Re: New property added to BioChemEntity

Hi

I still believe that BioChemEntity is a type only.

As you will have seen in the other email thread about the protein example using BioChemEntity we can use multiple types in the type statement. For something that we have a Bioschemas Profile for, the expected URI will be stated, i.e. SIO:protein for the protein profile. For something that we don’t have a profile for, then none of our tooling will have dedicated support for it. They could make a best effort, but it would be similar to what the structured data testing tool does when we introduce BioChemEnity

However, when we identify that we want to represent a new type, we can start the process of creating a new profile. The first thing to do here would be to identify the use cases that we want to support and then identifying the terms to use.

Best regards

Alasdair


On 25 Oct 2017, at 15:20, Leyla Garcia <ljgarcia@ebi.ac.uk<mailto:ljgarcia@ebi.ac.uk>> wrote:

Hi Alasdair,

It is great news that some feedback from Dan is coming soon! I am so looking forward to it!

About BioChemEntity being a type and not a profile. If, as Justin pointed out, we are going to have BioChemEntity with no profile, I would say we need a BioChemEntity Profile similar to what we do with LabProtocol. However, I recognize that getting a profile for some BioChemEntity will be challenging so maybe having all optional for those not-yet-profiled entities is a good idea. I am happy if we go for all optional for BioChemEntity corresponding to no profile.

Regards,


On 25/10/2017 14:41, Gray, Alasdair J G wrote:
Hi Leyla

Sorry I’ve not had time to fully catch up with your proposal. I’ve been busy working on the data platform proposal.

One quick response to your first email is that BioChemEntity is a type not a profile. Therefore there is nothing that is mandatory.

Second, I’ve been chatting with Dan here at ISWC discussing how these things can be integrated into schema. I’ve got some feedback on our current proposal but need to write it up. I’ll send this in another email soon.

Alasdair

On 25 Oct 2017, at 15:32, Leyla Garcia <ljgarcia@ebi.ac.uk<mailto:ljgarcia@ebi.ac.uk>> wrote:

Hello,

There was a discussion last week about this new property, not many replies, no one objecting so I added it (and by doing that was hopping to get some more attention and more feedback). I guess at some point the reviewing committee will accept or reject, maybe based on what the community has said, still not sure about the process.

Why on top of AdditionalType? There are multiple ontologies describing what a protein/chemical/gene/etc. is. Usually groups will prefer to point to their own ontology.  Yes, we could have a list of all ontology terms allowed for, let's say, protein. That list will have to grow whenever a new ontology term gets in use. The one using it will have to inform some how, the profile responsible will have to double check and then add it, the validators and tools will need to know that that additionalType also refers to proteins. So having a simple label seems easier, I do not expect that many new profiles as ontology terms describing the same thing in slightly different ways. In a way, that label is the name of the profile if it were a proper type.

Mandatory or not, one or many, it all belongs to Bioschemas, so I would say that any BioChemEntity that does not have a profile, still should follow the minimums defined by Bioschemas. In that sense, if no specific profile available, "BioChemEntity" would be the profile to follow.

Any thoughts?

Regards,

On 25/10/2017 11:58, Justin Clark-Casey wrote:
Hello Leyla,

What about BioChemEntitys that do not yet have or may never have profiles? This is the generic case.

Why is this required on top of AdditionalType?

Regards,

Justin

On 25 Oct 2017 11:12, "Leyla Garcia" <ljgarcia@ebi.ac.uk<mailto:ljgarcia@ebi.ac.uk>> wrote:
Dear all,

A new property has been added to BioChemEntity. This property MUST contain the name of the profile so it will be easier for validators and tools to distinguished one profile from another.

property:  preferredLabel
expectedType:  Text
Description:  Indicates the preferred label to refer to a specific (sub)type of BioChemEntity Bioschemas description:  Profile name
Marginality:  Minimum Cardinality:  ONE Bioschemas description:  Bioschemas profiles Regards,


Alasdair J G Gray

Fellow of the Higher Education Academy
Assistant Professor in Computer Science,
School of Mathematical and Computer Sciences
(Athena SWAN Bronze Award)
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<http://www.macs.hw.ac.uk/%7Eajg33>
ORCID: http://orcid.org/0000-0002-5711-4872

Office: Earl Mountbatten Building 1.39
Twitter: @gray_alasdair

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Alasdair J G Gray

Fellow of the Higher Education Academy
Assistant Professor in Computer Science,
School of Mathematical and Computer Sciences
(Athena SWAN Bronze Award)
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