Introduction

1. About This Shiny App

• This app extracts information for medical identifiers such as CUI, LOINC, PheCode, CCS, and RxNorm.
• Enter multiple IDs in the left sidebar (separated by semicolons or newlines), or upload a CSV (the first column must be IDs).
• Choose output fields, preview the top 10 rows, and download the full results as CSV.

2. Data Sources and Versions

• All data are curated by PARSE via rigorous deduplication, normalization, and consolidation of authoritative source datasets, augmented with domain-specific harmonization.
• Data versions:
  • UMLS: 2021AB.
  • RxNorm: data as of 2024-06-11.
  • LOINC: v2.73.
• Official links:
  • UMLS: https://www.nlm.nih.gov/research/umls/
  • RxNorm: https://www.nlm.nih.gov/research/umls/rxnorm/
  • LOINC: https://loinc.org/
  • PheCode: https://phewascatalog.org/phecodes
  • CCS: https://www.hcup-us.ahrq.gov/toolssoftware/ccs/ccs.jsp

3. How to Use Shiny

• Paste IDs in the input box or upload a CSV (first column is IDs). Separate by semicolons or newlines.
• Supported ID formats (case-insensitive prefixes; mixed types allowed):
  • CUI: C\d{7} 7 digit numbers (e.g., C0018681)
  • LOINC:
    • LOINC:n-n (e.g., LOINC:2162-6)
    • n-n (e.g., 2162-6 → LOINC:2162-6)
    • LPn-n (e.g., LP14355-9)
  • PheCode:
    • PheCode:nnn(.n) (e.g., PheCode:714.1)
    • Xnnn(.n) (e.g., X714.1)
    • phe_nnn[_n] (e.g., phe_714_1 → PheCode:714.1)
  • CCS: CCS:nnn (e.g., CCS:233)
  • RxNorm:
    • RXNORM:n (4–9 digits) (e.g., RXNORM:191831)
    • plain 4–9 digit numbers (e.g., 191831)
• Select desired columns (e.g., id, term, groupid, groupdesc) and click Run.
• The table shows the top 10 rows; click Download CSV to export all results.

4. API Usage

• Endpoint: POST http://localhost:8000/query
• Parameters:
  • ids: string; multiple IDs separated by semicolons or newlines, e.g., C0018681;LOINC:2162-6;RXNORM:191831.
  • fields: comma-separated list of columns, e.g., id,term,groupid,groupdesc.
• curl example:

curl -X POST 'http://localhost:8000/query' \
  -d 'ids=C0018681;RXNORM:191831' \
  -d 'fields=id,term,groupid,groupdesc'

• R example:

httr::POST(
  "http://localhost:8000/query",
  body = list(
    ids = "C0018681;LOINC:2162-6;RXNORM:191831",
    fields = "id,term,groupid,groupdesc"
  ),
  encode = "form"
) |> httr::content()

• Returns JSON with the selected fields.