Finalise Ontological Terminology

[JackScanlon]

Task

[!TIP]
See the following repos for ontological/coding generation & processing:

• termspp → MeSH and x-ref mapping
• GOMED → SNOMED and x-ref mapping

1. Reference

1.1. Coding System Tables

Coding System	Dot Code	Non-Dot Code	New/Modifiable/Existing
SNOMED	[NONE]	code	New
MeSH	[NONE]	code	New
ICD-9	[NONE]	code	New
ICD-10	code	alt_code	Existing
OPSC-4	code_with_decimal	code_without_decimal	Existing
ReadCV2	read_code	[MISSING]	Modifiable
ReadCV3	[MISSING]	term_id	Modifiable

1.2. Ontology Tables

[!NOTE]

• TODO

2. Pre-Deployment Tasks

2.1. Uploading & Processing

1. Determine final procedure of uploading tables

   • GOMED outputs & assoc. scripts:

     • Upload SNOMED
     • Upload ICD-9 codes

   • termspp & assoc. scripts:

     • Upload MeSH codes
     • Upload MeSH mapping

2. Build x-ref table(s)

3. Post-upload processing

   • Write script to integrate ICD-9 & MeSH into Ontology

   • Measure mapping, e.g. ...

     • What % of ontological terms are mapped to other coding systems?
     • Which coding system mappings are weakly mapped?

2.2. Assignment

1. Refactor ontological assignment algorithm to account for new coding system(s)

2. Simplify ontological assignment:

   • Improve assignment algorithm by reducing matching threshold
   • Improve context of assignment(s)

3. Related Tasks

• Relates to #1714