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

Re: Protein representation with a Bioschemas context ()

From: Melanie Courtot <mcourtot@ebi.ac.uk>
Date: Mon, 13 Nov 2017 16:00:02 +0000
To: public-bioschemas@w3.org
Message-ID: <51154778-aadb-a920-0f13-b47652079bb4@ebi.ac.uk>
How does that currently work for schema.org, and could the same be used 
with Bioschemas?

Looking at Bioschemas as a markup language for existing data, we should 
aim for the lower adoption threshold possible, including unconstrained 
ontology terms, keeping required properties minimal, and not having an 
overly complicated structure with many new properties; I worry that 
otherwise people will just not use it.



On 10/11/2017 18:10, Justin Clark-Casey wrote:
> 'Data integration' is probably too strong a phrase for what I have in 
> mind.  I'm really thinking about discovery and how a search engine 
> (for example) may know/integrate that 2 different data sources are 
> talking about the same thing, so that the user gets the a 
> useful/linked set of search results.
>
> If a user wanted to find proteins transcribed by gene 'ABL1' 
> (following the examples), then I think it would be a lot simpler if 
> all the JSON-LD uses the term
> "http://semanticscience.org/resource/is-transcribed-from".  Otherwise 
> a search engine and maybe other applications would need to be aware of 
> all the mappings to other terms (I know OLS can/will provide this but 
> this will increase application complexity).
>
> I should be clear that this is thought programming on my part, I 
> haven't actually tried to implement anything yet :) It could well be 
> that there's a lot of value in sources using whatever terms are 
> optimal for them, and that costs of trying to co-ordinate IRIs are too 
> high.  But I do want to debate the possible tradeoffs.
>
> On Fri, Nov 10, 2017 at 5:39 PM, Melanie Courtot <mcourtot@ebi.ac.uk 
> <mailto:mcourtot@ebi.ac.uk>> wrote:
>
>     Is data integration really a use case for Bioschemas?  The stated
>     goal of Bioschemas is to extend schema.org <http://schema.org> to
>     provide markup for pages, and IIRC the use cases discussed at the
>     last meeting were about discovery and retrieval.
>
>     Cheers,
>     Melanie
>
>
>
>     On 10/11/2017 16:30, Justin Clark-Casey wrote:
>
>
>
>         On 10/11/17 14:21, ljgarcia wrote:
>
>             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.
>
>
>         If consuming applications have to use term mappings then this
>         will make them much harder to write, and in some cases might
>         make it impossible to integrate some information.  This might
>         only be a problem for code that is trying to integrate data
>         across websites, but this is an important use case.
>
>         At least for mandatory properties and types, and major
>         profiles (gene, protein, etc.), I would like to see pre-agreed
>         IRIs, rather than free choice or emerging consensus.  In some
>         ways, I don't think this is so different from what we are
>         doing with DataCatalog, Sample, TrainingMaterial, etc.
>
>
>             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 <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://identifiers.org/ncbigene/25>>
>                 <http://schema.org/name> "ABL1" .
>
>                 <http://identifiers.org/ncbigene/25
>                 <http://identifiers.org/ncbigene/25>>
>                 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type
>                 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>>
>                 <http://purl.obolibrary.org/obo/SO_0000704
>                 <http://purl.obolibrary.org/obo/SO_0000704>> .
>                 <http://identifiers.org/ncbigene/25
>                 <http://identifiers.org/ncbigene/25>>
>                 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type
>                 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>>
>                 <http://schema.org/BioChemEntity
>                 <http://schema.org/BioChemEntity>> .
>                 <http://identifiers.org/uniprot/P00519
>                 <http://identifiers.org/uniprot/P00519>>
>                 <http://schema.org/alternateName
>                 <http://schema.org/alternateName>> "ABL" .
>                 <http://identifiers.org/uniprot/P00519
>                 <http://identifiers.org/uniprot/P00519>>
>                 <http://schema.org/alternateName
>                 <http://schema.org/alternateName>> "JTK7" .
>                 <http://identifiers.org/uniprot/P00519
>                 <http://identifiers.org/uniprot/P00519>>
>                 <http://schema.org/description> "Non-receptor
>                 tyrosine-protein kinase
>                 that plays a role..." .
>                 <http://identifiers.org/uniprot/P00519
>                 <http://identifiers.org/uniprot/P00519>>
>                 <http://schema.org/name>
>                 "ABL1" .
>                 <http://identifiers.org/uniprot/P00519
>                 <http://identifiers.org/uniprot/P00519>>
