trust-data 20260911: 6 file(s)

Published by FLIP/trust/publish_trust_data.py. One copy of every artefact at an unversioned path; the data version is the tag 20260911 on this commit.

README.md

@@ -2,6 +2,8 @@
 license:
   - cc-by-sa-4.0
   - cc-by-nc-4.0
+  - cc-by-3.0
+  - cc-by-4.0
 pretty_name: FLIP mock trust data
 tags:
   - medical-imaging
@@ -18,7 +20,9 @@ Federated Learning Interoperability Platform. Everything here is either **synthe
 from a public research dataset** under its licence — no patient data. Licensing is **per project**
 (see the table and the per-project notes): the spleen- and cxr-derived content is **CC BY-SA 4.0**,
 the prostate-derived content (`prostate_project`) is **CC BY-NC 4.0** and therefore non-commercial;
-the DICOM vocabulary bundle keeps its own Apache 2.0.
+the pathology tables (`pathology_project`) are metadata derived from IDC's TCGA-BRCA collection
+(**CC BY 3.0**) and its Pan-Cancer-Nuclei-Seg annotations (**CC BY 4.0**); the DICOM vocabulary bundle
+keeps its own Apache 2.0.
 
 ## Versions
 
@@ -36,6 +40,7 @@ suffixed filename. Publishing a new version is one commit on `main` (the changed
 | `20260901` | `spleen_project` measurement rows carry the millimetre unit for SliceThickness (FLIP#1098); pgdata rebuilt |
 | `20260902` | `prostate_project` added — PI-CAI fold 0, the first cohort published for the seed pipeline alone (no snapshot) |
 | `20260903` | `prostate_project` DICOM re-cut with synthetic patient identities (name, birth date, referring physician, study description) — tables unchanged |
+| `20260911` | `pathology_project` added — 24 IDC TCGA-BRCA whole-slide images described in OMOP; **tables and the slide manifest only**, the imaging stays on IDC (no `dicom/` set) |
 
 Files with a version in their name or path (`trust<N>_pgdata_<v>.tar`, `omop-csv/<v>/`, …) are the
 pre-tag layout, kept only until every FLIP deployment fetches by tag; do not add to them.
@@ -45,8 +50,8 @@ pre-tag layout, kept only until every FLIP deployment fetches by tag; do not add
 | path | contents | licence | source |
 | --- | --- | --- | --- |
 | `omop-csv/<project>/*.csv` | OMOP CDM 5.4 tables for each mock cohort, one canonical dataset; every row carries `source_trust` | per project | generated by the converters in `FLIP/fl-tutorials/datasets/` |
-| `omop-csv/<project>/source/…` | the inputs each OMOP export was built from (DICOM metadata table; PI-CAI's marksheet) | per project | same |
-| `dicom/<project>.tar.gz` | the DICOM instances behind each cohort, `<accession>/*.dcm`, one archive per project | per project | see per-project notes below |
+| `omop-csv/<project>/source/…` | the inputs each OMOP export was built from (DICOM metadata table; PI-CAI's marksheet; the pathology slide manifest) | per project | same |
+| `dicom/<project>.tar.gz` | the DICOM instances behind each cohort, `<accession>/*.dcm`, one archive per project — only where the imaging is re-hosted here (`pathology_project` has none: its slides are fetched from IDC) | per project | see per-project notes below |
 | `trust<N>/trust<N>_pgdata.tar` | vocab-free PostgreSQL data volumes, two-trust snapshot (spleen + cxr) | CC BY-SA 4.0 | built from `omop-csv/` |
 | `trust<N>/trust<N>_orthanc_data.tar` | Orthanc storage volumes, two-trust snapshot (spleen + cxr) | CC BY-SA 4.0 | built from the DICOM sets |
 | `omop-vocab/vocab_dicom_*.zip` | the DICOM vocabulary for OMOP | Apache 2.0 | [DICOM2OMOP](https://github.com/paulnagy/DICOM2OMOP) |
@@ -102,6 +107,28 @@ the prostate-derived content is **non-commercial**. Reuse must credit the PI-CAI
 Citation) and may not be commercial; anyone using FLIP's mock data commercially must leave
 `prostate_project` out.
 
