Predefined subclasses for Spatial

Representative classes of the Spatial class are described below.

Subject entity

class Subject

a subclass of Spatial representing the subject of the study. Depending on whether it is a human being or not, it becomes either an Animal or a Participant.

If it is a tissue cut out from an individual, then it becomes a Tissue.

type

a required string property inherited as an Entity instance.

description

a required string property inherited as an Entity instance.

age

a required Age property indicating the age of this Subject.

license

a required property representing a license term or more that is related to this subject e.g. the license for the animal experiment, or the informed consent conditions with the human experiment.

parts

an optional property holding a Spatial or an array of them, as it is inherited from Spatial.

implants

an optional mapping property from names to Component instances, describing what additional Component instances are implanted, before or during experiments, to this Subject.

Possible Component entities include:

• implanted components (head-posts, cannula, chronic windows etc.)
• materials that are chronically introduced into the body (chronic drug admin., virus injection etc.)

Caution

Note the difference between implants and parts: parts refers to elements that are by definition part of the subject, whereas implants refers to those that are added in relation to (most likely, for the sake of) the experiment.

reference

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

Subclasses of Subject

class Animal

a subclass of Subject representing a non-human individual.

type

a required string property inherited as an Entity instance.

description

a required string property inherited as an Entity instance.

species-strain

a required Strain property indicating the species and strain of this Animal.

age

a required Age property, as it is inherited from Subject.

sex

a required Sex property of this Animal.

death

a required Death property, indicating when and how this Animal died.

license

a required license-term property, inherited from Subject.

parts

an optional property holding a Spatial or an array of them, as it is inherited from Spatial.

reference

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

TODO

is it better having a property indicating “experiment-specific”?

class Participant

a subclass of Subject representing a human individual.

type

a required string property inherited as an Entity instance.

description

a required string property inherited as an Entity instance.

age

a required Age property, as it is inherited from Subject.

sexuality

a required Sexuality property of this Participant.

license

a required license-term property, inherited from Subject.

parts

an optional property holding a Spatial or an array of them, as it is inherited from Spatial.

reference

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

TODO

add property details??

class Tissue

a subclass of Subject representing a tissue or an organ that is cut out from an individual.

type

a required string property inherited as an Entity instance.

description

a required string property inherited as an Entity instance.

origin

a required property referring to the Animal or the Participant where this Tissue instance originates from.

age

a required Age property, as it is inherited from Subject.

license

the required license-term property, inherited from Subject.

parts

an optional property holding a Spatial or an array of them, as it is inherited from Spatial.

reference

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

TODO

add property details

Component entity

class Component

a subclass of Spatial representing any chemical / physical component used for the study.

type

a required string property inherited as an Entity instance.

description

a required string property inherited as an Entity instance.

supplier

an optional (but recommended) property referring to an Individual who supplied this Material instance.

parts

an optional property holding a Spatial or an array of them, as it is inherited from Spatial.

reference

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

Material and its related classes

class Material

a subclass of Component representing any chemical / physical material used for the study.

Being a Material typically implies that it does not have a specific form. Normally, an experimenter uses a Material as a Substance or makes a Part out of it.

type

a required string property inherited as an Entity instance.

description

a required string property inherited as an Entity instance.

supplier

an optional (but recommended) property inherited from Component.

parts

an optional property holding a Spatial or an array of them, as it is inherited from Spatial.

reference

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

class Substance

a subclass of Material representing a (typically chemical) substance used for the study e.g. drug or some biochemical solutions.

type

a required string property inherited as an Entity instance.

description

a required string property inherited as an Entity instance.

supplier

an optional (but recommended) property inherited from Component.

parts

an optional property holding a Spatial or an array of them, as it is inherited from Spatial.

reference

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

class Part

a subclass of Spatial representing an artificial building block for the experiment.

Being a Part implies that it has a certain specific static shape, and has some specific static roles or functions for the experiment to work properly.

Typically, each Part is made of one single Material or two.

type

a required string property inherited as an Entity instance.

description

a required string property inherited as an Entity instance.

made-of

a required property referring to a Material that this Part is made of.

supplier

an optional (but recommended) property inherited from Component.

parts

an optional property holding a Spatial or an array of them, as it is inherited from Spatial.

reference

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

Apparatus and its related classes

class Apparatus

a subclass of Component representing an apparatus.

Being an apparatus may imply that many parts are configured in some specific ways to execute a specific role or a function.

type

a required string property inherited as an Entity instance.

model

a required string property representing the model name of this apparatus.

description

a required string property inherited as an Entity instance.

supplier

an optional (but recommended) property inherited from Component.

reference

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

parts

an optional property holding a Spatial or an array of them, as it is inherited from Spatial.

TODO

how to add any configurational parameter(s) for an Apparatus?

class Device

a subclass of Apparatus representing a device.

Being a Device implies that it reads or writes a Signal, and/or executes a Program in it.

type

a required string property inherited as an Entity instance.

model

a required string property representing the model name of this apparatus.

description

a required string property inherited as an Entity instance.

supplier

an optional (but recommended) property inherited from Component.

generates

an optional property consisting of a reference, or a list of references, to a Signal instance or more.

monitors

an optional property consisting of a reference, or a list of references, to a Signal instance or more.

runs

an optional property consisting of a reference, or a list of references, to a Program instance or more.

parts

an optional property holding a Spatial or an array of them, as it is inherited from Spatial.

reference

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