EchoSMs anatomical data store schema
Title: EchoSMs anatomical data store schema
Type object
Additional properties
Description: This document is the JSON schema for the echoSMs anatomical data store. It provides a standardised structure for storing fish and plankton acoustic scattering model data.
Property
Type
Title/Description
+ dataset_id
string
A unique identifier for this dataset, generated by the data storage system.
+ description
string
A description of the dataset.
+ anatomical_category
enum (of string)
The type of anatomy that this dataset contains.
+ anatomical_features
array of enum (of string)
The type of anatomical features in this dataset.
+ date_first_added
string
The date when these metadata were first created, in RFC9557 format.
+ date_last_modified
string
The date when these metadata were last modified, in RFC9557 format.
+ aphiaID
integer
The WoRMS aphiaID of the species in this dataset.
- class
string
Taxonomical hierarchy level of class that is consistent with WoRMS.
- order
string
Taxonomical hierarchy level of order that is consistent with WoRMS.
- family
string
Taxonomical hierarchy level of family that is consistent with WoRMS.
- genus
string
Taxonomical hierarchy level of genus that is consistent with WoRMS.
- species
string
Taxonomical hierarchy level of species that is consistent with WoRMS.
- vernacular_name
string
A vernacular name for the organism.
- reference
string
A literature reference for the dataset. If available, a DOI or URI is recommended.
- activity_name
string
Name of the data collection activity (if any), such as voyage code, project name, etc.
- location
string
Name or description of the location where organism was collected.
- latitude
number
Latitude of location where organism was collected (decimal degrees).
- longitude
number
Longitude of location where organism was collected (decimal degrees).
- depth
number
Depth below surface of organism collection location (m).
+ date_collection
string
The date or date range when the dataset was collected, in RFC9557 format.
+ date_image
string
The date when the dataset was imaged, in RFC9557 format.
- investigators
array of string
Names or identifying descriptions of persons or organisations that created this dataset.
- data_collection_description
string
Description of data collection details.
- note
string
Explanatory notes about the shape data.
+ imaging_method
enum (of string)
Method used to obtain the raw image data.
+ shape_method
enum (of string)
Method used to obtain the specimen shape.
- shape_method_processing
string
Description of processing used to convert raw images into shapes, including any manipulation of image data (for example, smoothing, edge enhancement, rotation, etc).
- model_type
enum (of string)
Original scattering model type.
- sound_speed_method
enum (of string)
Method used to obtain sound speed in the feature.
- mass_density_method
enum (of string)
Method used to obtain density in the feature.
+ shape_data_types
array of enum (of string)
Shape data types in this dataset.
+ dataset_size
number
Size of the entire dataset (including raw data) (MiB). Generated by the data store server.
+ specimens
array of object
Specimen data.
dataset_idDescription: A unique identifier for this dataset, generated by the data storage system.
descriptionDescription: A description of the dataset.
anatomical_categoryDescription: The type of anatomy that this dataset contains.
Must be one of:
* "tissue"
* "organ"
* "organ system"
* "organism"
* "other"
anatomical_features
Type array of enum (of string)
Description: The type of anatomical features in this dataset.
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
Must be one of:
* "body"
* "swimbladder"
* "backbone"
* "muscle"
* "other"
date_first_addedDescription: The date when these metadata were first created, in RFC9557 format.
date_last_modifiedDescription: The date when these metadata were last modified, in RFC9557 format.
aphiaIDDescription: The WoRMS aphiaID of the species in this dataset.
classDescription: Taxonomical hierarchy level of class that is consistent with WoRMS.
orderDescription: Taxonomical hierarchy level of order that is consistent with WoRMS.
familyDescription: Taxonomical hierarchy level of family that is consistent with WoRMS.
genusDescription: Taxonomical hierarchy level of genus that is consistent with WoRMS.
speciesDescription: Taxonomical hierarchy level of species that is consistent with WoRMS.
vernacular_nameDescription: A vernacular name for the organism.
referenceDescription: A literature reference for the dataset. If available, a DOI or URI is recommended.
activity_nameDescription: Name of the data collection activity (if any), such as voyage code, project name, etc.
locationDescription: Name or description of the location where organism was collected.
latitudeDescription: Latitude of location where organism was collected (decimal degrees).
Restrictions
Minimum ≥ -90
Maximum ≤ 90
longitudeDescription: Longitude of location where organism was collected (decimal degrees).
Restrictions
Minimum ≥ -180
Maximum ≤ 180
depthDescription: Depth below surface of organism collection location (m).
date_collectionDescription: The date or date range when the dataset was collected, in RFC9557 format.
date_imageDescription: The date when the dataset was imaged, in RFC9557 format.
investigatorsDescription: Names or identifying descriptions of persons or organisations that created this dataset.
