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[ENH] Added the specification for using HED libraries in BIDS #1106

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[ENH] Added the specification for using HED libraries in BIDS #1106

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6ce58dc
Added the specification for using HED libraries in BIDS
VisLab May 23, 2022
976559a
Added newline at end of hed appendices
VisLab May 23, 2022
6555ad5
Corrected the metadata.yml spacing
VisLab May 23, 2022
dc723e4
Added requirement that user-chosen prefixes be alphanumeric
VisLab May 24, 2022
d52c011
Merge branch 'master' of https://github.com/bids-standard/bids-specif…
VisLab Jun 9, 2022
8039ec9
Simplified HEDVersion to be array rather than object
VisLab Jun 9, 2022
ccf749b
Provided example using only SCORE library
VisLab Jun 9, 2022
ce26293
Made some typo and editorial corrections
VisLab Jun 9, 2022
a0a7b36
Changed base schema to standard schema
VisLab Jun 9, 2022
37e9b8f
Removed extra colon
VisLab Jun 9, 2022
42708ef
Update src/99-appendices/03-hed.md
VisLab Jun 11, 2022
f26bcd1
Update src/99-appendices/03-hed.md
VisLab Jun 11, 2022
cfea5f7
Merge branch 'master' into hed-library
sappelhoff Aug 29, 2022
5310be6
Update src/99-appendices/03-hed.md
sappelhoff Aug 29, 2022
a49df64
Update metadata.yaml
sappelhoff Aug 29, 2022
55d79a6
add new format: hed_version
sappelhoff Aug 30, 2022
5c7045d
line break pattern
sappelhoff Aug 30, 2022
6101459
Update src/schema/objects/metadata.yaml
sappelhoff Aug 30, 2022
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44 changes: 41 additions & 3 deletions src/99-appendices/03-hed.md
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Expand Up @@ -167,16 +167,16 @@ This allows for a proper validation of the HED annotations
(for example using the `bids-validator`).

Example: The following `dataset_description.json` file specifies that the
[`HED8.0.0.xml`](https://github.com/hed-standard/hed-specification/tree/master/hedxml/HED8.0.0.xml)
[`HED8.1.0.xml`](https://github.com/hed-standard/hed-specification/tree/master/hedxml/HED8.1.0.xml)
file from the `hedxml` directory of the
[`hed-specification`](https://github.com/hed-standard/hed-specification)
repository on GitHub should be used to validate the study event annotations.

```JSON
{
"Name": "A great experiment",
"BIDSVersion": "1.6.0",
"HEDVersion": "8.0.0"
"BIDSVersion": "1.7.0",
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"HEDVersion": "8.1.0"
}
```

Expand All @@ -185,3 +185,41 @@ any present HED information will be validated using the latest version of the HE
which is bound to result in problems.
Hence, it is strongly RECOMMENDED that the `HEDVersion` field be included when using HED
in a BIDS dataset.

### Using HED library schemas

HED also allows you to use one or more specialized vocabularies along with
the base vocabulary. These specialized vocabularies are developed by
communities of users and are available in the GitHub
[hed-schema-library](https://github.com/hed-standard/hed-schema-library) repository.

Example: The following `dataset_description.json` file specifies that the
[`HED8.1.0.xml`](https://github.com/hed-standard/hed-specification/tree/master/hedxml/HED8.1.0.xml)
base schema should be used along with the
SCORE library for clinical neurological annotation and a test library
located at [HED_score_0.0.1.xml](https://github.com/hed-standard/hed-schema-library/blob/main/library_schemas/score/hedxml/HED_score_0.0.1.xml) and [HED_testlib_1.0.2.xml](https://github.com/hed-standard/hed-schema-library/blob/main/library_schemas/testlib/hedxml/HED_testlib_1.0.2.xml), respectively.

```JSON
{
"Name": "A great experiment",
"BIDSVersion": "1.7.0",
"HEDVersion": {
"base": "8.1.0",
"libraries": {
"sc": "score_0.0.1",
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is this some "official" identity specification combining library and a version? if not, may be worth separating out, even if more verbose:

Suggested change
"sc": "score_0.0.1",
"sc": {"library": "score", "version": "0.0.1"},

or alike to make it explicit, and to allow in the future e.g. to expand with optional extra information (e.g. URL to the HED library which is not in the library of libraries i.e. hed-schema-library) but available from another library of libraries or may be even directly pointed to by that URL?

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Some version of what you suggest was the original plan (though URIs were never planned to be supported other than bids: schema paths within the dataset), but it was simplified during development after feedback from the HED community. @VisLab can provide more detail, which is escaping me.

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The suggestion is above is one that we have considered (see hed-specification issue#156). The actual format is only proposed at this point in the HED specification, and we would appreciate opinions and are open to changes.

We have gone through a number of versions of this, and originally we thought we would support a file within the bids data set itself and arbitrary URLs. The HED working group consensus was to start with the standard libraries and see how it goes, since the purpose is to have standardized vocabularies to make meaningful comparisons across datasets.

On a related note:
The hed-python tools allow a schema group to be passed into its BIDS data set constructor to override the specification in dataset_description. Right now the hed-javascript public interface (which is what BIDS uses) only passes in the data set and constructs the schema group internally.

I am mentioning this because another possibility is to allow a schema group to be passed in as part of the public interface to the hed-javascript validator (from bids) which would override the internal specification extracted from the dataset_description. This is relevant because we are going to have to do a major version bump to support the libraries because of another interface change and we could add this in as an option and allow BIDS to decide. @sappelhoff. @rwblair?

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The specification of which schemas are to be used to be used for validating a dataset are provided in a separate parameter, since hed-javascript cannot handle relative paths within the BIDS dataset directory and needs them parsed to use the absolute path. However, the actual Schema and Schemas types used by the validator to represent schemas are considered implementation details (despite being returned by the validator.buildSchema function) and not part of the stable API. In theory, the object passed as the second argument to validateBidsDataset can be any object conforming to the defined API, regardless of what datasetDescription.json says.

"ts": "testlib_1.0.2"
}
}
}
```
The `sc:` and `ts:` are user-chosen prefixes used to distinguish the sources
of the terms in the HED annotation.
These prefixes must be alphanumeric.
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In the following HED annotation:

```Text
Data-feature, sc:Photmyogenic-response, sc:Wicket-spikes
```

The tag `Data-feature` is from HED8.1.0,
while `Photmyogenic-response` and `Wicket-spikes` are from HED_score_0.0.1.
10 changes: 9 additions & 1 deletion src/schema/objects/metadata.yaml
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Expand Up @@ -1022,7 +1022,15 @@ HEDVersion:
description: |
If HED tags are used:
The version of the HED schema used to validate HED tags for study.
type: string
May include a single schema or a base schema and one or more library schema.
anyOf:
- type: string
- type: object
properties:
base:
type: string
libraries:
type: object
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Haematocrit:
name: Haematocrit
description: |
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4 changes: 2 additions & 2 deletions src/schema/rules/tabular_metadata.yaml
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Expand Up @@ -7,8 +7,8 @@ scans:
- .json
entities:
subject: required
session: optional # session is required if session is present in the dataset.
sessions: # This file may only exist if session is present in the dataset.
session: optional # session is required if session is present in the dataset.
sessions: # This file may only exist if session is present in the dataset.
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suffixes:
- sessions
extensions:
Expand Down