Clarification and Reorganization of High-Level Categories in miairr/data_elements

[ustervbo]

In the miairr/data_elements.rst, we mention having six high-level categories: Study and subject, sample collection, sample processing and sequencing, raw sequences, processing of sequence data, and processed AIRR sequences. However, the table only presents five levels:

• 1/study
• 1/subject
• 1/diagnosis and intervention
• 2/sample
• 3/process (cell)
• 3/process (nucleic acid)
• 3/process (nucleic acid [pcr])
• 3/process (sequencing)
• 4/data (raw reads)
• 5/process (computational)
• 5/data (processed sequence)

At first, it look like 5/data (processed sequence) should be 6/data (processed sequence), but looking at the TSV-file I see that 5/data (processed sequence) is all about registering the V(D)J germline reference database, which aligns it with 5/process (computational) as it is relevant for the software registered in Software tools and version numbers.

Is splitting the table in miairr/data_elements.rst into sections corresponding to each high-level category possible? This will prevent endless scrolling and make the grouping more clear. And we can explain the occult and enigmatic 6th level.

[javh]

From the call:

• DataProcessing.germline_database should be x-airr.subset: process (computational)
• Enable Rearrangement (x-airr.set: 6) row generation in MiAIRR TSV (in conf.py).
• Correct MiAIRR figure to move "V(D)J germline reference database" to set 5.
• Can we split the docs rendered table into sections or separate tables (with a toc)?
• Should we split some groups for v2.0?