Re: Revising the Bioschemas Profile Development Process

Sorry, managed to send the last email before I’d finished typing (the joys of working with an injured finger that is preventing my from typing properly).

The steering council believe that the DDE provides a significant improvement over our current approach, and we’ll now be taking the steps to move our profile development over to using DDE. We are aware that there are some aspects that may not be possible in the short term but hope that additional features will be added to the DDE as we go forward. Overall, this is a great opportunity for Bioschemas and the DDE team.

Before we can move over, we need to put the following in place:

  *   Tutorial on how to edit an existing profile
  *   Tutorial on how to create a new profile
  *   Develop a script to convert the DDE output into a form that can be published on a GitHub pages hosted website
  *   Setup GitHub actions to automate the process of publishing new profile revisions on the website

We hope that we can complete this process in the first quarter of 2022.

Best regards

Alasdair

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

Email: A.J.G.Gray@hw.ac.uk<mailto:A.J.G.Gray@hw.ac.uk>
Web: http://www.macs.hw.ac.uk/~ajg33
ORCID: http://orcid.org/0000-0002-5711-4872
Office: Earl Mountbatten Building 1.39
Twitter: @gray_alasdair


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From: Gray, Alasdair <A.J.G.Gray@hw.ac.uk>
Date: Friday, 10 December 2021 at 09:50
To: public-bioschemas@w3.org <public-bioschemas@w3.org>
Subject: Re: Revising the Bioschemas Profile Development Process
Hi All,

Just to let you know that the Steering Council met yesterday afternoon and discussed the pros and cons of moving to using the DDE as the profile editing environment. We believe

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

Email: A.J.G.Gray@hw.ac.uk<mailto:A.J.G.Gray@hw.ac.uk>
Web: http://www.macs.hw.ac.uk/~ajg33
ORCID: http://orcid.org/0000-0002-5711-4872
Office: Earl Mountbatten Building 1.39
Twitter: @gray_alasdair


Heriot-Watt is a global University, as a result my working hours may not be your working hours. Do not feel pressure to reply to this email outside your working hours.


To arrange a meeting: https://outlook.office365.com/owa/calendar/AlasdairGray@heriotwatt.onmicrosoft.com/bookings/

From: Gray, Alasdair <A.J.G.Gray@hw.ac.uk>
Date: Wednesday, 8 December 2021 at 11:31
To: public-bioschemas@w3.org <public-bioschemas@w3.org>
Subject: Re: Revising the Bioschemas Profile Development Process
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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

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

Email: A.J.G.Gray@hw.ac.uk<mailto:A.J.G.Gray@hw.ac.uk>
Web: http://www.macs.hw.ac.uk/~ajg33
ORCID: http://orcid.org/0000-0002-5711-4872
Office: Earl Mountbatten Building 1.39
Twitter: @gray_alasdair


Heriot-Watt is a global University, as a result my working hours may not be your working hours. Do not feel pressure to reply to this email outside your working hours.


To arrange a meeting: https://outlook.office365.com/owa/calendar/AlasdairGray@heriotwatt.onmicrosoft.com/bookings/

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.

Marco.

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.
https://docs.google.com/presentation/d/1pbpgovqiTUe9fwkJchL3SJ6txm6O7QHUTuc_0k-iZxY/edit#slide=id.gfa7382eed9_0_138

________________________________

Marco Brandizi <marco.brandizi@gmail.com<mailto:marco.brandizi@gmail.com>>
http://www.marcobrandizi.info

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