Rename "project" to "study"

yarikoptic · effigies · commit 315c08fb40d4 · 2025-06-12T05:20:20.000-04:00
While discussing with @jbpoline we wondered, if may be `study` would be a better descriptor to use here in favor of `project`. One of the rationales, is that e.g. in [BEP035](https://bids.neuroimaging.io/extensions/beps/bep_035.html) (attn @bids-standard/bep035) on Mega-analysis they introduce `study-` entity as a groupping element. It kinda then would match natively. we also mention "study" in various places in BIDS which seems to align nicely here ```shell ❯ git grep study src/CHANGES.md:- \[FIX] update physio bids name in longitudinal study page examples [#863](#863) ([Remi-Gau](https://github.com/Remi-Gau)) src/appendices/coordinate-systems.md:The following template identifiers are RECOMMENDED for individual- and study-specific reference src/appendices/coordinate-systems.md:In the case of multiple study templates, additional names may need to be defined. src/appendices/coordinate-systems.md:| study | Custom space defined using a group/study-specific template. This coordinate system requires specifying an additional file to be fully defined. | src/appendices/hed.md:numerical values that are similar across the recordings in the study. src/appendices/hed.md:repository on GitHub should be used to validate the study event annotations. src/common-principles.md: unless when appropriate given the study goals, for example, when scanning babies. src/introduction.md:> The data used in the study were organized using the src/modality-specific-files/genetic-descriptor.md: "Dataset": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001364.v1.p1", src/modality-specific-files/intracranial-electroencephalography.md:Note that the date and time information SHOULD be stored in the study key file src/modality-specific-files/magnetic-resonance-spectroscopy.md:acquisition parameters in filenames is helpful or necessary to distinguish datasets in a given study. src/modality-specific-files/motion.md:Note that the onsets of the recordings SHOULD be stored in the study key file [(`scans.tsv`)](../modality-agnostic-files.md#scans-file). src/modality-specific-files/positron-emission-tomography.md:This entity is OPTIONAL if only one tracer is used in the study, src/modality-specific-files/task-events.md:Please mind that this does not imply that only so called "event related" study designs src/schema/objects/common_principles.yaml: A set of neuroimaging and behavioral data acquired for a purpose of a particular study. src/schema/objects/common_principles.yaml: Session can (but doesn't have to) be synonymous to a visit in a longitudinal study. src/schema/objects/common_principles.yaml: A person or animal participating in the study. src/schema/objects/entities.yaml: For example, this should be used when a study includes two T1w images - src/schema/objects/entities.yaml: Session can (but doesn't have to) be synonymous to a visit in a longitudinal study. src/schema/objects/entities.yaml: A person or animal participating in the study. src/schema/objects/enums.yaml:study: src/schema/objects/enums.yaml: value: study src/schema/objects/enums.yaml: display_name: study src/schema/objects/enums.yaml: Custom space defined using a group/study-specific template. src/schema/objects/metadata.yaml: Reference to the study/studies on which the implementation is based. src/schema/objects/metadata.yaml: The version of the HED schema used to validate HED tags for study. tools/schemacode/src/bidsschematools/tests/data/broken_dataset_description.json:"EthicsApprovals": ["The original study from which this BIDS example dataset was derived was approved by the Ethics committee of Ghent University Hospital with identifier EC 2017/1103."] ``` and "project" mentionings are not particularly aligned. So, I think, we should just make it a "study", hence renaming accordingly.
diff --git a/src/common-principles.md b/src/common-principles.md
@@ -400,17 +400,17 @@ In particular, if a BIDS dataset contains a `derivatives/` subdirectory,
 the contents of that directory may be a heterogeneous mix of BIDS Derivatives
 datasets and non-compliant derivatives.
 
-## Project dataset
+## Study dataset
 
-BIDS allows one to organize the data for the entire project (original source data, raw BIDS, derivatives) as a valid BIDS dataset in the following way
+BIDS allows one to organize the data for the entire study (original source data, raw BIDS, derivatives) as a valid BIDS dataset in the following way
 
 <!-- This block generates a file tree.
 A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
 {{ MACROS___make_filetree_example(
     {
-    "my_project-1": {
+    "study-1": {
         "sourcedata": {
             "dicoms": {},
             "raw": {
@@ -438,7 +438,7 @@ In this example, `sourcedata/dicoms` is not nested inside
 The subdirectories of `derivatives` MAY be BIDS-compliant derivatives datasets
 (see [Non-compliant derivatives](#non-compliant-derivatives) for further discussion).
 The above example is a fully compliant BIDS dataset, providing a convention useful for organizing source, raw BIDS, and derived BIDS data while maintaining overall BIDS compliance.
-When using this convention, `dataset_description.json` MUST have `DatasetType` to be set to `"project"`.  It is also RECOMMENDED to set the `SourceDatasets`
+When using this convention, `dataset_description.json` MUST have `DatasetType` to be set to `"study"`.  It is also RECOMMENDED to set the `SourceDatasets`
 field in `dataset_description.json` of each subdirectory of `derivatives` to:
 
 ```JSON
diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml
@@ -360,14 +360,19 @@ individual:
     In context of surfaces this space has been referred to as `fsnative`.
 
     In order for this space to be interpretable, `SpatialReference` metadata MUST be provided.
-study:
+study__space:
   value: study
   display_name: study
   description: |
     Custom space defined using a group/study-specific template.
     This coordinate system requires specifying an additional file to be fully defined.
 
     In order for this space to be interpretable, `SpatialReference` metadata MUST be provided.
+study__datasettype:
+  value: study
+  display_name: study
+  description: |
+    A study BIDS dataset.
 scanner:
   value: scanner
   display_name: scanner
@@ -1319,11 +1324,6 @@ derivative:
   display_name: derivative
   description: |
     A derived BIDS dataset.
-project:
-  value: project
-  display_name: project
-  description: |
-    A project BIDS dataset.
 balanced:
   value: balanced
   display_name: balanced
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
@@ -583,7 +583,7 @@ DatasetType:
   enum:
     - $ref: objects.enums.raw.value
     - $ref: objects.enums.derivative.value
-    - $ref: objects.enums.project.value
+    - $ref: objects.enums.study__datasetype.value
 DecayCorrectionFactor:
   name: DecayCorrectionFactor
   display_name: Decay Correction Factor
diff --git a/src/schema/rules/checks/dataset.yaml b/src/schema/rules/checks/dataset.yaml
@@ -18,11 +18,11 @@ NoSubjectFolders:
   issue:
     code: NOSUBJECT_FOLDERS
     message: |
-      There should be no subject directories (labeled "sub-*") in the root of this project BIDS dataset.
+      There should be no subject directories (labeled "sub-*") in the root of this study BIDS dataset.
     level: warning
   selectors:
     - path == '/dataset_description.json'
-    - dataset.dataset_description.DatasetType == "project"
+    - dataset.dataset_description.DatasetType == "study"
   checks:
     - length(dataset.subjects.sub_dirs) == 0
 
