIAR_ID: + name: EMPIAR_ID + description: An Electron Microscopy Public Image Archive identifier + from_schema: metadata + base: string + pattern: ^EMPIAR-[0-9]+$ + EMDB_ID: + name: EMDB_ID + description: An Electron Microscopy Data Bank identifier + from_schema: metadata + base: string + pattern: ^EMD-[0-9]{4,5}$ + PDB_ID: + name: PDB_ID + description: A Protein Data Bank identifier + from_schema: metadata + base: string + pattern: ^pdb[0-9a-zA-Z]{4,8}$ + EMPIAR_EMDB_PDB_LIST: + name: EMPIAR_EMDB_PDB_LIST + description: A list of EMPIAR, EMDB, and PDB identifiers + from_schema: metadata + base: string + pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$ + EMPIAR_EMDB_DOI_PDB_LIST: + name: EMPIAR_EMDB_DOI_PDB_LIST + description: A list of EMPIAR, EMDB, DOI, and PDB identifiers + from_schema: metadata + base: string + pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$ +enums: + annotation_file_source_enum: + name: annotation_file_source_enum + description: How the annotation file was acquired + from_schema: metadata + permissible_values: + dataset_author: + text: dataset_author + description: Annotation submitted by dataset author + community: + text: community + description: Annotation submitted by community member + portal_standard: + text: portal_standard + description: Annotation submitted by portal standardization + annotation_method_type_enum: + name: annotation_method_type_enum + description: Describes how the annotations were generated. + from_schema: metadata + permissible_values: + manual: + text: manual + description: Annotations were generated manually. + automated: + text: automated + description: Annotations were generated automatically. + hybrid: + text: hybrid + description: Annotations were generated semi-automatically. + annotation_file_shape_type_enum: + name: annotation_file_shape_type_enum + description: Describes the shape of the annotation + from_schema: metadata + permissible_values: + SegmentationMask: + text: SegmentationMask + description: A binary mask volume + OrientedPoint: + text: OrientedPoint + description: A series of coordinates and an orientation + Point: + text: Point + description: A series of coordinates + InstanceSegmentation: + text: InstanceSegmentation + description: A volume with labels for multiple instances + annotation_method_link_type_enum: + name: annotation_method_link_type_enum + description: Describes the type of link associated to the annotation method. + from_schema: metadata + permissible_values: + documentation: + text: documentation + description: Links to the documentation related to the method. + models_weights: + text: models_weights + description: Links to the weights that the models used for generating annotations + were trained with. + other: + text: other + description: Link to resources that does not fit in the other categories. + source_code: + text: source_code + description: Links to the source code of the method. + website: + text: website + description: Links to a website of the method or tool used to generate the + annotation. + deposition_types_enum: + name: deposition_types_enum + description: Types of data a deposition has + from_schema: metadata + permissible_values: + annotation: + text: annotation + description: The deposition comprises of new annotations for existing datasets + dataset: + text: dataset + description: The deposition comprises of new dataset(s). + tomogram: + text: tomogram + description: The deposition comprises of new tomograms for existing datasets + sample_type_enum: + name: sample_type_enum + description: Type of sample imaged in a CryoET study. + from_schema: metadata + permissible_values: + cell: + text: cell + description: Tomographic data of whole cells or cell sections. + tissue: + text: tissue + description: Tomographic data of tissue sections. + organism: + text: organism + description: Tomographic data of sections through multicellular organisms. + organelle: + text: organelle + description: Tomographic data of purified organelles. + virus: + text: virus + description: Tomographic data of purified viruses or VLPs. + in_vitro: + text: in_vitro + description: Tomographic data of in vitro reconstituted systems or mixtures + of proteins. + in_silico: + text: in_silico + description: Simulated tomographic data. + other: + text: other + description: Other type of sample. + tiltseries_camera_acquire_mode_enum: + name: tiltseries_camera_acquire_mode_enum + description: Camera acquisition mode + from_schema: metadata + permissible_values: + counting: + text: counting + description: Counting mode + superresolution: + text: superresolution + description: Super-resolution mode + linear: + text: linear + description: Linear mode + cds: + text: cds + description: Correlated double sampling mode + tiltseries_microscope_manufacturer_enum: + name: tiltseries_microscope_manufacturer_enum + description: Microscope manufacturer + from_schema: metadata + permissible_values: + FEI: + text: FEI + description: FEI Company + TFS: + text: TFS + description: Thermo Fisher Scientific + JEOL: + text: JEOL + description: JEOL Ltd. + fiducial_alignment_status_enum: + name: fiducial_alignment_status_enum + description: Fiducial Alignment method + from_schema: metadata + permissible_values: + FIDUCIAL: + text: FIDUCIAL + description: Alignment computed based on fiducial markers + NON_FIDUCIAL: + text: NON_FIDUCIAL + description: Alignment computed without fiducial markers + tomogram_processing_enum: + name: tomogram_processing_enum + description: Tomogram processing method + from_schema: metadata + permissible_values: + denoised: + text: denoised + description: Tomogram was denoised + filtered: + text: filtered + description: Tomogram was filtered + raw: + text: raw + description: Tomogram was not processed + tomogram_reconstruction_method_enum: + name: tomogram_reconstruction_method_enum + description: Tomogram reconstruction method + from_schema: metadata + permissible_values: + SART: + text: SART + description: Simultaneous Algebraic Reconstruction Technique + Fourier Space: + text: Fourier Space + description: Fourier space reconstruction + SIRT: + text: SIRT + description: Simultaneous Iterative Reconstruction Technique + WBP: + text: WBP + description: Weighted Back-Projection + Unknown: + text: Unknown + description: Unknown reconstruction method + tomogram_type_enum: + name: tomogram_type_enum + description: Tomogram type + from_schema: metadata + permissible_values: + CANONICAL: + text: CANONICAL + description: Canonical tomogram (basis geometry for all annotations) + UNKNOWN: + text: UNKNOWN + description: Tomogram's was not submitted by the dataset author + alignment_type_enum: + name: alignment_type_enum + description: Type of alignment + from_schema: metadata + permissible_values: + LOCAL: + text: LOCAL + description: per-section non-rigid alignment available + GLOBAL: + text: GLOBAL + description: only per-section rigid alignment available +classes: + PicturePath: + name: PicturePath + description: A set of paths to representative images of a piece of data. + from_schema: metadata + attributes: + snapshot: + name: snapshot + description: Path to the dataset preview image relative to the dataset directory + root. + from_schema: metadata + exact_mappings: + - cdp-common:snapshot + alias: snapshot + owner: PicturePath + domain_of: + - PicturePath + range: URLorS3URI + recommended: true + inlined: true + inlined_as_list: true + pattern: ^(((https?|s3)://)|cryoetportal-rawdatasets-dev).*$ + thumbnail: + name: thumbnail + description: Path to the thumbnail of preview image relative to the dataset + directory root. + from_schema: metadata + exact_mappings: + - cdp-common:thumbnail + alias: thumbnail + owner: PicturePath + domain_of: + - PicturePath + range: URLorS3URI + recommended: true + inlined: true + inlined_as_list: true + pattern: ^(((https?|s3)://)|cryoetportal-rawdatasets-dev).*$ + Author: + name: Author + description: Author of a scientific data entity. + from_schema: metadata + mixins: + - AuthorMixin + attributes: + ORCID: + name: ORCID + description: The ORCID identifier for the author. + from_schema: metadata + exact_mappings: + - cdp-common:author_orcid + alias: ORCID + owner: Author + domain_of: + - Author + range: ORCID + recommended: true + inlined: true + inlined_as_list: true + pattern: '[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$' + name: + name: name + description: The full name of the author. + from_schema: metadata + exact_mappings: + - cdp-common:author_name + alias: name + owner: Author + domain_of: + - AuthorMixin + - OrganismDetails + - TissueDetails + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + required: true + inlined: true + inlined_as_list: true + email: + name: email + description: The email address of the author. + from_schema: metadata + exact_mappings: + - cdp-common:author_email + alias: email + owner: Author + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_name: + name: affiliation_name + description: The name of the author's affiliation. + from_schema: metadata + exact_mappings: + - cdp-common:author_affiliation_name + alias: affiliation_name + owner: Author + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_address: + name: affiliation_address + description: The address of the author's affiliation. + from_schema: metadata + exact_mappings: + - cdp-common:author_affiliation_address + alias: affiliation_address + owner: Author + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_identifier: + name: affiliation_identifier + description: A Research Organization Registry (ROR) identifier. + from_schema: metadata + exact_mappings: + - cdp-common:author_affiliation_identifier + alias: affiliation_identifier + owner: Author + domain_of: + - AuthorMixin + range: string + recommended: true + inlined: true + inlined_as_list: true + corresponding_author_status: + name: corresponding_author_status + description: Whether the author is a corresponding author. + from_schema: metadata + exact_mappings: + - cdp-common:author_corresponding_author_status + ifabsent: 'False' + alias: corresponding_author_status + owner: Author + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + primary_author_status: + name: primary_author_status + description: Whether the author is a primary author. + from_schema: metadata + exact_mappings: + - cdp-common:author_primary_author_status + ifabsent: 'False' + alias: primary_author_status + owner: Author + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + FundingDetails: + name: FundingDetails + description: A funding source for a scientific data entity (base for JSON and + DB representation). + from_schema: metadata + attributes: + funding_agency_name: + name: funding_agency_name + description: The name of the funding source. + from_schema: metadata + exact_mappings: + - cdp-common:funding_agency_name + alias: funding_agency_name + owner: FundingDetails + domain_of: + - FundingDetails + range: string + recommended: true + inlined: true + inlined_as_list: true + grant_id: + name: grant_id + description: Grant identifier provided by the funding agency + from_schema: metadata + exact_mappings: + - cdp-common:funding_grant_id + alias: grant_id + owner: FundingDetails + domain_of: + - FundingDetails + range: string + recommended: true + inlined: true + inlined_as_list: true + DateStamp: + name: DateStamp + description: A set of dates at which a data item was deposited, published and + last modified. + from_schema: metadata + mixins: + - DateStampedEntityMixin + attributes: + deposition_date: + name: deposition_date + description: The date a data item was received by the cryoET data portal. + from_schema: metadata + exact_mappings: + - cdp-common:deposition_date + alias: deposition_date + owner: DateStamp + domain_of: + - DateStampedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + release_date: + name: release_date + description: The date a data item was received by the cryoET data portal. + from_schema: metadata + exact_mappings: + - cdp-common:release_date + alias: release_date + owner: DateStamp + domain_of: + - DateStampedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + last_modified_date: + name: last_modified_date + description: The date a piece of data was last modified on the cryoET data + portal. + from_schema: metadata + exact_mappings: + - cdp-common:last_modified_date + alias: last_modified_date + owner: DateStamp + domain_of: + - DateStampedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + DateStampedEntity: + name: DateStampedEntity + description: An entity with associated deposition, release and last modified dates. + from_schema: metadata + attributes: + dates: + name: dates + description: A set of dates at which a data item was deposited, published + and last modified. + from_schema: metadata + alias: dates + owner: DateStampedEntity + domain_of: + - DateStampedEntity + range: DateStamp + required: true + inlined: true + inlined_as_list: true + AuthoredEntity: + name: AuthoredEntity + description: An entity with associated authors. + from_schema: metadata + attributes: + authors: + name: authors + description: Author of a scientific data entity. + from_schema: metadata + list_elements_ordered: true + alias: authors + owner: AuthoredEntity + domain_of: + - AuthoredEntity + range: Author + required: true + multivalued: true + inlined: true + inlined_as_list: true + minimum_cardinality: 1 + FundedEntity: + name: FundedEntity + description: An entity with associated funding sources. + from_schema: metadata + attributes: + funding: + name: funding + description: A funding source for a scientific data entity (base for JSON + and DB representation). + from_schema: metadata + list_elements_ordered: true + alias: funding + owner: FundedEntity + domain_of: + - FundedEntity + range: FundingDetails + recommended: true + multivalued: true + inlined: true + inlined_as_list: true + CrossReferences: + name: CrossReferences + description: A set of cross-references to other databases and publications. + from_schema: metadata + mixins: + - CrossReferencesMixin + attributes: + publications: + name: publications + description: Comma-separated list of DOIs for publications associated with + the dataset. + from_schema: metadata + alias: publications + owner: CrossReferences + domain_of: + - CrossReferencesMixin + range: DOI_LIST + recommended: true + inlined: true + inlined_as_list: true + pattern: (^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+(\s*,\s*(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+)*$)|(^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+(\s*,\s*(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+)*$) + related_database_entries: + name: related_database_entries + description: Comma-separated list of related database entries for the dataset. + from_schema: metadata + alias: related_database_entries + owner: CrossReferences + domain_of: + - CrossReferencesMixin + range: EMPIAR_EMDB_PDB_LIST + recommended: true + inlined: true + inlined_as_list: true + pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$) + related_database_links: + name: related_database_links + description: Comma-separated list of related database links for the dataset. + from_schema: metadata + alias: related_database_links + owner: CrossReferences + domain_of: + - CrossReferencesMixin + range: string + inlined: true + inlined_as_list: true + dataset_citations: + name: dataset_citations + description: Comma-separated list of DOIs for publications citing the dataset. + from_schema: metadata + alias: dataset_citations + owner: CrossReferences + domain_of: + - CrossReferencesMixin + range: string + inlined: true + inlined_as_list: true + CrossReferencedEntity: + name: CrossReferencedEntity + description: An entity with associated cross-references to other databases and + publications. + from_schema: metadata + mixin: true + attributes: + cross_references: + name: cross_references + description: A set of cross-references to other databases and publications. + from_schema: metadata + alias: cross_references + owner: CrossReferencedEntity + domain_of: + - CrossReferencedEntity + range: CrossReferences + inlined: true + inlined_as_list: true + PicturedEntity: + name: PicturedEntity + description: An entity with associated preview images. + from_schema: metadata + attributes: + key_photos: + name: key_photos + description: A set of paths to representative images of a piece of data. + from_schema: metadata + alias: key_photos + owner: PicturedEntity + domain_of: + - PicturedEntity + range: PicturePath + required: true + inlined: true + inlined_as_list: true + OrganismDetails: + name: OrganismDetails + description: The species from which the sample was derived. + from_schema: metadata + attributes: + name: + name: name + description: Name of the organism from which a biological sample used in a + CryoET study is derived from, e.g. homo sapiens. + from_schema: metadata + exact_mappings: + - cdp-common:organism_name + alias: name + owner: OrganismDetails + domain_of: + - OrganismDetails + - TissueDetails + - CellType + - CellStrain + - CellComponent + - AnnotationObject + - AuthorMixin + range: string + required: true + inlined: true + inlined_as_list: true + taxonomy_id: + name: taxonomy_id + description: NCBI taxonomy identifier for the organism, e.g. 9606 + from_schema: metadata + exact_mappings: + - cdp-common:organism_taxid + alias: taxonomy_id + owner: OrganismDetails + domain_of: + - OrganismDetails + range: integer + recommended: true + inlined: true + inlined_as_list: true + minimum_value: 1 + TissueDetails: + name: TissueDetails + description: The type of tissue from which the sample was derived. + from_schema: metadata + attributes: + name: + name: name + description: Name of the tissue from which a biological sample used in a CryoET + study is derived from. + from_schema: metadata + exact_mappings: + - cdp-common:tissue_name + alias: name + owner: TissueDetails + domain_of: + - OrganismDetails + - TissueDetails + - CellType + - CellStrain + - CellComponent + - AnnotationObject + - AuthorMixin + range: string + required: true + inlined: true + inlined_as_list: true + id: + name: id + description: The UBERON identifier for the tissue. + from_schema: metadata + exact_mappings: + - cdp-common:tissue_id + alias: id + owner: TissueDetails + domain_of: + - TissueDetails + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: BTO_ID + recommended: true + inlined: true + inlined_as_list: true + pattern: ^BTO:[0-9]{7}$ + CellType: + name: CellType + description: The cell type from which the sample was derived. + from_schema: metadata + attributes: + name: + name: name + description: Name of the cell type from which a biological sample used in + a CryoET study is derived from. + from_schema: metadata + exact_mappings: + - cdp-common:cell_name + alias: name + owner: CellType + domain_of: + - OrganismDetails + - TissueDetails + - CellType + - CellStrain + - CellComponent + - AnnotationObject + - AuthorMixin + range: string + required: true + inlined: true + inlined_as_list: true + id: + name: id + description: Cell Ontology identifier for the cell type + from_schema: metadata + exact_mappings: + - cdp-common:cell_type_id + alias: id + owner: CellType + domain_of: + - TissueDetails + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: CL_ID + recommended: true + inlined: true + inlined_as_list: true + pattern: ^CL:[0-9]{7}$ + CellStrain: + name: CellStrain + description: The strain or cell line from which the sample was derived. + from_schema: metadata + attributes: + name: + name: name + description: Cell line or strain for the sample. + from_schema: metadata + exact_mappings: + - cdp-common:cell_strain_name + alias: name + owner: CellStrain + domain_of: + - OrganismDetails + - TissueDetails + - CellType + - CellStrain + - CellComponent + - AnnotationObject + - AuthorMixin + range: string + required: true + inlined: true + inlined_as_list: true + id: + name: id + description: A placeholder for any type of data. + from_schema: metadata + exact_mappings: + - cdp-common:cell_strain_id + alias: id + owner: CellStrain + domain_of: + - TissueDetails + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: Any + recommended: true + inlined: true + inlined_as_list: true + pattern: (WBStrain[0-9]{8}$)|(^[a-zA-Z]+:[0-9]+$) + any_of: + - range: WORMBASE_ID + - range: ONTOLOGY_ID + CellComponent: + name: CellComponent + description: The cellular component from which the sample was derived. + from_schema: metadata + attributes: + name: + name: name + description: Name of the cellular component. + from_schema: metadata + exact_mappings: + - cdp-common:cell_component_name + alias: name + owner: CellComponent + domain_of: + - OrganismDetails + - TissueDetails + - CellType + - CellStrain + - CellComponent + - AnnotationObject + - AuthorMixin + range: string + required: true + inlined: true + inlined_as_list: true + id: + name: id + description: The GO identifier for the cellular component. + from_schema: metadata + exact_mappings: + - cdp-common:cell_component_id + alias: id + owner: CellComponent + domain_of: + - TissueDetails + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: GO_ID + recommended: true + inlined: true + inlined_as_list: true + pattern: ^GO:[0-9]{7}$ + ExperimentMetadata: + name: ExperimentMetadata + description: Metadata describing sample and sample preparation methods used in + a cryoET dataset. + from_schema: metadata + attributes: + sample_type: + name: sample_type + description: Type of sample imaged in a CryoET study. + from_schema: metadata + exact_mappings: + - cdp-common:preparation_sample_type + alias: sample_type + owner: ExperimentMetadata + domain_of: + - ExperimentMetadata + range: sample_type_enum + required: true + inlined: true + inlined_as_list: true + pattern: (^cell$)|(^tissue$)|(^organism$)|(^organelle$)|(^virus$)|(^in_vitro$)|(^in_silico$)|(^other$) + sample_preparation: + name: sample_preparation + description: Describes how the sample was prepared. + from_schema: metadata + exact_mappings: + - cdp-common:sample_preparation + alias: sample_preparation + owner: ExperimentMetadata + domain_of: + - ExperimentMetadata + range: string + recommended: true + inlined: true + inlined_as_list: true + grid_preparation: + name: grid_preparation + description: Describes Cryo-ET grid preparation. + from_schema: metadata + exact_mappings: + - cdp-common:grid_preparation + alias: grid_preparation + owner: ExperimentMetadata + domain_of: + - ExperimentMetadata + range: string + recommended: true + inlined: true + inlined_as_list: true + other_setup: + name: other_setup + description: Describes other setup not covered by sample preparation or grid + preparation that may make this dataset unique in the same publication. + from_schema: metadata + exact_mappings: + - cdp-common:preparation_other_setup + alias: other_setup + owner: ExperimentMetadata + domain_of: + - ExperimentMetadata + range: string + recommended: true + inlined: true + inlined_as_list: true + organism: + name: organism + description: The species from which the sample was derived. + from_schema: metadata + alias: organism + owner: ExperimentMetadata + domain_of: + - ExperimentMetadata + range: OrganismDetails + inlined: true + inlined_as_list: true + tissue: + name: tissue + description: The type of tissue from which the sample was derived. + from_schema: metadata + alias: tissue + owner: ExperimentMetadata + domain_of: + - ExperimentMetadata + range: TissueDetails + inlined: true + inlined_as_list: true + cell_type: + name: cell_type + description: The cell type from which the sample was derived. + from_schema: metadata + alias: cell_type + owner: ExperimentMetadata + domain_of: + - ExperimentMetadata + range: CellType + inlined: true + inlined_as_list: true + cell_strain: + name: cell_strain + description: The strain or cell line from which the sample was derived. + from_schema: metadata + alias: cell_strain + owner: ExperimentMetadata + domain_of: + - ExperimentMetadata + range: CellStrain + inlined: true + inlined_as_list: true + cell_component: + name: cell_component + description: The cellular component from which the sample was derived. + from_schema: metadata + alias: cell_component + owner: ExperimentMetadata + domain_of: + - ExperimentMetadata + range: CellComponent + inlined: true + inlined_as_list: true + Dataset: + name: Dataset + description: High-level description of a cryoET dataset. + from_schema: metadata + mixins: + - DateStampedEntity + - AuthoredEntity + - FundedEntity + - CrossReferencedEntity + - ExperimentMetadata + attributes: + dataset_identifier: + name: dataset_identifier + description: An identifier for a CryoET dataset, assigned by the Data Portal. + Used to identify the dataset as the directory name in data tree. + from_schema: metadata + exact_mappings: + - cdp-common:dataset_identifier + alias: dataset_identifier + owner: Dataset + domain_of: + - Dataset + range: integer + required: true + inlined: true + inlined_as_list: true + dataset_title: + name: dataset_title + description: Title of a CryoET dataset. + from_schema: metadata + exact_mappings: + - cdp-common:dataset_title + alias: dataset_title + owner: Dataset + domain_of: + - Dataset + range: string + required: true + inlined: true + inlined_as_list: true + dataset_description: + name: dataset_description + description: A short description of a CryoET dataset, similar to an abstract + for a journal article or dataset. + from_schema: metadata + exact_mappings: + - cdp-common:dataset_description + alias: dataset_description + owner: Dataset + domain_of: + - Dataset + range: string + required: true + inlined: true + inlined_as_list: true + dates: + name: dates + description: A set of dates at which a data item was deposited, published + and last modified. + from_schema: metadata + alias: dates + owner: Dataset + domain_of: + - DateStampedEntity + range: DateStamp + required: true + inlined: true + inlined_as_list: true + authors: + name: authors + description: Author of a scientific data entity. + from_schema: metadata + list_elements_ordered: true + alias: authors + owner: Dataset + domain_of: + - AuthoredEntity + range: Author + required: true + multivalued: true + inlined: true + inlined_as_list: true + minimum_cardinality: 1 + funding: + name: funding + description: A funding source for a scientific data entity (base for JSON + and DB representation). + from_schema: metadata + list_elements_ordered: true + alias: funding + owner: Dataset + domain_of: + - FundedEntity + range: FundingDetails + recommended: true + multivalued: true + inlined: true + inlined_as_list: true + cross_references: + name: cross_references + description: A set of cross-references to other databases and publications. + from_schema: metadata + alias: cross_references + owner: Dataset + domain_of: + - CrossReferencedEntity + range: CrossReferences + inlined: true + inlined_as_list: true + sample_type: + name: sample_type + description: Type of sample imaged in a CryoET study. + from_schema: metadata + exact_mappings: + - cdp-common:preparation_sample_type + alias: sample_type + owner: Dataset + domain_of: + - ExperimentMetadata + range: sample_type_enum + required: true + inlined: true + inlined_as_list: true + pattern: (^cell$)|(^tissue$)|(^organism$)|(^organelle$)|(^virus$)|(^in_vitro$)|(^in_silico$)|(^other$) + sample_preparation: + name: sample_preparation + description: Describes how the sample was prepared. + from_schema: metadata + exact_mappings: + - cdp-common:sample_preparation + alias: sample_preparation + owner: Dataset + domain_of: + - ExperimentMetadata + range: string + recommended: true + inlined: true + inlined_as_list: true + grid_preparation: + name: grid_preparation + description: Describes Cryo-ET grid preparation. + from_schema: metadata + exact_mappings: + - cdp-common:grid_preparation + alias: grid_preparation + owner: Dataset + domain_of: + - ExperimentMetadata + range: string + recommended: true + inlined: true + inlined_as_list: true + other_setup: + name: other_setup + description: Describes other setup not covered by sample preparation or grid + preparation that may make this dataset unique in the same publication. + from_schema: metadata + exact_mappings: + - cdp-common:preparation_other_setup + alias: other_setup + owner: Dataset + domain_of: + - ExperimentMetadata + range: string + recommended: true + inlined: true + inlined_as_list: true + organism: + name: organism + description: The species from which the sample was derived. + from_schema: metadata + alias: organism + owner: Dataset + domain_of: + - ExperimentMetadata + range: OrganismDetails + inlined: true + inlined_as_list: true + tissue: + name: tissue + description: The type of tissue from which the sample was derived. + from_schema: metadata + alias: tissue + owner: Dataset + domain_of: + - ExperimentMetadata + range: TissueDetails + inlined: true + inlined_as_list: true + cell_type: + name: cell_type + description: The cell type from which the sample was derived. + from_schema: metadata + alias: cell_type + owner: Dataset + domain_of: + - ExperimentMetadata + range: CellType + inlined: true + inlined_as_list: true + cell_strain: + name: cell_strain + description: The strain or cell line from which the sample was derived. + from_schema: metadata + alias: cell_strain + owner: Dataset + domain_of: + - ExperimentMetadata + range: CellStrain + inlined: true + inlined_as_list: true + cell_component: + name: cell_component + description: The cellular component from which the sample was derived. + from_schema: metadata + alias: cell_component + owner: Dataset + domain_of: + - ExperimentMetadata + range: CellComponent + inlined: true + inlined_as_list: true + Deposition: + name: Deposition + description: Metadata describing a deposition. + from_schema: metadata + mixins: + - DateStampedEntity + - AuthoredEntity + - CrossReferencedEntity + attributes: + deposition_description: + name: deposition_description + description: A short description of the deposition, similar to an abstract + for a journal article or dataset. + from_schema: metadata + exact_mappings: + - cdp-common:deposition_description + alias: deposition_description + owner: Deposition + domain_of: + - Deposition + range: string + required: true + inlined: true + inlined_as_list: true + deposition_identifier: + name: deposition_identifier + description: An identifier for a CryoET deposition, assigned by the Data Portal. + Used to identify the deposition the entity is a part of. + from_schema: metadata + exact_mappings: + - cdp-common:deposition_identifier + alias: deposition_identifier + owner: Deposition + domain_of: + - Deposition + range: integer + required: true + inlined: true + inlined_as_list: true + deposition_title: + name: deposition_title + description: Title of a CryoET deposition. + from_schema: metadata + exact_mappings: + - cdp-common:deposition_title + alias: deposition_title + owner: Deposition + domain_of: + - Deposition + range: string + required: true + inlined: true + inlined_as_list: true + deposition_types: + name: deposition_types + description: Type of data in the deposition (e.g. dataset, annotation, tomogram) + from_schema: metadata + exact_mappings: + - cdp-common:deposition_types + alias: deposition_types + owner: Deposition + domain_of: + - Deposition + range: deposition_types_enum + required: true + multivalued: true + inlined: true + inlined_as_list: true + pattern: (^annotation$)|(^dataset$)|(^tomogram$) + minimum_cardinality: 1 + dates: + name: dates + description: A set of dates at which a data item was deposited, published + and last modified. + from_schema: metadata + alias: dates + owner: Deposition + domain_of: + - DateStampedEntity + range: DateStamp + required: true + inlined: true + inlined_as_list: true + authors: + name: authors + description: Author of a scientific data entity. + from_schema: metadata + list_elements_ordered: true + alias: authors + owner: Deposition + domain_of: + - AuthoredEntity + range: Author + required: true + multivalued: true + inlined: true + inlined_as_list: true + minimum_cardinality: 1 + cross_references: + name: cross_references + description: A set of cross-references to other databases and publications. + from_schema: metadata + alias: cross_references + owner: Deposition + domain_of: + - CrossReferencedEntity + range: CrossReferences + inlined: true + inlined_as_list: true + CameraDetails: + name: CameraDetails + description: The camera used to collect the tilt series. + from_schema: metadata + attributes: + acquire_mode: + name: acquire_mode + description: A placeholder for any type of data. + from_schema: metadata + exact_mappings: + - cdp-common:tiltseries_camera_acquire_mode + alias: acquire_mode + owner: CameraDetails + domain_of: + - CameraDetails + range: Any + inlined: true + inlined_as_list: true + pattern: (^[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$)|((^counting$)|(^superresolution$)|(^linear$)|(^cds$)) + any_of: + - range: StringFormattedString + - range: tiltseries_camera_acquire_mode_enum + manufacturer: + name: manufacturer + description: Name of the camera manufacturer + from_schema: metadata + exact_mappings: + - cdp-common:tiltseries_camera_manufacturer + alias: manufacturer + owner: CameraDetails + domain_of: + - CameraDetails + - MicroscopeDetails + range: string + required: true + inlined: true + inlined_as_list: true + model: + name: model + description: Camera model name + from_schema: metadata + exact_mappings: + - cdp-common:tiltseries_camera_model + alias: model + owner: CameraDetails + domain_of: + - CameraDetails + - MicroscopeDetails + range: string + required: true + inlined: true + inlined_as_list: true + MicroscopeDetails: + name: MicroscopeDetails + description: The microscope used to collect the tilt series. + from_schema: metadata + attributes: + additional_info: + name: additional_info + description: Other microscope optical setup information, in addition to energy + filter, phase plate and image corrector + from_schema: metadata + exact_mappings: + - cdp-common:tiltseries_microscope_additional_info + alias: additional_info + owner: MicroscopeDetails + domain_of: + - MicroscopeDetails + range: string + inlined: true + inlined_as_list: true + manufacturer: + name: manufacturer + description: A placeholder for any type of data. + from_schema: metadata + alias: manufacturer + owner: MicroscopeDetails + domain_of: + - CameraDetails + - MicroscopeDetails + range: Any + inlined: true + inlined_as_list: true + pattern: ^[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + any_of: + - range: tiltseries_microscope_manufacturer + - range: StringFormattedString + model: + name: model + description: Microscope model name + from_schema: metadata + exact_mappings: + - cdp-common:tiltseries_microscope_model + alias: model + owner: MicroscopeDetails + domain_of: + - CameraDetails + - MicroscopeDetails + range: string + required: true + inlined: true + inlined_as_list: true + MicroscopeOpticalSetup: + name: MicroscopeOpticalSetup + description: The optical setup of the microscope used to collect the tilt series. + from_schema: metadata + attributes: + energy_filter: + name: energy_filter + description: Energy filter setup used + from_schema: metadata + exact_mappings: + - cdp-common:tiltseries_microscope_energy_filter + alias: energy_filter + owner: MicroscopeOpticalSetup + domain_of: + - MicroscopeOpticalSetup + range: string + required: true + inlined: true + inlined_as_list: true + phase_plate: + name: phase_plate + description: Phase plate configuration + from_schema: metadata + exact_mappings: + - cdp-common:tiltseries_microscope_phase_plate + alias: phase_plate + owner: MicroscopeOpticalSetup + domain_of: + - MicroscopeOpticalSetup + range: string + inlined: true + inlined_as_list: true + image_corrector: + name: image_corrector + description: Image corrector setup + from_schema: metadata + exact_mappings: + - cdp-common:tiltseries_microscope_image_corrector + alias: image_corrector + owner: MicroscopeOpticalSetup + domain_of: + - MicroscopeOpticalSetup + range: string + inlined: true + inlined_as_list: true + TiltRange: + name: TiltRange + description: The range of tilt angles in the tilt series. + from_schema: metadata + attributes: + min: + name: min + description: A placeholder for any type of data. + from_schema: metadata + alias: min + owner: TiltRange + domain_of: + - TiltRange + range: Any + inlined: true + inlined_as_list: true + pattern: ^float[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + any_of: + - range: tiltseries_tilt_min + - range: FloatFormattedString + max: + name: max + description: A placeholder for any type of data. + from_schema: metadata + alias: max + owner: TiltRange + domain_of: + - TiltRange + range: Any + inlined: true + inlined_as_list: true + pattern: ^float[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + any_of: + - range: tiltseries_tilt_max + - range: FloatFormattedString + TiltSeries: + name: TiltSeries + description: Metadata describing a tilt series. + from_schema: metadata + attributes: + acceleration_voltage: + name: acceleration_voltage + description: Electron Microscope Accelerator voltage in volts + from_schema: metadata + exact_mappings: + - cdp-common:tiltseries_acceleration_voltage + alias: acceleration_voltage + owner: TiltSeries + domain_of: + - TiltSeries + range: float + required: true + inlined: true + inlined_as_list: true + minimum_value: 20000 + unit: + symbol: V + descriptive_name: volts + aligned_tiltseries_binning: + name: aligned_tiltseries_binning + description: A placeholder for any type of data. + from_schema: metadata + ifabsent: float(1) + alias: aligned_tiltseries_binning + owner: TiltSeries + domain_of: + - TiltSeries + range: Any + inlined: true + inlined_as_list: true + pattern: ^float[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + any_of: + - range: tiltseries_aligned_tiltseries_binning + - range: FloatFormattedString + binning_from_frames: + name: binning_from_frames + description: A placeholder for any type of data. + from_schema: metadata + ifabsent: float(1) + alias: binning_from_frames + owner: TiltSeries + domain_of: + - TiltSeries + range: Any + inlined: true + inlined_as_list: true + pattern: ^float[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + any_of: + - range: tiltseries_binning_from_frames + - range: FloatFormattedString + camera: + name: camera + description: The camera used to collect the tilt series. + from_schema: metadata + alias: camera + owner: TiltSeries + domain_of: + - TiltSeries + range: CameraDetails + required: true + inlined: true + inlined_as_list: true + data_acquisition_software: + name: data_acquisition_software + description: Software used to collect data + from_schema: metadata + exact_mappings: + - cdp-common:tiltseries_data_acquisition_software + alias: data_acquisition_software + owner: TiltSeries + domain_of: + - TiltSeries + range: string + required: true + inlined: true + inlined_as_list: true + frames_count: + name: frames_count + description: Number of frames associated with this tiltseries + from_schema: metadata + exact_mappings: + - cdp-common:tiltseries_frames_count + alias: frames_count + owner: TiltSeries + domain_of: + - TiltSeries + range: integer + inlined: true + inlined_as_list: true + is_aligned: + name: is_aligned + description: Whether this tilt series is aligned + from_schema: metadata + exact_mappings: + - cdp-common:tiltseries_is_aligned + alias: is_aligned + owner: TiltSeries + domain_of: + - TiltSeries + range: boolean + required: true + inlined: true + inlined_as_list: true + microscope: + name: microscope + description: The microscope used to collect the tilt series. + from_schema: metadata + alias: microscope + owner: TiltSeries + domain_of: + - TiltSeries + range: MicroscopeDetails + required: true + inlined: true + inlined_as_list: true + microscope_optical_setup: + name: microscope_optical_setup + description: The optical setup of the microscope used to collect the tilt + series. + from_schema: metadata + alias: microscope_optical_setup + owner: TiltSeries + domain_of: + - TiltSeries + range: MicroscopeOpticalSetup + required: true + inlined: true + inlined_as_list: true + related_empiar_entry: + name: related_empiar_entry + description: If a tilt series is deposited into EMPIAR, enter the EMPIAR dataset + identifier + from_schema: metadata + exact_mappings: + - cdp-common:tiltseries_related_empiar_entry + alias: related_empiar_entry + owner: TiltSeries + domain_of: + - TiltSeries + range: EMPIAR_ID + inlined: true + inlined_as_list: true + pattern: ^EMPIAR-[0-9]+$ + spherical_aberration_constant: + name: spherical_aberration_constant + description: A placeholder for any type of data. + from_schema: metadata + alias: spherical_aberration_constant + owner: TiltSeries + domain_of: + - TiltSeries + range: Any + inlined: true + inlined_as_list: true + pattern: ^float[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + any_of: + - range: tiltseries_spherical_aberration_constant + - range: FloatFormattedString + tilt_alignment_software: + name: tilt_alignment_software + description: Software used for tilt alignment + from_schema: metadata + exact_mappings: + - cdp-common:tiltseries_tilt_alignment_software + alias: tilt_alignment_software + owner: TiltSeries + domain_of: + - TiltSeries + range: string + inlined: true + inlined_as_list: true + tilt_axis: + name: tilt_axis + description: A placeholder for any type of data. + from_schema: metadata + alias: tilt_axis + owner: TiltSeries + domain_of: + - TiltSeries + range: Any + inlined: true + inlined_as_list: true + pattern: ^float[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + any_of: + - range: tiltseries_tilt_axis + - range: FloatFormattedString + tilt_range: + name: tilt_range + description: The range of tilt angles in the tilt series. + from_schema: metadata + alias: tilt_range + owner: TiltSeries + domain_of: + - TiltSeries + range: TiltRange + required: true + inlined: true + inlined_as_list: true + tilt_series_quality: + name: tilt_series_quality + description: A placeholder for any type of data. + from_schema: metadata + alias: tilt_series_quality + owner: TiltSeries + domain_of: + - TiltSeries + range: Any + inlined: true + inlined_as_list: true + pattern: ^int[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + any_of: + - range: tiltseries_tilt_series_quality + - range: IntegerFormattedString + tilt_step: + name: tilt_step + description: A placeholder for any type of data. + from_schema: metadata + alias: tilt_step + owner: TiltSeries + domain_of: + - TiltSeries + range: Any + inlined: true + inlined_as_list: true + pattern: ^float[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + any_of: + - range: tiltseries_tilt_step + - range: FloatFormattedString + tilting_scheme: + name: tilting_scheme + description: The order of stage tilting during acquisition of the data + from_schema: metadata + exact_mappings: + - cdp-common:tiltseries_tilting_scheme + alias: tilting_scheme + owner: TiltSeries + domain_of: + - TiltSeries + range: string + required: true + inlined: true + inlined_as_list: true + total_flux: + name: total_flux + description: A placeholder for any type of data. + from_schema: metadata + alias: total_flux + owner: TiltSeries + domain_of: + - TiltSeries + range: Any + inlined: true + inlined_as_list: true + pattern: ^float[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + any_of: + - range: tiltseries_total_flux + - range: FloatFormattedString + pixel_spacing: + name: pixel_spacing + description: A placeholder for any type of data. + from_schema: metadata + alias: pixel_spacing + owner: TiltSeries + domain_of: + - TiltSeries + range: Any + inlined: true + inlined_as_list: true + pattern: ^float[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + any_of: + - range: tiltseries_pixel_spacing + - range: FloatFormattedString + TomogramSize: + name: TomogramSize + description: The size of a tomogram in voxels in each dimension. + from_schema: metadata + attributes: + x: + name: x + description: Number of pixels in the 3D data fast axis + from_schema: metadata + alias: x + owner: TomogramSize + domain_of: + - TomogramSize + - TomogramOffset + range: integer + required: true + inlined: true + inlined_as_list: true + minimum_value: 0 + unit: + symbol: px + descriptive_name: pixels + y: + name: y + description: Number of pixels in the 3D data medium axis + from_schema: metadata + alias: y + owner: TomogramSize + domain_of: + - TomogramSize + - TomogramOffset + range: integer + required: true + inlined: true + inlined_as_list: true + minimum_value: 0 + unit: + symbol: px + descriptive_name: pixels + z: + name: z + description: Number of pixels in the 3D data slow axis. This is the image + projection direction at zero stage tilt + from_schema: metadata + alias: z + owner: TomogramSize + domain_of: + - TomogramSize + - TomogramOffset + range: integer + required: true + inlined: true + inlined_as_list: true + minimum_value: 0 + unit: + symbol: px + descriptive_name: pixels + TomogramOffset: + name: TomogramOffset + description: The offset of a tomogram in voxels in each dimension relative to + the canonical tomogram. + from_schema: metadata + attributes: + x: + name: x + description: x offset data relative to the canonical tomogram in pixels + from_schema: metadata + alias: x + owner: TomogramOffset + domain_of: + - TomogramSize + - TomogramOffset + range: integer + required: true + inlined: true + inlined_as_list: true + unit: + symbol: px + descriptive_name: pixels + y: + name: y + description: y offset data relative to the canonical tomogram in pixels + from_schema: metadata + alias: y + owner: TomogramOffset + domain_of: + - TomogramSize + - TomogramOffset + range: integer + required: true + inlined: true + inlined_as_list: true + unit: + symbol: px + descriptive_name: pixels + z: + name: z + description: z offset data relative to the canonical tomogram in pixels + from_schema: metadata + alias: z + owner: TomogramOffset + domain_of: + - TomogramSize + - TomogramOffset + range: integer + required: true + inlined: true + inlined_as_list: true + unit: + symbol: px + descriptive_name: pixels + Tomogram: + name: Tomogram + description: Metadata describing a tomogram. + from_schema: metadata + mixins: + - AuthoredEntity + attributes: + voxel_spacing: + name: voxel_spacing + description: A placeholder for any type of data. + from_schema: metadata + alias: voxel_spacing + owner: Tomogram + domain_of: + - Tomogram + range: Any + inlined: true + inlined_as_list: true + pattern: ^float[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + any_of: + - range: tomogram_voxel_spacing + - range: FloatFormattedString + fiducial_alignment_status: + name: fiducial_alignment_status + description: A placeholder for any type of data. + from_schema: metadata + alias: fiducial_alignment_status + owner: Tomogram + domain_of: + - Tomogram + range: Any + inlined: true + inlined_as_list: true + pattern: ^[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + any_of: + - range: tomogram_fiducial_alignment_status + - range: StringFormattedString + ctf_corrected: + name: ctf_corrected + description: Whether this tomogram is CTF corrected + from_schema: metadata + exact_mappings: + - cdp-common:tomogram_ctf_corrected + alias: ctf_corrected + owner: Tomogram + domain_of: + - Tomogram + range: boolean + recommended: true + inlined: true + inlined_as_list: true + align_software: + name: align_software + description: Software used for alignment + from_schema: metadata + exact_mappings: + - cdp-common:tomogram_align_software + alias: align_software + owner: Tomogram + domain_of: + - Tomogram + range: string + inlined: true + inlined_as_list: true + reconstruction_method: + name: reconstruction_method + description: A placeholder for any type of data. + from_schema: metadata + alias: reconstruction_method + owner: Tomogram + domain_of: + - Tomogram + range: Any + inlined: true + inlined_as_list: true + pattern: ^[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$ + any_of: + - range: tomogram_reconstruction_method + - range: StringFormattedString + reconstruction_software: + name: reconstruction_software + description: Name of software used for reconstruction + from_schema: metadata + exact_mappings: + - cdp-common:tomogram_reconstruction_software + alias: reconstruction_software + owner: Tomogram + domain_of: + - Tomogram + range: string + required: true + inlined: true + inlined_as_list: true + processing: + name: processing + description: Describe additional processing used to derive the tomogram + from_schema: metadata + exact_mappings: + - cdp-common:tomogram_processing + alias: processing + owner: Tomogram + domain_of: + - Tomogram + range: tomogram_processing_enum + required: true + inlined: true + inlined_as_list: true + pattern: (^denoised$)|(^filtered$)|(^raw$) + processing_software: + name: processing_software + description: Processing software used to derive the tomogram + from_schema: metadata + exact_mappings: + - cdp-common:tomogram_processing_software + alias: processing_software + owner: Tomogram + domain_of: + - Tomogram + range: string + recommended: true + inlined: true + inlined_as_list: true + tomogram_version: + name: tomogram_version + description: Version of tomogram + from_schema: metadata + exact_mappings: + - cdp-common:tomogram_version + alias: tomogram_version + owner: Tomogram + domain_of: + - Tomogram + range: VersionString + required: true + inlined: true + inlined_as_list: true + affine_transformation_matrix: + name: affine_transformation_matrix + description: The flip or rotation transformation of this author submitted + tomogram is indicated here + from_schema: metadata + array: + exact_number_dimensions: 2 + dimensions: + - exact_cardinality: 4 + - exact_cardinality: 4 + alias: affine_transformation_matrix + owner: Tomogram + domain_of: + - Tomogram + range: float + inlined: true + inlined_as_list: true + size: + name: size + description: The size of a tomogram in voxels in each dimension. + from_schema: metadata + alias: size + owner: Tomogram + domain_of: + - Tomogram + range: TomogramSize + inlined: true + inlined_as_list: true + offset: + name: offset + description: The offset of a tomogram in voxels in each dimension relative + to the canonical tomogram. + from_schema: metadata + alias: offset + owner: Tomogram + domain_of: + - Tomogram + range: TomogramOffset + required: true + inlined: true + inlined_as_list: true + authors: + name: authors + description: Author of a scientific data entity. + from_schema: metadata + list_elements_ordered: true + alias: authors + owner: Tomogram + domain_of: + - AuthoredEntity + range: Author + required: true + multivalued: true + inlined: true + inlined_as_list: true + minimum_cardinality: 1 + AnnotationConfidence: + name: AnnotationConfidence + description: Metadata describing the confidence of an annotation. + from_schema: metadata + attributes: + precision: + name: precision + description: Describe the confidence level of the annotation. Precision is + defined as the % of annotation objects being true positive + from_schema: metadata + exact_mappings: + - cdp-common:annotation_confidence_precision + alias: precision + owner: AnnotationConfidence + domain_of: + - AnnotationConfidence + range: float + inlined: true + inlined_as_list: true + minimum_value: 0 + maximum_value: 100 + unit: + symbol: '%' + descriptive_name: percentage + recall: + name: recall + description: Describe the confidence level of the annotation. Recall is defined + as the % of true positives being annotated correctly + from_schema: metadata + exact_mappings: + - cdp-common:annotation_confidence_recall + alias: recall + owner: AnnotationConfidence + domain_of: + - AnnotationConfidence + range: float + inlined: true + inlined_as_list: true + minimum_value: 0 + maximum_value: 100 + unit: + symbol: '%' + descriptive_name: percentage + ground_truth_used: + name: ground_truth_used + description: Annotation filename used as ground truth for precision and recall + from_schema: metadata + exact_mappings: + - cdp-common:annotation_ground_truth_used + alias: ground_truth_used + owner: AnnotationConfidence + domain_of: + - AnnotationConfidence + range: string + inlined: true + inlined_as_list: true + AnnotationObject: + name: AnnotationObject + description: Metadata describing the object being annotated. + from_schema: metadata + attributes: + id: + name: id + description: Gene Ontology Cellular Component identifier for the annotation + object + from_schema: metadata + exact_mappings: + - cdp-common:annotation_object_id + alias: id + owner: AnnotationObject + domain_of: + - TissueDetails + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: GO_ID + required: true + inlined: true + inlined_as_list: true + pattern: ^GO:[0-9]{7}$ + name: + name: name + description: Name of the object being annotated (e.g. ribosome, nuclear pore + complex, actin filament, membrane) + from_schema: metadata + exact_mappings: + - cdp-common:annotation_object_name + alias: name + owner: AnnotationObject + domain_of: + - OrganismDetails + - TissueDetails + - CellType + - CellStrain + - CellComponent + - AnnotationObject + - AuthorMixin + range: string + required: true + inlined: true + inlined_as_list: true + description: + name: description + description: A textual description of the annotation object, can be a longer + description to include additional information not covered by the Annotation + object name and state. