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ave-dcd / mave_vocabulary

JSON Schema representation of MAVE controlled vocabulary terms
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Endogenous editing or in-vitro constructs #2

Closed ahwagner closed 1 year ago

ahwagner commented 1 year ago

This section of the README describes the use of controlled vocabulary terms for endogenous edit or in-vitro construct methods for library generation: https://github.com/ave-dcd/mave_vocabulary/blob/96d3dcc0f59330ddd1d2ddcbf0b5ef9ff54a5cc4/README.md?plain=1#L137-L139

My understanding is that an experiment may generate a library via one of these mechanisms, not both. This has implications in schema, as the fields and valuesets required for endogenous editing experiments are distinct from in-vitro construct experiments. Examples of experiments where both types of library generation methods are used together would be very informative.

In addition, these types refer to discrete subschemas for the VariantLibrary.generationMethod: https://github.com/ave-dcd/mave_vocabulary/blob/96d3dcc0f59330ddd1d2ddcbf0b5ef9ff54a5cc4/schema/experiment.yml#L197-L201

We should revise the README or schema to match, I suggest changing the README as the subschema approach allows for differences in required fields for in-vitro vs endogenous edit library methods.

afrubin commented 1 year ago

Agreed. Closed by https://github.com/ave-dcd/mave_vocabulary/pull/6