Synapse Annotations Schemas

This page describes how the DCC manages the content used to annotate files (keys, definitions, and ontological references). Sage Bionetworks has derived standards for how content is annotated Synapse. The synapseAnnotations Github repo includes schemas for individual terms. The terms are organized by modules in the terms/ folder. There are subfolders for each module, and the term names include the module. The mechanisms that manage and implement these annotations are described in the README.

Editing JSON schema

Each individual term is stored in its own JSON mini schema. This is a valid JSON Schema, such as the following:

{   $schema": "<http://json-schema.org/draft-07/schema#",>
    "$id": "<https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-experimentalData.specimenID-0.0.1",>
    "description": "Identifying string linked to a particular sample or specimen",
    "type": "string"
}

Templates for adding new terms are included in the term-templates/ directory.

To register these schemas in Synapse use the register-schemas.R script.

Procedure

1. Navigate to terms/modules/ directory

   • MODEL-AD terms currently reside in synapseAnnotations/terms/neuro

   • Q: Ask Kelsey about creating a MODEL-AD/ directory for those specific terms

2. Create or Edit an existing JSON schema file

3. Paste schema information

4. Edit $id line with Modulename and Key name.

5. Version number should start with 0.0.1 and be increased by one with each update.

6. Add new term, ontology citation, definition

7. Create branch structured like: ‘username-edit-type/‘

8. Add description of changes you want to commit

9. Request Reviewers

10. Data checks will start to run in the background.

11. Once the changes have been merged into master, need to run the XYZ script to update the metadata dictionary with the revised terms in synapseAnnotations.

Synapse Table of Metadata Terms: Link

AMP-AD Validation: syn20506363

Synapse Link

Synapse Table of Annotations