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

Re: Protein representation with a Bioschemas context ()

From: ljgarcia <ljgarcia@ebi.ac.uk>
Date: Fri, 10 Nov 2017 14:21:16 +0000
To: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
Cc: public-bioschemas@w3.org
Message-ID: <7dfa78cee70e5d4d50b2e0eebdb9f4c6@ebi.ac.uk>
Hi,

>> I thought we did not want to impose any IRI. Is there any reason why
>> we should?
> 
> But then we sacrifice the interoperability and understanding that we
> are striving for. If you look at the n-quads for the two examples
> (included at the end of this email) then you will see a different set
> of triples.

If there are mappings between the terms, that interoperability we want 
to achieve could still be achieved, could not it? With mappings, we 
still can transform any n-quads to the, let's say, canonical Bioschemas 
defined form. Would this not be a way? If a mapping cannot be found, 
then validation fails. Bioschemas should then use mapping tools and 
clearly state what the use mappings tool is.

Regards,

On 2017-11-10 14:07, Gray, Alasdair J G wrote:
>> On 10 Nov 2017, at 13:28, Leyla Garcia <ljgarcia@ebi.ac.uk> wrote:
>> I was under the same impression than Melanie. We agree on aliases
>> but providers can decide what is their preferred IRI for any of
>> them. A Bioschemas Protein context would just provide a default
>> context that can also be used as a template where IRIs (but not
>> aliases) can be modified. And of course, anyone could add more
>> aliases, Bioschemas will just not parse those outside the
>> default/template provided context.
>> 
>> I thought we did not want to impose any IRI. Is there any reason why
>> we should?
> 
> But then we sacrifice the interoperability and understanding that we
> are striving for. If you look at the n-quads for the two examples
> (included at the end of this email) then you will see a different set
> of triples. Aliases are only defined within the document. When you
> interpret them they give you different meanings. If we go down this
> route, we would need to make our tooling with knowledge of either all
> possible terms that will be used or mapping aware.
> 
> Alasdair
> 
> http://tinyurl.com/y9mu423y
> 
> <http://identifiers.org/ncbigene/25> <http://schema.org/name> "ABL1" .
> 
> <http://identifiers.org/ncbigene/25>
> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>
> <http://purl.obolibrary.org/obo/SO_0000704> .
> <http://identifiers.org/ncbigene/25>
> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>
> <http://schema.org/BioChemEntity> .
> <http://identifiers.org/uniprot/P00519>
> <http://schema.org/alternateName> "ABL" .
> <http://identifiers.org/uniprot/P00519>
> <http://schema.org/alternateName> "JTK7" .
> <http://identifiers.org/uniprot/P00519>
> <http://schema.org/description> "Non-receptor tyrosine-protein kinase
> that plays a role..." .
> <http://identifiers.org/uniprot/P00519> <http://schema.org/name>
> "ABL1" .
> <http://identifiers.org/uniprot/P00519>
> <http://semanticscience.org/resource/SIO_000001>
> <http://pfam.xfam.org/clan/CL0001> .
> <http://identifiers.org/uniprot/P00519>
> <http://semanticscience.org/resource/SIO_010081>
> <http://identifiers.org/ncbigene/25> .
> <http://identifiers.org/uniprot/P00519>
> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>
> <http://purl.obolibrary.org/obo/PR_000000001> .
> <http://identifiers.org/uniprot/P00519>
> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>
> <http://schema.org/BioChemEntity> .
> 
> http://tinyurl.com/yd5snze2
> 
> <http://identifiers.org/ncbigene/25> <http://schema.org/name> "ABL1" .
> 
> <http://identifiers.org/ncbigene/25>
> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>
> <http://purl.obolibrary.org/obo/OGI_0000004> .
> <http://identifiers.org/ncbigene/25>
> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>
> <http://schema.org/BioChemEntity> .
> <http://identifiers.org/uniprot/P00519>
> <http://purl.obolibrary.org/obo/RO_0002510>
> <http://identifiers.org/ncbigene/25> .
> <http://identifiers.org/uniprot/P00519>
> <http://schema.org/alternateName> "ABL" .
> <http://identifiers.org/uniprot/P00519>
> <http://schema.org/alternateName> "JTK7" .
> <http://identifiers.org/uniprot/P00519>
> <http://schema.org/description> "Non-receptor tyrosine-protein kinase
> that plays a role..." .
> <http://identifiers.org/uniprot/P00519> <http://schema.org/name>
> "ABL1" .
> <http://identifiers.org/uniprot/P00519>
> <http://semanticscience.org/resource/SIO_000001>
> <http://pfam.xfam.org/clan/CL0001> .
> <http://identifiers.org/uniprot/P00519>
> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>
> <http://purl.obolibrary.org/obo/NCIT_C17021> .
> <http://identifiers.org/uniprot/P00519>
> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>
> <http://schema.org/BioChemEntity> .
> 
> 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 Friday, 10 November 2017 14:21:47 UTC

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