This schema defines a structure for storing fish and plankton acoustic scattering model data, mainly for input to the echoSMs anatomical datastore.
The reference version of the schema (formatted as a JSON-schema file) will always be available in the echoSMs github repository.
No Additional PropertiesA Universally Unique IDentifier for this specimen as per RFC9562. Generated by the datastore.
A version number that increments whenever this specimen is updated. Generated and updated by the datastore.
Value must be greater or equal to 1
The timestamp when this specimen dataset was last modified, in RFC9557 format, including the timezone. Generated and updated by the datastore.
A note about the changes in this version.
Names or identifying descriptions of persons or organisations that updated or created this dataset.
No Additional ItemsA Universally Unique IDentifier for a dataset as RFC9562. Datasets are used only to group multiple specimens together. They contain no information that is not already in the specimen metadata.
A name for the dataset.
A description of the specimen.
No Additional ItemsThe type of anatomy that this dataset contains.
Taxonomical hierarchy level of class that is consistent with WoRMS.
Taxonomical hierarchy level of order that is consistent with WoRMS.
Taxonomical hierarchy level of family that is consistent with WoRMS.
Taxonomical hierarchy level of genus that is consistent with WoRMS.
Taxonomical hierarchy level of species that is consistent with WoRMS.
Vernacular names for the organism.
No Additional ItemsA literature reference for the dataset. If available, a DOI or URI is recommended.
Name of the data collection activity (if any), such as voyage code, project name, etc.
Name or description of the location where organism was collected.
Latitude of location where organism was collected.
Value must be greater or equal to -90 and lesser or equal to 90
Units for latitude. Positive values indicate north of the equator.
Longitude of location where organism was collected.
Value must be greater or equal to -180 and lesser or equal to 180
Units for longitude. Positive values indicate east of the prime meridian.
Depth below surface of organism collection location.
Value must be greater or equal to 0
Units for depth.
The date when the specimen was collected in RFC9557 format. Use an empty string if the date is unknown.
""
The date when the dataset was imaged, in RFC9557 format. Use an empty string if the date is unknown.
""
Description of data collection details.
Explanatory notes about the shape data.
No Additional ItemsMethod used to obtain the raw image data.
Method used to obtain the specimen shape.
Description of processing used to convert raw images into shapes, including any manipulation of image data (for example, smoothing, edge enhancement, rotation, etc).
Original scattering model type.
Method used to obtain sound speed in the specimen.
Use of an empirical relationship between density and sound speed
Specific value:"density to sound speed relationship"
Estimated from the time taken for an acoustic pulse to travel from a source to destination transducer through the object being measured
Specific value:"time-of-flight"
Sound speed is determined by measuring the reflection time from the back of a tissue sample using a single transducer (vs the two used in a typical time-of-flight measurement)
Specific value:"pulse-echo"
Inferred or inverted from a fitted scattering model or other approach
Specific value:"inverted"
Obtained from an existing publication, report, etc
Specific value:"literature"
The method used to estimate the sound speed is unknown
Specific value:"unknown"
The method used to estimate the sound speed is not one of the listed methods
Specific value:"other"
Method used to obtain density in the specimen
Conversion of computer tomography Hounsfield unit numbers into density
Specific value:"CT density"
Division of object mass by it's volume, measured using liquid displacement
Specific value:"liquid displacement"
Obtained from an existing publication, report, etc
Specific value:"literature"
Density is determined by mixing two liquids of known densities until the animal reaches neutral buoyancy
Specific value:"titration"
Gravimetric displacement that determines an animal's volume by weighing the mass of seawater required to return a graduated cylinder to its original volume after the animal has been added
Specific value:"pipette"
Density is calculated by weighing animals in two different fluids of known densities
Specific value:"dual-density"
Weighted average of known densities of an animal's chemical components, such as water, lipids, proteins, and other contribution sources
Specific value:"from composition"
Inferred or inverted from a fitted scattering model or other approach
Specific value:"inverted"
The method used to estimate the density is unknown
Specific value:"unknown"
The method used to estimate the density is not one of the listed methods
Specific value:"other"
Size of the entire dataset (including raw data). Generated by the datastore server.
