v3.2.0

Oxford OMOP data mapper v3.2.0

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What's Changed

• fix cosd observation id by @holtyad in #277
• Rtds - Provider and Observation by @khayamAmin in #278
• Fix SQL syntax error in ConditionOccurrenceRecorder duplicate detection by @Copilot in #281
• [WIP] Update mapping of unknown concepts to 0 instead of null by @Copilot in #280
• Bump Microsoft.Extensions.Configuration.Json and Microsoft.Extensions.Hosting by @dependabot[bot] in #283
• Bump Microsoft.NET.Test.Sdk from 18.0.0 to 18.0.1 by @dependabot[bot] in #284
• Bump MSTest.TestFramework from 4.0.1 to 4.0.2 by @dependabot[bot] in #286
• Added base queries for all known COSD elements in schema version 8.1 … by @james-cockayne in #287
• restructure cosd folder by @holtyad in #288
• Bump MSTest.TestAdapter from 4.0.1 to 4.0.2 by @dependabot[bot] in #290
• Add COSD lung mappings by @holtyad in #289
• COSD lung measurements by @holtyad in #291
• final cosd measurement mappings by @holtyad in #292
• Insert only distinct records to avoid bug where although the source r… by @james-cockayne in #295
• Bump JetBrains.Annotations from 2025.2.2 to 2025.2.4 by @dependabot[bot] in #293
• Trim lookup key before doing a lookup. by @james-cockayne in #296
• New COSD mappings by @holtyad in #294
• New regression fixes by @khayamAmin in #298
• Bump NUnit3TestAdapter from 5.2.0 to 6.0.0 by @dependabot[bot] in #297
• Feature/out of domain mappings by @james-cockayne in #299
• Observation SQL fixes by @khayamAmin in #300
• Map unknown concepts to 0 rather than null. When mapping from known c… by @james-cockayne in #279
• Bump Microsoft.Extensions.Configuration.Json and Microsoft.Extensions.Hosting by @dependabot[bot] in #302
• Fix bug where concept map recorded the target domain as at the source… by @james-cockayne in #303
• COSD breast condition / procedure mappings by @holtyad in #304
• Bump DuckDB.NET.Data.Full from 1.4.1 to 1.4.3 by @dependabot[bot] in #305
• Fix bug where a concept could be mapped to an unknown concept rather … by @james-cockayne in #306
• update supported docs by @holtyad in #310
• COSD breast mappings by @holtyad in #309
• Bump NUnit3TestAdapter from 6.0.0 to 6.0.1 by @dependabot[bot] in #311
• Added observation_source_value mappings by @james-cockayne in #314
• Bump Microsoft.Extensions.Configuration.Json and Microsoft.Extensions.Hosting by @dependabot[bot] in #317
• Bump NUnit3TestAdapter from 6.0.1 to 6.1.0 by @dependabot[bot] in #315
• Breast mappings by @holtyad in #313
• Try fix bug where some patients did not have a linked NHS number. by @james-cockayne in #318
• Cosd mappings by @holtyad in #319
• Final cosd breast measurements by @holtyad in #320
• Cosd Measurement Mappings by @holtyad in #321

New Contributors

• @Copilot made their first contribution in #281

Full Changelog: v3.1.1...v3.2.0

v3.1.1

Oxford OMOP data mapper v3.1.1

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Full Changelog: v3.1.0...v3.1.1

v3.1.0

Oxford OMOP data mapper v3.1.0

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What's Changed

• Bump Microsoft.Extensions.Configuration.Json and Microsoft.Extensions.Hosting by @dependabot[bot] in #273
• fix url resolver by @holtyad in #274
• Feature/lab observations by @holtyad in #270
• Bump MSTest.TestFramework from 3.10.4 to 4.0.1 by @dependabot[bot] in #269
• Feature/sact visit and observation by @khayamAmin in #267
• Fix dqd observations by @holtyad in #276
• Feature/restore cosd by @james-cockayne in #275