>                 <http://semanticscience.org/resource/SIO_000001
>                 <http://semanticscience.org/resource/SIO_000001>>
>                 <http://pfam.xfam.org/clan/CL0001
>                 <http://pfam.xfam.org/clan/CL0001>> .
>                 <http://identifiers.org/uniprot/P00519
>                 <http://identifiers.org/uniprot/P00519>>
>                 <http://semanticscience.org/resource/SIO_010081
>                 <http://semanticscience.org/resource/SIO_010081>>
>                 <http://identifiers.org/ncbigene/25
>                 <http://identifiers.org/ncbigene/25>> .
>                 <http://identifiers.org/uniprot/P00519
>                 <http://identifiers.org/uniprot/P00519>>
>                 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type
>                 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>>
>                 <http://purl.obolibrary.org/obo/PR_000000001
>                 <http://purl.obolibrary.org/obo/PR_000000001>> .
>                 <http://identifiers.org/uniprot/P00519
>                 <http://identifiers.org/uniprot/P00519>>
>                 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type
>                 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>>
>                 <http://schema.org/BioChemEntity
>                 <http://schema.org/BioChemEntity>> .
>
>                 http://tinyurl.com/yd5snze2
>
>                 <http://identifiers.org/ncbigene/25
>                 <http://identifiers.org/ncbigene/25>>
>                 <http://schema.org/name> "ABL1" .
>
>                 <http://identifiers.org/ncbigene/25
>                 <http://identifiers.org/ncbigene/25>>
>                 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type
>                 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>>
>                 <http://purl.obolibrary.org/obo/OGI_0000004
>                 <http://purl.obolibrary.org/obo/OGI_0000004>> .
>                 <http://identifiers.org/ncbigene/25
>                 <http://identifiers.org/ncbigene/25>>
>                 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type
>                 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>>
>                 <http://schema.org/BioChemEntity
>                 <http://schema.org/BioChemEntity>> .
>                 <http://identifiers.org/uniprot/P00519
>                 <http://identifiers.org/uniprot/P00519>>
>                 <http://purl.obolibrary.org/obo/RO_0002510
>                 <http://purl.obolibrary.org/obo/RO_0002510>>
>                 <http://identifiers.org/ncbigene/25
>                 <http://identifiers.org/ncbigene/25>> .
>                 <http://identifiers.org/uniprot/P00519
>                 <http://identifiers.org/uniprot/P00519>>
>                 <http://schema.org/alternateName
>                 <http://schema.org/alternateName>> "ABL" .
>                 <http://identifiers.org/uniprot/P00519
>                 <http://identifiers.org/uniprot/P00519>>
>                 <http://schema.org/alternateName
>                 <http://schema.org/alternateName>> "JTK7" .
>                 <http://identifiers.org/uniprot/P00519
>                 <http://identifiers.org/uniprot/P00519>>
>                 <http://schema.org/description> "Non-receptor
>                 tyrosine-protein kinase
>                 that plays a role..." .
>                 <http://identifiers.org/uniprot/P00519
>                 <http://identifiers.org/uniprot/P00519>>
>                 <http://schema.org/name>
>                 "ABL1" .
>                 <http://identifiers.org/uniprot/P00519
>                 <http://identifiers.org/uniprot/P00519>>
>                 <http://semanticscience.org/resource/SIO_000001
>                 <http://semanticscience.org/resource/SIO_000001>>
>                 <http://pfam.xfam.org/clan/CL0001
>                 <http://pfam.xfam.org/clan/CL0001>> .
>                 <http://identifiers.org/uniprot/P00519
>                 <http://identifiers.org/uniprot/P00519>>
>                 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type
>                 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>>
>                 <http://purl.obolibrary.org/obo/NCIT_C17021
>                 <http://purl.obolibrary.org/obo/NCIT_C17021>> .
>                 <http://identifiers.org/uniprot/P00519
>                 <http://identifiers.org/uniprot/P00519>>
>                 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type
>                 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type>>
>                 <http://schema.org/BioChemEntity
>                 <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
>                 <http://www.macs.hw.ac.uk/%7Eajg33>
>                 ORCID: http://orcid.org/0000-0002-5711-4872
>                 <http://orcid.org/0000-0002-5711-4872>
>                 Office: Earl Mountbatten Building 1.39
>                 Twitter: @gray_alasdair
>
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Received on Monday, 13 November 2017 16:00:30 UTC

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