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Re: [Urgent] Proposed changes to Bioschemas

From: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
Date: Thu, 1 Nov 2018 12:13:37 +0000
To: ljgarcia <ljgarcia@ebi.ac.uk>
CC: Tony Burdett <tburdett@ebi.ac.uk>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Message-ID: <949F6CF1-5C2A-49BC-8971-119EBA55C114@hw.ac.uk>
Tony, Melanie,

Thanks for doing the due diligence and going through the proposal with the Samples point of view.

As Leyla has said, we can add a Sample type at this point as well. This would be very much inline with this proposal. The one question is should Sample inherit from BioChemEntity or directly from Thing? I guess this would be very linked to whether BioChemEntity inherits from Thing or Intangible. If it inherits from the latter then it would be contradictory in my mind for a Sample to inherit from BioChemEnity, rather the Sample would be an instance of the BioChemEntity?

The only other issue is then the use of https://schema.org/dataset. The current definition of this property would mean that Sample is somehow a catalog. I think what you are trying to say is that this information about the specific sample is contained in a specific dataset. I think the https://schema.org/mainEntityOfPage property is a better fit based on the descriptions (although the human readable property name is not great).

I think all your other properties are already included in schema.org<http://schema.org>.

Would you like me to draft up the Sample type with its properties and add it to the existing document?

Alasdair


On 31 Oct 2018, at 18:30, ljgarcia <ljgarcia@ebi.ac.uk<mailto:ljgarcia@ebi.ac.uk>> wrote:

Hi Tony, Melanie, Alasdair,

If MarRef and others are already using Samples as a type, I think it is just a matter to formalize it, i.e., including Sample as a type as part of this proposal shared by Alasdair.

@Alasdair, you have gone through the profiles already. Do you think it is possible to add Sample on this first round? I am aware that your deadline was today but Sample profile is mature enough and in use so nothing should changed when promoted to type, although new things could be added if needed.

Gene and Protein had been discussed by the community but none of them was being used already, there is some room for more changes on those and that has been seen on the discussions. But with Sample, everything that is already in place should be kept.

Any thoughts?

Regards,





On 2018-10-31 17:54, Tony Burdett wrote:
Hi Alasdair,
On 31/10/2018 14:12, Gray, Alasdair J G wrote:
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.
Melanie is doing a more detailed analysis now and commenting on the
proposal document. The existing Sample deployments require some
mechanism to identify those BioChemEntities that are samples (whether
this is via a property describing the type as an ontology URI or
having a dedicated Sample type doesn't really matter, but the MarRef
implementation assumes Sample as a new type) and the ability to link
from PropertyValue to CategoryCode. We've built implementations on the
assumption these will form part of the proposal and I think it would
be good to keep these in order to send the right message to those
early adopters who are using bioschemas markup for something other
than search indexing.
Thanks,
Tony

--
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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Received on Thursday, 1 November 2018 12:14:07 UTC

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