Full Changelog: v3.0.0...v3.1.0

v3.0.0

Oxford OMOP data mapper v3.0.0

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What's Changed

• remove drugs after death by @holtyad in #211
• add event_id in prescribing by @holtyad in #210
• Bump JetBrains.Annotations from 2024.3.0 to 2025.2.0 by @dependabot[bot] in #212
• Bump Microsoft.Data.SqlClient and 2 others by @dependabot[bot] in #214
• Added support for processing Oxford's spine death data. Added support… by @james-cockayne in #215
• Bump Microsoft.Extensions.Configuration.Json and Microsoft.Extensions.Hosting by @dependabot[bot] in #216
• Feature/csv pagination by @james-cockayne in #221
• Bump MSTest.TestFramework from 3.10.0 to 3.10.1 by @dependabot[bot] in #220
• Feature/azure sql retry by @james-cockayne in #222
• Bump MSTest.TestFramework from 3.10.1 to 3.10.2 by @dependabot[bot] in #226
• Bump NUnit from 4.3.2 to 4.4.0 by @dependabot[bot] in #224
• Bump MSTest.TestAdapter from 3.10.0 to 3.10.2 by @dependabot[bot] in #225
• Bump NUnit3TestAdapter from 5.0.0 to 5.1.0 by @dependabot[bot] in #223
• Feature/memory performance experiment by @james-cockayne in #228
• Bump Microsoft.Data.SqlClient from 6.1.0 to 6.1.1 by @dependabot[bot] in #227
• add rtds mappings by @holtyad in #218
• Do not request the next batch if the current batch was not full. by @james-cockayne in #229
• add dqd correction from CI build by @holtyad in #232
• Bugfix/sact row merging by @james-cockayne in #233
• Bump MSTest.TestAdapter from 3.10.2 to 3.10.3 by @dependabot[bot] in #231
• In the case that we have a SNOMED code that cannot be mapped to stand… by @james-cockayne in #234
• Bump MSTest.TestFramework from 3.10.2 to 3.10.3 by @dependabot[bot] in #230
• add zeros to lookup by @holtyad in #237
• Bump JetBrains.Annotations from 2025.2.0 to 2025.2.1 by @dependabot[bot] in #236
• Fix RTDS mappings by @holtyad in #238
• Bump JetBrains.Annotations from 2025.2.1 to 2025.2.2 by @dependabot[bot] in #239
• Bump MSTest.TestAdapter from 3.10.3 to 3.10.4 by @dependabot[bot] in #240
• Swap int to string in record.cs files by @holtyad in #242
• Bump MSTest.TestFramework from 3.10.3 to 3.10.4 by @dependabot[bot] in #241
• make lookup case insensitive by @holtyad in #235
• Extend non standard to standard concept map to handle DMD+d ingredien… by @james-cockayne in #243
• Bump Microsoft.Extensions.Configuration.Json from 9.0.8 to 9.0.9 by @dependabot[bot] in #246
• Bump Newtonsoft.Json from 13.0.3 to 13.0.4 by @dependabot[bot] in #248
• Widen list of reasons why we may want to retry a query. by @james-cockayne in #249
• Bump Microsoft.Extensions.Hosting from 9.0.8 to 9.0.9 by @dependabot[bot] in #247
• fix RTDS join on ID column by @holtyad in #251
• Fix dqd errors by @holtyad in #252
• Bump rexml from 3.4.0 to 3.4.2 by @dependabot[bot] in #250
• add supported docs by @holtyad in #253
• Added SACT - Provider, Care Site and Measurement by @khayamAmin in #257
• Feature/duckdb by @james-cockayne in #262
• Bump Microsoft.NET.Test.Sdk from 17.14.1 to 18.0.0 by @dependabot[bot] in #256
• Bump NUnit3TestAdapter from 5.1.0 to 5.2.0 by @dependabot[bot] in #258
• Lab data mappings by @holtyad in #263
• Feature/duckdb cpu performance by @james-cockayne in #264
• Optimise finalise scripts by @james-cockayne in #271
• Bump DuckDB.NET.Data.Full from 1.3.2 to 1.4.1 by @dependabot[bot] in #265

Full Changelog: v2.1.0...v3.0.0

v2.1.1

Oxford OMOP data mapper v2.1.1

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What's Changed

• Feature/gp staging by @james-cockayne in #196
• Feature/prescribing concept by @james-cockayne in #200
• Bump MSTest.TestAdapter and MSTest.TestFramework by @dependabot[bot] in #201
• Feature/many to one concept map by @james-cockayne in #199
• Prescription Lookup by @holtyad in #198
• Alter era calculating stored procedure to use temp tables to improve performance. by @james-cockayne in #203
• Include non dictionary fields in the mapping svg by @james-cockayne in #202
• Feature/prescription lookup by @khayamAmin in #204
• OxfordGP Drug Exposure Mappings by @holtyad in #205
• Use DW unique identifier as the RecordConnectionIdentifier by @james-cockayne in #207
• lowercase mappings bug by @holtyad in #208
• Bump Microsoft.Extensions.Configuration.Json and Microsoft.Extensions.Hosting by @dependabot[bot] in #209
• Added new vocabulary entry by @james-cockayne in #206