+### `pathology_project`
+
+**Tables and a manifest only — no imaging.** Twenty-four haematoxylin-and-eosin whole-slide images
+from the **TCGA-BRCA** collection of the [NCI Imaging Data Commons](https://portal.imaging.datacommons.cancer.gov/)
+(DICOM Slide Microscopy), one slide per patient, twelve from each of two TCGA tissue source sites
+(A8, A7 → `source_trust` 1 and 2). The slides and their Pan-Cancer-Nuclei-Seg nuclei annotations
+(DICOM Microscopy Bulk Simple Annotations) are **not re-hosted here**: FLIP's tutorial downloads
+them from IDC's public buckets at run time (`make -C fl-tutorials download-idc-pathology-data`), and
+the annotations reach a trust's XNAT by data enrichment. What is published is the small thing that
+makes a run reproducible — `source/manifest.csv`, the lockfile naming every selected slide (its UIDs,
+site and the IDC index version the selection was resolved against, since IDC issues versioned
+releases and series come and go) — and the four OMOP tables derived from it. The OMOP rows are
+metadata: TCGA barcodes as `person_source_value`/`accession_id`, study and series UIDs, IDC's
+recorded study dates, and the Slide microscopy modality concept. TCGA pathology DICOM is
+de-identified, so demographics are OMOP's "No matching concept" (0) and `year_of_birth` is the
+deliberately implausible sentinel 1900 rather than an invented value.
+
+**Licence: CC BY 3.0 for the TCGA-BRCA-derived metadata and CC BY 4.0 for the annotation-derived
+columns**, as IDC records for the collection and the `pan_cancer_nuclei_seg_dicom` analysis result
+respectively (the `license_short_name` column of the IDC index). Attribution to TCGA / the NCI
+Imaging Data Commons and, for the annotations, to Hou et al. (see Citation) is required.
+
 ## Provenance
 
 The code that produced every table here is in the FLIP repository under
@@ -123,3 +150,12 @@ If you use the prostate-derived content, cite the PI-CAI challenge and its publi
 
 > Saha, A., Twilt, J. J., Bosma, J. S., van Ginneken, B. et al. The PI-CAI Challenge: Public Training
 > and Development Dataset (2022). Zenodo. https://doi.org/10.5281/zenodo.6624726
+
+If you use the pathology-derived content, cite the NCI Imaging Data Commons and the nuclei annotations:
+
+> Fedorov, A., Longabaugh, W. J. R., Pot, D. et al. NCI Imaging Data Commons. *Cancer Research* 81(16),
+> 4188–4193 (2021). https://doi.org/10.1158/0008-5472.CAN-21-0950
+
+> Hou, L., Gupta, R., Van Arnam, J. S. et al. Dataset of segmented nuclei in hematoxylin and eosin
+> stained histopathology images of ten cancer types. *Sci Data* 7, 185 (2020).
+> https://doi.org/10.1038/s41597-020-0528-1