Value must be greater or equal to 0
Units for dataset_size. Generated by the datastore server.
The viewpoint of the imaging x-ray machine to the anatomical feature.
The exposure time setting of the imaging x-ray machine.
Unit of exposure time.
Focal length setting of the imaging x-ray machine.
Unit of focal length.
The kilovoltage peak setting of the imaging x-ray machine.
The milliamperage setting of the imaging x-ray machine.
A name that identifies the specimen.
Condition of the specimen when it was imaged.
Length of the specimen.
Value must be greater or equal to 0
Units for lengths, dimensions, and sizes.
Weight of the specimen.
Value must be greater or equal to 0
Units for weight.
Sex of specimen
Type of length measurement.
Type of shape data used for this specimen.
Data that specifies the shapes in the specimen.
Must contain a minimum of 1 items
Represents a three-dimensional shape using a dorsal and lateral outline.
No Additional Properties"outline"
Units for lengths, dimensions, and sizes.
Type of reflecting boundary for this shape.
x-coordinate of shape centreline.
Must contain a minimum of 1 items
y-coordinate of shape centreline.
Must contain a minimum of 1 items
z-coordinate of shape centreline.
Must contain a minimum of 1 items
Height of the shape at each centreline point.
Must contain a minimum of 1 items
Value must be greater or equal to 0
Width of the shape at each centreline point.
Must contain a minimum of 1 items
Value must be greater or equal to 0
Mass density of shape.
Must contain a minimum of 1 items
Value must be greater or equal to 0
Units for mass density.
Compressional sound speed in shape.
Must contain a minimum of 1 items
Value must be greater or equal to 0
Units for sound speed.
Transversal (shear) sound speed in shape.
Must contain a minimum of 1 items
Value must be greater or equal to 0
Units for sound speed.
Ratio of mass densities of the shape and the surrounding material or shape.
Must contain a minimum of 1 items
Value must be greater or equal to 0
Ratio of compressional sound speed of the and the surrounding material or shape.
Must contain a minimum of 1 items
Value must be greater or equal to 0
Young's modulus, E, of the shape.
Must contain a minimum of 1 items
Value must be greater or equal to 0
Units for Young's modulus.
Represents a three-dimensional shape using a triangulated mesh.
No Additional Properties"surface"
Units for lengths, dimensions, and sizes.
Type of reflecting boundary for this shape.
x-coordinates of surface nodes.
Must contain a minimum of 1 items
y-coordinates of surface nodes.
Must contain a minimum of 1 items
z-coordinates of surface nodes.
Must contain a minimum of 1 items
Zero-based indices into x, y, and z that define node 0 of a surface triangle.
Must contain a minimum of 1 items
Value must be greater or equal to 0
Zero-based indices into x, y, and z that define node 1 of a surface triangle.
Must contain a minimum of 1 items
Value must be greater or equal to 0
Zero-based indices into x, y, and z that define node 2 of a surface triangle.
Must contain a minimum of 1 items
Value must be greater or equal to 0
x-component of outward-pointing normal vector for each facet.
Must contain a minimum of 1 items
y-component of outward-pointing normal vector for each facet.
Must contain a minimum of 1 items
z-component of outward-pointing normal vector for each facet.
Must contain a minimum of 1 items
Mass density of shape.
Value must be greater or equal to 0
Must contain a minimum of 1 items
Must contain a maximum of 1 items
Value must be greater or equal to 0
Units for mass density.
Compressional sound speed in shape.
Value must be greater or equal to 0
Must contain a minimum of 1 items
Must contain a maximum of 1 items
Value must be greater or equal to 0
Units for sound speed.
Transversal (shear) sound speed in shape.
Value must be greater or equal to 0
Must contain a minimum of 1 items
Must contain a maximum of 1 items
Value must be greater or equal to 0
Units for sound speed.
Ratio of mass densities of the shape and the surrounding material or shape.
