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 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.

Each term is stored in a JSON mini-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"
}

Editing Schemas

• Github rep: https://github.com/Sage-Bionetworks/synapseAnnotations

  • Guidance: 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 Schemas: https://github.com/Sage-Bionetworks/synapseAnnotations/tree/master/terms/neuro

  • https://www.ebi.ac.uk/ols/index

• Edit JSON Schema file

  • Copy and Paste Schema template into the new file

  • Edit $id line with <MODULENAME> and <KEY>

  • Version numbers start with 0.0.1 and should be incremented with each update

  • Edit term:

    • Term

    • Definition

    • Ontology citation for the included definition ( https://www.ebi.ac.uk/ols/index )

  • Commit changes to a new branch

• Schema validation checks will start to run in the background. These must successfully PASS.

• Open a Pull Request and select DCC curators as reviewers

• With PRs merged, the Metadata Dictionary needs to be updated.

Update Schemas

• 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