omop-csv/pathology_project/image_occurrence.csv

@@ -0,0 +1,25 @@
+image_occurrence_id,person_id,procedure_occurrence_id,visit_occurrence_id,anatomic_site_concept_id,image_occurrence_date,image_study_uid,image_series_uid,modality_concept_id,accession_id,source_trust
+4000002,4000002,4000002,4000002,4298444,2024-02-17,2.25.305523966109504368018351018821035186810,1.3.6.1.4.1.5962.99.1.1343238082.2143638158.1637725810626.2.0,2128009266,TCGA-A8-A0AB,1
+4000003,4000003,4000003,4000003,4298444,2024-02-17,2.25.192399737675737361415977896880090698760,1.3.6.1.4.1.5962.99.1.1328235411.2034776796.1637710807955.2.0,2128009266,TCGA-A8-A081,1
+4000004,4000004,4000004,4000004,4298444,2024-02-17,2.25.119835570115797028422844848264053387008,1.3.6.1.4.1.5962.99.1.1298374454.577926621.1637680946998.2.0,2128009266,TCGA-A8-A096,1
+4000005,4000005,4000005,4000005,4298444,2024-02-17,2.25.220751785271985364724971555318215948627,1.3.6.1.4.1.5962.99.1.1296583235.86538995.1637679155779.2.0,2128009266,TCGA-A8-A08O,1
+4000006,4000006,4000006,4000006,4298444,2024-02-16,2.25.169784672318826886132580208430669334731,1.3.6.1.4.1.5962.99.1.1225071011.983645337.1637607643555.2.0,2128009266,TCGA-A8-A09E,1
+4000007,4000007,4000007,4000007,4298444,2024-02-17,2.25.138702317045524558976015668865792470767,1.3.6.1.4.1.5962.99.1.1259953117.294735783.1637642525661.2.0,2128009266,TCGA-A8-A0A9,1
+4000008,4000008,4000008,4000008,4298444,2024-02-17,2.25.299977009049451329321651806359296628715,1.3.6.1.4.1.5962.99.1.1367267308.1768023270.1637749839852.2.0,2128009266,TCGA-A8-A09V,1
+4000009,4000009,4000009,4000009,4298444,2024-02-17,2.25.103585145459164662599223054785921756905,1.3.6.1.4.1.5962.99.1.1220544723.1270762659.1637603117267.2.0,2128009266,TCGA-A8-A08R,1
+4000010,4000010,4000010,4000010,4298444,2024-02-17,2.25.68399676442636907535169301560976352834,1.3.6.1.4.1.5962.99.1.1220038490.599051918.1637602611034.2.0,2128009266,TCGA-A8-A07P,1
+4000011,4000011,4000011,4000011,4298444,2024-02-17,2.25.325210512961201802780816078357976766997,1.3.6.1.4.1.5962.99.1.1340678228.1109027337.1637723250772.2.0,2128009266,TCGA-A8-A07S,1
+4000012,4000012,4000012,4000012,4298444,2024-02-17,2.25.240724300011212187002949156753856238593,1.3.6.1.4.1.5962.99.1.1357615950.126653566.1637740188494.2.0,2128009266,TCGA-A8-A09T,1
+4000013,4000013,4000013,4000013,4298444,2024-02-17,2.25.180569379270056488293474013124856658992,1.3.6.1.4.1.5962.99.1.1326894461.1402752791.1637709467005.2.0,2128009266,TCGA-A8-A06Y,1
+4000014,4000014,4000014,4000014,4298444,2013-07-19,2.25.330868272658484346572731257805283834134,1.3.6.1.4.1.5962.99.1.1245512436.1024397970.1637628084980.2.0,2128009266,TCGA-A7-A6VX,2
+4000015,4000015,4000015,4000015,4298444,2012-04-11,2.25.153733541112255149777482802193058778928,1.3.6.1.4.1.5962.99.1.1364956540.241659483.1637747529084.2.0,2128009266,TCGA-A7-A13G,2
+4000016,4000016,4000016,4000016,4298444,2012-11-07,2.25.162394393184651528111512810448509291989,1.3.6.1.4.1.5962.99.1.1295987467.1597207152.1637678560011.2.0,2128009266,TCGA-A7-A4SF,2
+4000017,4000017,4000017,4000017,4298444,2012-01-03,2.25.68516411604766662277254001788210261148,1.3.6.1.4.1.5962.99.1.1242004905.590606254.1637624577449.2.0,2128009266,TCGA-A7-A3IZ,2
+4000018,4000018,4000018,4000018,4298444,2012-06-29,2.25.264568583337383073020388294229059814033,1.3.6.1.4.1.5962.99.1.1333244898.288348353.1637715817442.2.0,2128009266,TCGA-A7-A0DC,2
+4000019,4000019,4000019,4000019,4298444,2010-06-16,2.25.153831939308446900240606182874660117400,1.3.6.1.4.1.5962.99.1.1262650191.1557751999.1637645222735.2.0,2128009266,TCGA-A7-A0D9,2
+4000020,4000020,4000020,4000020,4298444,2012-01-03,2.25.269771148612352137450652923295602650839,1.3.6.1.4.1.5962.99.1.1225893494.594288157.1637608466038.2.0,2128009266,TCGA-A7-A3IY,2
+4000021,4000021,4000021,4000021,4298444,2010-05-03,2.25.91976047339731422292449180535012148857,1.3.6.1.4.1.5962.99.1.1286568999.785070502.1637669141543.2.0,2128009266,TCGA-A7-A0CJ,2
+4000022,4000022,4000022,4000022,4298444,2013-03-15,2.25.65395507133293104927112704105662895570,1.3.6.1.4.1.5962.99.1.1319843813.1020557758.1637702416357.2.0,2128009266,TCGA-A7-A5ZW,2
+4000023,4000023,4000023,4000023,4298444,2012-01-03,2.25.216116207995006814699560813680532103282,1.3.6.1.4.1.5962.99.1.1228037969.1349381979.1637610610513.2.0,2128009266,TCGA-A7-A3J0,2
+4000024,4000024,4000024,4000024,4298444,2012-06-07,2.25.221353562383464887241573616278760448828,1.3.6.1.4.1.5962.99.1.1225679957.427673716.1637608252501.2.0,2128009266,TCGA-A7-A0CD,2
+4000025,4000025,4000025,4000025,4298444,2010-07-30,2.25.252894393418284940524351551819828261668,1.3.6.1.4.1.5962.99.1.1362849508.831342304.1637745422052.2.0,2128009266,TCGA-A7-A0CH,2

