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This The DCC has derived standards for how content is annotated in Synapse and this page describes how the DCC manages the content used to annotate files (management of the keys, definitions, and ontological references ). Sage Bionetworks has derived standards for how content is annotated Synapse. used to annotate files.

General info: Synapse Annotations
Community-approved Terms: Table of Annotations

Schemas

The synapseAnnotations Github repo includes schemas for individual metadata terms. The Each term is stored in a JSON mini-schema and the terms are organized by modules in the each terms/<module>/ 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:

Code Block

language	json

{   $schema": "<http://json-schema.org/draft-07/schema#",>
    "$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

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

NOTE: Terms specific to MODEL-AD are stored here: synapseAnnotations/terms/neuro

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Create or Edit an existing JSON schema file.

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Copy and Paste schema template.

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Edit $id line with Modulename and Key name.

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

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

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

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Add a brief description of changes to commit

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Github: GitHub - Sage-Bionetworks/synapseAnnotations (README)
JSON Schemas: synapseAnnotations/terms
MODEL-AD Schemas: synapseAnnotations/terms/neuro
https://sagebionetworks.jira.com/wiki/spaces/SBC/pages/2363523282/Manage+metadata+templates+annotations#Metadata-templates-(JSON)

Edit JSON Schema

Copy a template from: synapseAnnotations/term-templates
Edit new file
- Edit $id line with <MODULENAME> and <KEY>
- Increment version with each update
- Add Term, Definition, and a source for Definition (https://www.ebi.ac.uk/ols/index )
- Commit changes to a new branch
Schema validation checks will automatically start to run in the background.

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Address any errors until validation passes
Open a Pull Request and select DCC reviewers

Update Schemas

Once the

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Synapse Table of Metadata Terms: Link

AMP-AD Validation: syn20506363

Synapse Link

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PRs are merged, it is necessary to update the Metadata Dictionary
Navigate to: /Users/ryaxley/Documents/GitHub/synapseAnnotations
To register the schemas in Synapse run the register-schemas.R script
- Help: ./register-schemas.R --help
- Register all schemas: ./register-schemas.R terms/*/*.json
- Verify if this script runs automatically as part of the Github workflow
To update the Synapse annotations table:
- ./update-annotations-table.R

Generate Template

Github sysbioDCCjsonschemas repo
SysBio Metadata Templates: https://github.com/Sage-Bionetworks/sysbioDCCjsonschemas/tree/master/schema_metadata_templates
Construct a JSON schema file to generate XLS template
Make sure to register latest versions of JSON schemas
To create a Synapse table of all terms in metadata templates:
- create_Syn_table_from_Syn_schemas.py
For example, to generate a Metadata Template:
- create_template_from_Syn_schema_sorted.py