SAFEHR-data · docsteveharris · Apr 12, 2024 · Apr 11, 2024 · Apr 11, 2024 · Apr 11, 2024
diff --git a/.gitignore b/.gitignore
@@ -4,6 +4,7 @@ _site
 .jekyll-metadata
 vendor
 *.pyc
+*.DS_Store
 
 # Environment files
 .env
diff --git a/_projects/uclh_cchic_s0/_01_detail.md b/_projects/uclh_cchic_s0/_01_detail.md
@@ -0,0 +1,41 @@
+
+##### Theme : 
+Critical Care Health Informatics Collaborative (CC-HIC)
+
+##### Supporting Document / Problem Statement:
+N/A
+
+##### Correlated Data Source:
+hic-cc (v003) vocab data
+
+##### Generation Rules
+* Using hic cc v003 vocabulary table only
+* All table date fields should be correlated to birth date / visit date / death date
+* Should have an age between 18 and 100 at the moment of the visit.
+* Patient Race Based on 2011 Race Census figure in England and Wales
+* Male and Female (probability 50:50)
+* 15% of the death rate, with an average of 25000 death day
+* measurement value_as_number between 30-180, any type
+* At least 1 record on procedure_occurrence record
+* 20% of person records have a link in procedure_occurrence with the concept of "Plain chest X-ray"
+
+##### Restriction:
+No Clinical Data can be used for learning
+
+##### Remark:
+* Version 0
+* Generated by man-made rule/story generator
+* Structural correct, all tables linked with the relationship
+
+##### Table
+1. condition_occurrence
+2. death
+3. device_exposure
+4. drug_exposure
+5. measurement
+6. observation
+7. observation_period
+8. person
+9. procedure_occurrence
+10. specimen
+11. visit_occurrence
diff --git a/_projects/uclh_cchic_s0/_02_appendix.md b/_projects/uclh_cchic_s0/_02_appendix.md
@@ -0,0 +1,23 @@
+
+##### 2011 Race Census figure in England and Wales
+
+| Ethnic Group                                                                                   | Population(%) |
+|------------------------------------------------------------------------------------------------|---------------|
+| Asian or Asian British: Bangladeshi | 1.1 |
+| Asian or Asian British: Chinese | 0.7 |
+| Asian or Asian British: Indian | 3.1 |
+| Asian or Asian British: Pakistani | 2.7 |
+| Asian or Asian British: any other Asian background | 1.6 |
+| Black or African or Caribbean or Black British: African | 2.5 |
+| Black or African or Caribbean or Black British: Caribbean | 1 |
+| Black or African or Caribbean or Black British: other Black or African or Caribbean background | 0.5 |
+| Mixed multiple ethnic groups: White and Asian | 0.8 |
+| Mixed multiple ethnic groups: White and Black African | 0.4 |
+| Mixed multiple ethnic groups: White and Black Caribbean | 0.9 |
+| Mixed multiple ethnic groups: any other Mixed or multiple ethnic background | 0.8 |
+| White: English or Welsh or Scottish or Northern Irish or British | 74.4 |
+| White: Irish | 0.9 |
+| White: Gypsy or Irish Traveller | 0.1 |
+| White: any other White background | 6.4 |
+| Other ethnic group: any other ethnic group | 1.6 |
+| Other ethnic group: Arab | 0.6 |
diff --git a/_projects/uclh_cchic_s0/_03_data.html b/_projects/uclh_cchic_s0/_03_data.html
@@ -0,0 +1,20 @@
+<body>
+    <h5>Synthetic Data CSV file</h5>
+    <div class="alert alert-warning">
+        <strong>Warning!</strong> We will publish here our synthetic data once it's approved for publication by the people at UCL Research Data Repository.
