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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 latest approved Synapse Annotations are available in a searchable Table of Annotations.

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.

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Annotation schemas in JSON

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

1. Create Github issue if needed in https://github.com/Sage-Bionetworks/synapseAnnotations/tree/masterissues

2. Term information is stored in JSON schemas in the synapseAnnotations/terms directory.
   NOTE: Terms specific to MODEL-AD are stored

   here

   in: synapseAnnotations/terms/neuro

3. Create a JSON schema file or Edit edit an existing JSON schema fileone.

4. Copy and Paste schema template.

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

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

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

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

9. Add a brief description of changes to commit

10. Data checks will start to run in the background. All data checks must successfully pass.

11. Initiate Once desired changes are committed, initiate a Pull Request and select DCC curators as reviewers.

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

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1. To register these schemas in Synapse run the register-schemas.R script.

Links

Ontology Lookup Service: https://www.ebi.ac.uk/ols/index

AMP-AD Validation : syn20506363

Synapse Link

Synapse Table of Annotations(dccvalidator + dccmonitor data)