Full Changelog: v2.0.0...v2.1.1

v2.1.0

Oxford OMOP data mapper v2.1.0

Tagged Container images

What's Changed

• Feature/gp staging by @james-cockayne in #196
• Feature/prescribing concept by @james-cockayne in #200
• Bump MSTest.TestAdapter and MSTest.TestFramework by @dependabot[bot] in #201
• Feature/many to one concept map by @james-cockayne in #199
• Prescription Lookup by @holtyad in #198
• Alter era calculating stored procedure to use temp tables to improve performance. by @james-cockayne in #203
• Include non dictionary fields in the mapping svg by @james-cockayne in #202
• Feature/prescription lookup by @khayamAmin in #204
• OxfordGP Drug Exposure Mappings by @holtyad in #205
• Use DW unique identifier as the RecordConnectionIdentifier by @james-cockayne in #207
• lowercase mappings bug by @holtyad in #208
• Bump Microsoft.Extensions.Configuration.Json and Microsoft.Extensions.Hosting by @dependabot[bot] in #209
• Added new vocabulary entry by @james-cockayne in #206

Full Changelog: v2.0.0...v2.1.0

v2.0.0

Oxford OMOP data mapper v2.0.0

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What's Changed

• add docs for db patching tool by @holtyad in #43
• Bump CsvHelper from 31.0.2 to 33.0.1 by @dependabot in #42
• Bump MSTest.TestAdapter from 3.2.2 to 3.4.3 by @dependabot in #40
• Bump webrick from 1.8.1 to 1.8.2 by @dependabot in #46
• Bump google-protobuf from 3.25.3 to 3.25.5 by @dependabot in #45
• Bump rexml from 3.2.6 to 3.3.9 by @dependabot in #44
• Bump MSTest.TestFramework from 3.2.2 to 3.4.3 by @dependabot in #39
• Bump Microsoft.NET.Test.Sdk from 17.9.0 to 17.10.0 by @dependabot in #32
• Bump Dapper from 2.1.35 to 2.1.44 by @dependabot in #25
• Feature/oxmop 11 stage apc by @james-cockayne-ad in #56
• Bump JetBrains.Annotations from 2023.3.0 to 2024.3.0 by @dependabot in #47
• Bump NUnit3TestAdapter from 4.5.0 to 4.6.0 by @dependabot in #48
• Bump NSubstitute from 5.1.0 to 5.3.0 by @dependabot in #49
• Bump Microsoft.Extensions.Configuration.Json and Microsoft.Extensions.Hosting by @dependabot in #50
• Bump MSTest.TestAdapter from 3.4.3 to 3.6.3 by @dependabot in #51
• Bump System.Data.SqlClient from 4.8.6 to 4.9.0 by @dependabot in #52
• Bump MSTest.TestFramework from 3.4.3 to 3.6.3 by @dependabot in #54
• Bump NUnit from 4.1.0 to 4.2.2 by @dependabot in #53
• Bump Microsoft.NET.Test.Sdk from 17.10.0 to 17.11.1 by @dependabot in #55
• fix/carriage returns and add unit tests by @holtyad in #58
• Fix remaining build warnings. by @james-cockayne-ad in #59
• DataQualityDashboard QA validation pipeline by @holtyad in #61
• Bump Microsoft.NET.Test.Sdk from 17.11.1 to 17.12.0 by @dependabot in #60
• VPN connectivity dashboard pipeline fix by @holtyad in #62
• Feature/oxmop 22 by @james-cockayne-ad in #63
• Bump MSTest.TestFramework from 3.6.3 to 3.6.4 by @dependabot in #65
• Feature/sus transform by @james-cockayne-ad in #68
• Fix bug where procedure_source_value was set to the date rather than … by @james-cockayne-ad in #66
• Fix bug where SUS OP staging tables could not be cleared. by @james-cockayne-ad in #67
• Added additional vocabularies by @james-cockayne-ad in #70
• Added known data quality dashboard test failures. Make run.ps1 script… by @james-cockayne-ad in #69
• Bump NUnit from 4.2.2 to 4.3.0 by @dependabot in #72
• Add outpatient person, location & death by @holtyad in #73
• Fix bug where OP OPCS procedure data was not staged properly. by @james-cockayne-ad in #74
• Add inpatient care_site and provider by @holtyad in #71
• Bump coverlet.collector from 6.0.2 to 6.0.3 by @dependabot in #81
• Bump NUnit from 4.3.0 to 4.3.2 by @dependabot in #80
• Bump MSTest.TestFramework from 3.6.4 to 3.7.0 by @dependabot in #76
• Fix data quality dashboard errors field_fkdomain_condition_occurrence… by @james-cockayne-ad in #79
• Bump MSTest.TestAdapter from 3.6.4 to 3.7.0 by @dependabot in #77
• Add outpatient procedure and condition occurrance by @holtyad in #75
• Fix bug where some discharge and admission codes were non standard. by @james-cockayne-ad in #82
• Add SUS APC referral observation by @holtyad in #84
• Use concept 0 for genders other than male/female as it is the only ot… by @james-cockayne-ad in #85
• Update purge command to also rebuild era tables. by @james-cockayne-ad in #83
• Fix bug where some mapped ICD10/ICDO3/OPCS4 codes were not standard o… by @james-cockayne-ad in #86
• Fix to replace DateConverter with DateAndTimeCombiner by @holtyad in #87
• Bump MSTest.TestAdapter from 3.7.0 to 3.7.1 by @dependabot in #91
• Bump Microsoft.Extensions.Configuration.Json and Microsoft.Extensions.Hosting by @dependabot in #92
• add condition and procedure occurrence fixes by @holtyad in #89
• Bump MSTest.TestFramework from 3.7.0 to 3.7.1 by @dependabot in #90
• Bump Microsoft.Data.SqlClient from 5.2.2 to 6.0.0 by @dependabot in #93
• add location, visit_occurrence and visit_detail fixes by @holtyad in #95
• Bump coverlet.collector from 6.0.3 to 6.0.4 by @dependabot in #96
• Update HospitalProviderSpellNumber Data Type by @holtyad in #97
• Differentiate between standard and non standard ICD10 code resolvers.… by @james-cockayne-ad in #98
• add measurements and concept relationship resolver by @holtyad in #94
• Fix to use non standard selector in measurements by @holtyad in #100
• Bump MSTest.TestFramework from 3.7.1 to 3.7.2 by @dependabot in #102
• Bump MSTest.TestAdapter from 3.7.1 to 3.7.2 by @dependabot in #101
• Add OP Observations & Visits by @holtyad in #99
• Simplify relationship resolver. by @james-cockayne-ad in #104
• Feature/oxomop 18 stage ae data by @james-cockayne-ad in #103
• Remove DB references by @holtyad in #105
• Add OP CareSite, Provider & Visits fix by @holtyad in #106
• Bump Microsoft.Data.SqlClient from 6.0.0 to 6.0.1 by @dependabot in #107
• Bump MSTest.TestAdapter from 3.7.2 to 3.7.3 by @dependabot in #108
• Add AE Person, Location & Death by @holtyad in #110
• OP QA updates by @holtyad in #111
• Bump MSTest.TestFramework from 3.7.2 to 3.7.3 by @dependabot in #109
• Bump Dapper from 2.1.44 to 2.1.66 by @dependabot in #114
• Visit Occurrence / Detail updates by @holtyad in #112
• AE Conditions & Visits by @holtyad in #113
• Bump NUnit3TestAdapter from 4.6.0 to 5.0.0 by @dependabot in #117
• Bump Microsoft.NET.Test.Sdk from 17.12.0 to 17.13.0 by @dependabot in #116
• Added support for staging CCMDS data. by @james...

