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. See Synapse Annotations for general information. Approved terms are available in a searchable
General info: Synapse Annotations
Community-approved Terms: Table of Annotations
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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.
Annotation schemas in JSON
Templates for adding new terms are included in the term-templates/ directory. Each individual term is stored in its own JSON mini schema. This is a valid JSON Schema, such as the following:
| Code Block | ||
|---|---|---|
| ||
{ $schema": "<http://json-schema.org/draft-07/schema#",>
"$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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Create Github issue if needed in https://github.com/Sage-Bionetworks/synapseAnnotations/issues
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Term information is stored in JSON schemas in the synapseAnnotations/terms directory.
NOTE: Terms specific to MODEL-AD are stored in: synapseAnnotations/terms/neuro
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Create a JSON schema file or edit an existing one.
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Copy and Paste schema template.
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Edit $id line with Modulename and Key name.
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Version numbers start with 0.0.1 and should be incremented with each update.
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Add new term, a brief definition, and an ontology citation for the included definition.
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Create a branch name formatted like ‘username-edit-type/‘
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Add a brief description of changes to commit
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Data checks will start to run in the background. All data checks must successfully pass.
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Once desired changes are committed, initiate a Pull Request and select DCC curators as reviewers.
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Github: GitHub - Sage-Bionetworks/synapseAnnotations (README)
JSON Schemas: synapseAnnotations/terms
MODEL-AD Schemas: synapseAnnotations/terms/neuro
Edit JSON Schema
Copy a template from: synapseAnnotations/term-templates
Edit new file
Edit
$idline 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 reviewers
Update Schemas
Once the PRs are merged, 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.
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R --helpRegister all schemas
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:
./register-schemas.R terms/*/*.json
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Verify if this script runs automatically as part of the Github workflow
To update the Synapse annotations table
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./update-annotations-table.R
Generate Template
Links
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Github sysbioDCCjsonschemas repo
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Add/Remove terms from XLS template file. Alternatively, this can be done programmatically with JSON.
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
New templates must be uploaded manually to: https://www.
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