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Re: Why is PhysicalThing.additionalType recommended rather than mandatory

From: Dan Brickley <danbri@danbri.org>
Date: Tue, 19 Sep 2017 16:11:58 +0100
Message-ID: <CAFfrAFpeTgTfMqf0UCWd2-L=wiHN=Grjb-YhU7DWQTViQTwgRA@mail.gmail.com>
To: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
Cc: Michel Dumontier <michel.dumontier@stanford.edu>, Leyla Garcia <ljgarcia@ebi.ac.uk>, Justin Clark-Casey <justinccdev@gmail.com>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
On 19 September 2017 at 16:07, Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>

> Perhaps we should have a separation between the proposal of new types and
> their usage for certain resources.

Yup! To be clear, Schema.org definitions aren't going to say anything about
"mandatory", but we are interested in collecting pointers to
application-specific profiles that say "in such and such a context, the
following data shape is needed to achieve [some outcome]". If you can write
those down in Shex or SHACL format, so much the better :)


> It is clear that we need a new type for BiologicalEntity, it is not clear
> to me that Proteins, Genes, and Samples all need to have the same
> mandatory, recommended, and optional set of properties. Perhaps for new
> types, we should stick to Schema.org <http://schema.org> style
> descriptions and then only introduce MG, CD, and CV in usage profiles
> (specifications) over these types.
> Alasdair
> On 19 Sep 2017, at 15:55, Michel Dumontier <michel.dumontier@stanford.edu>
> wrote:
> I also think many types should be allowed.  whether it should be mandatory
> depends on whether it must indicate an exact match, or it could link to a
> more general type where the exact concept is lacking.
> m.
> On Tue, Sep 19, 2017 at 2:36 PM, Leyla Garcia <ljgarcia@ebi.ac.uk> wrote:
>> On 19/09/2017 12:35, Justin Clark-Casey wrote:
>>> I see that PhysicalThing.additionalType is shown as recommended [1]
>>> whereas BiologicalEntity.biologicalType [2] was mandatory.  What is the
>>> reason for this change?  I thought that this was one for the most critical
>>> properties (since most entity types will not have their own Bioschemas
>>> subclass).
>>> [1] http://bioschemas.org/bsc_specs/PhysicalEntity/specification/
>>> [2] https://docs.google.com/document/d/1XASuESIHU3bi1aXMxQS5-rCO
>>> QX0ugjMNkh68VF4co4Q
>>> -- Justin
>> I might be wrong but I think the specifications are still work in
>> progress. I am taking your comment as a suggestion for PhysicalEntity.
>> Still, we should take a second look to M/R/O for PhysicalEntity and Record
>> and get to some agreements as a group. I think the point you raised makes
>> sense, additionalType should be mandatory (and it has been modified as
>> such). However, I am wondering if anyone has a case where the biological
>> type cannot be provided. Also, is ONE enough? Should be allowed MANY for
>> that field? And, if we allow many, will sameAs be assumed by applications?
>> 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
> 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 Tuesday, 19 September 2017 15:12:24 UTC

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