+    </div>
+    <br/>
+    <ul>
+        <li><a href="data/condition_occurrence.csv">condition_occurrence.csv</a></li>
+        <li><a href="data/death.csv">death.csv</a></li>
+        <li><a href="data/device_exposure.csv">device_exposure.csv</a></li>
+        <li><a href="data/drug_exposure.csv">drug_exposure.csv</a></li>
+        <li><a href="data/measurement.csv">measurement.csv</a></li>
+        <li><a href="data/observation.csv">observation.csv</a></li>
+        <li><a href="data/observation_period.csv">observation_period.csv</a></li>
+        <li><a href="data/person.csv">person.csv</a></li>
+        <li><a href="data/procedure_occurrence.csv">procedure_occurrence.csv</a></li>
+        <li><a href="data/specimen.csv">specimen.csv</a></li>
+        <li><a href="data/visit_occurrence.csv">visit_occurrence.csv</a></li>
+    </ul>
+</body>
diff --git a/_projects/uclh_cchic_s0/authors.txt b/_projects/uclh_cchic_s0/authors.txt
@@ -0,0 +1 @@
+NIHR BRC SAFTHER Team
diff --git a/_projects/uclh_cchic_s0/data/condition_occurrence.csv b/_projects/uclh_cchic_s0/data/condition_occurrence.csv
@@ -0,0 +1,101 @@
+condition_occurrence_id,person_id,condition_concept_id,condition_start_date,condition_start_datetime,condition_end_date,condition_end_datetime,condition_type_concept_id,condition_status_concept_id,stop_reason,provider_id,visit_occurrence_id,visit_detail_id,condition_source_value,condition_source_concept_id,condition_status_source_value
+2443,2451,32895,1999-09-21,1999-09-21 16:17:17.767006,2009-12-19,2009-12-19 17:35:13.694854,32854,32896,,,2451,,,45757117,
+2444,2452,32911,1976-11-02,1976-11-02 21:57:23.312813,1983-06-03,1983-06-03 13:23:12.613786,32830,32902,,,2452,,,45757060,
+2445,2453,32902,1996-03-27,1996-03-27 03:16:14.229761,1997-10-22,1997-10-22 13:01:33.951073,32842,32907,,,2453,,,45757077,
+2446,2454,32896,1969-08-20,1969-08-20 07:50:54.642154,2006-04-19,2006-04-19 20:22:40.923065,32830,32903,,,2454,,,45757146,
+2447,2455,32904,1986-02-07,1986-02-07 15:33:33.114652,2008-01-10,2008-01-10 08:42:51.729807,32838,32907,,,2455,,,45757094,
+2448,2456,32905,2020-06-01,2020-06-01 22:54:41.610866,2020-08-10,2020-08-10 01:08:48.220549,32844,32895,,,2456,,,45757128,
+2449,2457,32895,2009-12-19,2009-12-19 20:19:02.294577,2015-08-22,2015-08-22 01:00:13.670663,32863,32894,,,2457,,,45757081,
+2450,2458,32891,1963-03-13,1963-03-13 14:57:22.842345,1963-12-20,1963-12-20 13:42:38.234994,32855,32890,,,2458,,,45757139,
+2451,2459,32898,1994-08-15,1994-08-15 15:05:05.508819,1994-09-10,1994-09-10 20:39:24.427335,32863,32907,,,2459,,,45757110,
+2452,2460,32901,1972-01-28,1972-01-28 13:41:57.004696,1972-02-02,1972-02-02 12:02:37.9271,32871,32898,,,2460,,,45757077,
+2453,2461,32893,2003-06-09,2003-06-09 21:56:27.977,2009-11-13,2009-11-13 23:46:39.426975,32826,32907,,,2461,,,45757104,
+2454,2462,32894,2009-05-02,2009-05-02 11:05:27.581414,2010-07-31,2010-07-31 15:11:23.029061,703249,32893,,,2462,,,45757135,