1.0.0

Oxford Omop Data Mapper v1.0.0 Release Notes

Current Aims

The current scope for the transformation at source data level is as follows:

Source Data Set	Version(s) Supported
CDS - Commissioning Data Sets	EMIS Infoflex 6.2 fixed width multiline text format
COSD - Cancer Outcomes and Services Dataset	v8-1 and v9-0-1 xml formats
SACT - Systemic Anti-Cancer Therapy Data Set	v3.0
RTDS - Radiotherapy Data Set	Varian ARIA Oncology Information System format

The current scope for the transformation at table and field level has been selected based on the HDR UK minimum field set for cohorting queries. In addition to this, any other mandatory OMOP fields for the respective tables have been considered. Some additional tables and fields have been included as these were picked up as part of the analysis process. To see which fields and tables have been considered, please see the transformation documentation section of the site.

Supported Transformations

OMOP Table	CDS	COSD	RTDS	SACT
Location	✔	✔	✔	✔
Person	✔️	✔️	✔️	✔️
Condition Occurrence	✔️	✔️
Visit Occurrence	✔️
Visit Details	✔️
Measurement	✔️ ❗	✔️
Death	✔️	✔
Procedure Occurrence	✔️	✔️
Drug Exposure	✔
Observation	✔	✔️

Getting Started

To get started with Data Migration Tool v1.0.0, visit our official website for download instructions, comprehensive documentation, and more.