Re: Protein representation with and without BioChemEntity

Hi Alasdair,

Some biologists speak in terms of gene products, for example, describing
FMO3 (ncbigene:2328) as catalyzing the conversion of nicotine
to nicotine-N-oxide <https://www.wikipathways.org/index.php/Pathway:WP1600>,
even though it's actually the FMO3 enzyme, not the gene, that does the
catalysis.

Could I describe this using the scheme you're proposing?

Thanks,
Anders Riutta

On Wed, Nov 1, 2017 at 8:56 AM, Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
wrote:

> 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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