Experimental Measurement

The subject of the Experimental Model Schema is represented by an Individual element. 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).

Probably we want to model this on the ro-crate JSON-LD model, therefore I am not trying to fill out details here

Suggestion

The data that is current in MPD looks like this

.. code-block:: console

"animaldata": [
{
  "animal_id": "F148-1-dob2015-01-09",
  "animal_projid": 519,
  "measnum": 89013,
  "projsym": "JaxCC1",
  "sex": "f",
  "stocknum": "021236",
  "strain": "CC002/UncJ",
  "strainid": 1502,
  "value": 2117.0,
  "varname": "distance_total_OF",
  "zscore": -0.78
},
{
  "animal_id": "F148-2-dob2015-01-09",
  "animal_projid": 519,
  "measnum": 89013,
  "projsym": "JaxCC1",
  "sex": "f",
  "stocknum": "021236",
  "strain": "CC002/UncJ",
  "strainid": 1502,
  "value": 2887.0,
  "varname": "distance_total_OF",
  "zscore": 0.78
}, ....

and like this

.. code-block:: console

measures_info": [
    {
      "ageweeks": "7-9wks",
      "association": null,
      "datatype": null,
      "descrip": "total distance traveled, 20 min test",
      "descrip2": null,
      "extname": "distance_traveled_total",
      "file_column": null,
      "granularity": "animal",
      "intervention": null,
      "is_baseline": false,
      "is_control": false,
      "is_covar": null,
      "is_measure": true,
      "keymeasnum": 89013,
      "label": null,
      "listorder": 9013,
      "magnitude": null,
      "measnum": 89013,
      "method": "open field test",
      "mpdsector": "css",
      "native_method": "open field",
      "nstrainstested": 18,
      "paneldesc": "CC",
      "private": null,
      "projsym": "JaxCC1",
      "projyear": "2018",
      "reference": null,
      "seriestype": null,
      "sextested": "both",
      "sourceparm": "jaxcc_oft",
      "supplemental": null,
      "units": "cm",
      "upload_factors": null,
      "varname": "distance_total_OF"
    }
  ]

It seems to me that this is mixing information about the experiment itself with information about the measurement and other items. We would want to "normalize" this in database parlance. It seems to me it would be a good idea to create an ontology to represent information about the types of experiments we perform at JAX under the assumption that these experimental designs are stable with time.

We have here an Open Field Test: The Open Field task is a simple sensorimotor test used to determine general activity levels, gross locomotor activity, and exploration habits in rodent models.

We could represent this as follows

.. code-block:: console

id: MEO:0000001
label: open-field test total distance traveled

id: MEO:0000002
label: open-field test total distance traveled in 10 minutes
is_a: MEO:0000001 ! open-field test total distance traveled

id: MEO:0000002
label: open-field test total distance traveled in 20 minutes
is_a: MEO:0000001 ! open-field test total distance traveled

Then, we would refer to this term instead of the descrip, descrip2, extname, measnum, and method fields (and possibly some of the other fields) in the EMS.

In bioconnect, I am seeing things like this -- JAXAS000001 longitudinal mass measurement assay, but it is unclear where to get info about JAXAS000001 -- is this intended to be a controlled terminology or ontology?

Data model

Example

The following example is typical but does not make use of all of the optional fields of this element.

.. code-block:: yaml

todo: id: "todo"

Explanations

todo