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
General info: Synapse Annotations
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Community-approved Terms: Table of Annotations
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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.
Github: GitHub - Sage-Bionetworks/synapseAnnotations (README)
JSON Schemas: synapseAnnotations/terms
MODEL-AD Schemas: synapseAnnotations/terms/neuro
Edit JSON Schema
Copy needed a template from: synapseAnnotations/term-templates
Paste into 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 curators as reviewers
Update Schemas
Once the PRs are approvedmerged, 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, run :
./update-annotations-table.R
Generate Template
Github sysbioDCCjsonschemas repo
SysBio Metadata Templates: https://github.com/Sage-Bionetworks/sysbioDCCjsonschemas/tree/master/schema_metadata_templates
Edit terms in XLS template or construct Construct a JSON schema file to do this programmaticallyEnsure generate XLS template
Make sure to register latest versions of JSON schemas have been registered. How to
To create a Synapse table of all terms in metadata templates:
create_Syn_table_from_Syn_schemas.py
To For example, to generate a Metadata Template:
create_template_from_Syn_schema_sorted.py
Code Block cd /Users/ryaxley~/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
New templates must be uploaded manually to: https://www.synapse.org/#!Synapse:syn18512044
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