+2455,2463,32906,1976-10-19,1976-10-19 01:25:48.271393,1982-12-05,1982-12-05 11:22:45.792149,32869,32904,,,2463,,,45757143,
+2456,2464,32890,2020-02-12,2020-02-12 04:53:03.495486,2021-03-14,2021-03-14 07:19:07.730283,32852,32908,,,2464,,,45757119,
+2457,2465,32897,1996-09-30,1996-09-30 07:41:08.921501,1997-06-28,1997-06-28 12:47:15.35059,32879,32895,,,2465,,,45757096,
+2458,2466,32900,1988-05-31,1988-05-31 16:28:08.64905,1988-10-17,1988-10-17 23:31:19.215215,32824,32896,,,2466,,,45757143,
+2459,2467,32895,2011-10-22,2011-10-22 18:21:00.760983,2012-02-03,2012-02-03 16:01:22.485727,32857,32901,,,2467,,,45757154,
+2460,2468,32893,2002-05-03,2002-05-03 12:50:31.555859,2002-05-08,2002-05-08 10:40:17.172959,32814,32899,,,2468,,,45757097,
+2461,2469,32909,1966-08-05,1966-08-05 02:43:41.375501,1980-02-26,1980-02-26 15:03:20.406352,32868,32891,,,2469,,,45757130,
+2462,2470,32904,1974-07-11,1974-07-11 13:32:01.884333,1981-02-14,1981-02-14 19:05:53.64581,32830,32898,,,2470,,,45757062,
+2463,2471,32903,2016-11-13,2016-11-13 10:54:29.922582,2019-05-08,2019-05-08 18:13:52.081241,32813,32898,,,2471,,,45757116,
+2464,2472,32902,2021-05-26,2021-05-26 14:11:53.6601,2021-07-15,2021-07-15 18:44:49.363089,32859,32901,,,2472,,,45757100,
+2465,2473,32907,2023-10-11,2023-10-11 09:17:21.402501,2023-10-13,2023-10-13 16:10:50.417459,32829,32905,,,2473,,,45757076,
+2466,2474,32899,1994-12-27,1994-12-27 06:13:51.890934,1994-01-30,1994-01-30 07:27:32.816874,32876,32908,,,2474,,,45757108,
+2467,2475,32911,2022-01-15,2022-01-15 06:14:36.618526,2022-03-18,2022-03-18 01:00:18.341538,32885,32896,,,2475,,,45757140,
+2468,2476,32906,2021-02-23,2021-02-23 17:14:45.279515,2021-06-15,2021-06-15 12:07:39.646936,32834,32910,,,2476,,,45757107,
+2469,2477,32908,2004-06-05,2004-06-05 00:10:24.536635,2004-08-17,2004-08-17 11:21:45.532473,32814,32902,,,2477,,,45757119,
+2470,2478,32894,2010-08-30,2010-08-30 06:57:34.392817,2015-03-01,2015-03-01 06:28:41.754635,32853,32901,,,2478,,,45757091,
+2471,2479,32905,2015-02-15,2015-02-15 05:42:38.875951,2015-05-17,2015-05-17 20:33:36.051963,32814,32905,,,2479,,,45757078,
+2472,2480,32909,2004-05-25,2004-05-25 21:17:58.022796,2013-11-29,2013-11-29 09:39:11.920891,32819,32893,,,2480,,,45757112,
+2473,2481,32901,2011-08-19,2011-08-19 19:06:29.697335,2016-09-20,2016-09-20 16:13:55.482479,32809,32891,,,2481,,,45757116,
+2474,2482,32911,2018-07-23,2018-07-23 18:12:38.788933,2020-07-07,2020-07-07 20:49:17.806019,32813,32895,,,2482,,,45757141,
+2475,2483,32902,1967-03-25,1967-03-25 16:54:51.089477,1982-02-26,1982-02-26 18:14:13.71137,32830,32904,,,2483,,,45757057,
+2476,2484,32895,1991-04-17,1991-04-17 17:00:55.846369,2003-02-27,2003-02-27 13:33:17.243893,32842,32892,,,2484,,,45757093,
+2477,2485,32892,1980-02-20,1980-02-20 03:33:31.650876,1981-01-27,1981-01-27 20:36:25.172883,32880,32902,,,2485,,,45757056,
+2478,2486,32909,2021-11-19,2021-11-19 18:28:52.380142,2022-02-08,2022-02-08 17:23:32.49452,32875,32897,,,2486,,,45757105,