Array restrictions
Min items N/A
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
data_collection_descriptionDescription: Description of data collection details.
noteDescription: Explanatory notes about the shape data.
imaging_methodDescription: Method used to obtain the raw image data.
Must be one of:
* "radiograph"
* "CT"
* "MRI"
* "photograph"
* "3D scanner"
* "unknown"
* "other"
* "not applicable"
shape_methodDescription: Method used to obtain the specimen shape.
Must be one of:
* "manual outline of image(s)"
* "automated outline of images(s)"
* "3D scan of object"
* "not applicable"
* "unknown"
* "other"
shape_method_processingDescription: Description of processing used to convert raw images into shapes, including any manipulation of image data (for example, smoothing, edge enhancement, rotation, etc).
model_typeDescription: Original scattering model type.
Must be one of:
* "KRM"
* "KA"
* "DWBA"
* "PTDWBA"
* "FEM"
* "BEM"
* "MFS"
* "unknown"
* "other"
sound_speed_methodDescription: Method used to obtain sound speed in the feature.
Must be one of:
* "density to sound speed relationship"
* "time-of-flight"
* "literature"
* "unknown"
* "other"
mass_density_methodDescription: Method used to obtain density in the feature.
Must be one of:
* "CT density"
* "liquid displacement"
* "literature"
* "unknown"
* "other"
shape_data_types
Type array of enum (of string)
Description: Shape data types in this dataset.
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
Must be one of:
* "surface"
* "voxels"
* "outline"
dataset_sizeDescription: Size of the entire dataset (including raw data) (MiB). Generated by the data store server.
specimensDescription: Specimen data.
Array restrictions
Min items N/A
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
Type object
Additional properties
Property
Type
Title/Description
+ specimen_id
string
A name that uniquely identifies each specimen in a dataset.
+ specimen_condition
enum (of string)
Condition of the specimen when it was imaged.
+ length
number
Length of the specimen (m).
- weight
number
Weight of the specimen (kg).
- sex
enum (of string)
Sex of specimen
+ length_type
enum (of string)
Type of length measurement.
+ shape_type
enum (of string)
Type of shape data used for this specimen.
+ shapes
array of object
Shape data.
specimen_idDescription: A name that uniquely identifies each specimen in a dataset.
specimen_conditionDescription: Condition of the specimen when it was imaged.
Must be one of:
* "fresh"
* "frozen"
* "thawed"
* "unknown"
* "other"
lengthDescription: Length of the specimen (m).
weightDescription: Weight of the specimen (kg).
sexDescription: Sex of specimen
Must be one of:
* "female"
* "male"
* "immature"
* "unknown"
length_typeDescription: Type of length measurement.
Must be one of:
* "total length"
* "fork length"
* "standard length"
* "lower jaw fork length"
* "total width"
* "carapace length"
* "curved fork length"
* "disc width"
* "stretched total length"
* "CCAMLR krill - front of eye to tip of telson"
* "unknown"
* "other"
shape_typeDescription: Type of shape data used for this specimen.
Must be one of:
* "outline"
* "surface"
* "voxels"
shapesDescription: Shape data.
Array restrictions
Min items N/A
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
Type combining
Additional properties
Property
Type
Title/Description
+ name
string
Name of the shape, e.g., 'body', 'swimbladder', 'bone', 'inclusion', etc.
item 0
Type object
Additional properties
Property
Type
Title/Description
- shape_type
const
-
+ x
array of number
x-coordinate of shape centreline (m).
+ y
array of number
y-coordinate of shape centreline (m).
+ z
array of number
z-coordinate of shape centreline (m).
+ height
array of number
Height of the shape at each centreline point (m).
+ width
array of number
Width of the shape at each centreline point (m).
- mass_density
array of number
Mass density of shape (kg/m³).
- sound_speed_compressional
array of number
Compressional sound speed in shape (m/s).
- sound_speed_shear
array of number
Transversal (shear) sound speed in shape (m/s).
- mass_density_ratio
array of number
Ratio of mass densities of the shape and the surrounding material or shape.
- sound_speed_ratio
array of number
Ratio of compressional sound speed of the and the surrounding material or shape (m/s).
- youngs_modulus
array of number
Young's modulus, E, of the shape (Pa).
+ boundary
enum (of string)
Type of reflecting boundary for this shape.
shape_typeSpecific value: "outline"
xDescription: x-coordinate of shape centreline (m).
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
Each item of this array must be
Description
x items -
yDescription: y-coordinate of shape centreline (m).
