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 PropertiesThe license that applies to this specimen data. Only some Creative Commons licenses are permitted (to ensure that the data remain freely available and usable).
These data have no license. Use this option as a last resort as it can create uncertainty about how the data can be used. May be appropriate for historical data where the data creater or owner cannot provide a license (although CC0 could be used in that case).
Specific value:"no license"
CC Zero. No Copyright. The person who associated a work with this deed has dedicated the work to the public domain by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. Canonical URL: https://creativecommons.org/publicdomain/zero/1.0/.
Specific value:"CC0 1.0"
CC BY. You are free to:
share - copy and redistribute the material in any medium or format for any purpose, even commercially,
adapt - remix, transform, and build upon the material for any purpose, even commercially.
attribution - you must give appropriate credit, provide a link to the license, and indicate if changes were made.
Canonical URL: https://creativecommons.org/licenses/by/4.0/.
"CC BY 4.0"
CC BY. You are free to:
share - copy and redistribute the material in any medium or format for any purpose, even commercially,
adapt - remix, transform, and build upon the material for any purpose, even commercially.
attribution - you must give appropriate credit, provide a link to the license, and indicate if changes were made,
sharealike - if you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original.
Canonical URL: https://creativecommons.org/licenses/by-sa/4.0/.
"CC BY-SA 4.0"
A Universally Unique IDentifier for this specimen as per RFC9562. Populated by the datastore if empty.
A version number that increments whenever this specimen is updated. Any existing value is overwritten 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. Any existing timestamp is overwritten by the datastore.
A note about the changes in this version. Can be an empty string but a short note is very much recommended.
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.
The WoRMS aphiaID of the specimen's species. Use a value of 0 if the specimen is not from a species.
Value must be greater or equal to 0
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). Any value is overwritten by the datastore server.
Value must be greater or equal to 0
Units for dataset_size.
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. Is a superset of the ICES AC_Sex vocabulary
Type of length measurement. Is a superset of the ICES AC_LengthMeasurementType vocabulary
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.
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 ItemsType 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.
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 Itemsx-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"
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 ItemsVoxel 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"
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 ItemsVoxel 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 fromed by the union of one or more geometric shapes.
"geometric"
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 ItemsMass 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.
Units for lengths, dimensions, and sizes.
The units used for pitch, roll, and yaw attributes
The simple geometries that make up this shape.
Must contain a minimum of 1 items
An optionally uniformly bent cylinder. When pitch, roll, and yaw are zero, the cylinder lies along the x-axis of the echoSMs coordinate system.
No Additional Properties"cylinder"
Radius of the cylinder.
Value must be greater or equal to 0.0
Length of the cylinder.
Value must be greater or equal to 0.0
Bend radius of the cylinder, taken along the centreline of the cylinder. Bending occurs in the x-z plane. If this property is absent, the cylinder is not bent.
Value must be greater or equal to 0.0
The direction in which the cylinder is bent.
The ends of the cylinder will bend upwards (in the echoSMs coordinate system this in the negative z-direction).
Specific value:"up"
The ends of the cylinder will bend downwards (in the echoSMs coordinate system this in the positive z-direction).
Specific value:"down"
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
The location of the shape's centroid, ordered (x, y, z) as per the echoSMs coordinate system.
Must contain a minimum of 3 items
Must contain a maximum of 3 items
A sphere, prolate spheroid, or oblate spheroid. The polar axis of the spheroid 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 0.0
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 0.0
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 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
The location of the shape's centroid, ordered (x, y, z) as per the echoSMs coordinate system.
Must contain a minimum of 3 items
Must contain a maximum of 3 items