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1. Create Github issue if needed in https://github.com/Sage-Bionetworks/synapseAnnotations/issues

2. Term information is stored in JSON schemas in the synapseAnnotations/terms directory.
   NOTE: Terms specific to MODEL-AD are stored in: synapseAnnotations/terms/neuro

3. Create a JSON schema file or edit an existing one.

4. Copy and Paste schema template.

5. Edit $id line with Modulename and Key name.

6. Version numbers start with 0.0.1 and should be incremented with each update.

7. Add new term, a brief definition, and an ontology citation for the included definition.

8. Create a branch name formatted like ‘username-edit-type/‘

9. Add a brief description of changes to commit

10. Data checks will start to run in the background. All data checks must successfully pass.

11. Once desired changes are committed, initiate a Pull Request and select DCC curators as reviewers.

12. Once the changes PRs have been merged into master, need to run script to update the metadata dictionary needs to be updated with the latest version of terms. To register these 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

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

14. Github sysbioDCCjsonschemas repo

15. Add/Remove terms from XLS template file. Alternatively, this can be done programmatically with JSON.

Links

Ontology Lookup Service: https://www.ebi.ac.uk/ols/index

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