omop-csv/pathology_project/person.csv

@@ -0,0 +1,25 @@
+person_id,gender_concept_id,year_of_birth,race_concept_id,ethnicity_concept_id,person_source_value,source_trust
+4000002,0,1900,0,0,TCGA-A8-A0AB,1
+4000003,0,1900,0,0,TCGA-A8-A081,1
+4000004,0,1900,0,0,TCGA-A8-A096,1
+4000005,0,1900,0,0,TCGA-A8-A08O,1
+4000006,0,1900,0,0,TCGA-A8-A09E,1
+4000007,0,1900,0,0,TCGA-A8-A0A9,1
+4000008,0,1900,0,0,TCGA-A8-A09V,1
+4000009,0,1900,0,0,TCGA-A8-A08R,1
+4000010,0,1900,0,0,TCGA-A8-A07P,1
+4000011,0,1900,0,0,TCGA-A8-A07S,1
+4000012,0,1900,0,0,TCGA-A8-A09T,1
+4000013,0,1900,0,0,TCGA-A8-A06Y,1
+4000014,0,1900,0,0,TCGA-A7-A6VX,2
+4000015,0,1900,0,0,TCGA-A7-A13G,2
+4000016,0,1900,0,0,TCGA-A7-A4SF,2
+4000017,0,1900,0,0,TCGA-A7-A3IZ,2
+4000018,0,1900,0,0,TCGA-A7-A0DC,2
+4000019,0,1900,0,0,TCGA-A7-A0D9,2
+4000020,0,1900,0,0,TCGA-A7-A3IY,2
+4000021,0,1900,0,0,TCGA-A7-A0CJ,2
+4000022,0,1900,0,0,TCGA-A7-A5ZW,2
+4000023,0,1900,0,0,TCGA-A7-A3J0,2
+4000024,0,1900,0,0,TCGA-A7-A0CD,2
+4000025,0,1900,0,0,TCGA-A7-A0CH,2

