Data model content updates to support GH docs

[Bankso]

Relative to #49 and #66

Draft of the MC2 data model dictionary, using GitHub pages deployment, is here: https://mc2-center.github.io/data-models/

Potential actions that could improve documentation quality (should determine necessity/priority for the following):

• review all Component and Attribute entries and add descriptions where missing/incomplete
• review Valid Values and add descriptions, ontology references
• implement hierarchy for Valid Values

[aclayton555]

in 24-3, at least first two bullets are readily do-able. Third bullet might be more difficult so need to scope this further and see how far we can get.

[Bankso]

Currently reviewing components, attributes, and valid values

For hierarchy/structure, I did some preliminary analysis with GPT and ontology scoping, documented here:
https://docs.google.com/document/d/1Vs-X4laTfih2YpoouF0njCCSQmcC4AIpsmgmCdl5b9c/edit?usp=sharing

Summary: it seems doable, but it will be a lot of work. To help minimize effort required, I'll source from existing ontologies for structure and devise mappings when needed.

In terms of implementation, I think defining pair-wise relationships will be sufficient, since the information will be carried forward in each mapping. A generic example would be:

Take five terms: RNA-seq, scRNA-seq, ATAC-seq, scATAC-seq, WGS
Highest level group: Genomic technique
Possible second level groups: bulk, single-cell, transcriptomics, epigenomics, RNA, DNA (lots of options, is the point)

Organizing terms would occur in a CSV, using the column names:
Technique (should replace assay), Parent, [all other info captured]

Then relationships are easy to define and structure is easily inferred, using Genomic --> bulk, single-cell --> RNA-seq, scRNA-seq, ATAC-seq, scATAC-seq, WGS

Technique, Parent
Genomic, None
Bulk, Genomic
Single-cell, Genomic
RNA-seq, Bulk
ATAC-seq, Bulk
WGS, Bulk
scRNA-seq, Single-cell
scATAC-seq, Single-cell
.
.
.

[aclayton555]

Suggest to chat with ANV to see how this was designed and implemented in NF

[aclayton555]

• Continue working through building this out
• For search purposes, FTS may not necessitate this hierarchy, so that use case can be deprioritized until we know if FTS is favourable.

[aclayton555]

24-6: No updates this sprint. Carry into next sprint

[Bankso]

I will continue to collate valid value definitions here for assays, tissues, and tumor types here: https://docs.google.com/spreadsheets/d/1YL8kDB_tdvGDYqDy4x8zlBauLPDxc24W4tLEArJh0kQ/edit?usp=sharing

In addition, there are many valid value sets that are missing descriptions/definitions, like file formats, licenses, input/output formats, etc. Next step here is identify all value types that would benefit from this exercise and note them here.

[aclayton555]

24-7/8 close out: have new models add (per #115 )

[aclayton555]

24-9: Secondary to site visit priorities.

Will require some work to add new components. Might be some room for automation to help pull this information easier as the data model updates