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[SCHEMA] Add metadata term files #774

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Jul 13, 2021
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acc3b9a
[SCHEMA] Add metadata term files (#762)
tsalo Apr 13, 2021
2ecfc88
Improve make_metadata_table docstring.
tsalo Apr 13, 2021
b5f182c
Start addressing inconsistencies between rendered and hardcoded tables.
tsalo Apr 13, 2021
63b2027
Merge branch 'master' into metadata-schema
tsalo Apr 14, 2021
4d6cd67
Fix typos in PET metadata
tsalo Apr 26, 2021
c2a02ec
Add metadata fields from qMRI appendix.
tsalo Apr 26, 2021
e8607d2
Fix.
tsalo Apr 26, 2021
c29aa2f
Address duplicate datatypes.
tsalo Apr 26, 2021
58926cf
Wrap example strings in code.
tsalo Apr 26, 2021
675f9f5
Use enum for n/a instead of pattern.
tsalo Apr 26, 2021
4dcab2b
Replace "string" with "n/a" when appropriate.
tsalo Apr 26, 2021
ae7715c
Address some inconsistencies.
tsalo Apr 26, 2021
db5ab58
Take a crack as SpatialReference.
tsalo Apr 26, 2021
47d6d0f
Apply suggestions from code review
tsalo Apr 27, 2021
947ad56
Update tools/schemacode/schema.py
effigies Apr 27, 2021
efffea9
search_structure --> dereference_yaml
tsalo Apr 27, 2021
3deb0a6
Use faster loading approach.
tsalo Apr 27, 2021
4161f1c
Fix deprecation link.
tsalo Apr 27, 2021
446cfe6
Apply suggestions from code review
tsalo Apr 28, 2021
abacfef
Update 01-magnetic-resonance-imaging-data.md
tsalo Apr 28, 2021
f00fdd0
Merge branch 'master' into metadata-schema
tsalo Apr 28, 2021
9ffbe7a
Add B0FieldIdentifier and B0FieldSource.
tsalo Apr 28, 2021
7167252
Revert type changes and add TODOs to check them.
tsalo Apr 28, 2021
96d6b13
Update tools/schemacode/schema.py
effigies Apr 28, 2021
e308008
Replace remaining relative links.
tsalo Apr 28, 2021
830029d
Merge branch 'metadata-schema' of https://github.com/bids-standard/bi…
tsalo Apr 28, 2021
e5bd6e7
Apply suggestions from code review
tsalo Apr 28, 2021
05f5c60
Add new coordinate systems from #775.
tsalo Apr 30, 2021
352930a
Grab hack from #781 (which wasn't merged).
tsalo Apr 30, 2021
d36b00e
Merge branch 'master' into metadata-schema
tsalo May 10, 2021
b7c94f8
Create HED.yaml
tsalo May 10, 2021
efd79f3
boldify table headers
Remi-Gau May 23, 2021
86bc69e
add device info metadata
Remi-Gau May 30, 2021
0737cab
fix table fences
Remi-Gau May 30, 2021
54a3174
fix cell padding
Remi-Gau May 30, 2021
4031283
fix cell padding
Remi-Gau May 30, 2021
8967140
Merge pull request #811 from Remi-Gau/remi-physio-metadata
sappelhoff May 31, 2021
d7a5615
Merge pull request #808 from Remi-Gau/fix_table_header
sappelhoff Jun 1, 2021
95e5599
Merge branch 'master' into metadata-schema
tsalo Jun 7, 2021
e5a5655
Fix up DICOM tags in metadata.
tsalo Jun 7, 2021
3e2a56d
Leverage "name" field for section-specific metadata definitions.
tsalo Jun 7, 2021
b8d0a75
Merge branch 'master' into metadata-schema
tsalo Jun 9, 2021
6ebde13
composite instances --> measurements
tsalo Jun 9, 2021
1405b23
Fix name of HED field.
tsalo Jun 16, 2021
f3fd1b5
Fix string formatting in coordinate system fields.
tsalo Jun 16, 2021
670ca5b
Move "preferably same as" to section-specific text.
tsalo Jun 16, 2021
39f5336
Standardize DICOM Tag format.
tsalo Jun 16, 2021
78499f1
Move mentions of DICOM Tags out of definitions.
tsalo Jun 16, 2021
0954aea
Apply suggestions from code review
tsalo Jun 17, 2021
6273e3d
Generalize SoftwareFilters example.
tsalo Jun 17, 2021
c0df0ad
Distinguish AnatomicalLandmarkCoordinates definitions.
tsalo Jun 17, 2021
30992ee
Rename fmapEchoTime to match new format.
tsalo Jun 17, 2021
6a7e001
Apply suggestions from code review
tsalo Jun 24, 2021
680257d
Apply suggestions from code review
tsalo Jun 29, 2021
c13df8d
Address review.
tsalo Jun 29, 2021
34d9435
Fix example manufacturer names.
tsalo Jun 29, 2021
9ffaa12
Merge branch 'master' into metadata-schema
tsalo Jun 29, 2021
313de15
TEMPORARY: fix osipi URL (revert when osipi.org is back)
sappelhoff Jun 30, 2021
316453f
Fix regex for identifying macros.
tsalo Jun 30, 2021
890b364
Partially address review.
tsalo Jun 30, 2021
e5c130e
Do not assume minItems is 1 for array terms.
tsalo Jun 30, 2021
90c00d2
composite instances --> measurements (again)
tsalo Jul 1, 2021
af31fec
Update src/schema/metadata/MagneticFieldStrength.yaml
tsalo Jul 1, 2021
d9b3576
Update description to PharmaceuticalDoseTime
mnoergaard Jul 5, 2021
4a9bf0d
Update 09-positron-emission-tomography.md
mnoergaard Jul 5, 2021
def5ae3
fix table pipe alignment
sappelhoff Jul 5, 2021
9e6c75d
add pharmaceuticaldosetime fix to schema
sappelhoff Jul 5, 2021
26450b0
fix str examples
sappelhoff Jul 5, 2021
7bb90d8
Apply suggestions from code review
tsalo Jul 5, 2021
a803334
Update src/schema/metadata/RepetitionTimeExcitation.yaml
tsalo Jul 5, 2021
371a7e1
Merge branch 'master' into metadata-schema
tsalo Jul 13, 2021
34760d8
Add DoseCalibrationFactor.
tsalo Jul 13, 2021
85d60e2
Update ScanDate definition and deprecate it.
tsalo Jul 13, 2021
0c76b93
Remove hardcoded tables.
tsalo Jul 13, 2021
763c90a
Remove unused links.
tsalo Jul 13, 2021
43166e1
Update tools/schemacode/schema.py
tsalo Jul 13, 2021
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13 changes: 13 additions & 0 deletions src/02-common-principles.md
Original file line number Diff line number Diff line change
Expand Up @@ -508,6 +508,19 @@ Note that if a field name included in the data dictionary matches a column name
then that field MUST contain a description of the corresponding column,
using an object containing the following fields:

