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Re: Protein representation with and without BioChemEntity

From: ljgarcia <ljgarcia@ebi.ac.uk>
Date: Mon, 06 Nov 2017 10:35:00 +0000
To: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
Cc: Melanie Courtot <mcourtot@ebi.ac.uk>, Michel Dumontier <michel.dumontier@gmail.com>, public-bioschemas@w3.org
Message-ID: <8af81880422ec7113fa3f587f933623e@ebi.ac.uk>
Hi Alasdair, all,

If we are going to use a second context with aliases defined by 
Bioschemas profiles, would it not make sense for that second context be 
one provided by Bioschemas? If we have a Bioschemas context, that 
context will take care of define the aliases and collate the possible 
corresponding ontology terms. In this way we keep it simple for users 
and avoid multiple cases (camel and others), for minimum and recommended 
properties at least. A third party property would always be possible for 
optional properties, giving proority to any of those already coined in 

I am aware that this Bioschemas context would be somehow "defining our 
own terms" but it could simplify Bioschemas adoption by making it simple 
for data providers and consumers, and leaving the ontology mapping and 
collation to Bioschemas itself. This Bioschemas context would also go 
beyond the scope of a particular document.


On 2017-11-06 10:16, Gray, Alasdair J G wrote:
> Hi
> I appreciate the argument for not wanting to say that one ontology
> term is better than another, and also that we do not want to get into
> the area of defining our own terms.
> However, the benefit of Bioschemas comes from us agreeing as a
> community that we are going to use a particular subset of terms.
> Thus I believe that a profile should select a particular term to use.
> Where possible this should be from schema.org [3], but where such a
> term does not exist we should be selecting one, hopefully using a
> widely used term.
> With the Proteins profile we have selected several terms for use and
> stating these with additionalProperty.
> Of course, people are free to use equivalence of terms to convert
> these for ingestion, but I believed that we do need to keep the
> profiles simple to encourage take up.
> Alasdair
>> On 3 Nov 2017, at 13:43, Melanie Courtot <mcourtot@ebi.ac.uk> wrote:
>> +1
>> As said below, either existing mappings or some tools - OxO,
>> BioPortal or else; I didn't mean to add a constraint there.
>> For the relations at least users will need to make sure there is a
>> way to get to a "known" entity for validation. Do we know how that
>> could look like?
>> Let's say for example some datasets use
>> "http://semanticscience.org/resource/is-transcribed-from" [1] and
>> some use "http://purl.obolibrary.org/obo/RO_0002510 [2]" (and I'm
>> sure there are other relations than SIO and RO, using those as
>> working examples, not saying either SIO or RO should be required),
>> how would that work for the protein profile?
>  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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> [1] http://semanticscience.org/resource/is-transcribed-from
> [2] http://purl.obolibrary.org/obo/RO_0002510
> [3] http://schema.org
Received on Monday, 6 November 2017 10:35:28 UTC

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