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Annotation Schemas

Owned by Rich Yaxley (Unlicensed)
Last updated: Dec 31, 2021
2 min read

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.

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.

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

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