diff --git a/staging/hca-centre-for-inflammation-research-liver/SI Table 1 - Patient metadata.xlsx b/staging/hca-centre-for-inflammation-research-liver/SI Table 1 - Patient metadata.xlsx
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diff --git a/staging/hca-centre-for-inflammation-research-liver/index.html b/staging/hca-centre-for-inflammation-research-liver/index.html
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--- /dev/null
+++ b/staging/hca-centre-for-inflammation-research-liver/index.html
@@ -0,0 +1,31 @@
+
+
+
+
+ CCF-EUI with custom data
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/staging/hca-centre-for-inflammation-research-liver/registrations.yaml b/staging/hca-centre-for-inflammation-research-liver/registrations.yaml
new file mode 100644
index 0000000..e677d4d
--- /dev/null
+++ b/staging/hca-centre-for-inflammation-research-liver/registrations.yaml
@@ -0,0 +1,394 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/hubmapconsortium/hra-rui-locations-processor/main/registrations.schema.json
+
+- consortium_name: UEdinburgh
+ provider_name: CIR/UEdinburgh
+ provider_uuid: b27cb053-cf97-498b-b9d6-0854155e9df6
+ defaults:
+ id: https://www.ed.ac.uk/inflammation-research/research
+ thumbnail: assets/logo.jpg
+ link: https://www.ed.ac.uk/inflammation-research/research
+ donors:
+ - id: HEA1
+ sex: Female
+ age: 62
+ label: Female, Age 62, Patient HEA1
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Healthy.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Healthy tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: HEA2
+ sex: Male
+ age: 70
+ label: Male, Age 70, Patient HEA2
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Male_Healthy.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Healthy tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: HEA3
+ sex: Male
+ age: 39
+ label: Male, Age 39, Patient HEA3
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Male_Healthy.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Healthy tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: HEA4
+ sex: Male
+ age: 59
+ label: Male, Age 59, Patient HEA4
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Male_Healthy.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Healthy tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: HEA5
+ sex: Male
+ age: 70
+ label: Male, Age 70, Patient HEA5
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Male_Healthy.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Healthy tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: HEA6
+ sex: Male
+ age: 71
+ label: Male, Age 71, Patient HEA6
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Male_Healthy.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Healthy tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: HEA7
+ sex: Male
+ age: 67
+ label: Male, Age 67, Patient HEA7
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Male_Healthy.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Healthy tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: HEA8
+ sex: Female
+ age: 64
+ label: Female, Age 64, Patient HEA8
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Healthy.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Healthy tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: HEA9
+ sex: Female
+ age: 57
+ label: Female, Age 57, Patient HEA9
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Healthy.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Healthy tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: HEA10
+ sex: Male
+ age: 80
+ label: Male, Age 80, Patient HEA10
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Male_Healthy.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Healthy tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: APAP1
+ sex: Male
+ age: 19
+ label: Male, Age 19, Patient APAP1
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Male_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: APAP2
+ sex: Female
+ age: 23
+ label: Female, Age 23, Patient APAP2
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: APAP3
+ sex: Male
+ age: 66
+ label: Male, Age 66, Patient APAP3
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Male_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: APAP4
+ sex: Male
+ age: 38
+ label: Male, Age 28, Patient APAP4
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Male_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: APAP5
+ sex: Female
+ age: 37
+ label: Female, Age 37, Patient APAP5
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: APAP6
+ sex: Female
+ age: 45
+ label: Female, Age 45, Patient APAP6