+2479,2487,32891,2019-01-08,2019-01-08 20:20:28.153608,2019-03-24,2019-03-24 19:23:36.924522,32827,32906,,,2487,,,45757070,
+2480,2488,32908,2011-06-17,2011-06-17 07:06:31.14859,2011-07-24,2011-07-24 12:10:49.064287,32825,32898,,,2488,,,45757140,
+2481,2489,32900,1981-02-08,1981-02-08 20:06:11.949652,1983-04-01,1983-04-01 02:17:39.664337,32820,32902,,,2489,,,45757155,
+2482,2490,32903,1981-06-03,1981-06-03 11:43:28.819981,1981-11-11,1981-11-11 19:11:21.237103,32839,32895,,,2490,,,45757070,
+2483,2491,32901,2022-10-08,2022-10-08 13:02:45.77798,2022-10-28,2022-10-28 13:13:58.3035,32852,32908,,,2491,,,45757102,
+2484,2492,32897,2009-01-29,2009-01-29 06:34:31.87623,2015-04-20,2015-04-20 03:24:15.802315,32809,32909,,,2492,,,45757143,
+2485,2493,32897,2010-04-12,2010-04-12 23:01:47.551578,2011-08-09,2011-08-09 13:04:38.356685,32861,32911,,,2493,,,45757147,
+2486,2494,32904,2015-09-14,2015-09-14 07:06:41.142271,2020-07-08,2020-07-08 19:52:21.844275,32844,32895,,,2494,,,45757118,
+2487,2495,32907,1998-06-16,1998-06-16 18:45:02.80421,1999-04-06,1999-04-06 04:36:40.400886,32844,32911,,,2495,,,45757099,
+2488,2496,32902,2017-11-15,2017-11-15 11:09:31.892345,2019-01-10,2019-01-10 10:14:46.720458,32814,32905,,,2496,,,45757102,
+2489,2497,32909,2023-07-27,2023-07-27 00:45:12.720818,2023-07-30,2023-07-30 01:08:35.645668,32830,32899,,,2497,,,45757135,
+2490,2498,32900,2014-02-23,2014-02-23 18:14:56.48261,2014-02-23,2014-02-23 13:59:11.377742,32850,32897,,,2498,,,45757125,
+2491,2499,32903,1996-10-25,1996-10-25 15:24:52.42201,1997-04-01,1997-04-01 11:43:42.145373,703249,32904,,,2499,,,45757135,
+2492,2500,32902,2015-01-30,2015-01-30 15:22:30.037603,2015-02-16,2015-02-16 10:10:39.177572,32872,32911,,,2500,,,45757108,
+2493,2501,32909,2017-10-22,2017-10-22 11:52:13.178603,2017-12-18,2017-12-18 12:39:45.854484,32849,32895,,,2501,,,45757149,
+2494,2502,32891,2008-09-30,2008-09-30 22:34:53.416918,2008-11-28,2008-11-28 06:15:04.936984,32886,32894,,,2502,,,45757111,
+2495,2503,32894,2005-09-04,2005-09-04 09:48:51.334592,2011-02-19,2011-02-19 07:43:25.546219,32885,32890,,,2503,,,45757149,
+2496,2504,32900,1984-01-10,1984-01-10 02:03:04.195627,1984-04-17,1984-04-17 14:26:01.563233,32859,32906,,,2504,,,45757147,
+2497,2505,32898,2008-02-05,2008-02-05 13:17:53.774246,2014-03-24,2014-03-24 15:20:09.970651,32825,32894,,,2505,,,45757144,
+2498,2506,32911,1973-01-18,1973-01-18 18:44:21.33449,2001-12-19,2001-12-19 20:15:53.577317,32856,32911,,,2506,,,45757129,
+2499,2507,32903,1993-09-19,1993-09-19 00:50:25.756616,2014-01-25,2014-01-25 16:53:13.324949,32843,32904,,,2507,,,45757112,
+2500,2508,32901,2023-05-15,2023-05-15 07:46:58.453056,2023-05-24,2023-05-24 12:09:30.493321,32813,32903,,,2508,,,45757112,
+2501,2509,32905,1962-03-21,1962-03-21 07:44:20.319079,1973-08-05,1973-08-05 21:25:26.653515,32849,32900,,,2509,,,45757140,
