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 new file mode 100644 index 0000000..1885b45 Binary files /dev/null and b/staging/hca-centre-for-inflammation-research-liver/SI Table 1 - Patient metadata.xlsx differ diff --git a/staging/hca-centre-for-inflammation-research-liver/assets/logo.jpg b/staging/hca-centre-for-inflammation-research-liver/assets/logo.jpg new file mode 100644 index 0000000..4593d54 Binary files /dev/null and b/staging/hca-centre-for-inflammation-research-liver/assets/logo.jpg differ diff --git a/staging/hca-centre-for-inflammation-research-liver/index.html b/staging/hca-centre-for-inflammation-research-liver/index.html new file mode 100644 index 0000000..69ae598 --- /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, + 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"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": 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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", + "label": "Female, Age 62, Patient HEA1", + "description": "Entered 8/24/2023, Jordan Portman, UEdinburgh", + "link": "https://www.ed.ac.uk/inflammation-research/research", + "consortium_name": "UEdinburgh", + "provider_name": "CIR/UEdinburgh", + "provider_uuid": "b27cb053-cf97-498b-b9d6-0854155e9df6", + "age": 62, + "sex": "Female", + "samples": [ + { + "@id": "HEA1#TissueBlock1", + "@type": "Sample", + "sample_type": "Tissue Block", + "label": "Registered 8/24/2023, Jordan Portman, UEdinburgh", + "description": 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