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: APAP7
+ sex: Female
+ age: 48
+ label: Female, Age 48, Patient APAP6
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: APAP8
+ sex: Female
+ age: 46
+ label: Female, Age 46, Patient APAP8
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: APAP9
+ sex: Male
+ age: 41
+ label: Male, Age 41, Patient APAP9
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Male_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: APAP10
+ sex: Female
+ age: 48
+ label: Female, Age 48, Patient APAP10
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: NAE1
+ sex: Male
+ age: 32
+ label: Male, Age 32, Patient NAE1
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Male_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: NAE2
+ sex: Male
+ age: 53
+ label: Male, Age 53, Patient NAE2
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Male_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: NAE3
+ sex: Female
+ age: 48
+ label: Female, Age 48, Patient NAE3
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: NAE4
+ sex: Female
+ age: 58
+ label: Female, Age 58, Patient NAE4
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: NAE5
+ sex: Female
+ age: 60
+ label: Female, Age 60, Patient NAE5
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: NAE6
+ sex: Male
+ age: 29
+ label: Male, Age 29, Patient NAE4
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Male_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: NAE7
+ sex: Female
+ age: 60
+ label: Female, Age 60, Patient NAE7
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: NAE8
+ sex: Female
+ age: 59
+ label: Female, Age 59, Patient NAE8
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: NAE9
+ sex: Female
+ age: 68
+ label: Female, Age 68, Patient NAE9
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: NAE10
+ sex: Female
+ age: 56
+ label: Female, Age 56, Patient NAE10
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: NAE11
+ sex: Female
+ age: 61
+ label: Female, Age 61, Patient NAE11
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
+ - id: NAE12
+ sex: Female
+ age: 50
+ label: Female, Age 50, Patient NAE12
+ description: Entered 8/24/2023, Jordan Portman, UEdinburgh
+ samples:
+ - rui_location: Female_Disease.json
+ label: Registered 8/24/2023, Jordan Portman, UEdinburgh
+ description: Diseased tissue block
+ datasets:
+ - technology: OTHER
+ - link: https://www.ed.ac.uk/inflammation-research/research
\ No newline at end of file
diff --git a/staging/hca-centre-for-inflammation-research-liver/registrations/Female_Disease.json b/staging/hca-centre-for-inflammation-research-liver/registrations/Female_Disease.json
new file mode 100644
index 0000000..efe645c
--- /dev/null
+++ b/staging/hca-centre-for-inflammation-research-liver/registrations/Female_Disease.json
@@ -0,0 +1,37 @@
+{
+ "@context": "https://hubmapconsortium.github.io/ccf-ontology/ccf-context.jsonld",
+ "@id": "http://purl.org/ccf/1.5/92c7d973-67c3-4548-b386-51591184367e",
+ "@type": "SpatialEntity",
+ "creator": "Jordan Portman",
+ "creator_first_name": "Jordan",
+ "creator_last_name": "Portman",
+ "creation_date": "2023-08-24",
+ "ccf_annotations": [
+ "http://purl.obolibrary.org/obo/UBERON_0001149",
+ "http://purl.obolibrary.org/obo/UBERON_0016479"
+ ],
+ "x_dimension": 10,
+ "y_dimension": 10,
+ "z_dimension": 10,
+ "dimension_units": "millimeter",
+ "placement": {
+ "@context": "https://hubmapconsortium.github.io/ccf-ontology/ccf-context.jsonld",
+ "@id": "http://purl.org/ccf/1.5/92c7d973-67c3-4548-b386-51591184367e_placement",
+ "@type": "SpatialPlacement",
+ "target": "http://purl.org/ccf/latest/ccf.owl#VHFLiver",
+ "placement_date": "2023-08-24",
+ "x_scaling": 1,
+ "y_scaling": 1,
+ "z_scaling": 1,
+ "scaling_units": "ratio",
+ "x_rotation": 71,
+ "y_rotation": 0,
+ "z_rotation": 15,
+ "rotation_order": "XYZ",
+ "rotation_units": "degree",
+ "x_translation": 45.692,
+ "y_translation": 135.983,
+ "z_translation": 120.138,
+ "translation_units": "millimeter"
+ }
+}
\ No newline at end of file
diff --git a/staging/hca-centre-for-inflammation-research-liver/registrations/Female_Healthy.json b/staging/hca-centre-for-inflammation-research-liver/registrations/Female_Healthy.json
new file mode 100644
index 0000000..15205a2
--- /dev/null
+++ b/staging/hca-centre-for-inflammation-research-liver/registrations/Female_Healthy.json
@@ -0,0 +1,37 @@
+{
+ "@context": "https://hubmapconsortium.github.io/ccf-ontology/ccf-context.jsonld",
+ "@id": "http://purl.org/ccf/1.5/952347f5-d5fc-4fa8-9bdf-5488ec52a511",
+ "@type": "SpatialEntity",
+ "creator": "Jordan Portman",