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
Each item of this array must be
Description
y items -
zDescription: z-coordinate of shape centreline (m).
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
Each item of this array must be
Description
z items -
heightDescription: Height of the shape at each centreline point (m).
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
widthDescription: Width of the shape at each centreline point (m).
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
Each item of this array must be
Description
width items -
mass_densityDescription: Mass density of shape (kg/m³).
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
sound_speed_compressionalDescription: Compressional sound speed in shape (m/s).
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
sound_speed_shearDescription: Transversal (shear) sound speed in shape (m/s).
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
mass_density_ratioDescription: Ratio of mass densities of the shape and the surrounding material or shape.
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
sound_speed_ratioDescription: Ratio of compressional sound speed of the and the surrounding material or shape (m/s).
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
youngs_modulusDescription: Young's modulus, E, of the shape (Pa).
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
boundary
Type enum (of string)
Defined in #/$defs/boundary
Description: Type of reflecting boundary for this shape.
Must be one of:
* "hard"
* "soft"
* "fluid"
item 1
Type object
Additional properties
Property
Type
Title/Description
- shape_type
const
-
+ x
array of number
x-coordinates of surface nodes (m).
+ y
array of number
y-coordinates of surface nodes (m).
+ z
array of number
z-coordinates of surface nodes (m).
+ facets_0
array of integer
Zero-based indices into x, y, and z that define node 0 of a surface triangle.
+ facets_1
array of integer
Zero-based indices into x, y, and z that define node 1 of a surface triangle.
+ facets_2
array of integer
Zero-based indices into x, y, and z that define node 2 of a surface triangle.
+ normals_x
array of number
x-component of outward-pointing normal vector for each facet.
+ normals_y
array of number
y-component of outward-pointing normal vector for each facet.
+ normals_z
array of number
z-component of outward-pointing normal vector for each facet.
- mass_density
number
Mass density of shape (kg/m³).
- sound_speed_compressional
number
Compressional sound speed in shape (m/s).
- sound_speed_shear
number
Transversal (shear) sound speed in shape (m/s).
- mass_density_ratio
number
Ratio of mass densities of the shape and the surrounding material or shape.
- sound_speed_ratio
number
Ratio of compressional sound speed of the and the surrounding material or shape (m/s).
- youngs_modulus
number
Young's modulus, E, of the shape (Pa).
+ boundary
enum (of string)
Type of reflecting boundary for this shape.
shape_typeSpecific value: "surface"
xDescription: x-coordinates of surface nodes (m).
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
Each item of this array must be
Description
x items -
yDescription: y-coordinates of surface nodes (m).
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
Each item of this array must be
Description
y items -
zDescription: z-coordinates of surface nodes (m).
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
Each item of this array must be
Description
z items -
facets_0Description: Zero-based indices into x, y, and z that define node 0 of a surface triangle.
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
facets_1Description: Zero-based indices into x, y, and z that define node 1 of a surface triangle.
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
facets_2Description: Zero-based indices into x, y, and z that define node 2 of a surface triangle.
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
normals_xDescription: x-component of outward-pointing normal vector for each facet.
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
normals_yDescription: y-component of outward-pointing normal vector for each facet.
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
normals_zDescription: z-component of outward-pointing normal vector for each facet.
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
mass_densityDescription: Mass density of shape (kg/m³).
sound_speed_compressionalDescription: Compressional sound speed in shape (m/s).
sound_speed_shearDescription: Transversal (shear) sound speed in shape (m/s).
mass_density_ratioDescription: Ratio of mass densities of the shape and the surrounding material or shape.
sound_speed_ratioDescription: Ratio of compressional sound speed of the and the surrounding material or shape (m/s).
youngs_modulusDescription: Young's modulus, E, of the shape (Pa).
boundary
Type enum (of string)
Defined in #/$defs/boundary
Description: Type of reflecting boundary for this shape.
Must be one of:
* "hard"
* "soft"
* "fluid"
item 2
Type object
Additional properties
shape_typeSpecific value: "voxels"
voxel_sizeDescription: Voxel size, ordered x, y, z (m).
Array restrictions
Min items 3
Max items 3
Items unicity False
Additional items False
Tuple validation See below
mass_densityDescription: Mass density of voxels (kg/m³).
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
sound_speed_compressionalDescription: Compressional sound speed of voxels (kg/m³).
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
Array restrictions
Min items 1
Max items N/A
Items unicity False
Additional items False
Tuple validation See below
nameDescription: Name of the shape, e.g., 'body', 'swimbladder', 'bone', 'inclusion', etc.
Generated using json-schema-for-humans on 2025-08-31 at 08:34:51 +0000
Property 
Property 