Malabsorption due to gastrointestinal surgery

PH3554 / 8621

OpenSAFELY

Jan 26, 2026

REGISTERING DOI...

OpenCodelists Phenotype

  1. Overview

    Codelist ID
    opensafely/malabsorption-due-to-gastrointestinal-surgery
    Version ID
    4c26d322
    Coding System
    SNOMED CT codes
    Collections
    OpenCodelistPhenotype Library
    Tags
    No data

  2. Definition

    This codelist was taken from OpenCodelists, created by OpenSAFELY. We recommend viewing this Phenotype on the OpenCodelist website to view the most recent version.

    This codelist aims to identify gastrointestinal surgeries resulting in malabsorption of vitamin D. It is developed for the purpose of the vitamin D study (indications for vitamin D testing/ prescribing).

    © University of Oxford for the Bennett Institute for Applied Data Science 2025. This work may be copied freely for non-commercial research and study.

  3. Methodology

    Search terms: Roux-en-Y Gastric Bypass, sleeve gastrectomy, duodenal bypass, duodenal switch, gastric bypass, ileal bypass, pancreatic diversion.

    The aim was to identify specific surgical procedures most likely to lead to vit. D deficiency: sleeve gastrectomy (esp. Biliopancreatic diversion with duodenal switch (BPD/DS)) and gastric bypass (esp. RYGB). Related weight-loss procedures, especially those affecting duodenal and ileal absorption (e.g. duodenal bypass liner), were included. Similarly, procedures where the duodenum is bypassed (as this is where most vit D. absorption occurs) were included.

    Large umbrella terms likely to include these surgeries (e.g. gastrojejustomy) were included; other terms were excluded.

    Gastric banding was excluded, as BOMMS guidelines state that following gastric banding: "Routine monitoring is usually not required unless the patient has symptomatic vitamin D deficiency".

  4. References

    Source Reference

    https://www.opencodelists.org/codelist/opensafely/malabsorption-due-to-gastrointestinal-surgery/4c26d322

    References

  5. Clinical Codelist

  6. API

    To Export Phenotype Details:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH3554/version/8621/detail/?format=json
    R Package

    # Download here

    library(ConceptLibraryClient)


    # Connect to API

    client = ConceptLibraryClient::Connection$new(public=TRUE)


    # Get details of Phenotype

    phenotype_details = client$phenotypes$get_detail(
     'PH3554',
     version_id=8621
    )

    Py Package

    # Download here

    from pyconceptlibraryclient import Client


    # Connect to API

    client = Client(public=True)


    # Get details of Phenotype

    phenotype_detail = client.phenotypes.get_detail(
     'PH3554',
     version_id=8621
    )

    To Export Phenotype Code List:

    FormatAPI
    JSON site_root/api/v1/phenotypes/PH3554/version/8621/export/codes/?format=json
    R Package

    # Download here

    library(ConceptLibraryClient)


    # Connect to API

    client = ConceptLibraryClient::Connection$new(public=TRUE)


    # Get codelist of Phenotype

    phenotype_codelist = client$phenotypes$get_codelist(
     'PH3554',
     version_id=8621
    )

    Py Package

    # Download here

    from pyconceptlibraryclient import Client


    # Connect to API

    client = Client(public=True)


    # Get codelist of Phenotype

    phenotype_codelist = client.phenotypes.get_codelist(
     'PH3554',
     version_id=8621
    )

  7. Version History

    Version IDNameOwnerPublish date
    Malabsorption due to gastrointestinal surgery ieuan.scanlon2026-01-26 23:21