Basic progress monitor for mappings

[matentzn]

We need a way to understand how far we are along the mapping process and how far we still need to go.

Functional requirements:

• We have statistics and tables about:
  • Number of ICD terms (100%)
  • ICD terms that are
    • not mapped
      • unmapped-in-scope: but in scope (it is a disease)
      • unmapped-excluded: but excluded (because out of scope)
    • mapped.
  • unmapped-in-scope, unmapped-excluded and mapped add up to 100%.

Inputs to analysis:

• Exclusion table (Create list of ICD terms excluded from our mapping monarch-initiative/mondo#4570): sync from here.
• Mappings (Ingest Mondo mappings #4, @hrshdhgd will share link to a mondo-icd sssom mapping when its there)
• ICD10 (owl file).

Output:

• a table with all ICD codes that have a column category that is either unmapped-excluded, mapped or unmapped-in-scope
• Summary summary statistics across

### Example Table:

code	category
ICD10CM:ABC	unmapped-in-scope
ICD10CM:A12	unmapped-excluded

Non-functional requirements:

• We need to be able to do the same for any incoming ontology - the code should be agnostic to which ontology, mappingset etc it takes as an input
• Should be delivered as a Makefile goal here

analysis/icd10cm-mapping-progress.tsv: mirror/icd10cm.owl exclusions/icd10.tsv mappings/icd10cm.sssom.tsv
     python........

[joeflack4]

Oh, you got to making an issue for this. And it is detailed. Thank you Nico!

There's a chance I can start this today or tomorrow. Otherwise I can start next Thursday.

[joeflack4]

@hrshdhgd Can you link ICD10CM exact matches?

[hrshdhgd]

@hrshdhgd Can you link ICD10CM exact matches?

https://raw.githubusercontent.com/monarch-initiative/mondo/45f95c89d96d38db3d10b69cbb88a514afe01bff/src/ontology/mappings/mondo_exactmatch_icd10cm.sssom.tsv