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Re: New property added to BioChemEntity

From: Leyla Garcia <ljgarcia@ebi.ac.uk>
Date: Wed, 25 Oct 2017 15:20:41 +0100
To: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
Cc: Justin Clark-Casey <justinccdev@gmail.com>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Message-ID: <5b528830-0457-3f2b-4d5f-fe648d023d6a@ebi.ac.uk>
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: MinimumCardinality: ONEBioschemas 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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Received on Wednesday, 25 October 2017 14:21:10 UTC

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