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Re: Protein representation with and without BioChemEntity

From: Justin Clark-Casey <justinccdev@gmail.com>
Date: Wed, 1 Nov 2017 16:18:26 +0000
Message-ID: <CAME9NR_LxH5dwzoryH2NGvd3yV5KJTc+bG9jMVb1E5zcx38CEw@mail.gmail.com>
To: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
Cc: "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Direct term reuse sounds like a good choice to me, especially as

a) it's the mechanism that schema.org themselves have to add existing
ontology classes and terms to the structured data
b) will make applications much easier to write as they can use existing
general tooling
c) allows us to do everything we were doing with AdditionalProperty and
d) still allows us to define profiles without having to move everything
through schema.org

-- Justin

On Wed, Nov 1, 2017 at 3:56 PM, Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>

> Hi All,
> Apologies for the delay in sending this email. I have been working with
> Carole on submitting an Implementation Study proposal to the Data Platform
> for more work on Bioschemas.
> For representing a specific bioscience type, e.g. a protein, we currently
> have a proposal for using a generic wrapper approach that we then
> specialise, e.g. BioChemEntity specialised with a Protein profile.
> Protein profile
> http://bioschemas.org/specifications/Protein/specification/
> BioChemEntity type
> http://bioschemas.org/specifications/BioChemEntity/specification/
> To help understand the various advantages and disadvantages of this
> approach, Kenneth and I have drawn up an example of marking up a specific
> protein first using the current proposal and second  if we were to do the
> same with a specific ProteinEntity. Below are the examples and some
> analysis of them.
> *BioChemEntity Example*
> Minimum markup using BioChemEntity
> https://github.com/BioSchemas/specifications/blob/master/
> PhysicalEntity/examples/BioChemEntity-min.jsonld
> Minimum + Recommended markup using BioChemEntity
> https://github.com/BioSchemas/specifications/blob/master/
> PhysicalEntity/examples/BioChemEntity-min%2Brec.jsonld
> <https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntity-min+rec.jsonld>
> One thing to note is that the minimum + recommended markup is not an
> additive extension of the minimum markup. Due to the use of the
> AdditionalProperty relationship, you need to use an JSON array and add the
> properties from the recommended level within the existing array.
> An advantage of this approach is that it reuses terms from existing
> ontologies and we can represent types that do not currently exist in
> Schema.org <http://schema.org>, e.g. Genes, Chemicals, etc.
> *ProteinEntity example*
> Minimum markup using ProteinEntity
> https://github.com/BioSchemas/specifications/blob/master/
> PhysicalEntity/examples/ProteinEntity-min.jsonld
> Minimum + Recommended markup using ProteinEntity
> https://github.com/BioSchemas/specifications/blob/master/
> PhysicalEntity/examples/ProteinEntity-min%2Brec.jsonld
> <https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/ProteinEntity-min+rec.jsonld>
> While the markup in these examples using ProteinEntity is easier to
> interpret, the number of items that need to be changed to markup another
> protein is the same as in the BioChemEntity approach. The simplified markup
> should enable easier adoption, although we could help the current proposal
> of using BioChemEntity by using highlighting on the Bioschemas site to show
> which terms need to be changed.
> A major downside of this approach is that we would need to add all the
> types to Schema.org <http://schema.org> or host them at Bioschemas.org
> <http://bioschemas.org>. While these could be mapped to existing terms,
> we would be accused of duplicating existing ontology terms.
> *Direct term reuse example*
> Last week, I showed the above examples to Dan (we were at ISWC together).
> He pointed out that the additionalProperty relation was added to allow the
> use of property/value pairs where the properties do not exist in an
> ontology. We are in the situation where the properties we are using come
> from ontologies. Dan suggested that we just use them directly. Note that
> the example also exploits the fact that you can define multiple types.
> Minimum markup using BioChemEntity and term reuse
> https://github.com/BioSchemas/specifications/blob/master/
> PhysicalEntity/examples/BioChemEntityAlt-min.jsonld
> Minimum + Recommended markup using BioChemEntity and term reuse
> https://github.com/BioSchemas/specifications/blob/master/
> PhysicalEntity/examples/BioChemEntityAlt-min%2Brec.jsonld
> <https://github.com/BioSchemas/specifications/blob/master/PhysicalEntity/examples/BioChemEntityAlt-min+rec.jsonld>
> As you will see, this seems to have the advantages of both the above
> approaches. The markup is more straightforward than the additionalProperty
> approach, but exploits reusing existing domain ontologies. The tooling and
> exploitation will be much more straightforward.
> I invite you all to review and comment on these different examples. Do we
> believe that the BioChemEntity with term reuse (the third set of examples)
> is an appropriate path going forward?
> Best regards
> Alasdair
> PS Sorry for the long email
> 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 Wednesday, 1 November 2017 16:18:56 UTC

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