[PR #3] [MERGED] necessary scripts for lung cancer ADAM #9

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opened 2026-03-23 20:29:37 +00:00 by mirror · 0 comments

mirror commented

2026-03-23 20:29:37 +00:00

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📋 Pull Request Information

Original PR: https://github.com/RADar-AZDelta/AZDelta-OMOP-CDM/pull/3
Author: @lbertelo01
Created: 8/23/2022
Status: ✅ Merged
Merged: 9/14/2022
Merged by: @StijnDupulthys

Base: main ← Head: Louise-proposals

📝 Commits (3)

1cf3caf necessary scripts for lung cancer ADAM
c37b758 longchirurgie - check mapping procedure_concept_id
a18d07e custom concepts

📊 Changes

83 files changed (+5681 additions, -0 deletions)

View changed files

➕ condition_occurrence/awell_baselineclinicalform.sql.jinja (+62 -0)
➕ condition_occurrence/condition_concept_id/awell_antwoorden_baselineclinical_usagi.csv (+73 -0)
➕ condition_occurrence/condition_concept_id/awell_vragen_baselineclinical_usagi.csv (+23 -0)
➕ condition_occurrence/condition_concept_id/custom/awell_condition_concept.csv (+6 -0)
➕ condition_occurrence/condition_concept_id/custom/moc_condition_concept.csv (+6 -0)
➕ condition_occurrence/condition_concept_id/vragenlijsten_hix_antwoorden_MOC.sql.jinja (+13 -0)
➕ condition_occurrence/condition_concept_id/vragenlijsten_hix_antwoorden_MOC_usagi.csv (+570 -0)
➕ condition_occurrence/condition_concept_id/vragenlijsten_hix_vragen_MOC.sql.jinja (+12 -0)
➕ condition_occurrence/condition_concept_id/vragenlijsten_hix_vragen_MOC_usagi.csv (+77 -0)
➕ condition_occurrence/conditions_in_moc.sql.jinja (+47 -0)
➕ episode/awell_treatment.sql.jinja (+76 -0)
➕ episode/episode_concept_id/kuur_usagi.csv (+2 -0)
➕ episode/episode_concept_id/radiotherapie_usagi.csv (+4 -0)
➕ episode/episode_concept_id/therapie_awell_yearly_followup_usagi.csv (+5 -0)
➕ episode/episode_object_concept_id/awell_start_treatment.sql.jinja (+33 -0)
➕ episode/episode_object_concept_id/awell_start_treatment_usagi.csv (+30 -0)
➕ episode/episode_object_concept_id/custom/kuur_concept.csv (+47 -0)
➕ episode/episode_object_concept_id/kuur.sql.jinja (+10 -0)
➕ episode/episode_object_concept_id/kuur_usagi.csv (+175 -0)
➕ episode/episode_type_concept_id/mzg_usagi.csv (+2 -0)

...and 63 more files

📄 Description

In script condition_occurrence - conditions_in_moc.sql.jinja and baselineclinicalform_awell.sql.jinja, this contains mutations (ALK, BRAF, …) from lung tumors. I have put this the condition_status_concept_id to 'secondary diagnosis' but I am not 100% sure of this, please verify.
No condition_source_concept_id usagi files were added for the new scripts, let me know if this is necessary.
Episode: every line of radiotherapy is 1 record in the episode table (unlike before where every day radiotherapy occurred was a record with start-date=end-date). TODO: add each record to procedure_occurrence?
Does the master omop contain length, weight, bmi in the measurement table?
Observation table does not hold a 'value_as_datetime' column in version 5.4 so I stored datetimes as strings in the value_as_string column

_{🔄 This issue represents a GitHub Pull Request. It cannot be merged through Gitea due to API limitations.}

