[ { "phenotype_id": "PH4139", "phenotype_version_id": 9357, "name": "Cholelithiasis", "definition": "Cholelithiasis involves the presence of gallstones (see the image below), which are concretions that form in the biliary tract.\n\nUKB baseline self reported fields.\n", "implementation": "The earliest record across all sources is obtained.\n", "publications": [ { "doi": "https://doi.org/10.1038/s41598-025-05838-9", "details": "Torralbo, Ana and Davitte, Jonathan M. and Croteau-Chonka, Damien C. and Ytsma, Cai R. and Tomlinson, Christopher and Fitzpatrick, Natalie and Chung, Sheng-Chia and Fatemifar, Ghazaleh and Cortes, Adrian S. and Richardson, Tom G. and Barclay, Matthew and Carrasco Zanini Sanchez, Julia and Finan, Chris and Hemingway, Harry and Hingorani, Aroon D. and Kuan Po Ai, Valerie and Langenberg, Claudia and Lyratzopoulos, Georgios and Lumbers, Tom and Pietzner, Maik and Shah, Anoop Dinesh and Thygesen, Johan Hilge and Zelenka, Natalie and Whittaker, John C. and Ehm, Margaret G. and Denaxas, Spiros, A Computational Framework for Defining and Validating Reproducible Phenotyping Algorithms of 313 Diseases in the UK Biobank.", "primary": true } ], "validation": "Phenotypes underwent a multi\\-layered validation approach that included a) evaluating data source concordance, b) age\\-sex incidence and baseline prevalence patterns, c) an external comparison to a representative and unselected UK EHR dataset, d) modifiable risk factor associations, and e) genetic correlations with external genome\\-wide association studies (GWAS). Results showed consistent disease distributions by age and sex, high ranked correlation with general population prevalence estimates, confirmed risk factor associations, and significant genetic correlations with external GWAS.\n", "citation_requirements": null, "created": "2026-06-08T20:07:47.122562Z", "author": "Torralbo, A; Davitte, J M; Croteau-Chonka, D C; Ytsma, C; Tomlinson, C; Fitzpatrick, N K; Chung, S C; Fatemifar, G; Cortes, A S; Richardson, T G; Barclay, M; Carrasco Zanini, J; Finan, C; Hemingway, H; Hingorani, A; Kuan, V; Langenberg, C; Lyratzopoulos, G; Lumbers, R T; Pietzner, M; Shah, A D; Thygesen, J H; Zelenka, N; Whittaker, J C; Ehm, M G; Denaxas, S", "collections": [ { "name": "Phenotype Library", "value": 18 }, { "name": "UK Biobank", "value": 32 } ], "tags": null, "organisation": null, "world_access": 1, "updated": "2026-06-08T20:07:47.115262Z", "sex": [ { "name": "Both", "value": "3" } ], "type": [ { "name": "Disease or syndrome", "value": "2" } ], "trials": null, "ontology": [ { "name": "Calculus in biliary tract (disorder)", "value": 675250 } ], "phenoflowid": null, "data_sources": [ { "name": "UK Biobank", "value": 13, "uid": "6a9f93ad-2434-41d9-93bf-6e9d2eee04e5", "url": "https://healthdatagateway.org/en/dataset/700", "datasource_id": 700 }, { "name": "Patient Episode Dataset for Wales (PEDW)", "value": 40, "uid": "4c33a5d2-164c-41d7-9797-dc2b008cc852", "url": "https://healthdatagateway.org/en/dataset/318", "datasource_id": 318 }, { "name": "Scottish Cancer Registry (SMR06)", "value": 417, "uid": "ad36dc03-1856-44de-99b0-1af6f312d86b", "url": "https://healthdatagateway.org/en/dataset/79", "datasource_id": 79 }, { "name": "Cancer Registration Data", "value": 788, "uid": "6904a2ff-ab44-4dd6-b9ec-25d3cad29e43", "url": "https://healthdatagateway.org/en/dataset/880", "datasource_id": 880 } ], "endorsements": null, "project_name": null, "coding_system": [ { "name": "UKBioBank codes", "value": 12 }, { "name": "ICD10 codes", "value": 4 }, { "name": "Read codes v3", "value": 6 }, { "name": "OPCS4 codes", "value": 7 } ], "corresp_author": "Ana Torralbo", "event_date_range": null, "concept_information": [ { "concept_id": 9854, "concept_version_id": 