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Re: Revising the Bioschemas Profile Development Process

From: Gray, Alasdair <A.J.G.Gray@hw.ac.uk>
Date: Wed, 8 Dec 2021 11:30:14 +0000
To: "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Message-ID: <LNXP265MB1068523FE083EA51E53C86B0B66F9@LNXP265MB1068.GBRP265.PROD.OUTLOOK.COM>
Hi Marco,

Thanks for the input into this discussion.

With our current approach, it is not practical to have people edit the source code directly since the GSheets are seen as the normative form with others being generated from it, i.e. if edits are made to the webpage version then these have to be transcribed back to the GSheets.

While we are trying to continue support for a UI editing approach by adopting DDE, it would also make it feasible for others to directly edit the JSON-LD files that contain the JSON-Schema. However, this would require checks that the resulting file conforms to the expected structure so that it can still be rendered and edited in the DDE.

With the proposed DDE approach, the JSON-LD file with the JSON-Schema contained would be the normative form of the profile and these would be hosted on GitHub for others to exploit.

Best regards


Alasdair J G Gray
Associate Professor in Computer Science,
School of Mathematical and Computer Sciences
Heriot-Watt University, Edinburgh, UK.

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From: Marco Brandizi <marco.brandizi@gmail.com>
Date: Tuesday, 23 November 2021 at 23:07
To: public-bioschemas@w3.org <public-bioschemas@w3.org>
Subject: Re: Revising the Bioschemas Profile Development Process
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Hi Alasdair,

I haven't clear if it will also be possible to propose new profiles or changes to existing profiles by sending in source code, in formats like JSON-Schema or SHACL, using tools like github pull requests. I think the same approach would also be important to work on new types or changes to them.

While I understand that certain users prefer graphical UIs, there are other kind of users (ie, geeks), who are more comfortable with code and plain text files. Moreover, such machine-readable specifications are useful for a number of other applications (eg, validating local datasets, building local UIs, developing new profiles/types while modelling new data sets).

Of course, I'm not thinking of this as an alternative to tools like the DDE (I might end up using that too), but of having both options, with the ability to export JSON-Schema or alike from a tool like the DDE.


On 23/11/2021 13:40, Gray, Alasdair wrote:

We believe that the Data Discovery Engine<https://discovery.biothings.io/view/bioschemas/> (DDE) supports most of what we want to achieve (the whole process is outlined at the end of this email). During the recent BioHackathon we have been exploring and testing the functionality offered by DDE, and identifying what processes would be needed to convert the DDE representation to the website, which we believe can be automated with GitHub actions. This slide shows some screenshots of where we have got to.


Marco Brandizi <marco.brandizi@gmail.com<mailto:marco.brandizi@gmail.com>>


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Received on Wednesday, 8 December 2021 11:30:33 UTC

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