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_object_description + alias: description + owner: AnnotationObject + domain_of: + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + state: + name: state + description: Molecule state annotated (e.g. open, closed) + from_schema: metadata + exact_mappings: + - cdp-common:annotation_object_state + alias: state + owner: AnnotationObject + domain_of: + - AnnotationObject + range: string + inlined: true + inlined_as_list: true + AnnotationSourceFile: + name: AnnotationSourceFile + description: File and sourcing data for an annotation. Represents an entry in + annotation.sources. + from_schema: metadata + attributes: + file_format: + name: file_format + description: File format for this file + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_format + alias: file_format + owner: AnnotationSourceFile + domain_of: + - AnnotationSourceFile + range: string + required: true + inlined: true + inlined_as_list: true + glob_string: + name: glob_string + description: Glob string to match annotation files in the dataset. Required + if annotation_source_file_glob_strings is not provided. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_glob_string + alias: glob_string + owner: AnnotationSourceFile + domain_of: + - AnnotationSourceFile + range: string + required: false + inlined: true + inlined_as_list: true + glob_strings: + name: glob_strings + description: Glob strings to match annotation files in the dataset. Required + if annotation_source_file_glob_string is not provided. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_glob_strings + alias: glob_strings + owner: AnnotationSourceFile + domain_of: + - AnnotationSourceFile + range: string + required: false + multivalued: true + inlined: true + inlined_as_list: true + is_visualization_default: + name: is_visualization_default + description: This annotation will be rendered in neuroglancer by default. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_is_visualization_default + ifabsent: 'False' + alias: is_visualization_default + owner: AnnotationSourceFile + domain_of: + - AnnotationSourceFile + range: boolean + inlined: true + inlined_as_list: true + AnnotationOrientedPointFile: + name: AnnotationOrientedPointFile + description: File and sourcing data for an oriented point annotation. Annotation + that identifies points along with orientation in the volume. + from_schema: metadata + aliases: + - OrientedPoint + is_a: AnnotationSourceFile + attributes: + binning: + name: binning + description: The binning factor for a point / oriented point / instance segmentation + annotation file. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_binning + ifabsent: float(1) + alias: binning + owner: AnnotationOrientedPointFile + domain_of: + - AnnotationOrientedPointFile + - AnnotationPointFile + range: float + inlined: true + inlined_as_list: true + minimum_value: 0 + filter_value: + name: filter_value + description: The filter value for an oriented point / instance segmentation + annotation file. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_filter_value + alias: filter_value + owner: AnnotationOrientedPointFile + domain_of: + - AnnotationOrientedPointFile + range: string + inlined: true + inlined_as_list: true + order: + name: order + description: The order of axes for an oriented point / instance segmentation + annotation file. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_order + ifabsent: string(xyz) + alias: order + owner: AnnotationOrientedPointFile + domain_of: + - AnnotationOrientedPointFile + range: string + inlined: true + inlined_as_list: true + file_format: + name: file_format + description: File format for this file + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_format + alias: file_format + owner: AnnotationOrientedPointFile + domain_of: + - AnnotationSourceFile + range: string + required: true + inlined: true + inlined_as_list: true + glob_string: + name: glob_string + description: Glob string to match annotation files in the dataset. Required + if annotation_source_file_glob_strings is not provided. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_glob_string + alias: glob_string + owner: AnnotationOrientedPointFile + domain_of: + - AnnotationSourceFile + range: string + required: false + inlined: true + inlined_as_list: true + glob_strings: + name: glob_strings + description: Glob strings to match annotation files in the dataset. Required + if annotation_source_file_glob_string is not provided. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_glob_strings + alias: glob_strings + owner: AnnotationOrientedPointFile + domain_of: + - AnnotationSourceFile + range: string + required: false + multivalued: true + inlined: true + inlined_as_list: true + is_visualization_default: + name: is_visualization_default + description: This annotation will be rendered in neuroglancer by default. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_is_visualization_default + ifabsent: 'False' + alias: is_visualization_default + owner: AnnotationOrientedPointFile + domain_of: + - AnnotationSourceFile + range: boolean + inlined: true + inlined_as_list: true + AnnotationInstanceSegmentationFile: + name: AnnotationInstanceSegmentationFile + description: File and sourcing data for an instance segmentation annotation. Annotation + that identifies individual instances of object shapes. + from_schema: metadata + aliases: + - InstanceSegmentation + is_a: AnnotationOrientedPointFile + attributes: + binning: + name: binning + description: The binning factor for a point / oriented point / instance segmentation + annotation file. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_binning + ifabsent: float(1) + alias: binning + owner: AnnotationInstanceSegmentationFile + domain_of: + - AnnotationOrientedPointFile + - AnnotationPointFile + range: float + inlined: true + inlined_as_list: true + minimum_value: 0 + filter_value: + name: filter_value + description: The filter value for an oriented point / instance segmentation + annotation file. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_filter_value + alias: filter_value + owner: AnnotationInstanceSegmentationFile + domain_of: + - AnnotationOrientedPointFile + range: string + inlined: true + inlined_as_list: true + order: + name: order + description: The order of axes for an oriented point / instance segmentation + annotation file. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_order + ifabsent: string(xyz) + alias: order + owner: AnnotationInstanceSegmentationFile + domain_of: + - AnnotationOrientedPointFile + range: string + inlined: true + inlined_as_list: true + file_format: + name: file_format + description: File format for this file + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_format + alias: file_format + owner: AnnotationInstanceSegmentationFile + domain_of: + - AnnotationSourceFile + range: string + required: true + inlined: true + inlined_as_list: true + glob_string: + name: glob_string + description: Glob string to match annotation files in the dataset. Required + if annotation_source_file_glob_strings is not provided. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_glob_string + alias: glob_string + owner: AnnotationInstanceSegmentationFile + domain_of: + - AnnotationSourceFile + range: string + required: false + inlined: true + inlined_as_list: true + glob_strings: + name: glob_strings + description: Glob strings to match annotation files in the dataset. Required + if annotation_source_file_glob_string is not provided. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_glob_strings + alias: glob_strings + owner: AnnotationInstanceSegmentationFile + domain_of: + - AnnotationSourceFile + range: string + required: false + multivalued: true + inlined: true + inlined_as_list: true + is_visualization_default: + name: is_visualization_default + description: This annotation will be rendered in neuroglancer by default. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_is_visualization_default + ifabsent: 'False' + alias: is_visualization_default + owner: AnnotationInstanceSegmentationFile + domain_of: + - AnnotationSourceFile + range: boolean + inlined: true + inlined_as_list: true + AnnotationPointFile: + name: AnnotationPointFile + description: File and sourcing data for a point annotation. Annotation that identifies + points in the volume. + from_schema: metadata + aliases: + - Point + is_a: AnnotationSourceFile + attributes: + binning: + name: binning + description: The binning factor for a point / oriented point / instance segmentation + annotation file. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_binning + ifabsent: float(1) + alias: binning + owner: AnnotationPointFile + domain_of: + - AnnotationOrientedPointFile + - AnnotationPointFile + range: float + inlined: true + inlined_as_list: true + minimum_value: 0 + columns: + name: columns + description: The columns used in a point annotation file. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_columns + ifabsent: string(xyz) + alias: columns + owner: AnnotationPointFile + domain_of: + - AnnotationPointFile + range: string + inlined: true + inlined_as_list: true + delimiter: + name: delimiter + description: The delimiter used in a point annotation file. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_delimiter + ifabsent: string(,) + alias: delimiter + owner: AnnotationPointFile + domain_of: + - AnnotationPointFile + range: string + inlined: true + inlined_as_list: true + file_format: + name: file_format + description: File format for this file + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_format + alias: file_format + owner: AnnotationPointFile + domain_of: + - AnnotationSourceFile + range: string + required: true + inlined: true + inlined_as_list: true + glob_string: + name: glob_string + description: Glob string to match annotation files in the dataset. Required + if annotation_source_file_glob_strings is not provided. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_glob_string + alias: glob_string + owner: AnnotationPointFile + domain_of: + - AnnotationSourceFile + range: string + required: false + inlined: true + inlined_as_list: true + glob_strings: + name: glob_strings + description: Glob strings to match annotation files in the dataset. Required + if annotation_source_file_glob_string is not provided. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_glob_strings + alias: glob_strings + owner: AnnotationPointFile + domain_of: + - AnnotationSourceFile + range: string + required: false + multivalued: true + inlined: true + inlined_as_list: true + is_visualization_default: + name: is_visualization_default + description: This annotation will be rendered in neuroglancer by default. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_is_visualization_default + ifabsent: 'False' + alias: is_visualization_default + owner: AnnotationPointFile + domain_of: + - AnnotationSourceFile + range: boolean + inlined: true + inlined_as_list: true + AnnotationSegmentationMaskFile: + name: AnnotationSegmentationMaskFile + description: File and sourcing data for a segmentation mask annotation. Annotation + that identifies an object. + from_schema: metadata + aliases: + - SegmentationMask + is_a: AnnotationSourceFile + attributes: + file_format: + name: file_format + description: File format for this file + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_format + alias: file_format + owner: AnnotationSegmentationMaskFile + domain_of: + - AnnotationSourceFile + range: string + required: true + inlined: true + inlined_as_list: true + glob_string: + name: glob_string + description: Glob string to match annotation files in the dataset. Required + if annotation_source_file_glob_strings is not provided. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_glob_string + alias: glob_string + owner: AnnotationSegmentationMaskFile + domain_of: + - AnnotationSourceFile + range: string + required: false + inlined: true + inlined_as_list: true + glob_strings: + name: glob_strings + description: Glob strings to match annotation files in the dataset. Required + if annotation_source_file_glob_string is not provided. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_glob_strings + alias: glob_strings + owner: AnnotationSegmentationMaskFile + domain_of: + - AnnotationSourceFile + range: string + required: false + multivalued: true + inlined: true + inlined_as_list: true + is_visualization_default: + name: is_visualization_default + description: This annotation will be rendered in neuroglancer by default. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_is_visualization_default + ifabsent: 'False' + alias: is_visualization_default + owner: AnnotationSegmentationMaskFile + domain_of: + - AnnotationSourceFile + range: boolean + inlined: true + inlined_as_list: true + AnnotationSemanticSegmentationMaskFile: + name: AnnotationSemanticSegmentationMaskFile + description: File and sourcing data for a semantic segmentation mask annotation. + Annotation that identifies classes of objects. + from_schema: metadata + aliases: + - SemanticSegmentationMask + is_a: AnnotationSourceFile + attributes: + mask_label: + name: mask_label + description: The mask label for a semantic segmentation mask annotation file. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_mask_label + ifabsent: int(1) + alias: mask_label + owner: AnnotationSemanticSegmentationMaskFile + domain_of: + - AnnotationSemanticSegmentationMaskFile + range: integer + inlined: true + inlined_as_list: true + file_format: + name: file_format + description: File format for this file + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_format + alias: file_format + owner: AnnotationSemanticSegmentationMaskFile + domain_of: + - AnnotationSourceFile + range: string + required: true + inlined: true + inlined_as_list: true + glob_string: + name: glob_string + description: Glob string to match annotation files in the dataset. Required + if annotation_source_file_glob_strings is not provided. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_glob_string + alias: glob_string + owner: AnnotationSemanticSegmentationMaskFile + domain_of: + - AnnotationSourceFile + range: string + required: false + inlined: true + inlined_as_list: true + glob_strings: + name: glob_strings + description: Glob strings to match annotation files in the dataset. Required + if annotation_source_file_glob_string is not provided. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_glob_strings + alias: glob_strings + owner: AnnotationSemanticSegmentationMaskFile + domain_of: + - AnnotationSourceFile + range: string + required: false + multivalued: true + inlined: true + inlined_as_list: true + is_visualization_default: + name: is_visualization_default + description: This annotation will be rendered in neuroglancer by default. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_source_file_is_visualization_default + ifabsent: 'False' + alias: is_visualization_default + owner: AnnotationSemanticSegmentationMaskFile + domain_of: + - AnnotationSourceFile + range: boolean + inlined: true + inlined_as_list: true + Annotation: + name: Annotation + description: Metadata describing an annotation. + from_schema: metadata + mixins: + - DateStampedEntity + - AuthoredEntity + attributes: + annotation_method: + name: annotation_method + description: Describe how the annotation is made (e.g. Manual, crYoLO, Positive + Unlabeled Learning, template matching) + from_schema: metadata + exact_mappings: + - cdp-common:annotation_method + alias: annotation_method + owner: Annotation + domain_of: + - Annotation + range: string + required: true + inlined: true + inlined_as_list: true + annotation_object: + name: annotation_object + description: Metadata describing the object being annotated. + from_schema: metadata + alias: annotation_object + owner: Annotation + domain_of: + - Annotation + range: AnnotationObject + required: true + inlined: true + inlined_as_list: true + annotation_publications: + name: annotation_publications + description: List of publication IDs (EMPIAR, EMDB, DOI) that describe this + annotation method. Comma separated. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_publications + alias: annotation_publications + owner: Annotation + domain_of: + - Annotation + range: EMPIAR_EMDB_DOI_PDB_LIST + inlined: true + inlined_as_list: true + pattern: ^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$ + annotation_software: + name: annotation_software + description: Software used for generating this annotation + from_schema: metadata + exact_mappings: + - cdp-common:annotation_software + alias: annotation_software + owner: Annotation + domain_of: + - Annotation + range: string + recommended: true + inlined: true + inlined_as_list: true + confidence: + name: confidence + description: Metadata describing the confidence of an annotation. + from_schema: metadata + alias: confidence + owner: Annotation + domain_of: + - Annotation + range: AnnotationConfidence + inlined: true + inlined_as_list: true + files: + name: files + description: File and sourcing data for an annotation. Represents an entry + in annotation.sources. + from_schema: metadata + list_elements_ordered: true + alias: files + owner: Annotation + domain_of: + - Annotation + range: AnnotationSourceFile + multivalued: true + inlined: true + inlined_as_list: true + ground_truth_status: + name: ground_truth_status + description: Whether an annotation is considered ground truth, as determined + by the annotator. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_ground_truth_status + ifabsent: 'False' + alias: ground_truth_status + owner: Annotation + domain_of: + - Annotation + range: boolean + recommended: true + inlined: true + inlined_as_list: true + is_curator_recommended: + name: is_curator_recommended + description: This annotation is recommended by the curator to be preferred + for this object type. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_is_curator_recommended + ifabsent: 'False' + alias: is_curator_recommended + owner: Annotation + domain_of: + - Annotation + range: boolean + inlined: true + inlined_as_list: true + method_type: + name: method_type + description: Classification of the annotation method based on supervision. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_method_type + alias: method_type + owner: Annotation + domain_of: + - Annotation + range: annotation_method_type_enum + required: true + inlined: true + inlined_as_list: true + pattern: (^manual$)|(^automated$)|(^hybrid$) + object_count: + name: object_count + description: Number of objects identified + from_schema: metadata + exact_mappings: + - cdp-common:annotation_object_count + alias: object_count + owner: Annotation + domain_of: + - Annotation + range: integer + inlined: true + inlined_as_list: true + version: + name: version + description: Version of annotation. + from_schema: metadata + exact_mappings: + - cdp-common:annotation_version + alias: version + owner: Annotation + domain_of: + - Annotation + range: VersionString + inlined: true + inlined_as_list: true + dates: + name: dates + description: A set of dates at which a data item was deposited, published + and last modified. + from_schema: metadata + alias: dates + owner: Annotation + domain_of: + - DateStampedEntity + range: DateStamp + required: true + inlined: true + inlined_as_list: true + authors: + name: authors + description: Author of a scientific data entity. + from_schema: metadata + list_elements_ordered: true + alias: authors + owner: Annotation + domain_of: + - AuthoredEntity + range: Author + required: true + multivalued: true + inlined: true + inlined_as_list: true + minimum_cardinality: 1 + Any: + name: Any + description: A placeholder for any type of data. + from_schema: metadata + class_uri: linkml:Any + DateStampedEntityMixin: + name: DateStampedEntityMixin + description: A set of dates at which a data item was deposited, published and + last modified. + from_schema: metadata + mixin: true + attributes: + deposition_date: + name: deposition_date + description: The date a data item was received by the cryoET data portal. + from_schema: metadata + exact_mappings: + - cdp-common:deposition_date + alias: deposition_date + owner: DateStampedEntityMixin + domain_of: + - DateStampedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + release_date: + name: release_date + description: The date a data item was received by the cryoET data portal. + from_schema: metadata + exact_mappings: + - cdp-common:release_date + alias: release_date + owner: DateStampedEntityMixin + domain_of: + - DateStampedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + last_modified_date: + name: last_modified_date + description: The date a piece of data was last modified on the cryoET data + portal. + from_schema: metadata + exact_mappings: + - cdp-common:last_modified_date + alias: last_modified_date + owner: DateStampedEntityMixin + domain_of: + - DateStampedEntityMixin + range: string + required: true + inlined: true + inlined_as_list: true + CrossReferencesMixin: + name: CrossReferencesMixin + description: A set of cross-references to other databases and publications. + from_schema: metadata + mixin: true + attributes: + publications: + name: publications + description: Comma-separated list of DOIs for publications associated with + the dataset. + from_schema: metadata + alias: publications + owner: CrossReferencesMixin + domain_of: + - CrossReferencesMixin + range: DOI_LIST + recommended: true + inlined: true + inlined_as_list: true + pattern: (^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+(\s*,\s*(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+)*$)|(^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+(\s*,\s*(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+)*$) + related_database_entries: + name: related_database_entries + description: Comma-separated list of related database entries for the dataset. + from_schema: metadata + alias: related_database_entries + owner: CrossReferencesMixin + domain_of: + - CrossReferencesMixin + range: EMPIAR_EMDB_PDB_LIST + recommended: true + inlined: true + inlined_as_list: true + pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$) + related_database_links: + name: related_database_links + description: Comma-separated list of related database links for the dataset. + from_schema: metadata + alias: related_database_links + owner: CrossReferencesMixin + domain_of: + - CrossReferencesMixin + range: string + inlined: true + inlined_as_list: true + dataset_citations: + name: dataset_citations + description: Comma-separated list of DOIs for publications citing the dataset. + from_schema: metadata + alias: dataset_citations + owner: CrossReferencesMixin + domain_of: + - CrossReferencesMixin + range: string + inlined: true + inlined_as_list: true + AuthorMixin: + name: AuthorMixin + description: An entity with author data + from_schema: metadata + mixin: true + attributes: + name: + name: name + description: The full name of the author. + from_schema: metadata + exact_mappings: + - cdp-common:author_name + alias: name + owner: AuthorMixin + domain_of: + - AuthorMixin + - OrganismDetails + - TissueDetails + - CellType + - CellStrain + - CellComponent + - AnnotationObject + range: string + required: true + inlined: true + inlined_as_list: true + email: + name: email + description: The email address of the author. + from_schema: metadata + exact_mappings: + - cdp-common:author_email + alias: email + owner: AuthorMixin + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_name: + name: affiliation_name + description: The name of the author's affiliation. + from_schema: metadata + exact_mappings: + - cdp-common:author_affiliation_name + alias: affiliation_name + owner: AuthorMixin + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_address: + name: affiliation_address + description: The address of the author's affiliation. + from_schema: metadata + exact_mappings: + - cdp-common:author_affiliation_address + alias: affiliation_address + owner: AuthorMixin + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + affiliation_identifier: + name: affiliation_identifier + description: A Research Organization Registry (ROR) identifier. + from_schema: metadata + exact_mappings: + - cdp-common:author_affiliation_identifier + alias: affiliation_identifier + owner: AuthorMixin + domain_of: + - AuthorMixin + range: string + recommended: true + inlined: true + inlined_as_list: true + corresponding_author_status: + name: corresponding_author_status + description: Whether the author is a corresponding author. + from_schema: metadata + exact_mappings: + - cdp-common:author_corresponding_author_status + ifabsent: 'False' + alias: corresponding_author_status + owner: AuthorMixin + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true + primary_author_status: + name: primary_author_status + description: Whether the author is a primary author. + from_schema: metadata + exact_mappings: + - cdp-common:author_primary_author_status + ifabsent: 'False' + alias: primary_author_status + owner: AuthorMixin + domain_of: + - AuthorMixin + range: string + inlined: true + inlined_as_list: true +source_file: core/v2.0.0/metadata.yaml diff --git a/schema/core/v2.0.0/common.yaml b/schema/core/v2.0.0/common.yaml new file mode 100644 index 000000000..46618809b --- /dev/null +++ b/schema/core/v2.0.0/common.yaml @@ -0,0 +1,1263 @@ +id: common +name: cdp-common +version: 1.1.0 +prefixes: + linkml: https://w3id.org/linkml/ + cdp-common: common + ROR: https://ror.org/ + UBERON: http://purl.obolibrary.org/obo/UBERON_ + CL: http://purl.obolibrary.org/obo/CL_ + GO: http://purl.obolibrary.org/obo/GO_ + IAO: http://purl.obolibrary.org/obo/IAO_ + FOAF: http://xmlns.com/foaf/0.1/ +imports: + - linkml:types +default_prefix: cdp-common +default_range: string + + +slots: + # ============================================================================ + # Snapshot / Thumbnail + # ============================================================================ + snapshot: + description: >- + Path to the dataset preview image relative to the dataset directory root. + range: URLorS3URI + recommended: true + + thumbnail: + description: >- + Path to the thumbnail of preview image relative to the dataset directory root. + range: URLorS3URI + recommended: true + + # ============================================================================ + # Dates (re-used in Dataset, Tomogram, Tiltseries, Annotation) + # ============================================================================ + deposition_date: + range: date + required: true + description: >- + The date a data item was received by the cryoET data portal. + + release_date: + range: date + required: true + description: >- + The date a data item was received by the cryoET data portal. + + last_modified_date: + range: date + required: true + description: >- + The date a piece of data was last modified on the cryoET data portal. + # ============================================================================ + + # ============================================================================ + # Author slots + # ============================================================================ + author_orcid: + range: ORCID + description: >- + The ORCID identifier for the author. + recommended: true + + author_name: + range: string + required: true + description: >- + The full name of the author. + close_mappings: + - FOAF:name + + author_email: + range: string + description: >- + The email address of the author. + close_mappings: + - FOAF:mbox + + author_affiliation_name: + range: string + description: >- + The name of the author's affiliation. + + author_affiliation_address: + range: string + description: >- + The address of the author's affiliation. + + author_affiliation_identifier: + description: >- + A Research Organization Registry (ROR) identifier. + range: string + pattern: '^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$' + recommended: true + + author_corresponding_author_status: + range: boolean + description: >- + Whether the author is a corresponding author. + ifabsent: false + + author_primary_author_status: + range: boolean + description: >- + Whether the author is a primary author. + ifabsent: false + + author_list_order: + range: integer + required: true + description: >- + The position of the author in the author list. + # ============================================================================ + + + # ============================================================================ + # Deposition slots + # ============================================================================ + deposition_identifier: + identifier: true + range: integer + required: true + description: >- + An identifier for a CryoET deposition, assigned by the Data Portal. Used to identify the deposition the entity is + a part of. + deposition_title: + range: string + required: true + description: >- + Title of a CryoET deposition. + deposition_description: + range: string + required: true + description: >- + A short description of the deposition, similar to an abstract for a journal article or dataset. + deposition_types: + range: deposition_types_enum + required: true + multivalued: true + description: >- + Type of data in the deposition (e.g. dataset, annotation, tomogram) + # ============================================================================ + + # ============================================================================ + # Dataset slots + # ============================================================================ + dataset_identifier: + identifier: true + range: integer + required: true + description: >- + An identifier for a CryoET dataset, assigned by the Data Portal. Used to identify the dataset as the directory + name in data tree. + dataset_title: + range: string + required: true + description: >- + Title of a CryoET dataset. + dataset_description: + range: string + required: true + description: >- + A short description of a CryoET dataset, similar to an abstract for a journal article or dataset. + + dataset_key_photo_url: + range: string + description: >- + URL for the dataset preview image. + dataset_key_photo_thumbnail_url: + range: string + description: >- + URL for the thumbnail of preview image. + dataset_s3_prefix: + range: string + description: >- + The S3 public bucket path where this dataset is contained. + dataset_https_prefix: + range: string + description: >- + The HTTPS directory path where this dataset is contained. + # ============================================================================ + + # ============================================================================ + # Funding information slots + # ============================================================================ + funding_agency_name: + range: string + recommended: true + description: The name of the funding source. + funding_grant_id: + range: string + recommended: true + description: Grant identifier provided by the funding agency + # ============================================================================ + + # ============================================================================ + # Experimental metadata slots + # ============================================================================ + # Organism/Species + organism_name: + range: string + required: true + description: >- + Name of the organism from which a biological sample used in a CryoET study is derived from, e.g. homo sapiens. + organism_taxid: + range: integer + minimum_value: 1 + recommended: true + description: >- + NCBI taxonomy identifier for the organism, e.g. 9606 + + # Tissue + tissue_name: + range: string + required: true + description: >- + Name of the tissue from which a biological sample used in a CryoET study is derived from. + tissue_id: + range: BTO_ID + recommended: true + description: >- + The UBERON identifier for the tissue. + + # Cell Type + cell_name: + range: string + required: true + description: >- + Name of the cell type from which a biological sample used in a CryoET study is derived from. + cell_type_id: + range: CL_ID + recommended: true + description: >- + Cell Ontology identifier for the cell type + + # Cell Strain + cell_strain_name: + range: string + required: true + description: >- + Cell line or strain for the sample. + cell_strain_id: + any_of: + - range: WORMBASE_ID + - range: ONTOLOGY_ID + recommended: true + description: >- + Link to more information about the cell strain. + + # Cell Component + cell_component_name: + range: string + required: true + description: >- + Name of the cellular component. + cell_component_id: + range: GO_ID + recommended: true + description: >- + The GO identifier for the cellular component. + + # Preparation + preparation_sample_type: + range: sample_type_enum + required: true + description: >- + Type of sample imaged in a CryoET study. + sample_preparation: + range: string + recommended: true + description: >- + Describes how the sample was prepared. + grid_preparation: + range: string + recommended: true + description: >- + Describes Cryo-ET grid preparation. + preparation_other_setup: + range: string + recommended: true + description: >- + Describes other setup not covered by sample preparation or grid preparation that may make this dataset unique in + the same