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

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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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JSON

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Templates

Each term is stored in its own a JSON mini-schema. This is a valid JSON Schema, such as the following:

{   $schema": "<http://json-schema.org/draft-07/schema#",>
    "$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"
}

Schema editing procedure

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Editing Schemas

• Open Github issue

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• in https://github.com/Sage-Bionetworks/synapseAnnotations/issues

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• • CONTRIBUTING.md - Sage-Bionetworks/synapseAnnotations

  • Templates: https://github.com/Sage-Bionetworks/synapseAnnotations/tree/master/term-templates

  • JSON schemas: https://github.com/Sage-Bionetworks/synapseAnnotations/tree/master/terms

  • MODEL-AD terms: https://github.com/Sage-Bionetworks/synapseAnnotations/tree/master/terms/neuro

• Create/Edit a JSON schema file

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• Copy and Paste schema template.

• Edit $id line with Modulename and Key name.

• Version numbers start with 0.0.1 and should be incremented 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 start to run in the background. All data checks must successfully pass.

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

• Once the PRs have been merged, the metadata dictionary needs to be updated with the latest version of terms. To register the schemas in Synapse run the register-schemas.R script.

  • To register all schemas, run ./register-schemas.R terms/*/*.json

  • Learn more about this script, run ./register-schemas.R --help

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

• Github sysbioDCCjsonschemas repo

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

Links

Ontology Lookup Service: https://www.ebi.ac.uk/ols/indexAMP-AD Validation (dccvalidator + dccmonitor data)