Protocol model

Table of contents

1. Introduction
2. Fields
3. Protocol type and subtypes
4. Creating and using a protocol
5. Permissions
6. API access

Introduction

A protocol is a reusable written method used by your lab, such as a standard operating procedure (SOP), a published protocol, or a lab procedure document. A procedure, specimen procedure, subject log, specimen log or procedure episode can reference the method instead of repeating it. Procedure, specimen procedure and procedure episode templates can also reference protocols.

A protocol describes how work is performed. It is a reference, not a template: selecting a protocol does not fill in any fields of the record. When you want values to be reused, use a template; a record can have both. A license records the authorization for the work; you can link the relevant licenses to the protocol.

This model with its direct connections only: drag to pan, Ctrl + scroll to zoom, click a model to select it, use the chevron to see its fields.

Fields

Field	Description
Name	Name shown in protocol selectors (required; string; maximum length: 255 characters). Include a version or date if you maintain several revisions. Example: “Craniotomy SOP v3 (2026-01)”
Protocol type	Kind of record the protocol applies to (required). Options: Breeding, Procedure, Specimen procedure, Subject log, Specimen log.
Subtypes	Specific types within the protocol type that the protocol covers (multiple selections). Leave empty for a general method.
Authenticated groups	Groups given access when the protocol is created (create only). Manage subsequent access from the protocol’s own page, where individual people can also be invited.
Description	Rich text description of the method.
URL	Optional link to the published method, such as protocols.io or a journal article (URL; maximum length: 200 characters).
Attachment	Optional protocol document: PDF, DOCX, XLSX, PPTX, ODT, CSV, Markdown (.md), or plain text (.txt), up to 15 MB. Downloads use signed URLs.
Licenses	Licenses that authorize this method (multiple selections). Adding a license requires Contributor on that license.
Public access	Designates if the protocol is publicly readable (boolean; default: False). Only owners can modify this setting.

Protocol type and subtypes

The protocol type determines where a protocol can be used:

Protocol type	API value	Used by	Subtypes drawn from
Breeding	breeding	Reserved for breeding protocols. Breedings do not yet have a protocol field.	None
Procedure	procedure	Procedures, procedure templates, procedure episodes and procedure episode templates	Procedure types
Specimen procedure	specimen_procedure	Specimen procedures and specimen procedure templates	Specimen procedure types
Subject log	subject_log	Subject logs	Subject log types
Specimen log	specimen_log	Specimen logs	Specimen log types

Subtypes optionally restrict a protocol to one or more types within the protocol type. A procedure protocol restricted to Craniotomy appears only when the procedure type is Craniotomy; one with no subtypes appears for every procedure type. Leave subtypes empty for a general method.

Selectors offer only protocols where you are at least a Contributor, filtered by type and subtype. Being able to read a colleague’s protocol is not enough to assert that your work followed it. Record the actual work and any deviations in the procedure or log itself.

Creating and using a protocol

1. Go to Personal Attributes → Protocols and add a protocol.
2. Enter a descriptive name and choose the protocol type. Select the groups that need access, then create the record.
3. Edit the protocol to add subtypes, a description, a URL or attachment, and any authorizing licenses.
4. Open a record of the matching type and select the protocol in its Protocol field.

For example, create “Handling SOP v2” with protocol type Subject log and subtype Handling. Each subject’s Handling log can reference that protocol while keeping its own dated entries and observations.

Permissions

Protocols have their own permissions, independent of the projects that reference them. The creator becomes an owner, and groups selected during creation receive access. Use the Manage tab to assign access to users and groups.

Role	Capabilities
Member	Read the protocol.
Contributor	Select the protocol on an experimental record. Does not allow editing the protocol itself.
Manager	Also manage members and access.
Owner	Also edit or delete the protocol, change public access, and assign managers or owners.

Making a project public does not make its protocols public. An owner must enable Public access on each protocol separately. Public protocols and their attachment download links are available through the public portal and API. Linked licenses keep their own sharing settings.

A protocol referenced by a procedure, procedure episode, subject log, or their templates cannot be deleted until those references are removed or reassigned. Deleting a protocol clears the link on specimen procedures, specimen procedure templates and specimen logs.

Visit the permissions page to learn more.

API access

The API allows for programmable access to protocols, enabling you to read, create, edit, and delete protocols through the API. Learn more about the fields and data structure on the Protocols API page.