Re: [Urgent] Proposed changes to Bioschemas

Tony,

On 31 Oct 2018, at 13:37, Tony Burdett <tburdett@ebi.ac.uk<mailto:tburdett@ebi.ac.uk>> wrote:

First - I'm totally supportive of the drive to propose a limited number of entities, I think this is a great idea, it seems highly pragmatic and well aligned with the original vision of the Bioschemas project.

Thanks for your response and generally being supportive of the approach.

But I do have some concerns about the process used to decide which new types should be put forward. What was the rationale for choosing this particular set of entities? Everyone involved in the Bioschemas efforts have spent quite a long period of time collecting detailed usecase and building or designing implementations that deliver on them. This proposal seems to have bypassed some of that work and with a very short time frame for comment. How did you evaluate this set of entities against the existing usecases and current implementations?

You are right to pull us up on this. Unfortunately time did not permit a wide discussion of the community to move this forward. In just over a week from now we will be at the Biohackathon with a lot of representatives from the ELIXIR Core Data Resources (CDRs) aiming to develop markup for their resources. The particular types (Protein and Gene) were chosen as they cover the majority of the CDRs. Both had reasonably well developed proposals which have been actively discussed in GitHub issues recently. It was these discussions that brought this to a head. Chemistry will be developed during the hackathon; at present the profile is just a shell.

Taxon ended up being prioritised since both Gene and Protein need it to be present. There was already a reasonably developed proposal so this was moved forward.


Speaking for the samples group, I don't think everyone involved has had time to evaluate the impact of this proposal on the samples driving usecases, including the MarRef deployment and Biobanks exchange work. At first reading I think this will make it harder to demonstrate utility for these deployments. If the samples usecases were deprioritized in favour of other more compelling examples, that's reasonable, but the proposal document doesn't indicate how this was determined and I'd like to have a chance to review the results of that decision-making process.

Sample was not prioritised at this point as I felt that we had a strong working example of this being used in live deployment based on the BioChemEntity, i.e. Sample has not been deprioritised. I do not believe that the proposal would affect Sample profile or the deployments, but please correct me if I am wrong. My intention had been to follow up with the Sample group, but time has not permitted this to happen. We are more than happy to have discussions on whether there is a need for a Sample type.

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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