SpecimenProcedureStage schemas

Detail schemas for the stages of a procedure or specimen procedure: a phase several materials take part in together, such as the induction of an anesthetic or one bath of a staining protocol.

This family is experimental: its schemas may change shape between releases without a version bump. Treat writes to these types as experimental.

Table of contents

1. How to use this family
2. Quick type map
3. Administration stage
4. Specimen processing stage

How to use this family

• These schemas describe JSON fields of the web forms (additional fields, repository links, specifications). The REST API returns the stored JSON as is.
• Every version is published at https://www.brainstem.org/schemas/SpecimenProcedureStage/<Type>/<version>.json and never changes; https://www.brainstem.org/schemas/SpecimenProcedureStage/<Type>.json is the current version and https://www.brainstem.org/schemas/SpecimenProcedureStage/<Type>/ lists the versions. See Public schemas.
• Quantities are objects {"value": <number>, "unit": "<code>"}. Property paths with [] are inside a repeatable list of rows. The server sets the schema version field itself.

Quick type map

Type code	Title	Version	Required properties	Schema
AdministrationStage	Administration stage	1.0.0	none	1.0.0.json
SpecimenProcessingStage	Specimen processing stage	1.0.1	none	1.0.1.json

Administration stage

• type code AdministrationStage · version 1.0.0 · schema

Records one stage of a substance delivery to the animal within an administration procedure, such as induction or maintenance of an anesthetic, with route, delivery method, gas concentration, volume, infusion rate and duration.

Property	Title	Shape	Required	Allowed values	Meaning
route	Route	choice		one of inhaled, ip, iv, sc, im, oral, topical, other	How this stage’s delivery entered the animal; leave empty for a stage that delivered nothing.
deliveryMethod	Delivery method	choice		one of anesthesia_chamber, nose_cone, face_mask, intubation, other	The apparatus an inhaled stage reached the animal through; leave empty for an injected stage.
gasConcentration	Gas concentration	quantity with unit		units % v/v, ppm; default {"unit": "% v/v"}	The inhaled agent’s fraction of the carrier gas during this stage, as set on the vaporizer.
volume	Volume	quantity with unit		units L, mL, µL; default {"unit": "mL"}	How much formulation was delivered in this stage; an inhaled stage has none.
rate	Infusion rate	quantity with unit		units L/min, mL/min, µL/min; default {"unit": "mL/min"}	How fast the formulation was infused in this stage; not the carrier-gas flow, and empty for a bolus.
duration	Duration	quantity with unit		units h, min, s; default {"unit": "min"}	How long this stage lasted, which is shorter than the whole event when it ran in several stages.

Illustrative payload:

{
    "route": "inhaled",
    "deliveryMethod": "anesthesia_chamber"
}

Specimen processing stage

• type code SpecimenProcessingStage · version 1.0.1 · schema

Records one stage of a specimen procedure, such as an incubation or wash, with contact duration and temperature, agitation, number of repeated cycles and bath volume.

Property	Title	Shape	Required	Allowed values	Meaning
duration	Applied/contact duration	quantity with unit		units d, h, min, s; default {"unit": "min"}	The contact or application duration for this processing stage.
temperature	Applied/contact temperature	quantity with unit		units °C; default {"unit": "°C"}	The temperature applied or maintained during this processing stage.
agitation	Agitation	choice		one of static, gentle_shaking, rotation, rocking, other	The agitation mode and setting used during this processing stage.
cycleCount	Number of repeated cycles	integer		≥ 1	Number of repeated cycles of the same treatment, e.g., for a wash step.
volume	Applied/contact bath volume	quantity with unit		units nL, µL, mL, L; default {"unit": "mL"}	Total solution volume contacting the target specimens, not stock volume drawn.

Illustrative payload:

{
    "duration": {
        "value": 1,
        "unit": "min"
    },
    "temperature": {
        "value": 1,
        "unit": "°C"
    }
}