Value must be greater or equal to 0
Must contain a minimum of 1 items
Must contain a maximum of 1 items
Value must be greater or equal to 0
Ratio of compressional sound speed of the and the surrounding material or shape.
Value must be greater or equal to 0
Must contain a minimum of 1 items
Must contain a maximum of 1 items
Value must be greater or equal to 0
Young's modulus, E, of the shape.
Value must be greater or equal to 0
Must contain a minimum of 1 items
Must contain a maximum of 1 items
Value must be greater or equal to 0
Units for Young's modulus.
Represents a three-dimensional shape using voxels.
No Additional Properties"voxels"
Voxel size, ordered x, y, z.
Must contain a minimum of 3 items
Must contain a maximum of 3 items
Value must be greater or equal to 0
Units for lengths, dimensions, and sizes.
Mass density of voxels.
Must contain a minimum of 1 items
Must contain a minimum of 1 items
Must contain a minimum of 1 items
Value must be greater or equal to 0
Units for mass density.
Compressional sound speed of voxels.
Must contain a minimum of 1 items
Must contain a minimum of 1 items
Must contain a minimum of 1 items
Value must be greater or equal to 0
Units for sound speed.
Represents a three-dimensional shape using categorised voxels.
No Additional Properties"categorised voxels"
Voxel size, ordered x, y, z.
Must contain a minimum of 3 items
Must contain a maximum of 3 items
Value must be greater or equal to 0
Units for lengths, dimensions, and sizes.
Voxel categories
Must contain a minimum of 1 items
Must contain a minimum of 1 items
Must contain a minimum of 1 items
Mass density of voxels categories.
Must contain a minimum of 1 items
Value must be greater or equal to 0
Units for mass density.
Compressional sound speed of voxel categories.
Must contain a minimum of 1 items
Value must be greater or equal to 0
Units for sound speed.
Represents a three-dimensional shape using the combination of one or more geometric shapes.
No Additional PropertiesThe centre of the cylinder for application of the origin, roll, pitch, and yaw is at radius=0 and halfway along the cylinder length.
No Additional Properties"cylinder"
Radius of the cylinder.
Value must be greater or equal to 0
Length of the cylinder.
Value must be greater or equal to 0
A sphere, prolate spheroid, or oblate spheroid. The polar axis of the spheroids lies along the x-axis of the echoSMs coordinate system (prior to application of any tilt, roll, and yaw). An oblate spheroid occurs when the equatorial radius is greater than the polar radius and a prolate spheroid when the polar radius is greater than the equatorial radius. A sphere is generated when the polar and equatorial radii are the same.
No Additional Properties"spheroid"
The equatorial radius of the spheroid. In the echoSMs coordinate system the equatorial radius is along the y- and z-axes.
Value must be greater or equal to 0
The polar radius of the spheroid. In the echoSMs coordinate system the polar axis is the x-axis.
Value must be greater or equal to 0
"geometric"
Geometric form of this shape
The units of the shape dimensions.
The units used for pitch, roll, and yaw attributes
The pitch of the shape in the echoSMs coordinate system.
Value must be greater or equal to 0.0 and lesser or equal to 180.0
The roll of the shape in the echoSMs coordinate system.
Value must be greater or equal to -90.0 and lesser or equal to 90.0
The yaw of the shape in the echoSMs coordinate system.
Value must be greater or equal to -180.0 and lesser or equal to 180.0
Mass density of the shape.
Value must be greater or equal to 0
Units for mass density.
Compressional sound speed of the shape.
Value must be greater or equal to 0
Units for sound speed.
Transversal (shear) sound speed in shape.
Value must be greater or equal to 0
Units for sound speed.
The location of the shape's centre, ordered (x, y, z) as per the echoSMs coordinate system.
Must contain a minimum of 3 items
Must contain a maximum of 3 items
The units of the origin coordinates.
Name for the shape.
Type of anatomical feature represented by this shape.
Was the shape straightened during the processing.
Was the shape smoothed during the processing.
Was the shape rotated during the processing.
Explanatory notes about the straightening, smoothing, and rotation of the shape.
No Additional Items