Predefined subclasses for Signal

Representative classes of the Signal class are described below.

Sampled and its subclasses

Sampled

class Sampled

for signal that is continuously sampled. An example of Sampled may be found here.

type

a required string property inherited as an Entity instance. This property must hold "Sampled" or the name of one of its subclasses.

description

a required string property inherited as an Entity instance.

role

a required string property referring to what role it plays in the context of this physiology experiment, as it is inherited from Signal.

quality

a required string property describing the physical quality that this signal is supposed to reflect, as it is inherited from Signal.

range

a required object property to describe what algebraic values this signal must hold, as it is inherited from Signal.

sampling-rate

a required Quantity property to specify the sampling rate of this signal.

generated-by

a required property indicating what spatial existence generates/emits this signal, as it is inherited from Signal.

monitored-by

a required property indicating what spatial existence monitors/reads this signal, as it is inherited from Signal.

reference

an optional string or [ string ] property inherited as an Entity instance.

There are several pre-defined subclasses. Although most physiology experiments (except for brain-imaging studies) can be described using the ones below, it is going to be possible at some point to define your own subclasses, too.

Scan

Scan is a subclass that represents loops of scans.

This class is the base class for “scanning”-type sampling methods as a whole. There are more common, usage-dependent sub-classes such as LineScan, Video, and Volume, so it is recommended to use them if your use case falls into one of them.

class Scan

represents any type of scanning method.

type

a required string property inherited as an Entity instance. This property must hold "Scan" or the name of one of its subclasses.

description

a required string property inherited as an Entity instance.

role

a required string property referring to what role it plays in the context of this physiology experiment, as it is inherited from Signal.

quality

a required string property describing the physical quality that this signal is supposed to reflect, as it is inherited from Signal.

range

a required object property to describe what algebraic values this signal must hold, as it is inherited from Signal.

sampling-rate

a required (pixel-)sampling rate of this signal, as it is inherited from Sampled.

size

a required Space property representing the number of pixels/voxels for each single scan.

For a Scan entity, this property probably holds a single-dimensional Space instance.

Caution

The current specification assumes that the number of pixels or voxels does not change dynamically during acquisition. If it changes from run to run, or during individual runs, consider holding this value as a variable.

generated-by

a required property indicating what spatial existence generates/emits this signal, as it is inherited from Signal.

monitored-by

a required property indicating what spatial existence monitors/reads this signal, as it is inherited from Signal.

scan-rate

an optional (but recommended) Quantity property representing the number of scans (i.e. sampling for size times) being run per unit time.

In most cases, the number is the inverse of the time taken to obtain size number of samples, but it may be exactly the same quantity as sampling-rate if e.g. sampling occurs simultaneously from multiple electrodes.

The unit is normally based on Hz.

reference

an optional string or [ string ] property inherited as an Entity instance.

Predefined subclasses of Scan

For the following subclasses, the defined properties are exactly the same as what Scan has, but a certain meaning is added in terms of ontology.

class LineScan

a subclass of Scan used to represent a line scan-based sampling. For properties, refer to Scan.

class MEA

a subclass of Scan used to represent a multi-electrode array. For properties, refer to Scan.

Note that, in this case, sampling-rate must be the same as scan-rate.

Caution

This class may be too specific to be pre-defined, and may subject to future deprecation.

class Video

a subclass of Scan used to represent video acquisition. For properties, refer to Scan.

The size property must hold a Space with more than two-dimensional. For example, the standard color videography will have three dimensions (i.e. width, height, and 3 color channels).

Note that, in the case of “standard” videography, sampling-rate can be the same as scan-rate, as it makes no sense to define the pixel-sampling rate (or pixel dwell-time, as it may be important for scanning microscopy).

class Volume

a subclass of Scan used to represent 3-D volume acquisition. For properties, refer to Scan.

The size property must hold a Space with more than three-demensional.

Event and its subclasses

Event

class Event

for signal that “occurs” discretely from time to time.

type

a required string property inherited as an Entity instance. This property must hold "Event" or the name of one of its subclasses.

description

a required string property inherited as an Entity instance.

role

a required string property referring to what role it plays in the context of this physiology experiment, as it is inherited from Signal.

quality

a required string property describing the physical quality that this event type is supposed to reflect, as it is inherited from Signal.

generated-by

a required property indicating what spatial existence generates/emits this event type, as it is inherited from Signal.

monitored-by

a required property indicating what spatial existence monitors/reads this event type, as it is inherited from Signal.

values

a required object property to describe what algebraic values this event type must hold, as it is inherited from Signal.

reference

an optional string or [ string ] property inherited as an Entity instance.

TODO

Image: image acquisition: needs size

State

class State

an abstract, discrete and instantaneous representation of a context, such as a state of a machine or a subject.

Note that, this property can hold some additional experiment-wise properties via the properties property.

type

a required string property inherited as an Entity instance. This property must hold "State" or the name of one of its subclasses.

description

a required string property inherited as an Entity instance.

role

a required string property referring to what role it plays in the context of this physiology experiment, as it is inherited from Signal.

quality

a required string property describing the physical quality that this state type is supposed to reflect, as it is inherited from Signal.

generated-by

a required property indicating what spatial existence generates/emits this state type, as it is inherited from Signal.

monitored-by

a required property indicating what spatial existence monitors/reads this state type, as it is inherited from Signal.

values

a required object property to describe what algebraic values this state type must hold, as it is inherited from Signal.

properties

an optional property that holds schematic descriptions of additional properties. The semantics follows that of JSON Schema.

reference

an optional string or [ string ] property inherited as an Entity instance.

TODO

add an example