From 984116ce1cdafb6c98b1a9fb8b92f3b949705625 Mon Sep 17 00:00:00 2001 From: Francois Date: Fri, 26 Jul 2024 16:16:10 +0100 Subject: [PATCH] updated example study output --- .../test/data/S-BIAD606/output.json | 58 +++------- .../test/data/S-BIAD634/output.json | 85 ++++---------- .../test/data/S-BIAD976/output.json | 72 +++--------- .../test/data/S-BIAD987/output.json | 108 ++++-------------- 4 files changed, 76 insertions(+), 247 deletions(-) diff --git a/bia-ingest-shared-models/test/data/S-BIAD606/output.json b/bia-ingest-shared-models/test/data/S-BIAD606/output.json index f0ba9918..1ab06093 100644 --- a/bia-ingest-shared-models/test/data/S-BIAD606/output.json +++ b/bia-ingest-shared-models/test/data/S-BIAD606/output.json @@ -30,37 +30,15 @@ "development", "segmentation" ], - "funding_statement": "Deutsche Forschungsgemeinschaft grant BR5039/3-1\nAssemble Plus grant as part of the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 730984", - "experimental_imaging_component": [ - "UUID-experimental-imaging-dataset-1" - ], - "annotation_component": [] + "funding_statement": "Deutsche Forschungsgemeinschaft grant BR5039/3-1\nAssemble Plus grant as part of the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 730984" }, { "uuid": "UUID-experimental-imaging-dataset-1", "title_id": "µCT data", "description": "Raw image stacks (3D tiff file format) of Pycnogonum litorale complete specimens and ROIs", - "image": [ - "UUID-experimentally-captured-image-1" - ], - "file": [ - "UUID-file-reference-1" - ], "submitted_in_study": "UUID-study-1", - "specimen_imaging_preparation_protocol": [ - "UUID-specimen-preparation-protocol-1" - ], - "acquisition_process": [ - "UUID-image-acquisition-1" - ], - "biological_entity": [ - "UUID-biosample-1" - ], - "specimen_growth_protocol": [], "analysis_method": [], "correlation_method": [], - "file_reference_count": 1, - "image_count": 1, "example_image_uri": [] }, { @@ -74,7 +52,7 @@ "title_id": "Pycnogonum litorale µCT", "protocol_description": "Dried specimens were placed in plastic tubes for overview scans. For higher resolution scans of the posterior body region with the regenerates, they were subsequently attached to plastic welding rods with hot glue. Scans were performed under 40 kV/200 μA/8 W or 30 kV/200 μA/6 W settings. Depending on the specimen size and region of interest, a 4×, 10×, or 20× objective was chosen. Exposure times were individually adjusted for each scan, ranging from 0.75 to 6.5 s. To reduce noise, binning 2 was applied during data acquisition. Tomography projections were reconstructed with the XMReconstructor software (Carl Zeiss Microscopy) with binning 1 (= full resolution) and TIFF format image stacks as output.", "imaging_instrument_description": "Xradia MicroXCT-200 (Carl Zeiss Microscopy)", - "imaging_method_name": "X-ray computed tomography", + "imaging_method_name": "X-ray computed tomography", "fbbi_id": [ "http://purl.obolibrary.org/obo/FBbi_00001002" ] @@ -95,27 +73,23 @@ "acquisition_process": [ "UUID-image-acquisition-1" ], - "representation": [ - "UUID-image-representation-1", - "UUID-image-representation-2", - "UUID-image-representation-3", - "UUID-image-representation-4", - "UUID-image-representation-5" - ], "submission_dataset": "UUID-experimental-imaging-dataset-1", - "subject": { - "imaging_preparation_protocol": [ - "UUID-specimen-preparation-protocol-1" - ], - "sample_of": [ - "UUID-biosample-1" - ], - "growth_protocol": [] - }, + "subject": "UUID-specimen-1", "attribute": {} }, + { + "uuid": "UUID-specimen-1", + "imaging_preparation_protocol": [ + "UUID-specimen-preparation-protocol-1" + ], + "sample_of": [ + "UUID-biosample-1" + ], + "growth_protocol": [] + }, { "uuid": "UUID-image-representation-1", + "representation_of": "UUID-experimentally-captured-image-1", "original_file_reference": [ "UUID12-file_reference" ], @@ -129,6 +103,7 @@ }, { "uuid": "UUID-image-representation-2", + "representation_of": "UUID-experimentally-captured-image-1", "original_file_reference": [], "image_format": "ome_ngff", "file_uri": [ @@ -140,6 +115,7 @@ }, { "uuid": "UUID-image-representation-3", + "representation_of": "UUID-experimentally-captured-image-1", "original_file_reference": [], "image_format": "ome_ngff", "file_uri": [ @@ -151,6 +127,7 @@ }, { "uuid": "UUID-image-representation-4", + "representation_of": "UUID-experimentally-captured-image-1", "original_file_reference": [], "image_format": "thumbnail", "file_uri": [ @@ -164,6 +141,7 @@ }, { "uuid": "UUID-image-representation-5", + "representation_of": "UUID-experimentally-captured-image-1", "original_file_reference": [], "image_format": "representative", "file_uri": [ diff --git a/bia-ingest-shared-models/test/data/S-BIAD634/output.json b/bia-ingest-shared-models/test/data/S-BIAD634/output.json index 7992e4eb..e83a09fc 100644 --- a/bia-ingest-shared-models/test/data/S-BIAD634/output.json +++ b/bia-ingest-shared-models/test/data/S-BIAD634/output.json @@ -170,47 +170,15 @@ "link": "https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BSST265", "description": "Original submission (not curated)" } - ], - "experimental_imaging_component": [ - "UUID-experimental-imaging-dataset-1" - ], - "annotation_component": [ - "UUID-annotation-dataset-1" ] }, { "uuid": "UUID-experimental-imaging-dataset-1", "title_id": "Fluorescence images", "description": "Fluorescent nuclear images of normal or cancer cells from different tissue origins and sample preparation types", - "image": [ - "UUID-experimentally-captured-image-1" - ], - "file": [ - "UUID-file-reference-1" - ], "submitted_in_study": "UUID-study-1", - "specimen_imaging_preparation_protocol": [ - "UUID-specimen-preparation-protocol-1", - "UUID-specimen-preparation-protocol-2", - "UUID-specimen-preparation-protocol-3", - "UUID-specimen-preparation-protocol-4" - ], - "acquisition_process": [ - "UUID-image-acquisition-1" - ], - "biological_entity": [ - "UUID-biosample-1", - "UUID-biosample-2", - "UUID-biosample-3", - "UUID-biosample-4", - "UUID-biosample-5", - "UUID-biosample-6" - ], - "specimen_growth_protocol": [], "analysis_method": [], "correlation_method": [], - "file_reference_count": 1, - "image_count": 1, "example_image_uri": [], "attribute": { "associatations": [ @@ -354,31 +322,11 @@ }, { "uuid": "UUID-experimentally-captured-image-1", + "submission_dataset": "UUID-experimental-imaging-dataset-1", "acquisition_process": [ "UUID-image-acquisition-1" ], - "representation": [ - "UUID-image-representation-1", - "UUID-image-representation-2" - ], - "submission_dataset": "UUID-experimental-imaging-dataset-1", - "subject": { - "imaging_preparation_protocol": [ - "UUID-specimen-preparation-protocol-1", - "UUID-specimen-preparation-protocol-2", - "UUID-specimen-preparation-protocol-3", - "UUID-specimen-preparation-protocol-4" - ], - "sample_of": [ - "UUID-biosample-1", - "UUID-biosample-2", - "UUID-biosample-3", - "UUID-biosample-4", - "UUID-biosample-5", - "UUID-biosample-6" - ], - "growth_protocol": [] - }, + "subject": "UUID-specimen-1", "attribute": { "file description": "Raw nuclear images in TIFF format", "Diagnosis": "normal (HaCaT)", @@ -396,8 +344,27 @@ "download_size": "1.3MiB" } }, + { + "uuid": "UUID-specimen-1", + "imaging_preparation_protocol": [ + "UUID-specimen-preparation-protocol-1", + "UUID-specimen-preparation-protocol-2", + "UUID-specimen-preparation-protocol-3", + "UUID-specimen-preparation-protocol-4" + ], + "sample_of": [ + "UUID-biosample-1", + "UUID-biosample-2", + "UUID-biosample-3", + "UUID-biosample-4", + "UUID-biosample-5", + "UUID-biosample-6" + ], + "growth_protocol": [] + }, { "uuid": "UUID-image-representation-1", + "representation_of": "UUID-experimentally-captured-image-1", "original_file_reference": [ "UUID-file-reference-1" ], @@ -411,6 +378,7 @@ }, { "uuid": "UUID-image-representation-2", + "representation_of": "UUID-experimentally-captured-image-1", "original_file_reference": [ "UUID12-file_reference" ], @@ -448,17 +416,8 @@ { "uuid": "UUID-annotation-dataset-1", "title_id": "Template image annotation dataset", - "image": [ - "UUID-derived-image-1" - ], - "file": [ - "UUID-file-reference-2" - ], - "annotation_file": [], "submitted_in_study": "UUID-study-1", "annotation_method": "UUID-annotation-method-1", - "file_reference_count": 1, - "image_count": 1, "example_image_uri": [] }, { diff --git a/bia-ingest-shared-models/test/data/S-BIAD976/output.json b/bia-ingest-shared-models/test/data/S-BIAD976/output.json index b129bbaf..4925bba6 100644 --- a/bia-ingest-shared-models/test/data/S-BIAD976/output.json +++ b/bia-ingest-shared-models/test/data/S-BIAD976/output.json @@ -64,34 +64,13 @@ "nucleus", "fluorescence" ], - "funding_statement": "This study was supported by R&D grants of Flanders Innovation & Entrepreneurship (IWT150003, 120511). ", - "experimental_imaging_component": [ - "UUID-experimental-imaging-dataset-1", - "UUID-experimental-imaging-dataset-2" - ], - "annotation_component": [] + "funding_statement": "This study was supported by R&D grants of Flanders Innovation & Entrepreneurship (IWT150003, 120511). " }, { "uuid": "UUID-experimental-imaging-dataset-1", "title_id": "Functional assay", "description": "Synchronous calcium bursting is measured in GCaMP6f-transduced primary cortical cultures from E18 mouse embryos.", - "image": [ - "UUID-experimentally-captured-image-1" - ], - "file": [ - "UUID-file-reference-1" - ], "submitted_in_study": "UUID1-study", - "specimen_preparation_method": [ - "UUID-specimen-preparation-protocol-1" - ], - "acquisition_method": [ - "UUID-image-acquisition-1" - ], - "biological_entity": [ - "UUID-biosample-1" - ], - "specimen_growth_protocol": [], "analysis_method": [ { "title_id": "Functional ", @@ -99,8 +78,6 @@ } ], "correlation_method": [], - "file_reference_count": 1, - "image_count": 1, "example_image_uri": [], "attribute": { "associatations": [ @@ -144,22 +121,7 @@ "uuid": "UUID-experimental-imaging-dataset-2", "title_id": "Morphological assay", "description": "Quantification of morphological neuronal connectivity in primary cortical cultures from E18 mouse embryos.", - "image": [ - "UUID-experimentally-captured-image-1" - ], - "file": [ - "UUID-file-reference-1" - ], "submitted_in_study": "UUID1-study", - "specimen_preparation_method": [ - "UUID-specimen_preparation-protocol-1" - ], - "acquisition_method": [ - "UUID-image-acquisition-2" - ], - "biological_entity": [ - "UUID-biosample-1" - ], "analysis_method": [ { "title_id": "Morphological", @@ -167,8 +129,6 @@ } ], "correlation_method": [], - "file_reference_count": 0, - "image_count": 0, "example_image_uri": [], "attribute": { "associatations": [ @@ -195,22 +155,8 @@ "acquisition_process": [ "UUID-image-acquisition-1" ], - "representation": [ - "UUID-image-representation-1", - "UUID-image-representation-2", - "UUID-image-representation-3", - "UUID-image-representation-4" - ], "submission_dataset": "UUID-experimental-imaging-dataset-1", - "subject": { - "imaging_preparation_protocol": [ - "UUID-specimen-preparation-protocol-1" - ], - "sample_of": [ - "UUID-biosample-1" - ], - "growth_protocol": [] - }, + "subject": "UUID-specimen-1", "attribute": { "Type": "Raw Data Time", "Rep": "1", @@ -220,8 +166,19 @@ "Condition": "B27" } }, + { + "uuid": "UUID-specimen-1", + "imaging_preparation_protocol": [ + "UUID-specimen-preparation-protocol-1" + ], + "sample_of": [ + "UUID-biosample-1" + ], + "growth_protocol": [] + }, { "uuid": "UUID-image-representation-1", + "representation_of": "UUID-experimentally-captured-image-1", "original_file_reference": [ "UUID-file-reference-1" ], @@ -235,6 +192,7 @@ }, { "uuid": "UUID-image-representation-2", + "representation_of": "UUID-experimentally-captured-image-1", "original_file_reference": [], "image_format": "ome_ngff", "file_uri": [ @@ -246,6 +204,7 @@ }, { "uuid": "UUID-image-representation-3", + "representation_of": "UUID-experimentally-captured-image-1", "original_file_reference": [ "UUID-file-reference-1" ], @@ -261,6 +220,7 @@ }, { "uuid": "UUID-image-representation-4", + "representation_of": "UUID-experimentally-captured-image-1", "original_file_reference": [ "UUID-file-reference-1" ], diff --git a/bia-ingest-shared-models/test/data/S-BIAD987/output.json b/bia-ingest-shared-models/test/data/S-BIAD987/output.json index 2779d672..7e0f1bb1 100644 --- a/bia-ingest-shared-models/test/data/S-BIAD987/output.json +++ b/bia-ingest-shared-models/test/data/S-BIAD987/output.json @@ -100,40 +100,16 @@ "mitochondrion", "plastid" ], - "funding_statement": "This work was supported by the NIAID Division of Intramural Research.", - "experimental_imaging_component": [ - "UUID-experimental-imaging-dataset-1", - "UUID-experimental-imaging-dataset-2", - "UUID-experimental-imaging-dataset-3", - "UUID-experimental-imaging-dataset-4" - ], - "annotation_component": [] + "funding_statement": "This work was supported by the NIAID Division of Intramural Research." }, { "uuid": "UUID-experimental-imaging-dataset-1", "title_id": "Day 2 Organelles", "description": "This component contains Airyscan-processed images of organelles from FACS-collected P. falciparum persisters and ring stages two days after treatment with DHA/sorbitol (“DHA”) and the vehicle control (“DMSO”), respectively. The apicoplast is shown in green, mitochondrion is shown in red, and nucleus are shown in blue. ", - "image": [ - "UUID-experimentally-captured-image-1" - ], - "file": [ - "UUID-file-reference-1" - ], "submitted_in_study": "UUID1-study", - "specimen_preparation_method": [ - "UUID-specimen-preparation-protocol-1" - ], - "acquisition_method": [ - "UUID-image-acquisition-1" - ], - "biological_entity": [ - "UUID-biosample-1" - ], "specimen_growth_protocol": [], "analysis_method": [], "correlation_method": [], - "file_reference_count": 1, - "image_count": 1, "example_image_uri": [], "attribute": { "associatations": [ @@ -149,23 +125,9 @@ "uuid": "UUID-experimental-imaging-dataset-2", "title_id": "Day 17 Organelles", "description": "This component contains Airyscan-processed images of apicoplasts, mitochondria, and nuclei from FACS-collected P. falciparum parasites 17 days after DHA/sorbitol treatment plus sorbitol selection.", - "image": [], - "file": [], "submitted_in_study": "UUID1-study", - "specimen_preparation_method": [ - "UUID-specimen-preparation-protocol-2" - ], - "acquisition_method": [ - "UUID-image-acquisition-1" - ], - "biological_entity": [ - "UUID-biosample-2" - ], - "specimen_growth_protocol": [], "analysis_method": [], "correlation_method": [], - "file_reference_count": 0, - "image_count": 0, "example_image_uri": [], "attribute": { "associatations": [ @@ -181,22 +143,9 @@ "uuid": "UUID-experimental-imaging-dataset-3", "title_id": "Day 5 Organelles", "description": "This component contains Airyscan-processed images of apicoplasts, mitochondria, and nuclei from FACS-collected P. falciparum parasites 5 days following initial treatment with DHA/sorbitol (\"DHA\") or vehicle control/sorbitol (“DMSO”) plus sorbitol selection. ", - "image": [], - "file": [], "submitted_in_study": "UUID1-study", - "specimen_preparation_method": [ - "UUID-specimen-preparation-protocol-2" - ], - "acquisition_method": [ - "UUID-image-acquisition-1" - ], - "biological_entity": [ - "UUID-biosample-2" - ], "analysis_method": [], "correlation_method": [], - "file_reference_count": 0, - "image_count": 0, "example_image_uri": [], "attribute": { "associatations": [ @@ -212,22 +161,9 @@ "uuid": "UUID-experimental-imaging-dataset-4", "title_id": "Day 11 Organelles", "description": "This study component contains Airyscan-processed images of apicoplasts, mitochondria, and nuclei from FACS-collected P. falciparum parasites 11 days following initial treatment with DHA/sorbitol (\"DHA\") or vehicle control/sorbitol (“DMSO”) plus sorbitol selection. ", - "image": [], - "file": [], "submitted_in_study": "UUID1-study", - "specimen_preparation_method": [ - "UUID-specimen-preparation-protocol-2" - ], - "acquisition_method": [ - "UUID-image-acquisition-1" - ], - "biological_entity": [ - "UUID-biosample-2" - ], "analysis_method": [], "correlation_method": [], - "file_reference_count": 0, - "image_count": 0, "example_image_uri": [], "attribute": { "associatations": [ @@ -273,26 +209,23 @@ "acquisition_process": [ "UUID-image-acquisition-1" ], - "representation": [ - "UUID-image-representation-1", - "UUID-image-representation-2", - "UUID-image-representation-3", - "UUID-image-representation-4" - ], "submission_dataset": "UUID-experimental-imaging-dataset-1", - "subject": { - "imaging_preparation_protocol": [ - "UUID-specimen-preparation-protocol-1" - ], - "sample_of": [ - "UUID-biosample-1" - ], - "growth_protocol": [] - }, + "subject": "UUID-specimen-1", "attribute": {} }, + { + "uuid": "UUID-specimen-1", + "imaging_preparation_protocol": [ + "UUID-specimen-preparation-protocol-1" + ], + "sample_of": [ + "UUID-biosample-1" + ], + "growth_protocol": [] + }, { "uuid": "UUID-image-representation-1", + "representation_of": "UUID-experimentally-captured-image-1", "original_file_reference": [ "UUID-file-reference-1" ], @@ -306,6 +239,7 @@ }, { "uuid": "UUID-image-representation-2", + "representation_of": "UUID-experimentally-captured-image-1", "original_file_reference": [], "image_format": "ome_ngff", "file_uri": [ @@ -316,10 +250,9 @@ "attribute": {} }, { - "uuid": "UUID-image-representation-1", - "original_file_reference": [ - "UUID-file-reference-1" - ], + "uuid": "UUID-image-representation-3", + "representation_of": "UUID-experimentally-captured-image-1", + "original_file_reference": [], "image_format": "thumbnail", "file_uri": [ "https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD987/d4c81718-25de-476d-9665-e6ef2680c696/d4c81718-25de-476d-9665-e6ef2680c696-thumbnail-256-256.png" @@ -331,10 +264,9 @@ "attribute": {} }, { - "uuid": "UUID-image-representation-1", - "original_file_reference": [ - "UUID-file-reference-1" - ], + "uuid": "UUID-image-representation-4", + "representation_of": "UUID-experimentally-captured-image-1", + "original_file_reference": [], "image_format": "representative", "file_uri": [ "https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD987/d4c81718-25de-476d-9665-e6ef2680c696/d4c81718-25de-476d-9665-e6ef2680c696-representative-512-512.png"