omop-csv/pathology_project/procedure_occurrence.csv

@@ -0,0 +1,25 @@
+procedure_occurrence_id,person_id,procedure_concept_id,procedure_date,procedure_type_concept_id,visit_occurrence_id,procedure_source_value,source_trust
+4000002,4000002,4047494,2024-02-17,32817,4000002,Histopathology slide,1
+4000003,4000003,4047494,2024-02-17,32817,4000003,Histopathology slide,1
+4000004,4000004,4047494,2024-02-17,32817,4000004,Histopathology slide,1
+4000005,4000005,4047494,2024-02-17,32817,4000005,Histopathology slide,1
+4000006,4000006,4047494,2024-02-16,32817,4000006,Histopathology slide,1
+4000007,4000007,4047494,2024-02-17,32817,4000007,Histopathology slide,1
+4000008,4000008,4047494,2024-02-17,32817,4000008,Histopathology slide,1
+4000009,4000009,4047494,2024-02-17,32817,4000009,Histopathology slide,1
+4000010,4000010,4047494,2024-02-17,32817,4000010,Histopathology slide,1
+4000011,4000011,4047494,2024-02-17,32817,4000011,Histopathology slide,1
+4000012,4000012,4047494,2024-02-17,32817,4000012,Histopathology slide,1
+4000013,4000013,4047494,2024-02-17,32817,4000013,Histopathology slide,1
+4000014,4000014,4047494,2013-07-19,32817,4000014,Histopathology slide,2
+4000015,4000015,4047494,2012-04-11,32817,4000015,Histopathology slide,2
+4000016,4000016,4047494,2012-11-07,32817,4000016,Histopathology slide,2
+4000017,4000017,4047494,2012-01-03,32817,4000017,Histopathology slide,2
+4000018,4000018,4047494,2012-06-29,32817,4000018,Histopathology slide,2
+4000019,4000019,4047494,2010-06-16,32817,4000019,Histopathology slide,2
+4000020,4000020,4047494,2012-01-03,32817,4000020,Histopathology slide,2
+4000021,4000021,4047494,2010-05-03,32817,4000021,Histopathology slide,2
+4000022,4000022,4047494,2013-03-15,32817,4000022,Histopathology slide,2
+4000023,4000023,4047494,2012-01-03,32817,4000023,Histopathology slide,2
+4000024,4000024,4047494,2012-06-07,32817,4000024,Histopathology slide,2
+4000025,4000025,4047494,2010-07-30,32817,4000025,Histopathology slide,2