{{ MACROS___make_metadata_table(
{
"LongName": "OPTIONAL",
"Description": (
"RECOMMENDED",
"The description of the column.",
),
"Levels": "RECOMMENDED",
"Units": "RECOMMENDED",
"TermURL": "RECOMMENDED",
}
) }}

| **Key name** | **Requirement level** | **Data type** | **Description** |
| ------------ | --------------------- | ------------------------- | --------------------------------------------------------------------------------------------------------------- |
| LongName | OPTIONAL | [string][] | Long (unabbreviated) name of the column. |
Expand Down
28 changes: 26 additions & 2 deletions src/03-modality-agnostic-files.md
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,23 @@ Templates:
The file `dataset_description.json` is a JSON file describing the dataset.
Every dataset MUST include this file with the following fields:

{{ MACROS___make_metadata_table(
{
"Name": "REQUIRED",
"BIDSVersion": "REQUIRED",
"HEDVersion": "RECOMMENDED",
"DatasetType": "RECOMMENDED",
"License": "RECOMMENDED",
"Authors": "OPTIONAL",
"Acknowledgements": "OPTIONAL",
"HowToAcknowledge": "OPTIONAL",
"Funding": "OPTIONAL",
"EthicsApprovals": "OPTIONAL",
"ReferencesAndLinks": "OPTIONAL",
"DatasetDOI": "OPTIONAL",
}
) }}

| **Key name** | **Requirement level** | **Data type** | **Description** |
|--------------------|-----------------------|--------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Name | REQUIRED | [string][] | Name of the dataset. |
Expand Down Expand Up @@ -69,6 +86,13 @@ In addition to the keys for raw BIDS datasets,
derived BIDS datasets include the following REQUIRED and RECOMMENDED
`dataset_description.json` keys:

{{ MACROS___make_metadata_table(
{
"GeneratedBy": "REQUIRED",
"SourceDatasets": "RECOMMENDED",
}
) }}

| **Key name** | **Requirement level** | **Data type** | **Description** |
|----------------|-----------------------|--------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| GeneratedBy | REQUIRED | [array][] of [objects][] | Used to specify provenance of the derived dataset. See table below for contents of each object. |
Expand Down Expand Up @@ -339,15 +363,15 @@ The purpose of this file is to describe timing and other properties of each
imaging acquisition sequence (each *run* file) within one session.

Each neural recording *file* SHOULD be described by exactly one row.
Some recordings consist of multiple parts, that span several files,
Some recordings consist of multiple parts, that span several files,
for example through `echo-`, `part-`, or `split-` entities.
Such recordings MUST be documented with one row per file.

Relative paths to files should be used under a compulsory `filename` header.

If acquisition time is included it should be listed under the `acq_time` header.
Acquisition time refers to when the first data point in each run was acquired.
Furthermore, if this header is provided, the acquisition times of all files that
Furthermore, if this header is provided, the acquisition times of all files that
belong to a recording MUST be identical.

Datetime should be expressed as described in [Units](./02-common-principles.md#units).
Expand Down
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