17339, "concept_name": "Non-cancer illness code, self-reported", "coding_system": { "id": 12, "name": "UKBioBank codes", "description": "UKBioBank codes" }, "phenotype_id": "PH4139", "phenotype_version_id": 9357, "phenotype_name": "Cholelithiasis", "code_attribute_header": [ "type" ], "codes": [ { "code": "1162", "description": "cholelithiasis/gall stones", "attributes": { "type": "any" } } ] }, { "concept_id": 9855, "concept_version_id": 17340, "concept_name": "Operation code", "coding_system": { "id": 12, "name": "UKBioBank codes", "description": "UKBioBank codes" }, "phenotype_id": "PH4139", "phenotype_version_id": 9357, "phenotype_name": "Cholelithiasis", "code_attribute_header": [ "type" ], "codes": [ { "code": "1528", "description": "gallstones removed", "attributes": { "type": "any" } } ] }, { "concept_id": 9856, "concept_version_id": 17341, "concept_name": "Diagnoses - main ICD10", "coding_system": { "id": 4, "name": "ICD10 codes", "description": "ICD10 Codes" }, "phenotype_id": "PH4139", "phenotype_version_id": 9357, "phenotype_name": "Cholelithiasis", "code_attribute_header": [ "type" ], "codes": [ { "code": "K80", "description": "Cholelithiasis", "attributes": { "type": "any" } } ] }, { "concept_id": 9857, "concept_version_id": 17342, "concept_name": "Diagnoses - secondary ICD10", "coding_system": { "id": 4, "name": "ICD10 codes", "description": "ICD10 Codes" }, "phenotype_id": "PH4139", "phenotype_version_id": 9357, "phenotype_name": "Cholelithiasis", "code_attribute_header": [ "type" ], "codes": [ { "code": "K80", "description": "Cholelithiasis", "attributes": { "type": "any" } } ] }, { "concept_id": 9858, "concept_version_id": 17343, "concept_name": "Operative procedures - main OPCS4", "coding_system": { "id": 7, "name": "OPCS4 codes", "description": "OPCS4 codes" }, "phenotype_id": "PH4139", "phenotype_version_id": 9357, "phenotype_name": "Cholelithiasis", "code_attribute_header": [ "type" ], "codes": [ { "code": "J18", "description": "cholecystectomy", "attributes": { "type": "any" } } ] }, { "concept_id": 9859, "concept_version_id": 17344, "concept_name": "Operative procedures - secondary OPCS4", "coding_system": { "id": 7, "name": "OPCS4 codes", "description": "OPCS4 codes" }, "phenotype_id": "PH4139", "phenotype_version_id": 9357, "phenotype_name": "Cholelithiasis", "code_attribute_header": [ "type" ], "codes": [ { "code": "J18", "description": "cholecystectomy", "attributes": { "type": "any" } } ] }, { "concept_id": 9860, "concept_version_id": 17345, "concept_name": "Underlying (primary) cause of death: ICD10", "coding_system": { "id": 4, "name": "ICD10 codes", "description": "ICD10 Codes" }, "phenotype_id": "PH4139", "phenotype_version_id": 9357, "phenotype_name": "Cholelithiasis", "code_attribute_header": [ "type" ], "codes": [ { "code": "K80", "description": "Cholelithiasis", "attributes": { "type": "any" } } ] }, { "concept_id": 9861, "concept_version_id": 17346, "concept_name": "Contributory (secondary) causes of death: ICD10", "coding_system": { "id": 4, "name": "ICD10 codes", "description": "ICD10 Codes" }, "phenotype_id": "PH4139", "phenotype_version_id": 9357, "phenotype_name": "Cholelithiasis", "code_attribute_header": [ "type" ], "codes": [ { "code": "K80", "description": "Cholelithiasis", "attributes": { "type": "any" } } ] }, { "concept_id": 9862, "concept_version_id": 17347, "concept_name": "GP clinical event records", "coding_system": { "id": 6, "name": "Read codes v3", "description": "Read codes v3" }, "phenotype_id": "PH4139", "phenotype_version_id": 9357, "phenotype_name": "Cholelithiasis", "code_attribute_header": [ "type" ], "codes": [ { "code": "14CE.00", "description": "H/O: gall