Describe the sequencing protocol within the preparation information

[wasade]

It would be nice for preparation information files to have a reserved column, perhaps qiita_protocol_types, which contains list[str] to describe the associated protocols. The terms for a protocol ideally are an enum and enforced. The primary need is to represent protocol information from the SPP, such as [EMP16S, KatharoSeq], where we always know the detail and it can be inherited from the sample sheet. Supporting this in the general case for studies created outside of the SPP would be great, but hard to cover the variations and we have less trust

[antgonza]

Just to confirm, what is the difference between library_construction_protocol and this new column?

[wasade]

That variable doesn't do what the issue describes. It is very difficult to bulk process data in qiita without a reliable controlled vocabulary describing the protocols used with a preparation. Multiple protocols can be applied like EMP16S and KatharoSeq. I have not seen an example of a variable provided by qiita which meets this important need

[ackermag]

ARe you asking for a protocol that could be used in a manuscript? We have never done that and have a short list of standard terminology that refers to standard protocols. For some new protocols (like TELL-Seq there is a short description and a link to a document that reflects the differences in the protocol that were being tested on each run.

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[wasade]

We discussed it a bunch at futuretech a while ago about how we can meaningfully capture protocol information so we can use it programmatically. I think I was asked by the group to create this issue. One of the suggestions was a tag system, and to have SPP specify the tags or something to that effect. The issue is we use combinations of protocols, and presumably SPP knows this information so if so it seems reasonable to reflect that in the produced prep