omop-csv/pathology_project/source/manifest.csv

@@ -0,0 +1,25 @@
+accession_id,site,tss,patient_id,slide_study_uid,slide_series_uid,slide_sop_instance_uid,annotation_series_uid,total_pixel_columns,total_pixel_rows,pixel_spacing_mm,study_date,slide_instance_mb,annotation_series_mb,idc_index_version
+TCGA-A8-A0AB,Trust_1,A8,TCGA-A8-A0AB,2.25.305523966109504368018351018821035186810,1.3.6.1.4.1.5962.99.1.1343238082.2143638158.1637725810626.2.0,1.3.6.1.4.1.5962.99.1.1343238082.2143638158.1637725810626.8.0,1.2.826.0.1.3680043.10.511.3.56403533861287743076629571100940444,35584,42752,0.0002325,2024-02-17,139.827614,29.813058,24.2.2
+TCGA-A8-A081,Trust_1,A8,TCGA-A8-A081,2.25.192399737675737361415977896880090698760,1.3.6.1.4.1.5962.99.1.1328235411.2034776796.1637710807955.2.0,1.3.6.1.4.1.5962.99.1.1328235411.2034776796.1637710807955.8.0,1.2.826.0.1.3680043.10.511.3.65676257618402188263560444822774483,28928,31488,0.0002325,2024-02-17,243.877284,37.603218,24.2.2
+TCGA-A8-A096,Trust_1,A8,TCGA-A8-A096,2.25.119835570115797028422844848264053387008,1.3.6.1.4.1.5962.99.1.1298374454.577926621.1637680946998.2.0,1.3.6.1.4.1.5962.99.1.1298374454.577926621.1637680946998.8.0,1.2.826.0.1.3680043.10.511.3.11207824219950204304234349540820717,37632,41216,0.0002325,2024-02-17,258.006132,37.949564,24.2.2
+TCGA-A8-A08O,Trust_1,A8,TCGA-A8-A08O,2.25.220751785271985364724971555318215948627,1.3.6.1.4.1.5962.99.1.1296583235.86538995.1637679155779.2.0,1.3.6.1.4.1.5962.99.1.1296583235.86538995.1637679155779.8.0,1.2.826.0.1.3680043.10.511.3.11976075682460354643307403001620073,43776,29440,0.0002325,2024-02-17,265.398286,33.60029,24.2.2
+TCGA-A8-A09E,Trust_1,A8,TCGA-A8-A09E,2.25.169784672318826886132580208430669334731,1.3.6.1.4.1.5962.99.1.1225071011.983645337.1637607643555.2.0,1.3.6.1.4.1.5962.99.1.1225071011.983645337.1637607643555.8.0,1.2.826.0.1.3680043.10.511.3.87890819835828812951806155190801784,31488,30976,0.0002325,2024-02-16,271.314432,34.511796,24.2.2
+TCGA-A8-A0A9,Trust_1,A8,TCGA-A8-A0A9,2.25.138702317045524558976015668865792470767,1.3.6.1.4.1.5962.99.1.1259953117.294735783.1637642525661.2.0,1.3.6.1.4.1.5962.99.1.1259953117.294735783.1637642525661.8.0,1.2.826.0.1.3680043.10.511.3.12355224368823972821040156932650477,38144,26368,0.0002325,2024-02-17,273.807038,41.303844,24.2.2
+TCGA-A8-A09V,Trust_1,A8,TCGA-A8-A09V,2.25.299977009049451329321651806359296628715,1.3.6.1.4.1.5962.99.1.1367267308.1768023270.1637749839852.2.0,1.3.6.1.4.1.5962.99.1.1367267308.1768023270.1637749839852.8.0,1.2.826.0.1.3680043.10.511.3.24982071129441089237349678361590179,32000,45312,0.0002325,2024-02-17,283.402294,31.810786,24.2.2
+TCGA-A8-A08R,Trust_1,A8,TCGA-A8-A08R,2.25.103585145459164662599223054785921756905,1.3.6.1.4.1.5962.99.1.1220544723.1270762659.1637603117267.2.0,1.3.6.1.4.1.5962.99.1.1220544723.1270762659.1637603117267.8.0,1.2.826.0.1.3680043.10.511.3.71901086447126194600234346641324538,38144,93440,0.0002325,2024-02-17,298.338258,21.83609,24.2.2
+TCGA-A8-A07P,Trust_1,A8,TCGA-A8-A07P,2.25.68399676442636907535169301560976352834,1.3.6.1.4.1.5962.99.1.1220038490.599051918.1637602611034.2.0,1.3.6.1.4.1.5962.99.1.1220038490.599051918.1637602611034.8.0,1.2.826.0.1.3680043.10.511.3.51776803487982560181076415694163104,27392,40192,0.0002325,2024-02-17,316.089946,31.750956,24.2.2
+TCGA-A8-A07S,Trust_1,A8,TCGA-A8-A07S,2.25.325210512961201802780816078357976766997,1.3.6.1.4.1.5962.99.1.1340678228.1109027337.1637723250772.2.0,1.3.6.1.4.1.5962.99.1.1340678228.1109027337.1637723250772.8.0,1.2.826.0.1.3680043.10.511.3.10893846000293134641114877650716859,38656,46848,0.0002325,2024-02-17,329.576332,44.105418,24.2.2
+TCGA-A8-A09T,Trust_1,A8,TCGA-A8-A09T,2.25.240724300011212187002949156753856238593,1.3.6.1.4.1.5962.99.1.1357615950.126653566.1637740188494.2.0,1.3.6.1.4.1.5962.99.1.1357615950.126653566.1637740188494.8.0,1.2.826.0.1.3680043.10.511.3.11250368212788472124393581643449070,37120,32512,0.0002325,2024-02-17,335.721764,42.293004,24.2.2
+TCGA-A8-A06Y,Trust_1,A8,TCGA-A8-A06Y,2.25.180569379270056488293474013124856658992,1.3.6.1.4.1.5962.99.1.1326894461.1402752791.1637709467005.2.0,1.3.6.1.4.1.5962.99.1.1326894461.1402752791.1637709467005.8.0,1.2.826.0.1.3680043.10.511.3.36758378264032531482667821926555498,46848,32000,0.0002325,2024-02-17,344.724066,31.235554,24.2.2
