Re: Enumerations and inference rules

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<http://schema.org> definition so that BiologicalEntity was included.

With regard to inferencing, schema.org<http://schema.org> 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<mailto: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<mailto:A.J.G.Gray@hw.ac.uk>>
To: ljgarcia <ljgarcia@ebi.ac.uk<mailto:ljgarcia@ebi.ac.uk>>

Hi Leyla

Could you resend this email as a question to the
public-bioschemas@w3.org<mailto: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<mailto: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) 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). 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<mailto:ljgarcia@ebi.ac.uk>> wrote:
Hi,
We need to use an enumeration
(http://health-lifesci.schema.org/Enumeration) 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<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

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



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










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