Animal

Individual experimental animals are represented by the Animal element of the Experimental Model Schema. This element intends to represent an individual model organism used in an experiment. Note that some experiment packets will refer to a cohort of individual models used for an experiment instead of an individual (See :ref:rstexperimentalcohort).

Data model

Field	Type	Multiplicity	Description
id	string	1..1	An arbitrary identifier. REQUIRED.
animal_identification_method_list	repeated AnimalIdentifier animal_identification_method_list	0..*	Methods used to identify this mouse in the experiment
sex	Sex	1..1	Sex of the model organism
taxonomy	OntologyClass	1..1	an :ref:rstontologyclass representing the species (e.g., NCBITaxon:10090 for Mus musculus)
strain	Strain	0..1	an :ref:rststrain representing the strain
animalOrigin	AnimalOrigin	0..1	a :ref:rstanimal_origin representing the provence of the animal

Example

The following example represents a single male C57BL/A mouse with an ear punch with the value "90".

{
"animalIdentificationMethodList": [{
    "id": "arbitrary.id",
    "identifier": {
        "id": "MGI:1234567",
        "label": "ear punch"
    },
    "identifierValue": "90"
}],
    "sex": "MALE",
"taxonomy": {
    "id": "NCBITaxon:10090",
    "label": "Mus musculus"
},
"strain": {
    "strainType": {
        "id": "MGI:2670463",
        "label": "C57BL/A"
    },
    "strainAttribute": ["INBRED_STRAIN"]
},
"animalOrigin": {
    "vendor": "anonynmous_vendor",
    "externalIdentifier": "arbitrary.external.id",
    "originIdentifierList": [{
        "idType": "jr_number",
        "idValue": "424242"
            }]
    }
}

Explanations

• animal_id

This element is the primary identifier for the individual animal and MUST be used in other parts of a message when referring to this individual. There are no further constraints on the identifier, which is application-specific.

• animal_project_id

TODO -- DOES THIS REFER TO THE EXPERIMENT -- PROVIDE DEFINITION HERE

• project_symbol

TODO -- WHY IS THIS NEEDED IN ADDITION TO THE animal_project_id?

• sex

An enumeration to denote the phenotypic sex of the individual animal. See :ref:rstsex.

• stock_number

WHAT IS THIS FOR AND DOES IT BELONG IN THE SCHEMA?

• taxonomy

The taxonomy identifier of the species of the the animal MUST be provided at its most specific level. We advise using the codes from the NCBI Taxonomy resource. For instance, NCBITaxon:10090 is mouse (Mus musculus) and or NCBITaxon:9615 is dog.

• strain

TODO -- Decide how to represent this

• strain_identifier

TODO -- Decide how to represent this