Page Comparison

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

...

• Community-approved Terms: Table of Annotations

...

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.

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"
}

...

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

  Guidance: CONTRIBUTING.md -

  : GitHub - Sage-Bionetworks/synapseAnnotations

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

  (README)

• 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

  sagebionetworks.

  ebi.ac.uk/ols/index

  jira.com/wiki/spaces/SBC/pages/2363523282/Manage+metadata+templates+annotations#Metadata-templates-(JSON)

Edit JSON Schema

...

• Copy

  and Paste Schema template into the

  a template from: synapseAnnotations/term-templates

• Edit new file

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

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

  • Edit term:

  • Term

  • Definition

  Ontology citation for the included definition

  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. These must successfully PASS.

• Address any errors until validation passes

• Open a Pull Request and select DCC curators as reviewersWith

Update Schemas

• Once the PRs are merged, it is necessary to update the Metadata Dictionary needs to be updated.

...

• Navigate to: /Users/ryaxley/Documents/GitHub/synapseAnnotations

• To register the schemas in Synapse run the register-schemas.R script

  • Help: ./register-schemas.

  • To register R --help

  • Register all schemas, run : ./register-schemas.R terms/*/*.jsonLearn more about this script, run ./register-schemas.R --help

  • 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

• 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.synapse.org/#!Synapse:syn18512044