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. See Synapse Annotations for general information, and search for community-approved terms in the 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 needed template from: synapseAnnotations/term-templates

• Paste into 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 curators as reviewers

Update Schemas

• Once the PRs are approved, 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 Github workflow

• To update the Synapse annotations table, run update-annotations-table.R

Generate Template

• Github sysbioDCCjsonschemas repo

• SysBio Metadata Templates: https://github.com/Sage-Bionetworks/sysbioDCCjsonschemas/tree/master/schema_metadata_templates

• Edit terms in XLS template or construct a JSON file to do this programmatically

• Ensure latest versions of JSON schemas have been registered. How to

• To create a Synapse table of all terms in metadata templates:

  • create_Syn_table_from_Syn_schemas.py

• To generate a Metadata Template:

  • create_template_from_Syn_schema.py

• cd /Users/ryaxley/Documents/GitHub/sysbioDCCjsonschemas/code/python/.
  python3 create_template_from_Syn_schema.py \
          sysbio.metadataTemplates-ad.manifest \ 
          manifest_test.xlsx excel

• New templates must be uploaded manually to: https://www.synapse.org/#!Synapse:syn18512044