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

Re: Enumerations and inference rules

From: J. Clark-Casey <jc955@cam.ac.uk>
Date: Wed, 14 Jun 2017 12:05:28 +0100
To: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
Cc: public-bioschemas@w3.org
Message-ID: <fafa7c7c0e93ec4aa8d8a3efddb66bd1@cam.ac.uk>
I'm surprised that isRelatedTo doesn't have Thing type, as it seems a 
very generic relation.  Otherwise schema.org could forever be adding 
more type choices, and BiologicalEntity seems even more specific than 
Product or Service.

I'm also surprised that isRelatedTo isn't a Thing property.

-- Justin

On 2017-06-08 16:29, Gray, Alasdair J G wrote:
> Hi Leyla,
> 
> With regard to the domain and range of schema:isRelatedTo, I think
> that we would be able to request an extension to the schema.org [6]
> definition so that BiologicalEntity was included.
> 
> With regard to inferencing, schema.org [6] tends not to enforce types
> or perform inferencing the way that OWL ontologies are typically used.
> This is due to the idea that these will be used loosely on the Web in
> general and would not be enforceable. However, in the bioschemas
> community we are planning to enforce typing and cardinality with our
> validation of resources so we would want to take more care.
> 
> Alasdair
> 
>> On 29 May 2017, at 13:32, Rodrigo Lopez <rls@ebi.ac.uk> wrote:
>> 
>> Hi,
>> 
>> IMHO: This depends largely on how inference is determined. In the
>> case of ProteinEntity the 'thing' can be determined by a protein
>> similarity search, such that 'thing' is related to other 'things'
>> (e.g. ProteinEntities), because their sequences share a certain
>> level of similarity or homology. This applies to 'things' within
>> datasets such as sequence databases (e.g. UniProtKB, PDBe sequences,
>> etc.). I also think that in this case, this is extends to Product as
>> per products in a dataset.
>> 
>> On the other hand, the 'Service' perspective can also be useful, in
>> that knowledge of the methods (the services) required/used to
>> determine similarity is taken into consideration. This applies to
>> different methods of determining sequence similarity and would apply
>> and extend to 'services' such as blast, fasta, HHMER, etc.
>> 
>> My two cents.
>> 
>> Kind regards,
>> 
>> R:)
>> 
>> On 25/05/2017 09:41, ljgarcia wrote:
>> 
>> -------- Original Message --------
>> Subject: Re: Enumerations
>> Date: 2017-05-24 17:52
>> From: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
>> To: ljgarcia <ljgarcia@ebi.ac.uk>
>> 
>> Hi Leyla
>> 
>> Could you resend this email as a question to the
>> public-bioschemas@w3.org list?
>> It would be good to have a record of these discussions.
>> 
>> Alasdair
>> 
>> On 24 May 2017, at 16:57, ljgarcia <ljgarcia@ebi.ac.uk> wrote:
>> 
>> Hi Alasdair,
>> 
>> Could we ask about inference rules as well?
>> 
>> For instance, we have the property isRelatedTo
>> (http://schema.org/isRelatedTo [1]) that is used in Product and
>> Service
>> and expects an object with type Product or Service. If I use the
>> same
>> property to say ProteinEntity isRelatedTo Thing, will it be
>> inferred
>> that ProteinEntity and Thing extend from either a Product or a
>> Service? Or simply isRelatedTo will be then used in Product,
>> Service
>> and ProteinEntity expecting an object with type Thing?
>> 
>> Also, we have the property dataset (http://schema.org/dataset [2]).
>> Would
>> it be right to use this same property in ProteinEntity - dataset -
>> Dataset or URL? Or because the way it is currently defined it can
>> only
>> take objects belonging to Dataset?
>> 
>> These questions together with some more documentation about
>> Ennumerations could be solved by email, so we save time tomorrow
>> for
>> discussing (live) other things.
>> 
>> Regards,
>> 
>> On 2017-05-24 13:06, Gray, Alasdair J G wrote:
>> Hi
>> On 4 May 2017, at 17:40, ljgarcia <ljgarcia@ebi.ac.uk> wrote:
>> Hi,
>> We need to use an enumeration
>> (http://health-lifesci.schema.org/Enumeration [3]) but have not
>> find
>> much more information about how to model this. any suggestions?
>> Sorry, I have no direct experience with it. Perhaps we can discuss
>> today or tomorrow.
>> Alasdair
>> 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 [4]
>> ORCID: http://orcid.org/0000-0002-5711-4872 [5]
>> Office: Earl Mountbatten Building 1.39
>> Twitter: @gray_alasdair
>> 
>> 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 [4]
>> ORCID: http://orcid.org/0000-0002-5711-4872 [5]
>> Office: Earl Mountbatten Building 1.39
>> Twitter: @gray_alasdair
> 
>  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 [4]
>  ORCID: http://orcid.org/0000-0002-5711-4872 [5]
>  Office: Earl Mountbatten Building 1.39
>  Twitter: @gray_alasdair
> 
>  Untitled Document
> 
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> Links:
> ------
> [1] http://schema.org/isRelatedTo
> [2] http://schema.org/dataset
> [3] http://health-lifesci.schema.org/Enumeration
> [4] http://www.macs.hw.ac.uk/~ajg33
> [5] http://orcid.org/0000-0002-5711-4872
> [6] http://schema.org
Received on Wednesday, 14 June 2017 11:06:00 UTC

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