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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.

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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).

When ETLing a "main" type, there are usually resources of other types that are related to it (e.g People, Organizations, Publications). It is necessary to enter information for these related types in a template of their own. For example, when ETLing a Monoclonal Antibody, you'll have separate files for related Hybridoma Cell Lines, People and Publications. 

Generate the following templates:

• A template for your " main " resource - use the most specific type possible (e.g. Plasmid 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

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• Plain text columns - you may enter any text. Avoid Do not include semi-colons, as they are used as the field separator (more on this below)
• Resource columns - represent linked resources. 
  • A value that matches the label of a resource in the repository (or a new resource) is expected. If you know the resource's URI, you may enter it here and thus avoid a look-up operation during ETL. 
  • The main resource type template will contain references to instances from secondary resource type template - references in the primary file need to use the exact name (ignoring case) entered in the secondary file for the correct linkage to occur. 
  • Resource columns are followed by Resource type columns; sometimes the resource type column is omitted if there are no possible values, i.e. the resource type ahs no subclasses)
• Referenced taxonomies - a value that matches an eagle-i ontology term or synonym is expected

Consult the tooltips in the header rows for more information about what is expected. Most columns (except for the "main" resource name and type) accept multiple values. Use a semicolon to separate the values

A few more guidelines and tips:

• You must always enter the Organization to which the resource is associated, either by name or by URI
  • It is best to use the Sweet to add the Organization (e.g. lab) to which these resources are associated, and then reference this name or URI in the files.
• If there is more than one value for a given column, enter values separated by ; (semicolon). Conversely, check your input file for the presence of ; in values that are not meant to be split and substitute for a different character.
• The first two columns (hidden) of a template are reserved for metadata. Please do not modify them or the name of the Tabs.
• Every resource (primary or secondary) needs to have a name and a type as a minimum. For simplification, the type column is omitted if there are no possible subclasses (e.g. Person, Human Subject). If the template has a type column, you must enter a value.

The actual ETL process

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

Special rules for embedded instances

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