+TCGA-A7-A6VX,Trust_2,A7,TCGA-A7-A6VX,2.25.330868272658484346572731257805283834134,1.3.6.1.4.1.5962.99.1.1245512436.1024397970.1637628084980.2.0,1.3.6.1.4.1.5962.99.1.1245512436.1024397970.1637628084980.8.0,1.2.826.0.1.3680043.10.511.3.96678489681723751396328685893712688,46648,35918,0.0002456,2013-07-19,105.48599,11.211174,24.2.2
+TCGA-A7-A13G,Trust_2,A7,TCGA-A7-A13G,2.25.153733541112255149777482802193058778928,1.3.6.1.4.1.5962.99.1.1364956540.241659483.1637747529084.2.0,1.3.6.1.4.1.5962.99.1.1364956540.241659483.1637747529084.8.0,1.2.826.0.1.3680043.10.511.3.11786936050699090881855007756857797,21896,76792,0.0002456,2012-04-11,118.214882,24.091824,24.2.2
+TCGA-A7-A4SF,Trust_2,A7,TCGA-A7-A4SF,2.25.162394393184651528111512810448509291989,1.3.6.1.4.1.5962.99.1.1295987467.1597207152.1637678560011.2.0,1.3.6.1.4.1.5962.99.1.1295987467.1597207152.1637678560011.8.0,1.2.826.0.1.3680043.10.511.3.98451891209799517027330943555072681,28560,40756,0.0002468,2012-11-07,123.10261,32.24399,24.2.2
+TCGA-A7-A3IZ,Trust_2,A7,TCGA-A7-A3IZ,2.25.68516411604766662277254001788210261148,1.3.6.1.4.1.5962.99.1.1242004905.590606254.1637624577449.2.0,1.3.6.1.4.1.5962.99.1.1242004905.590606254.1637624577449.8.0,1.2.826.0.1.3680043.10.511.3.99410141771380701384846414170333033,37128,32746,0.0002456,2012-01-03,159.005288,43.5814,24.2.2
+TCGA-A7-A0DC,Trust_2,A7,TCGA-A7-A0DC,2.25.264568583337383073020388294229059814033,1.3.6.1.4.1.5962.99.1.1333244898.288348353.1637715817442.2.0,1.3.6.1.4.1.5962.99.1.1333244898.288348353.1637715817442.8.0,1.2.826.0.1.3680043.10.511.3.49514007212870823249889665746342159,83776,31012,0.0002468,2012-06-29,194.74422,37.955312,24.2.2
+TCGA-A7-A0D9,Trust_2,A7,TCGA-A7-A0D9,2.25.153831939308446900240606182874660117400,1.3.6.1.4.1.5962.99.1.1262650191.1557751999.1637645222735.2.0,1.3.6.1.4.1.5962.99.1.1262650191.1557751999.1637645222735.8.0,1.2.826.0.1.3680043.10.511.3.88218669694964331769528856072273329,108528,26729,0.0002456,2010-06-16,204.046982,27.020022,24.2.2
+TCGA-A7-A3IY,Trust_2,A7,TCGA-A7-A3IY,2.25.269771148612352137450652923295602650839,1.3.6.1.4.1.5962.99.1.1225893494.594288157.1637608466038.2.0,1.3.6.1.4.1.5962.99.1.1225893494.594288157.1637608466038.8.0,1.2.826.0.1.3680043.10.511.3.11104345218602156492977722777579377,40936,74551,0.0002456,2012-01-03,210.702138,26.147536,24.2.2
+TCGA-A7-A0CJ,Trust_2,A7,TCGA-A7-A0CJ,2.25.91976047339731422292449180535012148857,1.3.6.1.4.1.5962.99.1.1286568999.785070502.1637669141543.2.0,1.3.6.1.4.1.5962.99.1.1286568999.785070502.1637669141543.8.0,1.2.826.0.1.3680043.10.511.3.72262868362446597888188752938942841,31416,77161,0.0002456,2010-05-03,211.947692,46.731352,24.2.2
+TCGA-A7-A5ZW,Trust_2,A7,TCGA-A7-A5ZW,2.25.65395507133293104927112704105662895570,1.3.6.1.4.1.5962.99.1.1319843813.1020557758.1637702416357.2.0,1.3.6.1.4.1.5962.99.1.1319843813.1020557758.1637702416357.8.0,1.2.826.0.1.3680043.10.511.3.81775070105310698489920890030170882,119952,24046,0.0002465,2013-03-15,213.317574,28.132846,24.2.2
+TCGA-A7-A3J0,Trust_2,A7,TCGA-A7-A3J0,2.25.216116207995006814699560813680532103282,1.3.6.1.4.1.5962.99.1.1228037969.1349381979.1637610610513.2.0,1.3.6.1.4.1.5962.99.1.1228037969.1349381979.1637610610513.8.0,1.2.826.0.1.3680043.10.511.3.67753289675507572540418328956192445,130424,24335,0.0002456,2012-01-03,222.806596,30.551406,24.2.2
+TCGA-A7-A0CD,Trust_2,A7,TCGA-A7-A0CD,2.25.221353562383464887241573616278760448828,1.3.6.1.4.1.5962.99.1.1225679957.427673716.1637608252501.2.0,1.3.6.1.4.1.5962.99.1.1225679957.427673716.1637608252501.8.0,1.2.826.0.1.3680043.10.511.3.14663082223063549584052796123120147,93296,45453,0.0002465,2012-06-07,238.828616,5.40048,24.2.2
+TCGA-A7-A0CH,Trust_2,A7,TCGA-A7-A0CH,2.25.252894393418284940524351551819828261668,1.3.6.1.4.1.5962.99.1.1362849508.831342304.1637745422052.2.0,1.3.6.1.4.1.5962.99.1.1362849508.831342304.1637745422052.8.0,1.2.826.0.1.3680043.10.511.3.68484908950097687838559163862974203,30464,90263,0.0002465,2010-07-30,248.907478,74.002816,24.2.2

