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Primary Malignancy_biliary tract

Kuan V, Denaxas S, Gonzalez-Izquierdo A, Direk K, Bhatti O, Husain S, Sutaria S, Hingorani M, Nitsch D, Parisinos C, Lumbers T, Mathur R, Sofat R, Casas JP, Wong I, Hemingway H, Hingorani A

Type
Disease or Syndrome
ID
PH247
Version ID
494
Valid event data range
01/01/1999 - 01/07/2016
Sex
Female, Male
Agreement Date
2019-05-20
Coding system
Read codes v2 ICD10 codes Med codes
Tags /Collections
CALIBER Phenotype Library

Definition

At the specified date, a patient is defined as having had Primary Malignancy biliary tract IF they meet the criteria for any of the following on or before the specified date. The earliest date on which the individual meets any of the following criteria on or before the specified date is defined as the first event date:

Primary care

  1. Primary Malignancy biliary tract diagnosis or history of diagnosis during a consultation

OR Secondary care

  1. ALL diagnoses of Primary Malignancy biliary tract or history of diagnosis during a hospitalization

Implementation


Publications

  • Kuan V., Denaxas S., Gonzalez-Izquierdo A. et al. A chronological map of 308 physical and mental health conditions from 4 million individuals in the National Health Service. The Lancet Digital Health - DOI 10.1016/S2589-7500(19)30012-3

Clinical Code List

Rows: 19
Code Description Disease Medcode Category
B151.00 Malignant neoplasm of intrahepatic bile ducts Primary Malignancy_biliary tract 16915.0 Diagnosis of Primary Malignancy_biliary tract
B151000 Malignant neoplasm of interlobular bile ducts Primary Malignancy_biliary tract 65124.0 Diagnosis of Primary Malignancy_biliary tract
B151200 Malignant neoplasm of intrahepatic biliary passages Primary Malignancy_biliary tract 89593.0 Diagnosis of Primary Malignancy_biliary tract
B151400 Malignant neoplasm of intrahepatic gall duct Primary Malignancy_biliary tract 58088.0 Diagnosis of Primary Malignancy_biliary tract
B151z00 Malignant neoplasm of intrahepatic bile ducts NOS Primary Malignancy_biliary tract 61643.0 Diagnosis of Primary Malignancy_biliary tract
B161.00 Malignant neoplasm of extrahepatic bile ducts Primary Malignancy_biliary tract 23433.0 Diagnosis of Primary Malignancy_biliary tract
B161000 Malignant neoplasm of cystic duct Primary Malignancy_biliary tract 72445.0 Diagnosis of Primary Malignancy_biliary tract
B161100 Malignant neoplasm of hepatic duct Primary Malignancy_biliary tract 52537.0 Diagnosis of Primary Malignancy_biliary tract
B161200 Malignant neoplasm of common bile duct Primary Malignancy_biliary tract 7982.0 Diagnosis of Primary Malignancy_biliary tract
B161211 Carcinoma common bile duct Primary Malignancy_biliary tract 36495.0 Diagnosis of Primary Malignancy_biliary tract
B161300 Malignant neoplasm of sphincter of Oddi Primary Malignancy_biliary tract 105613.0 Diagnosis of Primary Malignancy_biliary tract
B161z00 Malignant neoplasm of extrahepatic bile ducts NOS Primary Malignancy_biliary tract 74896.0 Diagnosis of Primary Malignancy_biliary tract
B162.00 Malignant neoplasm of ampulla of Vater Primary Malignancy_biliary tract 10949.0 Diagnosis of Primary Malignancy_biliary tract
B163.00 Malignant neoplasm, overlapping lesion of biliary tract Primary Malignancy_biliary tract 35039.0 Diagnosis of Primary Malignancy_biliary tract
BB5D100 [M]Cholangiocarcinoma Primary Malignancy_biliary tract 8711.0 Diagnosis of Primary Malignancy_biliary tract
BB5D111 [M]Bile duct carcinoma Primary Malignancy_biliary tract 40438.0 Diagnosis of Primary Malignancy_biliary tract
BB5D300 [M]Bile duct cystadenocarcinoma Primary Malignancy_biliary tract 41313.0 Diagnosis of Primary Malignancy_biliary tract
BB5D700 [M]Combined hepatocellular carcinoma and cholangiocarcinoma Primary Malignancy_biliary tract 107299.0 Diagnosis of Primary Malignancy_biliary tract
BB5D711 [M]Hepatocholangiocarcinoma Primary Malignancy_biliary tract 110147.0 Diagnosis of Primary Malignancy_biliary tract
Rows: 19
Code Description Disease ReadcodeDescr Readcode
105613.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract Malignant neoplasm of sphincter of Oddi B161300
107299.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract [M]Combined hepatocellular carcinoma and cholangiocarcinoma BB5D700
10949.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract Malignant neoplasm of ampulla of Vater B162.00
110147.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract [M]Hepatocholangiocarcinoma BB5D711
16915.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract Malignant neoplasm of intrahepatic bile ducts B151.00
23433.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract Malignant neoplasm of extrahepatic bile ducts B161.00
35039.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract Malignant neoplasm, overlapping lesion of biliary tract B163.00
36495.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract Carcinoma common bile duct B161211
40438.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract [M]Bile duct carcinoma BB5D111
41313.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract [M]Bile duct cystadenocarcinoma BB5D300
52537.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract Malignant neoplasm of hepatic duct B161100
58088.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract Malignant neoplasm of intrahepatic gall duct B151400
61643.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract Malignant neoplasm of intrahepatic bile ducts NOS B151z00
65124.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract Malignant neoplasm of interlobular bile ducts B151000
72445.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract Malignant neoplasm of cystic duct B161000
74896.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract Malignant neoplasm of extrahepatic bile ducts NOS B161z00
7982.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract Malignant neoplasm of common bile duct B161200
8711.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract [M]Cholangiocarcinoma BB5D100
89593.0 Diagnosis of Primary Malignancy_biliary tract Primary Malignancy_biliary tract Malignant neoplasm of intrahepatic biliary passages B151200
Rows: 2
Code Description Disease Category
C22.1 Malignant neoplasm: Intrahepatic bile duct carcinoma Primary Malignancy_biliary tract Diagnosis of Primary Malignancy_biliary tract
C24 Malignant neoplasm of other and unspecified parts of biliary tract Primary Malignancy_biliary tract Diagnosis of Primary Malignancy_biliary tract

API

To Export Phenotype Details:

Format API
XML site_root/api/v1/public/phenotypes/PH247/version/494/detail/?format=xml
JSON site_root/api/v1/public/phenotypes/PH247/version/494/detail/?format=json
R Package

# Download here

library(ConceptLibraryClient)


# Connect to API

client = connect_to_API(public=TRUE)


# Get details of phenotype

details = get_phenotype_detail_by_version('PH247', '494', api_client=client)

To Export Phenotype Code List:

Format API
XML site_root/api/v1/public/phenotypes/PH247/version/494/export/codes/?format=xml
JSON site_root/api/v1/public/phenotypes/PH247/version/494/export/codes/?format=json
CSV site_root/phenotypes/PH247/version/494/export/codes/
R Package

# Download here

library(ConceptLibraryClient)


# Connect to API

client = connect_to_API(public=TRUE)


# Get codelists of phenotype

codelists = get_phenotype_code_list('PH247', '494', api_client=client)

Version History

Version
ID
Name Owner Publish date
494 Primary Malignancy_biliary tract ieuan.scanlon 2021-10-06 currently shown

Export - export all codes into a csv file/JSON/XML for the current phenotype version.

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