Utilize existing LOINC mappings

[joeflack4]

Overview

There are some existing mappings we can potentially utilize.

Nico suggest to consult with him first before doing any sort of massive pipeline involving mappings.

Sub-tasks

• 1. From LOINC release files
• 2. From mapping commons
  • WIP: Add LOINC PART mappings monarch-initiative/monarch-mapping-commons#35 Nico: Contains some Uberon, CL, PRO, NCIT, GO and ChEBI mappings.
• 3. FDA UNII (UNique Ingredient Identifier codes)
  • Steven: UNII codes should be under this codesystem http://fdasis.nlm.nih.gov/
• 4. Cell Ontology
• Unsure where to obtain, but mentioned in the R01.
• 5. National Cancer Institute thesaurus
• Unsure where to obtain, but mentioned in the R01.

1. From LOINC release files

By the time of this writing, Shahim may or may not have partially or fully set this up. But there are plenty of existing mappings in the LOINC release. We need to make sure that these are included in our resulting output(s).

2. WIP: Add LOINC PART mappings #35

Note: drseb wrote:

All mappings except loinc2chebi_1.sssom.tsv were created using a semi-manual approach, in which software suggested mappings based on string comparisons, but a human would always review and possibly refine the mapping. loinc2chebi_1.sssom.tsv was obtained from compLoinc (Tim etc.)