+2502,2510,32894,2012-11-13,2012-11-13 12:50:17.473653,2013-05-27,2013-05-27 06:34:01.440474,32861,32905,,,2510,,,45757145,
+2503,2511,32898,2003-06-30,2003-06-30 06:19:55.759743,2004-02-09,2004-02-09 19:44:54.407809,32810,32895,,,2511,,,45757062,
+2504,2512,32891,2016-12-22,2016-12-22 21:15:17.757071,2017-02-20,2017-02-20 09:09:46.648247,32834,32904,,,2512,,,45757149,
+2505,2513,32891,1990-09-08,1990-09-08 09:21:51.01595,1991-03-21,1991-03-21 18:59:57.094138,32839,32898,,,2513,,,45757089,
+2506,2514,32893,2000-08-17,2000-08-17 08:30:47.857614,2004-03-24,2004-03-24 14:54:31.999989,705183,32904,,,2514,,,45757121,
+2507,2515,32897,2018-01-27,2018-01-27 00:13:32.916392,2018-07-16,2018-07-16 15:47:48.912172,32848,32909,,,2515,,,45757066,
+2508,2516,32891,1980-02-21,1980-02-21 04:12:18.594952,1997-06-09,1997-06-09 07:14:49.361138,32869,32890,,,2516,,,45757156,
+2509,2517,32896,2019-05-07,2019-05-07 19:46:23.060431,2020-02-17,2020-02-17 00:33:10.412458,32854,32902,,,2517,,,45757115,
+2510,2518,32906,2012-05-03,2012-05-03 20:49:27.758404,2013-06-01,2013-06-01 09:17:07.720954,32841,32895,,,2518,,,45757127,
+2511,2519,32901,1990-09-06,1990-09-06 16:24:22.336593,1992-11-14,1992-11-14 09:14:45.385989,32882,32909,,,2519,,,45757088,
+2512,2520,32891,1998-06-21,1998-06-21 01:49:51.925102,1999-01-11,1999-01-11 01:03:47.006497,32851,32890,,,2520,,,45757082,
+2513,2521,32894,2005-10-30,2005-10-30 17:20:23.765154,2007-12-29,2007-12-29 01:02:07.920228,32868,32901,,,2521,,,45757076,
+2514,2522,32902,2015-02-28,2015-02-28 08:52:10.414504,2015-10-26,2015-10-26 13:12:33.954844,32831,32907,,,2522,,,45757113,
+2515,2523,32893,1996-07-21,1996-07-21 14:11:41.516431,2005-04-16,2005-04-16 01:06:02.100855,32860,32894,,,2523,,,45757089,
+2516,2524,32903,2022-09-03,2022-09-03 05:48:26.808031,2022-09-05,2022-09-05 09:17:27.333742,32832,32896,,,2524,,,45757101,
+2517,2525,32911,2020-05-01,2020-05-01 00:19:00.329891,2020-10-31,2020-10-31 15:09:35.655276,32878,32903,,,2525,,,45757061,
+2518,2526,32890,2004-06-02,2004-06-02 12:03:26.736432,2004-06-20,2004-06-20 07:49:14.163596,32829,32903,,,2526,,,45757125,
+2519,2527,32891,2019-09-07,2019-09-07 13:13:10.954801,2020-05-16,2020-05-16 02:40:44.331659,32851,32895,,,2527,,,45757152,
+2520,2528,32899,2014-10-07,2014-10-07 06:30:12.164594,2011-07-23,2011-07-23 13:40:43.375512,32868,32902,,,2528,,,45757073,
+2521,2529,32911,2007-10-09,2007-10-09 14:28:36.825029,2015-02-19,2015-02-19 10:02:09.097847,32834,32895,,,2529,,,45757063,
+2522,2530,32911,2022-12-05,2022-12-05 00:05:41.263482,2023-02-23,2023-02-23 15:29:57.603426,32826,32899,,,2530,,,45757126,
+2523,2531,32892,2007-06-30,2007-06-30 07:40:48.330639,2008-12-03,2008-12-03 20:06:45.877167,32812,32890,,,2531,,,45757092,
+2524,2532,32906,1981-08-16,1981-08-16 05:49:52.48984,1993-03-23,1993-03-23 15:43:37.759673,32834,32901,,,2532,,,45757130,
+2525,2533,32904,1960-09-13,1960-09-13 21:04:32.684366,1975-05-02,1975-05-02 01:33:33.136984,32810,32895,,,2533,,,45757057,
