Procedures

Note

TODO: make a nice object diagram for “procedures” section

“procedures” section

A typical “procedures” section looks like the one below:

in: “procedures.json”

{
    "$schema": ".../amorphys.json#properties/procedures",
    "$description": "experimental procedures for each subject in the foraging project.",

    "phases": {

        "surgery": {
            "type":        "Phase",
            "description": "preparation of the animal before training begins, including probe implant.",

            "date":        { "$ref": "variables.json#subject/surgery-date" },
            "procedures":  [
                {
                    "type": "ketamine-xylazine-anesthesia",
                    "description": "Ket/Xyl anesthesia"
                },
                {
                    "type":          "ChronicPreparation",
                    "description":   "surface probe implant",
                    "manipulations": [
                        {
                            "@context":          "https://.../amorphys-manipulation",
                            "@id":               { "$ref": "materials.json#core-materials/probe" },
                            "implanted-to":      { "$ref": "materials.json#subject" },
                            "on-the-surface-of": { "$ref": "materials.json#subject/composition/frontal-lobe" },
                            "by-means-of":       {
                                ...
                            }
                        }
                    ]
                }
            ]
        },

        "session": {
            "type":  "array",
            "items": {
                "type":        "Phase",
                "description": "a behavioral session in the post-doc room.",

                "date":        { "$ref": "variables.json#sessions/session/session-date" },
                "procedures": [
                    {
                        "type":        "Acquisition",
                        "description": "acquisition from the surface probe",
                        "setup":       { "$ref": "setups.json#postdoc-room" },
                        "task":        { "$ref": "tasks.json#foraging-task" }
                    }
                ]
            }
        }
    },

    "order": {
        {
            "@context": "https://.../amorphys-temporal",
            "@id":      { "$ref": "../phases/session" },
            "after":    { "$ref": "../phases/surgery" }
        },
        ...
    }
}

class procedures

The procedures section of amorphys is a subclass of section. It consists of the blocks and order, both of which are required properties.

$description

a recommended string property inherited from section.

phases

a mapping from the phase names to Phase objects, or arrays of Phase objects.

If you perform the phase only once for each subject, the value must be a Phase entity; if you perform it repetitively on different days or periods, the value must be an array of Phase entity.

order

an array of Relationship instances representing the restrictions in the order between the specified Phase objects.