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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. Approved terms are available in a searchable

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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.

JSON Templates

Each term is stored in a JSON mini-schema, such as the following:

...

languagejson

...

.

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Editing Schemas

Edit JSON Schema

  • Copy a template from: synapseAnnotations/term-templates

  • Edit new file

    • Edit $id line with

    Modulename

    • <MODULENAME> and

    Key name.Version numbers start with 0.0.1 and should be incremented

    • <KEY>

    • Increment version with each update

    .

    • Add

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

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

  • Add a brief description of changes to commit

  • Data checks will

  • Schema validation checks will automatically start to run in the background. All data checks must successfully pass.Once desired changes are committed, initiate

  • Address any errors until validation passes

  • Open a Pull Request and select DCC curators as reviewers.

Update Schemas

  • Once the PRs have been are merged, the metadata dictionary needs to be updated with the latest version of terms. 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.

    • To register R --help

    • Register all schemas, run : ./register-schemas.R terms/*/*.jsonLearn more about this script, run ./register-schemas.R --help

    • Verify if this script runs automatically as part of the Github workflow

  • To update the Synapse annotations table, run :

    • ./update-annotations-table.R

Generate Template

  • Github sysbioDCCjsonschemas repo

  • Add/Remove terms from XLS template file. Alternatively, this can be done programmatically with JSON.

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  • 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

  • Code Block
    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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