bids-specification
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bids-standard
[ENH] Added the specification for using HED libraries in BIDS
This is a preliminary request for change in the BIDS specification to accommodate HED libraries.
The first official HED library schema (SCORE library for clinical neurological annotation) is close to release.
We will prepare a PR for the bids-validator to validate datasets using HED libraries as well as an example datasets for bids-examples when there is agreement on the format.
We would appreciate reviews and comments: @sappelhoff @Remi-Gau @tsalo (the yaml could be improved--please help) @happy5214 @IanCa, @dorahermes @dungscout96 @smakeig, @tpatpa.
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I would like to hold off for another week to allow more internal discussion.
In working on the example use cases using the score library, it has become apparent that many users will just want to use the score library when they are doing neurological annotation and not use the base schema at all.
We have the option of allowing the following so that users wouldn't have to prefix the score tags:
"HEDVersion": {
"base": "score_0.0.1",
"libraries": {
"bs": "8.0.0"
}
}
or also:
"HEDVersion": "score_0.0.1"
@tpatpa @dorahermes comments?
@tpatpa @happy5214 @dorahermes @sappelhoff @dungscout96 @tsalo @yarikoptic Please review. After discussion.... the proposal has been simplified... for the better.
This version is correct and has been agreed upon by the Hed Working Group. The bids-validator part isn't quite ready yet. I'll try to work on a PR for the BIDS validator side, which just needs a small change.
The modifications needed for the HED side aren't quite there yet, but we can probably write a by-pass temporarily. (We recommend that users check their validation using the Python validator until we get it completed.) @happy5214
As for a link to a library: the SCORE library official 1.0.0 was finished and out for community comment. @tpatpa @dorahermes need to give final approval and then we can release it and provide the stable link. (We know what the link will be but once we put the schema there, tools will start using it.)
It would be nice if this made it into the new release. What time frame do we have for finishing the validation side?
I think we should wait on the validation of the HEDVersion using a regular expression unless this is standard for BIDS and we have to do it. I would rather just pass the HEDVersion to the hed-validator and let it resolve the version. On the first pass, we would only support the straight version strings as shown in the example.
However, longer term we would support BIDS URI's, the PR of which I notice is also moving along.
The 1.8 release will probably come mid September. It'd be great to have the new hed features in by then!
I think we should wait on the validation of the
HEDVersionusing a regular expression unless this is standard for BIDS and we have to do it. I would rather just pass theHEDVersionto thehed-validatorand let it resolve the version. On the first pass, we would only support the straight version strings as shown in the example.
I believe BIDS has the primary responsibility to validate HEDVersion, whether or not we do our own validation, especially if it's as simple as adding a regex to an already-implemented framework. We implement the functionality on our end as a matter of convenience and expedience, but in the end this is a format defined by BIDS, not hed-validator.
We have now released hed-validator 3.8.0 on npm supporting HED library schema. Could we move this PR forward now that it has supporting PRs bids-standard/bids-validator#1496 and bids-standard/bids-examples#332?
I think all three PRs are ready to go. @sappelhoff @Remi-Gau @rwblair
I think the only open question is whether or not we want to add the regexp suggested by @happy5214 to the BIDS schema validation.
If you have strict rules about how versions for HED need to look like, then I think it'd be a good idea ... even if the regexp looks a bit unwieldy, as described in https://github.com/bids-standard/bids-specification/pull/1106#discussion_r895041453
cc @VisLab
I have added the hed_version format as suggested by @happy5214. If you disagree, we can discuss removing it again -- but I think it's a good idea to validate HED versions early on, and not only in the HED validator.
Yes the RegEx is fine. I had a chance to test on our set of testcases. Thanks....
I would prefer to defer adding this regular expression. We do use regular expressions as part of the checking of schema for the hed-validator, but they are not quite this regular expression. Let's put this on a todo list for a future PR.
On Mon, Aug 29, 2022 at 3:24 PM Stefan Appelhoff @.***> wrote:
I think the only open question is whether or not we want to add the regexp suggested by @happy5214 https://github.com/happy5214 to the BIDS schema validation.
If you have strict rules about how versions for HED need to look like, then I think it'd be a good idea ... even if the regexp looks a bit unwieldy, as described in #1106 (comment) https://github.com/bids-standard/bids-specification/pull/1106#discussion_r895041453
cc @VisLab https://github.com/VisLab
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