stones", "attributes": { "type": "prevalent" } }, { "code": "1965.", "description": "Biliary colic", "attributes": { "type": "any" } }, { "code": "1965.00", "description": "Biliary colic", "attributes": { "type": "any" } }, { "code": "1965.11", "description": "Biliary colic symptom", "attributes": { "type": "any" } }, { "code": "4775.00", "description": "Faeces: gall stones present", "attributes": { "type": "any" } }, { "code": "4G2..00", "description": "O/E: gall stone", "attributes": { "type": "any" } }, { "code": "4G21.00", "description": "O/E: cholesterol gall stone", "attributes": { "type": "any" } }, { "code": "4G22.00", "description": "O/E: pigment gall stone", "attributes": { "type": "any" } }, { "code": "4G2Z.00", "description": "O/E: gall stone NOS", "attributes": { "type": "any" } }, { "code": "7648700.0", "description": "Enterotomy and removal of gallstone", "attributes": { "type": "any" } }, { "code": "8CMWD00", "description": "On gallstone care pathway", "attributes": { "type": "any" } }, { "code": "J503000", "description": "Gallstone ileus", "attributes": { "type": "any" } }, { "code": "J64..00", "description": "Cholelithiasis", "attributes": { "type": "any" } }, { "code": "J640.00", "description": "Gallbladder calculus with acute cholecystitis", "attributes": { "type": "any" } }, { "code": "J640000", "description": "Gallbladder calculus with acute cholecystitis +no obstruct", "attributes": { "type": "any" } }, { "code": "J640100", "description": "Gallbladder calculus with acute cholecystitis + obstruction", "attributes": { "type": "any" } }, { "code": "J640z00", "description": "Gallbladder calculus with acute cholecystitis - obst NOS", "attributes": { "type": "any" } }, { "code": "J641.00", "description": "Gallbladder calculus with other cholecystitis", "attributes": { "type": "any" } }, { "code": "J641000", "description": "Gallbladder calculus with other cholecystitis +no obstruct", "attributes": { "type": "any" } }, { "code": "J64..11", "description": "Bile duct calculus", "attributes": { "type": "any" } }, { "code": "J641100", "description": "Gallbladder calculus with other cholecystitis + obstruct", "attributes": { "type": "any" } }, { "code": "J64..12", "description": "Calculus - biliary", "attributes": { "type": "any" } }, { "code": "J64..13", "description": "Cystic duct calculus", "attributes": { "type": "any" } }, { "code": "J64..14", "description": "Gallbladder calculus", "attributes": { "type": "any" } }, { "code": "J64..15", "description": "Gallstones", "attributes": { "type": "any" } }, { "code": "J64..16", "description": "Stone - biliary", "attributes": { "type": "any" } }, { "code": "J641z00", "description": "Gallbladder calculus with other cholecystitis - obstruct NOS", "attributes": { "type": "any" } }, { "code": "J642.00", "description": "Gallbladder calculus without mention of cholecystitis", "attributes": { "type": "any" } }, { "code": "J642000", "description": "Gallbladder calculus without mention cholecystitis +no obstr", "attributes": { "type": "any" } }, { "code": "J642100", "description": "Gallbladder calculus without mention cholecystitis + obstruc", "attributes": { "type": "any" } }, { "code": "J642.11", "description": "Gallbladder calculus without mention of cholecystitis", "attributes": { "type": "any" } }, { "code": "J642200", "description": "Biliary colic", "attributes": { "type": "any" } }, { "code": "J642z00", "description": "Gallbladder calculus without cholecystitis and obstruct NOS", "attributes": { "type": "any" } }, { "code": "J643.00", "description": "Bile duct calculus with acute cholecystitis", "attributes": { "type": "any" } }, { "code": "J643000", "description": "Bile duct calculus + acute cholecystitis and no obstruction", "attributes": { "type": "any" } }, { "code": "J643100", "description": "Bile