## 📋 Pull Request Information **Original PR:** https://github.com/RADar-AZDelta/AZDelta-OMOP-CDM/pull/3 **Author:** [@lbertelo01](https://github.com/lbertelo01) **Created:** 8/23/2022 **Status:** ✅ Merged **Merged:** 9/14/2022 **Merged by:** [@StijnDupulthys](https://github.com/StijnDupulthys) **Base:** `main` ← **Head:** `Louise-proposals` --- ### 📝 Commits (3) - [`1cf3caf`](https://github.com/RADar-AZDelta/AZDelta-OMOP-CDM/commit/1cf3caf305d4e9d1c78fdb52f70cd99f7cd4f9cb) necessary scripts for lung cancer ADAM - [`c37b758`](https://github.com/RADar-AZDelta/AZDelta-OMOP-CDM/commit/c37b7582bc1c4f7c62bfa8c2a4f7611caa9406c6) longchirurgie - check mapping procedure_concept_id - [`a18d07e`](https://github.com/RADar-AZDelta/AZDelta-OMOP-CDM/commit/a18d07ea7b8b44ac590accf2607cf24d90e0c97b) custom concepts ### 📊 Changes **83 files changed** (+5681 additions, -0 deletions) <details> <summary>View changed files</summary> ➕ `condition_occurrence/awell_baselineclinicalform.sql.jinja` (+62 -0) ➕ `condition_occurrence/condition_concept_id/awell_antwoorden_baselineclinical_usagi.csv` (+73 -0) ➕ `condition_occurrence/condition_concept_id/awell_vragen_baselineclinical_usagi.csv` (+23 -0) ➕ `condition_occurrence/condition_concept_id/custom/awell_condition_concept.csv` (+6 -0) ➕ `condition_occurrence/condition_concept_id/custom/moc_condition_concept.csv` (+6 -0) ➕ `condition_occurrence/condition_concept_id/vragenlijsten_hix_antwoorden_MOC.sql.jinja` (+13 -0) ➕ `condition_occurrence/condition_concept_id/vragenlijsten_hix_antwoorden_MOC_usagi.csv` (+570 -0) ➕ `condition_occurrence/condition_concept_id/vragenlijsten_hix_vragen_MOC.sql.jinja` (+12 -0) ➕ `condition_occurrence/condition_concept_id/vragenlijsten_hix_vragen_MOC_usagi.csv` (+77 -0) ➕ `condition_occurrence/conditions_in_moc.sql.jinja` (+47 -0) ➕ `episode/awell_treatment.sql.jinja` (+76 -0) ➕ `episode/episode_concept_id/kuur_usagi.csv` (+2 -0) ➕ `episode/episode_concept_id/radiotherapie_usagi.csv` (+4 -0) ➕ `episode/episode_concept_id/therapie_awell_yearly_followup_usagi.csv` (+5 -0) ➕ `episode/episode_object_concept_id/awell_start_treatment.sql.jinja` (+33 -0) ➕ `episode/episode_object_concept_id/awell_start_treatment_usagi.csv` (+30 -0) ➕ `episode/episode_object_concept_id/custom/kuur_concept.csv` (+47 -0) ➕ `episode/episode_object_concept_id/kuur.sql.jinja` (+10 -0) ➕ `episode/episode_object_concept_id/kuur_usagi.csv` (+175 -0) ➕ `episode/episode_type_concept_id/mzg_usagi.csv` (+2 -0) _...and 63 more files_ </details> ### 📄 Description 1) In script condition_occurrence - conditions_in_moc.sql.jinja and baselineclinicalform_awell.sql.jinja, this contains mutations (ALK, BRAF, …) from lung tumors. I have put this the condition_status_concept_id to 'secondary diagnosis' but I am not 100% sure of this, please verify. 2) No condition_source_concept_id usagi files were added for the new scripts, let me know if this is necessary. 3) Episode: every line of radiotherapy is 1 record in the episode table (unlike before where every day radiotherapy occurred was a record with start-date=end-date). TODO: add each record to procedure_occurrence? 4) Does the master omop contain length, weight, bmi in the measurement table? 5) Observation table does not hold a 'value_as_datetime' column in version 5.4 so I stored datetimes as strings in the value_as_string column --- <sub>🔄 This issue represents a GitHub Pull Request. It cannot be merged through Gitea due to API limitations.</sub>