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updated example study output #129

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updated example study output #129

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58 changes: 18 additions & 40 deletions bia-ingest-shared-models/test/data/S-BIAD606/output.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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": []
},
{
Expand All @@ -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"
]
Expand All @@ -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": [
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I'm leaning towards linking from Image Representation -> file reference, even if this will potentially be 1: A few.

I suspect File Reference -> Image Representation would be 1:1 most of the time judging by current code (only 1 image rep. gets linked back to a file reference - i'm assuming this is expected)

However, this feels better from the point of view of containing create/update operations. If you create a new image rep, you can link back to the original file references. This seems preferable compared to having to go the original file references and update them to point to the new image rep. Thoughts?

"UUID12-file_reference"
],
Expand All @@ -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": [
Expand All @@ -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": [
Expand All @@ -151,6 +127,7 @@
},
{
"uuid": "UUID-image-representation-4",
"representation_of": "UUID-experimentally-captured-image-1",
"original_file_reference": [],
"image_format": "thumbnail",
"file_uri": [
Expand All @@ -164,6 +141,7 @@
},
{
"uuid": "UUID-image-representation-5",
"representation_of": "UUID-experimentally-captured-image-1",
"original_file_reference": [],
"image_format": "representative",
"file_uri": [
Expand Down
85 changes: 22 additions & 63 deletions bia-ingest-shared-models/test/data/S-BIAD634/output.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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": [
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Typo: associatations written instead of associations!

Expand Down Expand Up @@ -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)",
Expand All @@ -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"
],
Expand All @@ -411,6 +378,7 @@
},
{
"uuid": "UUID-image-representation-2",
"representation_of": "UUID-experimentally-captured-image-1",
"original_file_reference": [
"UUID12-file_reference"
],
Expand Down Expand Up @@ -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": []
},
{
Expand Down
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