publication. + # ============================================================================ + + # ============================================================================ + # Run slots + # ============================================================================ + + # ============================================================================ + + # ============================================================================ + # TomogramVoxelSpacing slots + # ============================================================================ + + # ============================================================================ + + # ============================================================================ + # TiltSeries slots + # ============================================================================ + # id: + # range: integer + # description: Numeric identifier for this tilt series (this may change!) + #run (Run): An object relationship with the run this tiltseries is a part of + tiltseries_run_id: + range: integer + description: Reference to the run this tiltseries is a part of + tiltseries_acceleration_voltage: + range: float + minimum_value: 20000 + required: true + description: Electron Microscope Accelerator voltage in volts + unit: + descriptive_name: volts + symbol: V + tiltseries_aligned_tiltseries_binning: + range: float + minimum_value: 0 + description: Binning factor of the aligned tilt series + tiltseries_binning_from_frames: + range: float + minimum_value: 0 + description: Describes the binning factor from frames to tilt series file + tiltseries_camera_acquire_mode: + any_of: + - range: StringFormattedString + - range: tiltseries_camera_acquire_mode_enum + description: Camera acquisition mode + tiltseries_camera_manufacturer: + range: string + required: true + description: Name of the camera manufacturer + tiltseries_camera_model: + range: string + required: true + description: Camera model name + tiltseries_data_acquisition_software: + range: string + description: Software used to collect data + required: true + tiltseries_frames_count: + range: integer + description: Number of frames associated with this tiltseries + tiltseries_is_aligned: + range: boolean + required: true + description: Whether this tilt series is aligned + tiltseries_https_gain_file: + range: string + description: HTTPS path to the gain file for this tiltseries + tiltseries_https_angle_list: + range: string + description: HTTPS path to the angle list file for this tiltseries + tiltseries_https_collection_metadata: + range: string + description: HTTPS path to the collection metadata file for this tiltseries + tiltseries_https_mrc_bin1: + range: string + description: HTTPS path to this tiltseries in MRC format (no scaling) + tiltseries_https_omezarr_dir: + range: string + description: HTTPS path to this tiltseries in multiscale OME-Zarr format + tiltseries_microscope_additional_info: + range: string + description: Other microscope optical setup information, in addition to energy filter, phase plate and image corrector + tiltseries_microscope_energy_filter: + range: string + required: true + description: Energy filter setup used + tiltseries_microscope_image_corrector: + range: string + description: Image corrector setup + tiltseries_microscope_manufacturer: + range: tiltseries_microscope_manufacturer_enum + required: true + description: Name of the microscope manufacturer + tiltseries_microscope_model: + range: string + required: true + description: Microscope model name + tiltseries_microscope_phase_plate: + range: string + description: Phase plate configuration + tiltseries_pixel_spacing: + range: float + minimum_value: 0.001 + required: true + description: Pixel spacing for the tilt series + unit: + descriptive_name: Angstroms per pixel + symbol: Å/px + tiltseries_related_empiar_entry: + range: EMPIAR_ID + description: If a tilt series is deposited into EMPIAR, enter the EMPIAR dataset identifier + tiltseries_s3_gain_file: + range: string + description: S3 path to the gain file for this tiltseries + tiltseries_s3_angle_list: + range: string + description: S3 path to the angle list file for this tiltseries + tiltseries_s3_collection_metadata: + range: string + description: S3 path to the collection metadata file for this tiltseries + tiltseries_s3_mrc_bin1: + range: string + description: S3 path to this tiltseries in MRC format (no scaling) + tiltseries_s3_omezarr_dir: + range: string + description: S3 path to this tiltseries in multiscale OME-Zarr format + tiltseries_spherical_aberration_constant: + range: float + minimum_value: 0 + required: true + description: Spherical Aberration Constant of the objective lens in millimeters + unit: + descriptive_name: millimeters + symbol: mm + tiltseries_tilt_alignment_software: + range: string + description: Software used for tilt alignment + tiltseries_tilt_axis: + range: float + minimum_value: -360 + maximum_value: 360 + required: true + description: Rotation angle in degrees + unit: + descriptive_name: degrees + symbol: ° + tiltseries_tilt_max: + range: float + minimum_value: -90 + maximum_value: 90 + required: true + description: Maximal tilt angle in degrees + unit: + descriptive_name: degrees + symbol: ° + tiltseries_tilt_min: + range: float + minimum_value: -90 + maximum_value: 90 + required: true + description: Minimal tilt angle in degrees + unit: + descriptive_name: degrees + symbol: ° + tiltseries_tilt_series_quality: + range: integer + minimum_value: 1 + maximum_value: 5 + required: true + description: Author assessment of tilt series quality within the dataset (1-5, 5 is best) + tiltseries_tilt_step: + range: float + minimum_value: 0 + maximum_value: 90 + required: true + description: Tilt step in degrees + unit: + descriptive_name: degrees + symbol: ° + tiltseries_tilting_scheme: + range: string + required: true + description: The order of stage tilting during acquisition of the data + tiltseries_total_flux: + range: float + minimum_value: 0 + required: true + description: Number of Electrons reaching the specimen in a square Angstrom area for the entire tilt series + unit: + descriptive_name: electrons per square Angstrom + symbol: e^-/Å^2 + # ============================================================================ + + + # ============================================================================ + # Tomogram slots + # ============================================================================ + # tomogram affine_transformation_matrix is included in metadata.yaml for validation compatability purposes + tomogram_ctf_corrected: + range: boolean + description: Whether this tomogram is CTF corrected + recommended: true + #dataset (Dataset): An object relationship with the dataset this tomogram is a part of + tomogram_dataset_id: + range: integer + description: Reference to the dataset this tomogram is a part of + tomogram_fiducial_alignment_status: + range: fiducial_alignment_status_enum + required: true + description: Whether the tomographic alignment was computed based on fiducial markers. + tomogram_https_mrc_scale0: + range: string + description: HTTPS path to this tomogram in MRC format (no scaling) + tomogram_https_omezarr_dir: + range: string + description: HTTPS path to this tomogram in multiscale OME-Zarr format + tomogram_key_photo_thumbnail_url: + range: string + description: URL for the thumbnail of key photo + tomogram_key_photo_url: + range: string + description: URL for the key photo + tomogram_name: + range: string + description: Short name for this tomogram + tomogram_neuroglancer_config: + range: string + description: the compact json of neuroglancer config + tomogram_align_software: + range: string + description: Software used for alignment + tomogram_processing: + range: tomogram_processing_enum + required: true + description: Describe additional processing used to derive the tomogram + tomogram_processing_software: + range: string + description: Processing software used to derive the tomogram + recommended: true + tomogram_reconstruction_method: + range: tomogram_reconstruction_method_enum + required: true + description: Describe reconstruction method (WBP, SART, SIRT) + tomogram_reconstruction_software: + range: string + required: true + description: Name of software used for reconstruction + tomogram_s3_mrc_scale0: + range: string + description: S3 path to this tomogram in MRC format (no scaling) + tomogram_s3_omezarr_dir: + range: string + description: S3 path to this tomogram in multiscale OME-Zarr format + tomogram_scale0_dimensions: + range: string + description: comma separated x,y,z dimensions of the unscaled tomogram + tomogram_scale1_dimensions: + range: string + description: comma separated x,y,z dimensions of the scale1 tomogram + tomogram_scale2_dimensions: + range: string + description: comma separated x,y,z dimensions of the scale2 tomogram + tomogram_version: + range: VersionString + required: true + description: Version of tomogram + #tomogram_voxel_spacing (TomogramVoxelSpacing): An object relationship with a specific voxel spacing for this experiment run + tomogram_type: + range: string + description: "Tomogram purpose (ex: CANONICAL)" + tomogram_is_standardized: + range: boolean + description: Whether the tomogram was generated by per the portal standard specifications + tomogram_voxel_spacing: + range: float + minimum_value: 0.001 + required: true + description: Voxel spacing equal in all three axes in angstroms + unit: + descriptive_name: Angstroms per voxel + symbol: Å/voxel + # ============================================================================ + + # ============================================================================ + # Annotation slots + # ============================================================================ + #id (int): Numeric identifier (May change!) + annotation_method: + range: string + required: true + description: Describe how the annotation is made (e.g. Manual, crYoLO, Positive Unlabeled Learning, template matching) + annotation_method_type: + range: annotation_method_type_enum + required: true + description: Classification of the annotation method based on supervision. + annotation_publications: + range: EMPIAR_EMDB_DOI_PDB_LIST + description: List of publication IDs (EMPIAR, EMDB, DOI) that describe this annotation method. Comma separated. + annotation_software: + range: string + description: Software used for generating this annotation + recommended: true + #authors (list[Author]): An array relationship with the authors of this annotation + annotation_confidence_precision: + range: float + minimum_value: 0 + maximum_value: 100 + description: Describe the confidence level of the annotation. Precision is defined as the % of annotation objects being true positive + unit: + descriptive_name: percentage + symbol: '%' + annotation_confidence_recall: + range: float + minimum_value: 0 + maximum_value: 100 + description: Describe the confidence level of the annotation. Recall is defined as the % of true positives being annotated correctly + unit: + descriptive_name: percentage + symbol: '%' + #deposition_date (date): Date when an annotation set is initially received by the Data Portal. + annotation_ground_truth_status: + range: boolean + recommended: true + description: Whether an annotation is considered ground truth, as determined by the annotator. + ifabsent: false + annotation_ground_truth_used: + range: string + description: Annotation filename used as ground truth for precision and recall + https_metadata_path: + range: string + description: HTTPS path for the metadata json file for this annotation + #last_modified_date (date): Date when an annotation was last modified in the Data Portal + annotation_object_count: + range: integer + description: Number of objects identified + annotation_object_description: + range: string + description: A textual description of the annotation object, can be a longer description to include additional information not covered by the Annotation object name and state. + annotation_object_id: + range: GO_ID + required: true + description: Gene Ontology Cellular Component identifier for the annotation object + annotation_object_name: + range: string + required: true + description: Name of the object being annotated (e.g. ribosome, nuclear pore complex, actin filament, membrane) + annotation_object_state: + range: string + description: Molecule state annotated (e.g. open, closed) + #release_date (date): Date when annotation data is made public by the Data Portal. + #tomogram_voxel_spacing (TomogramVoxelSpacing): An object relationship with a specific voxel spacing for this annotation + tomogram_voxel_spacing_id: + range: integer + description: Reference to the tomogram voxel spacing group this annotation applies to + s3_metadata_path: + range: string + description: S3 path for the metadata json file for this annotation + annotation_is_curator_recommended: + range: boolean + description: This annotation is recommended by the curator to be preferred for this object type. + ifabsent: false + annotation_version: + range: VersionString + description: Version of annotation. + + # ============================================================================ + # Annotation Source File slots + # ============================================================================ + #id (int): Numeric identifier (May change!) + annotation_source_file_format: + range: string + required: true + description: File format for this file + annotation_source_file_https_path: + range: string + description: HTTPS url for the annotation file + annotation_source_file_s3_path: + range: string + description: S3 path for the annotation file + annotation_source_file_annotation_id: + range: integer + description: Reference to the annotation this file applies to + annotation_source_file_path: + range: string + description: Path to the annotation file relative to the dataset root. + annotation_source_file_glob_string: + range: string + required: false + description: Glob string to match annotation files in the dataset. Required if annotation_source_file_glob_strings is not provided. + annotation_source_file_glob_strings: + range: string + description: Glob strings to match annotation files in the dataset. Required if annotation_source_file_glob_string is not provided. + multivalued: true + required: false + annotation_source_file_is_visualization_default: + range: boolean + description: This annotation will be rendered in neuroglancer by default. + ifabsent: false + #Annotation (Annotation): The annotation this file is a part of + + # ============================================================================ + # Annotation Source File shape-specific slots + # ============================================================================ + annotation_source_file_binning: + range: float + description: The binning factor for a point / oriented point / instance segmentation annotation file. + ifabsent: 'float(1)' + minimum_value: 0 + annotation_source_file_columns: + range: string + description: The columns used in a point annotation file. + ifabsent: string(xyz) + annotation_source_file_delimiter: + range: string + description: The delimiter used in a point annotation file. + ifabsent: string(,) + annotation_source_file_filter_value: + range: string + description: The filter value for an oriented point / instance segmentation annotation file. + annotation_source_file_order: + range: string + description: The order of axes for an oriented point / instance segmentation annotation file. + ifabsent: string(xyz) + annotation_source_file_mask_label: + range: integer + description: The mask label for a semantic segmentation mask annotation file. + ifabsent: 'int(1)' + + # ============================================================================ + # Per Section Parameters fields + # ============================================================================ + per_section_z_index: + range: integer + description: z-index of the frame in the tiltseries + minimum_value: 0 + required: true + per_section_defocus: + range: float + description: defocus amount + minimum_value: 100 + maximum_value: 100 + unit: + descriptive_name: microns + symbol: µm + per_section_astigmatism: + range: float + description: Astigmatism amount for this frame + per_section_astigmatic_angle: + range: float + description: Angle of ast + minimum_value: -180 + maximum_value: 180 + unit: + descriptive_name: degrees + symbol: ° + + # ============================================================================ + # Alignment Parameters fields + # ============================================================================ + alignment_alignment_type: + range: alignment_type_enum + description: Type of alignment included, i.e. is a non-rigid alignment included? + + alignment_volume_x_dimension: + range: float + description: X dimension of the reconstruction volume in angstrom + unit: + descriptive_name: Angstrom + symbol: Å + + alignment_volume_y_dimension: + range: float + description: Y dimension of the reconstruction volume in angstrom + unit: + descriptive_name: Angstrom + symbol: Å + + alignment_volume_z_dimension: + range: float + description: Z dimension of the reconstruction volume in angstrom + unit: + descriptive_name: Angstrom + symbol: Å + + alignment_volume_x_offset: + range: float + description: X shift of the reconstruction volume in angstrom + unit: + descriptive_name: Angstrom + symbol: Å + + alignment_volume_y_offset: + range: float + description: Y shift of the reconstruction volume in angstrom + unit: + descriptive_name: Angstrom + symbol: Å + + alignment_volume_z_offset: + range: float + description: Z shift of the reconstruction volume in angstrom + unit: + descriptive_name: Angstrom + symbol: Å + + alignment_volume_x_rotation: + range: float + description: Additional X rotation of the reconstruction volume in degrees + unit: + descriptive_name: degrees + symbol: ° + + alignment_tilt_offset: + range: float + description: Additional tilt offset in degrees + unit: + descriptive_name: degrees + symbol: ° + + alignment_local_alignment_file: + range: string + description: Path to the local alignment file + + # ============================================================================ + # Per Section Alignment Parameters fields + # ============================================================================ + per_section_alignment_x_offset: + range: float + description: In-plane X-shift of the projection in angstrom + unit: + descriptive_name: Angstrom + symbol: Å + + per_section_alignment_y_offset: + range: float + description: In-plane Y-shift of the projection in angstrom + unit: + descriptive_name: Angstrom + symbol: Å + + per_section_alignment_in_plane_rotation: + range: float + description: In-plane rotation of the projection in degrees + unit: + descriptive_name: degrees + symbol: ° + + per_section_alignment_beam_tilt: + range: float + description: Beam tilt during projection in degrees + unit: + descriptive_name: degrees + symbol: ° + + per_section_alignment_tilt_angle: + range: float + description: Tilt angle of the projection in degrees + unit: + descriptive_name: degrees + symbol: ° + + # ============================================================================ + # API slots + # ============================================================================ + api_sequential_identifier: + range: integer + description: An identifier to refer to a specific instance of this type + required: true + api_author_list_order: + range: integer + description: The order that the author is listed as in the associated publication + required: true + api_file_format: + range: string + description: File format label + required: true + api_s3_path: + range: string + description: Path to the file in s3 + required: true + api_https_path: + range: string + description: Path to the file as an https url + required: true + api_s3_prefix: + range: string + description: Path to a directory containing data for this entity as an S3 url + required: true + api_https_prefix: + range: string + description: Path to a directory containing data for this entity as an HTTPS url + required: true + api_run_name: + range: string + description: Name of a run + required: true + api_tiltseries_tilt_range: + range: float + minimum_value: 0 + maximum_value: 180 + required: true + description: Total tilt range from min to max in degrees + unit: + descriptive_name: degrees + symbol: ° + api_tomogram_size_x: + range: float + minimum_value: 0 + required: true + description: Tomogram voxels in the x dimension + unit: + descriptive_name: voxels + symbol: voxel + api_tomogram_size_y: + range: float + minimum_value: 0 + required: true + description: Tomogram voxels in the y dimension + unit: + descriptive_name: voxels + symbol: voxel + api_tomogram_size_z: + range: float + minimum_value: 0 + required: true + description: Tomogram voxels in the z dimension + unit: + descriptive_name: voxels + symbol: voxel + api_tomogram_is_standardized: + range: boolean + required: true + description: Whether this tomogram was generated per the portal's standards + api_annotation_file_source: + range: annotation_file_source_enum + description: The source type for the annotation file + api_alignment: + range: string + required: true + description: Describe a tiltseries alignment + api_frame_raw_angle: + range: float + minimum_value: -90 + maximum_value: 90 + required: true + description: Camera angle for a frame + api_frame_acquisition_order: + range: integer + required: False + description: Frame's acquistion order within a tilt experiment + api_frame_dose: + range: float + required: true + description: The raw camera angle for a frame + unit: + descriptive_name: electrons per square angstrom + symbol: e-/Å2 + api_frame_https_gain_file: + range: string + description: HTTPS path to the gain file for this frame + api_frame_s3_gain_file: + range: string + description: S3 path to the gain file for this frame + api_frame_is_gain_corrected: + range: boolean + description: Whether this frame has been gain corrected + + +enums: + # ============================================================================ + # Controlled vocabularies + # ============================================================================ + annotation_file_source_enum: + description: How the annotation file was acquired + permissible_values: + dataset_author: + description: Annotation submitted by dataset author + community: + description: Annotation submitted by community member + portal_standard: + description: Annotation submitted by portal standardization + annotation_method_type_enum: + description: Describes how the annotations were generated. + permissible_values: + manual: + description: Annotations were generated manually. + automated: + description: Annotations were generated automatically. + hybrid: + description: Annotations were generated semi-automatically. + + annotation_file_shape_type_enum: + description: Describes the shape of the annotation + permissible_values: + SegmentationMask: + description: A binary mask volume + OrientedPoint: + description: A series of coordinates and an orientation + Point: + description: A series of coordinates + InstanceSegmentation: + description: A volume with labels for multiple instances + + annotation_method_link_type_enum: + description: Describes the type of link associated to the annotation method. + permissible_values: + documentation: + description: Links to the documentation related to the method. + models_weights: + description: Links to the weights that the models used for generating annotations were trained with. + other: + description: Link to resources that does not fit in the other categories. + source_code: + description: Links to the source code of the method. + website: + description: Links to a website of the method or tool used to generate the annotation. + + deposition_types_enum: + description: Types of data a deposition has + permissible_values: + annotation: + description: The deposition comprises of new annotations for existing datasets + dataset: + description: The deposition comprises of new dataset(s). + tomogram: + description: The deposition comprises of new tomograms for existing datasets + + sample_type_enum: + description: Type of sample imaged in a CryoET study. + permissible_values: + cell: + description: Tomographic data of whole cells or cell sections. + tissue: + description: Tomographic data of tissue sections. + organism: + description: Tomographic data of sections through multicellular organisms. + organelle: + description: Tomographic data of purified organelles. + virus: + description: Tomographic data of purified viruses or VLPs. + in_vitro: + description: Tomographic data of in vitro reconstituted systems or mixtures of proteins. + in_silico: + description: Simulated tomographic data. + other: + description: Other type of sample. + + tiltseries_camera_acquire_mode_enum: + description: Camera acquisition mode + permissible_values: + counting: + description: Counting mode + superresolution: + description: Super-resolution mode + linear: + description: Linear mode + cds: + description: Correlated double sampling mode + + tiltseries_microscope_manufacturer_enum: + description: Microscope manufacturer + permissible_values: + FEI: + description: FEI Company + TFS: + description: Thermo Fisher Scientific + JEOL: + description: JEOL Ltd. + + fiducial_alignment_status_enum: + description: Fiducial Alignment method + permissible_values: + FIDUCIAL: + description: Alignment computed based on fiducial markers + NON_FIDUCIAL: + description: Alignment computed without fiducial markers + + tomogram_processing_enum: + description: Tomogram processing method + permissible_values: + denoised: + description: Tomogram was denoised + filtered: + description: Tomogram was filtered + raw: + description: Tomogram was not processed + + tomogram_reconstruction_method_enum: + description: Tomogram reconstruction method + permissible_values: + SART: + description: Simultaneous Algebraic Reconstruction Technique + Fourier Space: + description: Fourier space reconstruction + SIRT: + description: Simultaneous Iterative Reconstruction Technique + WBP: + description: Weighted Back-Projection + Unknown: + description: Unknown reconstruction method + + tomogram_type_enum: + description: Tomogram type + permissible_values: + CANONICAL: + description: Canonical tomogram (basis geometry for all annotations) + UNKNOWN: + description: Tomogram's was not submitted by the dataset author + + alignment_type_enum: + description: Type of alignment + permissible_values: + LOCAL: + description: per-section non-rigid alignment available + GLOBAL: + description: only per-section rigid alignment available + +types: + StringFormattedString: + description: A formatted string (variable) that represents a string. + base: string + pattern: '^[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$' + + FloatFormattedString: + description: A formatted string that represents a floating point number. + base: string + pattern: '^float[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$' + + IntegerFormattedString: + description: A formatted string that represents an integer. + base: string + pattern: '^int[ ]*\{[a-zA-Z0-9_-]+\}[ ]*$' + + VersionString: + description: A version number (only major, minor versions) + base: float + minimum_value: 0 + + URLorS3URI: + description: A URL or S3 URI + base: string + # TODO: Temporary pattern allowing cryoetportal-rawdatasets-dev, but will be removed in the future + pattern: '^(((https?|s3)://)|cryoetportal-rawdatasets-dev).*$' + + ORCID: + description: A unique, persistent identifier for researchers, provided by ORCID. + base: string + pattern: '[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$' + + BTO_ID: + description: A BRENDA Tissue Ontology identifier + base: string + pattern: '^BTO:[0-9]{7}$' + + CL_ID: + description: A Cell Ontology identifier + base: string + pattern: '^CL:[0-9]{7}$' + + GO_ID: + description: A Gene Ontology identifier + base: string + pattern: '^GO:[0-9]{7}$' + + WORMBASE_ID: + description: A WormBase identifier + base: string + pattern: 'WBStrain[0-9]{8}$' + + ONTOLOGY_ID: + description: An ontology identifier + base: string + pattern: '^[a-zA-Z]+:[0-9]+$' + + DOI: + description: A Digital Object Identifier + base: string + pattern: '^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+$' + + DOI_LIST: + description: A list of Digital Object Identifiers + base: string + pattern: '^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+(\s*,\s*(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+)*$' + + EMPIAR_ID: + description: An Electron Microscopy Public Image Archive identifier + base: string + pattern: '^EMPIAR-[0-9]+$' + + EMDB_ID: + description: An Electron Microscopy Data Bank identifier + base: string + pattern: '^EMD-[0-9]{4,5}$' + + PDB_ID: + description: A Protein Data Bank identifier + base: string + pattern: '^pdb[0-9a-zA-Z]{4,8}$' + + EMPIAR_EMDB_PDB_LIST: + description: A list of EMPIAR, EMDB, and PDB identifiers + base: string + pattern: '^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$' + + EMPIAR_EMDB_DOI_PDB_LIST: + description: A list of EMPIAR, EMDB, DOI, and PDB identifiers + base: string + pattern: '^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+|pdb[0-9a-zA-Z]{4,8}))*$' + +classes: + Any: + class_uri: linkml:Any + description: A placeholder for any type of data. + + # ============================================================================ + # Mixins + # ============================================================================ + DateStampedEntityMixin: + description: A set of dates at which a data item was deposited, published and last modified. + mixin: true + attributes: + deposition_date: + exact_mappings: + - cdp-common:deposition_date + release_date: + exact_mappings: + - cdp-common:release_date + last_modified_date: + exact_mappings: + - cdp-common:last_modified_date + + # ============================================================================ + # Cross-references to other databases and publications + # ============================================================================ + CrossReferencesMixin: + description: A set of cross-references to other databases and publications. + mixin: true + attributes: + publications: + range: DOI_LIST + recommended: true + description: Comma-separated list of DOIs for publications associated with the dataset. + related_database_entries: + range: EMPIAR_EMDB_PDB_LIST + recommended: true + description: Comma-separated list of related database entries for the dataset. + related_database_links: # DEPRECATED + range: string + description: Comma-separated list of related database links for the dataset. + dataset_citations: # DEPRECATED + range: string + description: Comma-separated list of DOIs for publications citing the dataset. + + AuthorMixin: + description: An entity with author data + mixin: true + attributes: + name: + exact_mappings: + - cdp-common:author_name + email: + exact_mappings: + - cdp-common:author_email + affiliation_name: + exact_mappings: + - cdp-common:author_affiliation_name + affiliation_address: + exact_mappings: + - cdp-common:author_affiliation_address + affiliation_identifier: + exact_mappings: + - cdp-common:author_affiliation_identifier + corresponding_author_status: + exact_mappings: + - cdp-common:author_corresponding_author_status + primary_author_status: + exact_mappings: + - cdp-common:author_primary_author_status diff --git a/schema/core/v2.0.0/metadata.yaml b/schema/core/v2.0.0/metadata.yaml new file mode 100644 index 000000000..7e122ecec --- /dev/null +++ b/schema/core/v2.0.0/metadata.yaml @@ -0,0 +1,691 @@ +id: metadata +name: cdp-meta +version: 1.1.0 +prefixes: + linkml: https://w3id.org/linkml/ + cdp-meta: metadata + ORCID: https://orcid.org/ + ROR: https://ror.org/ + UBERON: http://purl.obolibrary.org/obo/UBERON_ + CL: http://purl.obolibrary.org/obo/CL_ + GO: http://purl.obolibrary.org/obo/GO_ + #cdp-common: common +imports: + - linkml:types +default_range: Any +default_prefix: cdp-meta + +classes: + # ============================================================================ + # Snapshot / Thumbnail + # ============================================================================ + + PicturePath: + description: A set of paths to representative images of a piece of data. + attributes: + snapshot: + exact_mappings: + - cdp-common:snapshot + thumbnail: + exact_mappings: + - cdp-common:thumbnail + + # ============================================================================ + + # ============================================================================ + # Author / Annotator + # ============================================================================ + Author: + mixins: + - AuthorMixin + description: >- + Author of a scientific data entity. + attributes: + ORCID: + exact_mappings: + - cdp-common:author_orcid + # ============================================================================ + + # ============================================================================ + # Funding source information + # ============================================================================ + # Updating name from Funding to FundingDetails to avoid conflict in case insensitive file names + FundingDetails: + description: A funding source for a scientific data entity (base for JSON and DB representation). + attributes: + funding_agency_name: + exact_mappings: + - cdp-common:funding_agency_name + grant_id: + exact_mappings: + - cdp-common:funding_grant_id + # ============================================================================ + + # ============================================================================ + # Deposition, release and last modified dates + # ============================================================================ + DateStamp: + description: A set of dates at which a data item was deposited, published and last modified. + mixins: + - DateStampedEntityMixin + + # ============================================================================ + # Meta-Mixins + # ============================================================================ + DateStampedEntity: + description: An entity with associated deposition, release and last modified dates. + attributes: + dates: + range: DateStamp + required: true + + AuthoredEntity: + description: An entity with associated authors. + attributes: + authors: + range: Author + required: true + description: An ordered list of authors of the entity. + multivalued: true + inlined_as_list: true + list_elements_ordered: true + + FundedEntity: + description: An entity with associated funding sources. + attributes: + funding: + range: FundingDetails + recommended: true + description: An ordered