Refactoring of the BIDS validator

41 views
Skip to first unread message

mganz

unread,
May 3, 2021, 5:20:31 PMMay 3
to bids-di...@googlegroups.com

Dear BIDS community,

within the new data sharing inititative for PET, OpenNeuroPET, there is some funding available for improving the BIDS validator. OpenNeuroPET has been in contact with SquishyMedia who has proposed the attached strategy for refactoring of the BIDS validator in order to make it easier accessile and future proof. We have discussed this with the BIDS maintainer team and they think it's a good way to move forward.

But BIDS community what do you think?

You cna also contribute to this discussion on the GitHub for the validator: https://github.com/bids-standard/bids-validator/issues/1277

Kind regards,

Melanie

--
Yours sincerely


Melanie Ganz-Benjaminsen
Asst. Prof., Researcher

Direct: + 45 35 45 67 18
Mail: melani...@nru.dk

Neurobiology Research Unit
Rigshospitalet, building 6931
Juliane Maries Vej 28, 3rd floor
DK-2100 Copenhagen, Denmark

Phone: +45 3545 6712
Fax: +45 3545 6713
URL:http://nru.dk


This e-mail and any attachment may contain confidential and privileged material intended for the addressee only. If you are not the addressee, you are notified that no part of the e-mail or any attachment may be disclosed, copied or distributed, and that any other action related to this e-mail or attachment is strictly prohibited, and may be unlawful. If you have received this e-mail by error, please notify the sender immediately by return e-mail, and delete this message.
OpenNeuro-PET declarative schema.pdf

Paola Di Maio

unread,
May 3, 2021, 7:43:08 PMMay 3
to bids-di...@googlegroups.com
Thank you for sharing
I think before working on the validator
BIDS should streamline and clean up the data model!
Its rather organically unclean.
If the validator is rewritten before the data model is streamlined
it could be money down the drain
PDM

--
We are all colleagues working together to shape brain imaging for tomorrow, please be respectful, gracious, and patient with your fellow group members.
---
You received this message because you are subscribed to the Google Groups "bids-discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to bids-discussi...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/bids-discussion/e2cd8b120c2988c07718dd6063dbc870%40nru.dk.

Chris Markiewicz

unread,
May 21, 2021, 8:30:01 AMMay 21
to bids-di...@googlegroups.com
Hi Paola,

I'm not clear on what your proposal (objection?) is here. If I understand correctly, you're referring to the BIDS-Terms effort from Dave Keator and colleagues to translate BIDS concepts to terms in an ontology? If that's correct, I see the translation of the standard to a declarative schema that can be validated as complementary but largely non-interfering. For what it's worth, the existing schema-fication that Taylor Salo has been leading has been done with some amount of communication with Dave, and I think we can say that we're not working at cross-purposes. I expect SquishyMedia will continue in a similar vein, as OpenNeuro will benefit from both a more community-maintainable validator and improved querying enabled by a rigorous data model.

If I'm misinterpreting your post, can you clarify your suggestion?

Best,
Chris


tibor...@gmail.com

unread,
May 21, 2021, 8:40:33 AMMay 21
to bids-di...@googlegroups.com

Hi all,

 

I think answering these questions can be largely based on our assumptions on what and how SquishyMedia would work. I think a data model should be ingrained into the validator; however, (1) if the validator is written in a way which allows generalisation across data models, then I agree that these two can be developed in parallel. On the other hand, (2) if the validator is specialized to a particular (say, current) data model, then any future development on the data model would require rewriting of the validator.

 

Also, even if the validator is flexible (case 1), its development cannot be agnostic to some generic concept(s) of the data model (e.g. format, complexity); therefore, some input from the data model development is, indeed, required to the development of the validator. The question here is whether the data model development is already at the level when it can provide these inputs.

 

Kind regards,

Tibor

 

Auer, Tibor M.D. Ph.D.

Research Fellow

School of Psychology, Faculty of Health and Medical Sciences

University of Surrey, Guildford GU2 7XH

T.A...@surrey.ac.uk

@TiborAuer

Paola Di Maio

unread,
May 22, 2021, 12:55:22 AMMay 22
to bids-di...@googlegroups.com
Hi Chris
is there a web page that summarises who is doing what/where?  
being the development of the BIDS specification distributed its entirely possible to put the cart before the ox
I am referring to some/several  discussions/efforts to revise the BIDS specification
(have seen a few but here is an example

The validator should be compiled after the specification has been updated
not before,   Dont think there is any cross purpose, but more like a workflow issue and a scoping
issue
 otherwise although it may be useful to parse a specific instance of BIDS 
may need to be done again and again


PDM

Paola Di Maio

unread,
May 22, 2021, 12:57:18 AMMay 22
to bids-di...@googlegroups.com
Yes Tibor, thanks for explaining this

Reply all
Reply to author
Forward
0 new messages