Annotation Schemas

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

• General info: Synapse Annotations

• Community-approved Terms: Table of Annotations

Schemas

The synapseAnnotations Github repo includes schemas for metadata terms. Each term is stored in a JSON mini-schema and the terms are organized by modules in each terms/<module>/ folder. There are subfolders for each module, and the term names include the module.

• 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.

• Address any errors until validation passes

• Open a Pull Request and select DCC reviewers

Update Schemas

• Once the 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

• cd ~/Documents/GitHub/sysbioDCCjsonschemas/code/python/. python3 create_template_from_Syn_schema_sorted.py \ sysbio.metadataTemplates-ad.manifest \ manifest_test.xlsx excel \ ~/Documents/GitHub/sysbioDCCjsonschemas/schema_metadata_templates/AD/manifest_metadata_template.json

• New templates must be uploaded manually to:

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