From c9cd4489c247d42cfce05955789647f032fd00c1 Mon Sep 17 00:00:00 2001
From: "Bruce W. Herr II" <bherr@indiana.edu>
Date: Tue, 24 Oct 2023 09:58:05 -0400
Subject: [PATCH] Implemented figure F4 data. Fixes #58

---
 data-processor/queries/figure-f4.rq | 46 +++++++++++++++++++++++++++++
 data/reports/figure-f4.csv          | 14 +++++++++
 2 files changed, 60 insertions(+)
 create mode 100644 data-processor/queries/figure-f4.rq
 create mode 100644 data/reports/figure-f4.csv

diff --git a/data-processor/queries/figure-f4.rq b/data-processor/queries/figure-f4.rq
new file mode 100644
index 0000000..b9286eb
--- /dev/null
+++ b/data-processor/queries/figure-f4.rq
@@ -0,0 +1,46 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX ASCTB-TEMP: <https://purl.org/ccf/ASCTB-TEMP_>
+PREFIX CL: <http://purl.obolibrary.org/obo/CL_>
+PREFIX FMA: <http://purl.org/sig/ont/fma/fma>
+PREFIX UBERON: <http://purl.obolibrary.org/obo/UBERON_>
+PREFIX ccf3d: <http://purl.org/ccf/latest/ccf.owl#>
+PREFIX ccf: <http://purl.org/ccf/>
+PREFIX ctpop: <https://cns-iu.github.io/hra-cell-type-populations-supporting-information/data/enriched_rui_locations.jsonld#>
+PREFIX dc: <http://purl.org/dc/terms/>
+PREFIX hubmap: <https://entity.api.hubmapconsortium.org/entities/>
+PREFIX rui: <http://purl.org/ccf/1.5/>
+
+# 3d ref organ | #meshes tagged with UBERON ID | total number of tissue blocks | sex | number of datasets
+SELECT
+	?organId
+    ?organ
+    ?sex
+    (COUNT(DISTINCT(?refOrganAs)) as ?organ_as_count)
+    (COUNT(DISTINCT(?rui_location)) as ?rui_location_count)
+	(COUNT(DISTINCT(?dataset)) as ?dataset_count)
+FROM ctpop:graph
+WHERE {
+  GRAPH ctpop:graph {
+    ?sample ccf:has_registration_location ?rui_location ;
+            ccf:generates_dataset ?dataset .
+
+    [] a ccf:SpatialPlacement ;
+      ccf:placement_for ?rui_location ;
+      ccf:placement_relative_to ?refOrgan .
+  }
+
+  GRAPH <https://purl.org/ccf/releases/2.2.1/ccf.owl> {
+    ?refOrgan ccf:has_reference_organ ?refOrgan ;
+    		  ccf:representation_of ?organIri ;
+          ccf:organ_owner_sex ?sex .
+    
+    ?refOrganAs ccf:has_reference_organ ?refOrgan .
+
+    ?organIri rdfs:label ?organ .
+    BIND(REPLACE(REPLACE(STR(?organIri), 'http://purl.obolibrary.org/obo/UBERON_', 'UBERON:'), 'http://purl.org/sig/ont/fma/fma', 'FMA:') as ?organId)
+    FILTER(?refOrganAs != ?refOrgan)
+  }
+}
+GROUP BY ?organId ?organ ?sex
+ORDER BY ?organ ?sex
diff --git a/data/reports/figure-f4.csv b/data/reports/figure-f4.csv
new file mode 100644
index 0000000..4f20583
--- /dev/null
+++ b/data/reports/figure-f4.csv
@@ -0,0 +1,14 @@
+organId,organ,sex,organ_as_count,rui_location_count,dataset_count
+FMA:57987,Set of lactiferous glands in right breast,Female,8,1,3
+UBERON:0000955,brain,Female,104,1,1
+UBERON:0000955,brain,Male,104,1,1
+UBERON:0000948,heart,Male,16,16,52
+UBERON:0000059,large intestine,Female,10,6,6
+UBERON:0000059,large intestine,Male,10,24,24
+UBERON:0004538,left kidney,Female,30,2,8
+UBERON:0004538,left kidney,Male,26,11,28
+UBERON:0000079,male reproductive system,Male,18,1,4
+UBERON:0004539,right kidney,Female,28,6,11
+UBERON:0004539,right kidney,Male,28,6,50
+UBERON:0002108,small intestine,Female,10,8,8
+UBERON:0002108,small intestine,Male,11,24,24
\ No newline at end of file