+2526,2534,32907,2012-07-19,2012-07-19 19:13:52.071611,2012-07-23,2012-07-23 02:20:06.604421,32882,32899,,,2534,,,45757060,
+2527,2535,32899,2010-09-19,2010-09-19 03:14:02.0221,2016-05-17,2016-05-17 02:05:52.218282,32867,32892,,,2535,,,45757136,
+2528,2536,32906,1993-03-21,1993-03-21 16:57:57.553571,1993-03-22,1993-03-22 16:24:50.980463,32844,32898,,,2536,,,45757150,
+2529,2537,32890,2018-05-29,2018-05-29 06:30:13.61261,2018-08-07,2018-08-07 00:02:49.960109,32860,32899,,,2537,,,45757057,
+2530,2538,32895,1994-03-18,1994-03-18 03:19:38.378893,1994-03-25,1994-03-25 14:50:50.494399,32872,32905,,,2538,,,45757056,
+2531,2539,32899,1986-02-17,1986-02-17 14:14:10.070595,1986-09-20,1986-09-20 14:59:12.053837,32865,32909,,,2539,,,45757128,
+2532,2540,32896,2018-10-11,2018-10-11 12:31:10.690896,2019-02-01,2019-02-01 12:59:55.264977,32877,32902,,,2540,,,45757122,
+2533,2541,32897,2011-11-17,2011-11-17 22:01:19.864847,2016-07-19,2016-07-19 01:21:47.255129,32843,32910,,,2541,,,45757115,
+2534,2542,32906,2011-01-25,2011-01-25 12:45:48.329206,2011-03-05,2011-03-05 04:08:47.056487,32834,32909,,,2542,,,45757075,
+2535,2543,32907,2017-01-30,2017-01-30 04:39:33.816673,2018-12-17,2018-12-17 16:27:10.514871,32819,32890,,,2543,,,45757081,
+2536,2544,32891,1984-12-07,1984-12-07 05:30:08.276708,1986-09-26,1986-09-26 21:12:37.813068,32847,32904,,,2544,,,45757136,
+2537,2545,32907,1969-12-10,1969-12-10 01:34:49.344358,2002-06-26,2002-06-26 18:54:21.836815,32820,32900,,,2545,,,45757134,
+2538,2546,32890,1994-03-28,1994-03-28 04:50:15.268827,1997-01-22,1997-01-22 05:40:35.855701,32840,32900,,,2546,,,45757125,
+2539,2547,32910,1960-03-17,1960-03-17 10:39:48.552524,1984-10-06,1984-10-06 12:07:13.477186,32864,32906,,,2547,,,45757136,
+2540,2548,32896,1983-04-10,1983-04-10 19:27:13.029461,2003-06-16,2003-06-16 08:24:42.743024,32830,32902,,,2548,,,45757144,
+2541,2549,32895,2018-12-08,2018-12-08 16:04:18.509784,2020-11-20,2020-11-20 15:19:11.38971,32867,32902,,,2549,,,45757069,
+2542,2550,32901,1960-07-06,1960-07-06 22:09:32.545403,1981-09-10,1981-09-10 19:24:29.013773,32831,32905,,,2550,,,45757073,
diff --git a/_projects/uclh_cchic_s0/data/death.csv b/_projects/uclh_cchic_s0/data/death.csv
@@ -0,0 +1,13 @@
+person_id,death_date,death_datetime,death_type_concept_id,cause_concept_id,cause_source_value,cause_source_concept_id
+2451,2015-09-09,2015-09-09 19:12:40.927984,,,,
+2457,2023-09-23,2023-09-23 10:39:23.052438,,,,
+2464,2023-01-14,2023-01-14 16:08:25.8573,,,,
+2474,1993-09-23,1993-09-23 23:16:14.294011,,,,
+2491,2023-07-24,2023-07-24 10:39:24.74315,,,,
+2496,2019-10-28,2019-10-28 06:30:18.102226,,,,
+2498,2014-02-23,2014-02-23 08:03:05.948063,,,,
+2499,1998-02-07,1998-02-07 18:45:35.790044,,,,
+2514,2007-06-29,2007-06-29 09:01:51.592632,,,,
+2528,2010-07-01,2010-07-01 12:36:06.149725,,,,
+2529,2023-12-26,2023-12-26 10:39:26.608424,,,,
+2541,2024-01-28,2024-01-28 10:39:27.166418,,,,