Re: Bioschemas Taxon profile specification

Hi,

We could consider using the defined terms, https://dataliberate.com/2018/06/18/schema-org-introduces-defined-terms/, to do that.

So have a protein be defined as 

           "@type": "DefinedTerm",
            "@id": "http://purl.obolibrary.org/obo/PR_000000001",
            "name": "Protein",
            "inDefinedTermSet": "http://bioschemas.org/terms",
            "description": "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.",
            "sameAs": "http://purl.obolibrary.org/obo/NCIT_C17021",
            "sameAs": "http://semanticscience.org/resource/SIO_010043"

(Using random examples of sameAs from https://www.ebi.ac.uk/ols/search?q=protein)

Cheers,
Melanie 


---
Melanie Courtot, PhD
EMBL-EBI
GA4GH/BioSamples project lead



> On 28 Jun 2018, at 15:18, ljgarcia <ljgarcia@ebi.ac.uk> wrote:
> 
> Hi,
> 
> I understood Franck's question in a different way.
> 
> Alasdair says
>> I also agree that a context file should be provided which has the
>> chosen types and terms in it, i.e. the context file would define
>> Protein to be the URI http://purl.obolibrary.org/obo/PR_000000001 <http://purl.obolibrary.org/obo/PR_000000001>.
> 
> I think what Franck is asking is how to choose http://purl.obolibrary.org/obo/PR_000000001 <http://purl.obolibrary.org/obo/PR_000000001> over other possible terms to define a Protein. For the taxon case, same as it happens with proteins, there are multiple possibilities. Franck, is this your question? If it is, I do not think there is any agreement on how to choose, other than going for well-known ontologies broadly accepted by the community of interest, even better if the term is mapped to other possible ones.
> 
> Regards,
> 
> On 2018-06-28 11:50, Gray, Alasdair J G wrote:
>>> On 27 Jun 2018, at 19:19, Justin Clark-Casey <justinccdev@gmail.com>
>>> wrote:
>>> I think we should have mandatory known @types and properties.  In
>>> my view, Bioschemas should be as easy as possible to write and
>>> consume.  Multiple options will increase cognitive load on writers
>>> (which one do I choose?  Why are these 2 examples using these
>>> different terms?) and open the door to greater inconsistency.
>>> Non-mandatory types will also raise the barriers for writing
>>> Bioschemas software that will have to be aware of equivalent
>>> mappings.
>> I completely agree that we should have a single approved type for
>> each profile, and likewise for each property a single chosen term.
>> This is the whole point of having the profiles.
>>> I would go one step further and say that Bioschemas should provide
>>> an http://bioschemas.org <http://bioschemas.org/> [1]context that will define types such as
>>> Taxon, rather than blessing particular ontology terms.
>> I also agree that a context file should be provided which has the
>> chosen types and terms in it, i.e. the context file would define
>> Protein to be the URI http://purl.obolibrary.org/obo/PR_000000001. To
>> be completely explicit, we would not be defining a type in the
>> bioschemas namespace, e.g. http://bioschemas.org/Protein.
>>> This context can also document equivalent terms in different
>>> ontologies.
>> I like the idea that this also contains mappings to the equivalent
>> terms in other ontologies.
>> Alasdair
>> 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
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