omop-csv/pathology_project/visit_occurrence.csv

@@ -0,0 +1,25 @@
+visit_occurrence_id,person_id,visit_concept_id,visit_start_date,visit_end_date,visit_type_concept_id,source_trust
+4000002,4000002,9201,2024-02-17,2024-02-17,32817,1
+4000003,4000003,9201,2024-02-17,2024-02-17,32817,1
+4000004,4000004,9201,2024-02-17,2024-02-17,32817,1
+4000005,4000005,9201,2024-02-17,2024-02-17,32817,1
+4000006,4000006,9201,2024-02-16,2024-02-16,32817,1
+4000007,4000007,9201,2024-02-17,2024-02-17,32817,1
+4000008,4000008,9201,2024-02-17,2024-02-17,32817,1
+4000009,4000009,9201,2024-02-17,2024-02-17,32817,1
+4000010,4000010,9201,2024-02-17,2024-02-17,32817,1
+4000011,4000011,9201,2024-02-17,2024-02-17,32817,1
+4000012,4000012,9201,2024-02-17,2024-02-17,32817,1
+4000013,4000013,9201,2024-02-17,2024-02-17,32817,1
+4000014,4000014,9201,2013-07-19,2013-07-19,32817,2
+4000015,4000015,9201,2012-04-11,2012-04-11,32817,2
+4000016,4000016,9201,2012-11-07,2012-11-07,32817,2
+4000017,4000017,9201,2012-01-03,2012-01-03,32817,2
+4000018,4000018,9201,2012-06-29,2012-06-29,32817,2
+4000019,4000019,9201,2010-06-16,2010-06-16,32817,2
+4000020,4000020,9201,2012-01-03,2012-01-03,32817,2
+4000021,4000021,9201,2010-05-03,2010-05-03,32817,2
+4000022,4000022,9201,2013-03-15,2013-03-15,32817,2
+4000023,4000023,9201,2012-01-03,2012-01-03,32817,2
+4000024,4000024,9201,2012-06-07,2012-06-07,32817,2
+4000025,4000025,9201,2010-07-30,2010-07-30,32817,2