+ "creator_first_name": "Jordan",
+ "creator_last_name": "Portman",
+ "creation_date": "2023-08-24",
+ "ccf_annotations": [
+ "http://purl.obolibrary.org/obo/UBERON_0016479",
+ "http://purl.obolibrary.org/obo/UBERON_0001115"
+ ],
+ "x_dimension": 10,
+ "y_dimension": 10,
+ "z_dimension": 10,
+ "dimension_units": "millimeter",
+ "placement": {
+ "@context": "https://hubmapconsortium.github.io/ccf-ontology/ccf-context.jsonld",
+ "@id": "http://purl.org/ccf/1.5/952347f5-d5fc-4fa8-9bdf-5488ec52a511_placement",
+ "@type": "SpatialPlacement",
+ "target": "http://purl.org/ccf/latest/ccf.owl#VHFLiver",
+ "placement_date": "2023-08-24",
+ "x_scaling": 1,
+ "y_scaling": 1,
+ "z_scaling": 1,
+ "scaling_units": "ratio",
+ "x_rotation": 63,
+ "y_rotation": -7,
+ "z_rotation": -16,
+ "rotation_order": "XYZ",
+ "rotation_units": "degree",
+ "x_translation": 186.607,
+ "y_translation": 90.986,
+ "z_translation": 138.638,
+ "translation_units": "millimeter"
+ }
+}
\ No newline at end of file
diff --git a/staging/hca-centre-for-inflammation-research-liver/registrations/Male_Disease.json b/staging/hca-centre-for-inflammation-research-liver/registrations/Male_Disease.json
new file mode 100644
index 0000000..7f801a6
--- /dev/null
+++ b/staging/hca-centre-for-inflammation-research-liver/registrations/Male_Disease.json
@@ -0,0 +1,37 @@
+{
+ "@context": "https://hubmapconsortium.github.io/ccf-ontology/ccf-context.jsonld",
+ "@id": "http://purl.org/ccf/1.5/62381536-7923-43da-8703-c744e4de0b25",
+ "@type": "SpatialEntity",
+ "creator": "Jordan Portman",
+ "creator_first_name": "Jordan",
+ "creator_last_name": "Portman",
+ "creation_date": "2023-08-24",
+ "ccf_annotations": [
+ "http://purl.obolibrary.org/obo/UBERON_0001149",
+ "http://purl.obolibrary.org/obo/UBERON_0016479"
+ ],
+ "x_dimension": 10,
+ "y_dimension": 10,
+ "z_dimension": 10,
+ "dimension_units": "millimeter",
+ "placement": {
+ "@context": "https://hubmapconsortium.github.io/ccf-ontology/ccf-context.jsonld",
+ "@id": "http://purl.org/ccf/1.5/62381536-7923-43da-8703-c744e4de0b25_placement",
+ "@type": "SpatialPlacement",
+ "target": "http://purl.org/ccf/latest/ccf.owl#VHMLiver",
+ "placement_date": "2023-08-24",
+ "x_scaling": 1,
+ "y_scaling": 1,
+ "z_scaling": 1,
+ "scaling_units": "ratio",
+ "x_rotation": 31,
+ "y_rotation": 0,
+ "z_rotation": 15,
+ "rotation_order": "XYZ",
+ "rotation_units": "degree",
+ "x_translation": 51.924,
+ "y_translation": 159.299,
+ "z_translation": 130.878,
+ "translation_units": "millimeter"
+ }
+}
\ No newline at end of file
diff --git a/staging/hca-centre-for-inflammation-research-liver/registrations/Male_Healthy.json b/staging/hca-centre-for-inflammation-research-liver/registrations/Male_Healthy.json
new file mode 100644
index 0000000..9db47b7
--- /dev/null
+++ b/staging/hca-centre-for-inflammation-research-liver/registrations/Male_Healthy.json
@@ -0,0 +1,37 @@
+{
+ "@context": "https://hubmapconsortium.github.io/ccf-ontology/ccf-context.jsonld",
+ "@id": "http://purl.org/ccf/1.5/2a823e94-6653-4c8c-b270-0c75bd1a58e8",
+ "@type": "SpatialEntity",
+ "creator": "Jordan Portman",
+ "creator_first_name": "Jordan",
+ "creator_last_name": "Portman",
+ "creation_date": "2023-08-24",
+ "ccf_annotations": [
+ "http://purl.obolibrary.org/obo/UBERON_0016479",
+ "http://purl.obolibrary.org/obo/UBERON_0001115"
+ ],
+ "x_dimension": 10,
+ "y_dimension": 10,
+ "z_dimension": 10,
+ "dimension_units": "millimeter",
+ "placement": {
+ "@context": "https://hubmapconsortium.github.io/ccf-ontology/ccf-context.jsonld",
+ "@id": "http://purl.org/ccf/1.5/2a823e94-6653-4c8c-b270-0c75bd1a58e8_placement",
+ "@type": "SpatialPlacement",
+ "target": "http://purl.org/ccf/latest/ccf.owl#VHMLiver",
+ "placement_date": "2023-08-24",
+ "x_scaling": 1,
+ "y_scaling": 1,
+ "z_scaling": 1,
+ "scaling_units": "ratio",
+ "x_rotation": 16,
+ "y_rotation": -4,
+ "z_rotation": 1,
+ "rotation_order": "XYZ",
+ "rotation_units": "degree",
+ "x_translation": 154.924,
+ "y_translation": 131.299,
+ "z_translation": 151.878,
+ "translation_units": "millimeter"
+ }
+}
\ No newline at end of file
diff --git a/staging/hca-centre-for-inflammation-research-liver/rui_locations.jsonld b/staging/hca-centre-for-inflammation-research-liver/rui_locations.jsonld
new file mode 100644
index 0000000..a0c4920
--- /dev/null
+++ b/staging/hca-centre-for-inflammation-research-liver/rui_locations.jsonld
@@ -0,0 +1,2533 @@
+{
+ "@context": "https://hubmapconsortium.github.io/ccf-ontology/ccf-context.jsonld",
+ "@graph": [
+ {
+ "@id": "HEA1",
+ "@type": "Donor",
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+}
\ No newline at end of file