W3C home > Mailing lists > Public > public-bioschemas@w3.org > October 2017

Re: New property added to BioChemEntity

From: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
Date: Wed, 25 Oct 2017 13:41:15 +0000
To: Leyla Garcia <ljgarcia@ebi.ac.uk>
CC: Justin Clark-Casey <justinccdev@gmail.com>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Message-ID: <A677AE60-89A9-41EB-B20A-C87ACE964B3F@hw.ac.uk>
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.


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


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?


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?



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
ORCID: http://orcid.org/0000-0002-5711-4872
Office: Earl Mountbatten Building 1.39
Twitter: @gray_alasdair


Heriot-Watt University is The Times & The Sunday Times International University of the Year 2018

Founded in 1821, Heriot-Watt is a leader in ideas and solutions. With campuses and students across the entire globe we span the world, delivering innovation and educational excellence in business, engineering, design and the physical, social and life sciences.

This email is generated from the Heriot-Watt University Group, which includes:

  1.  Heriot-Watt University, a Scottish charity registered under number SC000278
  2.  Edinburgh Business School a Charity Registered in Scotland, SC026900. Edinburgh Business School is a company limited by guarantee, registered in Scotland with registered number SC173556 and registered office at Heriot-Watt University Finance Office, Riccarton, Currie, Midlothian, EH14 4AS
  3.  Heriot- Watt Services Limited (Oriam), Scotland's national performance centre for sport. Heriot-Watt Services Limited is a private limited company registered is Scotland with registered number SC271030 and registered office at Research & Enterprise Services Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS.

The contents (including any attachments) are confidential. If you are not the intended recipient of this e-mail, any disclosure, copying, distribution or use of its contents is strictly prohibited, and you should please notify the sender immediately and then delete it (including any attachments) from your system.
Received on Wednesday, 25 October 2017 13:41:52 UTC

This archive was generated by hypermail 2.4.0 : Friday, 17 January 2020 19:07:59 UTC