Re: Protein representation with a Bioschemas context ()

On 10 Nov 2017, at 13:28, Leyla Garcia <ljgarcia@ebi.ac.uk<mailto: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<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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