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Synapse Annotations Schemas

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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. Term information is stored in JSON schemas in the https://github.com/Sage-Bionetworks/synapseAnnotations/tree/master/terms directory.

  2. Create or Edit an existing JSON schema file.

  3. Copy and Paste schema template.

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

  5. Version numbers start with 0.0.1 and need to be incremented with each update.

  6. Add new term, a brief definition, and an ontology citation for the included definition.

  7. Create a branch name formatted like ‘username-edit-type/‘

  8. Add a brief description of changes to commit

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

  10. Initiate a Pull Request and select reviewers

  11. Once the changes have been merged into master, need to run the script to update the metadata dictionary with the latest version of terms.

Synapse Table of Metadata Terms: Link

AMP-AD Validation: syn20506363

Synapse Link

Synapse Table of Annotations

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