Missing processed AIRR sequences in MiAIRR Data Elements table

[ustervbo]

In the section 'MiAIRR Data Elements', we write:

The AIRR Community has agreed to six high-level data sets that will guide the publication, curation, and sharing of AIRR-Seq data and metadata: Study and subject, sample collection, sample processing and sequencing, raw sequences, processing of sequence data, and processed AIRR sequences.

However, the table shown has only five sets. The last element of the table is 5 / data (processed sequence), which hints at a flawed numbering. The V(D)J germline reference database arguably belongs to 5 / process (computational).

What's missing from the table is the processed AIRR sequences. The reason seems to be a missing Rearrangement from:

tables = ['Study', 'Subject', 'Diagnosis', 'Sample', 'CellProcessing', 'NucleicAcidProcessing',
          'PCRTarget', 'SequencingRun', 'SequencingData', 'DataProcessing']

in conf.py. Looking at the schema, adding Rearrangement will add v_call, d_call, j_call, c_call, junction, junction_aa, duplicate_count, and cell_id to the table under set/section: 6 / data (processed sequence).

Additionally, germline_database in the schema should be modified so that subset: data (processed sequence) becomes subset: process (computational).

The opening paragraph could be rewritten to include the style of MiAIRR-to-NCBI Implementation:

The AIRR Community has agreed to six high-level data sets that will guide the publication, curation, and sharing of AIRR-Seq data and metadata. The levels are:

1. Study, subject, and diagnosis and intervention
2. Sample collection
3. Sample processing and sequencing
4. Raw sequencing data
5. Data processing
6. Processed sequences with a basic analysis results

[ustervbo]

Duplicate of #795