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 , 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.
JSON Templates
Each term is stored in a JSON mini-schema, such as the following:
Code Block | ||
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| ||
{ $schema": "<http://json-schema.org/draft-07/schema#",> "$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
Open Github issue in rep: https://github.com/Sage-Bionetworks/synapseAnnotations/issues
Guidance: CONTRIBUTING.md - Sage-Bionetworks/synapseAnnotations
Templates: https://github.com/Sage-Bionetworks/synapseAnnotations/tree/master/term-templates
JSON schemasSchemas: https://github.com/Sage-Bionetworks/synapseAnnotations/tree/master/terms
MODEL-AD termsSchemas: https://github.com/Sage-Bionetworks/synapseAnnotations/tree/master/terms/neuro
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
Create a branch name formatted like ‘username-edit-type/‘
Add a brief description of changes to commit
- Data
Commit changes to a new branch
Schema validation checks will start to run in the background. All data checks These must successfully passPASS.
Once desired changes are committed, initiate Open a Pull Request and select DCC curators as reviewers.
Once the With PRs have been merged, the metadata dictionary Metadata Dictionary needs to be updated with the latest version of terms. .
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
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