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The synapseAnnotations Github repo includes schemas for individual metadata terms. Each term is stored in a JSON mini-schema (see figure). The 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.

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• Github: GitHub - Sage-Bionetworks/synapseAnnotationsTemplates: synapseAnnotations/term-templates (README)

• JSON Schemas: synapseAnnotations/terms

• MODEL-AD Schemas: synapseAnnotations/terms/neuro

• Edit JSON Schema file

  Copy and Paste Schema template into the

  https://wwwsagebionetworks.ebi.ac.uk/ols/index

Edit Schema

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

Edit JSON Schema

• Copy needed template from: synapseAnnotations/term-templates

• Paste into new file

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

  • Version numbers start with 0.0.1 and should be incremented with 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 reviewers

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• Once the PRs are approved, 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.

  • 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 Github workflow

• To update the Synapse annotations table, run update-annotations-table.R

Generate Template

• Github sysbioDCCjsonschemas repoAdd

• /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

• Edit terms in XLS template or construct a JSON file to do this programmatically

• Ensure 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 generate a Metadata Template:

  • create_template_from_Syn_schema.py

• Code Block
  cd /Users/ryaxley/Documents/GitHub/sysbioDCCjsonschemas/code/python/. python3 create_template_from_Syn_schema.py \ sysbio.metadataTemplates-ad.manifest \ manifest_test.xlsx excel

• New templates must be uploaded manually to: https://www.synapse.org/#!Synapse:syn18512044