duct calculus + acute cholecystitis and obstruction", "attributes": { "type": "any" } }, { "code": "J643z00", "description": "Bile duct calculus + acute cholecystitis - obstruct NOS", "attributes": { "type": "any" } }, { "code": "J644.00", "description": "Bile duct calculus with other cholecystitis", "attributes": { "type": "any" } }, { "code": "J644000", "description": "Bile duct calculus + other cholecystitis and no obstruction", "attributes": { "type": "any" } }, { "code": "J644100", "description": "Bile duct calculus + other cholecystitis and obstruction", "attributes": { "type": "any" } }, { "code": "J644z00", "description": "Bile duct calculus + other cholecystitis - obstruction NOS", "attributes": { "type": "any" } }, { "code": "J645.00", "description": "Bile duct calculus without mention of cholecystitis", "attributes": { "type": "any" } }, { "code": "J645000", "description": "Bile duct calculus without cholecystitis, no obstruction", "attributes": { "type": "any" } }, { "code": "J645100", "description": "Bile duct calculus without cholecystitis with obstruction", "attributes": { "type": "any" } }, { "code": "J645.11", "description": "Choledocholithiasis", "attributes": { "type": "any" } }, { "code": "J645200", "description": "Bile duct calculus NOS", "attributes": { "type": "any" } }, { "code": "J645z00", "description": "Bile duct calculus without cholecystitis NOS", "attributes": { "type": "any" } }, { "code": "J646.00", "description": "Calculus of bile duct with cholangitis", "attributes": { "type": "any" } }, { "code": "J64z.", "description": "Cholelithiasis NOS", "attributes": { "type": "any" } }, { "code": "J64z.00", "description": "Cholelithiasis NOS", "attributes": { "type": "any" } }, { "code": "J64z000", "description": "Cholelithiasis without obstruction NOS", "attributes": { "type": "any" } }, { "code": "J64z100", "description": "Cholelithiasis with obstruction NOS", "attributes": { "type": "any" } }, { "code": "J64zz00", "description": "Cholelithiasis NOS", "attributes": { "type": "any" } }, { "code": "J670500", "description": "Gallstone acute pancreatitis", "attributes": { "type": "any" } }, { "code": "J671100", "description": "Gallstone chronic pancreatitis", "attributes": { "type": "any" } }, { "code": "Jyu8000", "description": "[X]Other cholelithiasis", "attributes": { "type": "any" } }, { "code": "X308i", "description": "Gallstone acute pancreatitis", "attributes": { "type": "any" } }, { "code": "X308u", "description": "Gallstone chronic pancreatitis", "attributes": { "type": "any" } }, { "code": "XaaBJ", "description": "On gallstone care pathway", "attributes": { "type": "any" } }, { "code": "XaB9c", "description": "Enterotomy and removal of gallstone", "attributes": { "type": "any" } }, { "code": "XaE6v", "description": "Bile duct calculus NOS", "attributes": { "type": "any" } }, { "code": "XaJCM", "description": "H/O: gall stones", "attributes": { "type": "prevalent" } }, { "code": "XE0bE", "description": "Bile duct calculus without mention of cholecystitis", "attributes": { "type": "any" } } ] } ], "status": 1, "doi": "https://doi.org/10.48533/8vbt-w629", "is_deleted": false, "publish_status": 2, "owner": "ieuan.scanlon", "template": { "id": 2, "name": "BHF Data Science Centre Phenotype", "description": "BHF Data Science Centre Phenotype definitions that describe a list of clinical codes, algorithms using clinical codes, or set of clinical trials. Visit the BHF Data Science Centre website to learn more: https://bhfdatasciencecentre.org", "version_id": 1 }, "versions": [ { "version_id": 9357, "version_name": "Cholelithiasis", "version_date": "2026-06-08T20:07:47.133749Z", "is_published": true, "is_latest": true } ] } ]