list of funding sources for the entity. + multivalued: true + inlined_as_list: true + list_elements_ordered: true + + CrossReferences: + description: A set of cross-references to other databases and publications. + mixins: + - CrossReferencesMixin + + CrossReferencedEntity: + mixin: true + description: An entity with associated cross-references to other databases and publications. + attributes: + cross_references: + range: CrossReferences + + PicturedEntity: + description: An entity with associated preview images. + attributes: + key_photos: + range: PicturePath + description: A set of paths to representative images of the entity. + required: true + # ============================================================================ + + # ============================================================================ + # Experimental metadata + # ============================================================================ + # Updating name from Organism to OrganismDetails to avoid conflict in case insensitive file names + OrganismDetails: + description: &desc_Organism The species from which the sample was derived. + attributes: + name: + exact_mappings: + - cdp-common:organism_name + taxonomy_id: + exact_mappings: + - cdp-common:organism_taxid + + # Updating name from Tissue to TissueDetails to avoid conflict in case insensitive file names + TissueDetails: + description: &desc_Tissue The type of tissue from which the sample was derived. + attributes: + name: + exact_mappings: + - cdp-common:tissue_name + id: + exact_mappings: + - cdp-common:tissue_id + + CellType: + description: &desc_CellType The cell type from which the sample was derived. + attributes: + name: + exact_mappings: + - cdp-common:cell_name + id: + exact_mappings: + - cdp-common:cell_type_id + + CellStrain: + description: &desc_CellStrain The strain or cell line from which the sample was derived. + attributes: + name: + exact_mappings: + - cdp-common:cell_strain_name + id: + exact_mappings: + - cdp-common:cell_strain_id + + CellComponent: + description: &desc_CellComponent The cellular component from which the sample was derived. + attributes: + name: + exact_mappings: + - cdp-common:cell_component_name + id: + exact_mappings: + - cdp-common:cell_component_id + + ExperimentMetadata: + description: Metadata describing sample and sample preparation methods used in a cryoET dataset. + attributes: + sample_type: + exact_mappings: + - cdp-common:preparation_sample_type + sample_preparation: + exact_mappings: + - cdp-common:sample_preparation + grid_preparation: + exact_mappings: + - cdp-common:grid_preparation + other_setup: + exact_mappings: + - cdp-common:preparation_other_setup + organism: + description: *desc_Organism + range: OrganismDetails + tissue: + description: *desc_Tissue + range: TissueDetails + cell_type: + description: *desc_CellType + range: CellType + cell_strain: + description: *desc_CellStrain + range: CellStrain + cell_component: + description: *desc_CellComponent + range: CellComponent + # ============================================================================ + + # ============================================================================ + # dataset_metadata.json + # ============================================================================ + Dataset: + description: High-level description of a cryoET dataset. + mixins: + - DateStampedEntity + - AuthoredEntity + - FundedEntity + - CrossReferencedEntity + - ExperimentMetadata + + attributes: + dataset_identifier: + exact_mappings: + - cdp-common:dataset_identifier + dataset_title: + exact_mappings: + - cdp-common:dataset_title + dataset_description: + exact_mappings: + - cdp-common:dataset_description + + # ============================================================================ + + # ============================================================================ + # Depositions metadata + # ============================================================================ + Deposition: + description: Metadata describing a deposition. + mixins: + - DateStampedEntity + - AuthoredEntity + - CrossReferencedEntity + + attributes: + deposition_description: + exact_mappings: + - cdp-common:deposition_description + deposition_identifier: + exact_mappings: + - cdp-common:deposition_identifier + deposition_title: + exact_mappings: + - cdp-common:deposition_title + deposition_types: + exact_mappings: + - cdp-common:deposition_types + + # ============================================================================ + # TiltSeries metadata + # ============================================================================ + # Updating name from Camera to CameraDetails to avoid conflict in case insensitive file names + CameraDetails: + description: &desc_camera The camera used to collect the tilt series. + attributes: + acquire_mode: + exact_mappings: + - cdp-common:tiltseries_camera_acquire_mode + manufacturer: + exact_mappings: + - cdp-common:tiltseries_camera_manufacturer + model: + exact_mappings: + - cdp-common:tiltseries_camera_model + + # Updating name from Microscope to MicroscopeDetails to avoid conflict in case insensitive file names + MicroscopeDetails: + description: &desc_microscope The microscope used to collect the tilt series. + attributes: + additional_info: + exact_mappings: + - cdp-common:tiltseries_microscope_additional_info + manufacturer: + any_of: + - range: cdp-common:tiltseries_microscope_manufacturer + - range: cdp-common:StringFormattedString + model: + exact_mappings: + - cdp-common:tiltseries_microscope_model + + MicroscopeOpticalSetup: + description: &desc_microscope_optical_setup The optical setup of the microscope used to collect the tilt series. + attributes: + energy_filter: + exact_mappings: + - cdp-common:tiltseries_microscope_energy_filter + phase_plate: + exact_mappings: + - cdp-common:tiltseries_microscope_phase_plate + image_corrector: + exact_mappings: + - cdp-common:tiltseries_microscope_image_corrector + + TiltRange: + description: &desc_tilt_range The range of tilt angles in the tilt series. + attributes: + min: + any_of: + - range: cdp-common:tiltseries_tilt_min + - range: cdp-common:FloatFormattedString + max: + any_of: + - range: cdp-common:tiltseries_tilt_max + - range: cdp-common:FloatFormattedString + # ============================================================================ + + # ============================================================================ + # tiltseries_metadata.json + # ============================================================================ + TiltSeries: + description: Metadata describing a tilt series. + + attributes: + acceleration_voltage: + exact_mappings: + - cdp-common:tiltseries_acceleration_voltage + aligned_tiltseries_binning: + any_of: + - range: cdp-common:tiltseries_aligned_tiltseries_binning + - range: cdp-common:FloatFormattedString + ifabsent: 'float(1)' + binning_from_frames: + any_of: + - range: cdp-common:tiltseries_binning_from_frames + - range: cdp-common:FloatFormattedString + ifabsent: 'float(1)' + camera: + description: *desc_camera + range: CameraDetails + required: true + data_acquisition_software: + exact_mappings: + - cdp-common:tiltseries_data_acquisition_software + frames_count: + exact_mappings: + - cdp-common:tiltseries_frames_count + is_aligned: + exact_mappings: + - cdp-common:tiltseries_is_aligned + microscope: + description: *desc_microscope + range: MicroscopeDetails + required: true + microscope_optical_setup: + description: *desc_microscope_optical_setup + range: MicroscopeOpticalSetup + required: true + related_empiar_entry: + exact_mappings: + - cdp-common:tiltseries_related_empiar_entry + spherical_aberration_constant: + any_of: + - range: cdp-common:tiltseries_spherical_aberration_constant + - range: cdp-common:FloatFormattedString + tilt_alignment_software: + exact_mappings: + - cdp-common:tiltseries_tilt_alignment_software + tilt_axis: + any_of: + - range: cdp-common:tiltseries_tilt_axis + - range: cdp-common:FloatFormattedString + tilt_range: + description: *desc_tilt_range + range: TiltRange + required: true + tilt_series_quality: + any_of: + - range: cdp-common:tiltseries_tilt_series_quality + - range: cdp-common:IntegerFormattedString + tilt_step: + any_of: + - range: cdp-common:tiltseries_tilt_step + - range: cdp-common:FloatFormattedString + tilting_scheme: + exact_mappings: + - cdp-common:tiltseries_tilting_scheme + total_flux: + any_of: + - range: cdp-common:tiltseries_total_flux + - range: cdp-common:FloatFormattedString + pixel_spacing: + any_of: + - range: cdp-common:tiltseries_pixel_spacing + - range: cdp-common:FloatFormattedString + # ============================================================================ + + TomogramSize: + description: &desc_tomogram_size The size of a tomogram in voxels in each dimension. + attributes: + x: + range: integer + minimum_value: 0 + # TODO: uncomment after any_of is fixed https://github.com/linkml/linkml/issues/1521 + # any_of: + # - range: integer + # minimum_value: 0 + # - range: IntegerFormattedString + required: true + description: Number of pixels in the 3D data fast axis + unit: + descriptive_name: pixels + symbol: px + y: + range: integer + minimum_value: 0 + # TODO: uncomment after any_of is fixed https://github.com/linkml/linkml/issues/1521 + # any_of: + # - range: integer + # minimum_value: 0 + # - range: IntegerFormattedString + required: true + description: Number of pixels in the 3D data medium axis + unit: + descriptive_name: pixels + symbol: px + z: + range: integer + minimum_value: 0 + # TODO: uncomment after any_of is fixed https://github.com/linkml/linkml/issues/1521 + # any_of: + # - range: integer + # minimum_value: 0 + # - range: IntegerFormattedString + required: true + description: Number of pixels in the 3D data slow axis. This is the image projection direction at zero stage tilt + unit: + descriptive_name: pixels + symbol: px + + TomogramOffset: + description: &desc_tomogram_offset The offset of a tomogram in voxels in each dimension relative to the canonical tomogram. + attributes: + x: + range: integer + # TODO: uncomment after any_of is fixed https://github.com/linkml/linkml/issues/1521 + # any_of: + # - range: integer + # - range: IntegerFormattedString + required: true + description: x offset data relative to the canonical tomogram in pixels + unit: + descriptive_name: pixels + symbol: px + y: + range: integer + # TODO: uncomment after any_of is fixed https://github.com/linkml/linkml/issues/1521 + # any_of: + # - range: integer + # - range: IntegerFormattedString + required: true + description: y offset data relative to the canonical tomogram in pixels + unit: + descriptive_name: pixels + symbol: px + z: + range: integer + # TODO: uncomment after any_of is fixed https://github.com/linkml/linkml/issues/1521 + # any_of: + # - range: integer + # - range: IntegerFormattedString + required: true + description: z offset data relative to the canonical tomogram in pixels + unit: + descriptive_name: pixels + symbol: px + + # ============================================================================ + + # ============================================================================ + # tomogram_metadata.json + # ============================================================================ + Tomogram: + description: Metadata describing a tomogram. + mixins: + - AuthoredEntity + + attributes: + voxel_spacing: + any_of: + - range: cdp-common:tomogram_voxel_spacing + - range: cdp-common:FloatFormattedString + fiducial_alignment_status: + any_of: + - range: cdp-common:tomogram_fiducial_alignment_status + - range: cdp-common:StringFormattedString + ctf_corrected: + exact_mappings: + - cdp-common:tomogram_ctf_corrected + align_software: + exact_mappings: + - cdp-common:tomogram_align_software + reconstruction_method: + any_of: + - range: cdp-common:tomogram_reconstruction_method + - range: cdp-common:StringFormattedString + reconstruction_software: + exact_mappings: + - cdp-common:tomogram_reconstruction_software + processing: + exact_mappings: + - cdp-common:tomogram_processing + processing_software: + exact_mappings: + - cdp-common:tomogram_processing_software + tomogram_version: + exact_mappings: + - cdp-common:tomogram_version + affine_transformation_matrix: + description: The flip or rotation transformation of this author submitted tomogram is indicated here + range: float + array: + exact_number_dimensions: 2 + dimensions: + - exact_cardinality: 4 + - exact_cardinality: 4 + size: + description: *desc_tomogram_size + range: TomogramSize + offset: + description: *desc_tomogram_offset + range: TomogramOffset + required: true + # ============================================================================ + + # ============================================================================ + # Annotation metadata + # ============================================================================ + AnnotationConfidence: + description: &desc_annotation_confidence Metadata describing the confidence of an annotation. + attributes: + precision: + exact_mappings: + - cdp-common:annotation_confidence_precision + recall: + exact_mappings: + - cdp-common:annotation_confidence_recall + ground_truth_used: + exact_mappings: + - cdp-common:annotation_ground_truth_used + + AnnotationObject: + description: &desc_annotation_object Metadata describing the object being annotated. + attributes: + id: + exact_mappings: + - cdp-common:annotation_object_id + name: + exact_mappings: + - cdp-common:annotation_object_name + description: + exact_mappings: + - cdp-common:annotation_object_description + state: + exact_mappings: + - cdp-common:annotation_object_state + + AnnotationSourceFile: + description: &desc_annotation_source_file File and sourcing data for an annotation. Represents an entry in annotation.sources. + attributes: + file_format: + exact_mappings: + - cdp-common:annotation_source_file_format + glob_string: + exact_mappings: + - cdp-common:annotation_source_file_glob_string + glob_strings: + exact_mappings: + - cdp-common:annotation_source_file_glob_strings + is_visualization_default: + exact_mappings: + - cdp-common:annotation_source_file_is_visualization_default + + AnnotationOrientedPointFile: + is_a: AnnotationSourceFile + aliases: + - OrientedPoint + description: File and sourcing data for an oriented point annotation. Annotation that identifies points along with orientation in the volume. + attributes: + binning: + exact_mappings: + - cdp-common:annotation_source_file_binning + filter_value: + exact_mappings: + - cdp-common:annotation_source_file_filter_value + order: + exact_mappings: + - cdp-common:annotation_source_file_order + + AnnotationInstanceSegmentationFile: + is_a: AnnotationOrientedPointFile + aliases: + - InstanceSegmentation + description: File and sourcing data for an instance segmentation annotation. Annotation that identifies individual instances of object shapes. + attributes: # no extended attributes + + AnnotationPointFile: + is_a: AnnotationSourceFile + aliases: + - Point + description: File and sourcing data for a point annotation. Annotation that identifies points in the volume. + attributes: + binning: + exact_mappings: + - cdp-common:annotation_source_file_binning + columns: + exact_mappings: + - cdp-common:annotation_source_file_columns + delimiter: + exact_mappings: + - cdp-common:annotation_source_file_delimiter + + AnnotationSegmentationMaskFile: + is_a: AnnotationSourceFile + aliases: + - SegmentationMask + description: File and sourcing data for a segmentation mask annotation. Annotation that identifies an object. + attributes: # no extended attributes + + AnnotationSemanticSegmentationMaskFile: + is_a: AnnotationSourceFile + aliases: + - SemanticSegmentationMask + description: File and sourcing data for a semantic segmentation mask annotation. Annotation that identifies classes of objects. + attributes: + mask_label: + exact_mappings: + - cdp-common:annotation_source_file_mask_label + + # ============================================================================ + + # ============================================================================ + # annotation_metadata.json + # ============================================================================ + Annotation: + description: Metadata describing an annotation. + mixins: + - DateStampedEntity + - AuthoredEntity + + attributes: + annotation_method: + exact_mappings: + - cdp-common:annotation_method + annotation_object: + description: *desc_annotation_object + range: AnnotationObject + required: true + annotation_publications: + exact_mappings: + - cdp-common:annotation_publications + annotation_software: + exact_mappings: + - cdp-common:annotation_software + confidence: + description: *desc_annotation_confidence + range: AnnotationConfidence + files: + description: *desc_annotation_source_file + range: AnnotationSourceFile + multivalued: true + inlined_as_list: true + list_elements_ordered: true + ground_truth_status: + exact_mappings: + - cdp-common:annotation_ground_truth_status + is_curator_recommended: + exact_mappings: + - cdp-common:annotation_is_curator_recommended + method_type: + exact_mappings: + - cdp-common:annotation_method_type + object_count: + exact_mappings: + - cdp-common:annotation_object_count + version: + exact_mappings: + - cdp-common:annotation_version + + # ============================================================================