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We usually write ad-hoc scripts that perform such transformations on the original data before copy-pasting individual columns into a SWIFT template. For controlled vocabulary fields, we produce mapping tables with the help of our domain experts and use them during these pre-processing steps.

Templates

SWIFT templates need to be generated using the toolkit version that corresponds to your eagle-i repository version (this is very important -if the versions don't match, you might end up with ontology terms that are not found during the ETL process).

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• A template for your main resource - use the most specific type possible (e.g. Monoclonal Antibody and not Reagent)
• Templates for the linked resources you need - consult the eagle-i ontology browser page of your main resource type to understand what types can be linked

Guidelines for filling the templates

Templates include different kinds of columns:

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ETL first the secondary resource type files (i.e. linked resources), then the main resource type file.

Special rules for embedded instances