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

Re: Protein representation with and without BioChemEntity

From: Justin Clark-Casey <jc955@cam.ac.uk>
Date: Tue, 7 Nov 2017 18:40:36 +0000
To: public-bioschemas@w3.org
Message-ID: <22399b33-fcf1-d88b-f00a-e077d695b8ad@cam.ac.uk>
Yes, my concern is that if we allow profiles to 'emerge' then we will see a proliferation of terms for the same property and types.  Which will make writing 
applications that integrate information over different databases (e.g. indexers) much harder and findability less comprehensive.

I would like to see an effort to create profiles and recommend terms before types are marked up, at least for types themselves and their mandatory properties. 
I also feel that pre-defining profiles will encourage adoption - if databases need to make fewer decisions then it will be less effort for them to do markup and 
assure them that bioschemas applications will recognize it.

-- Justin

On 06/11/17 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 <http://schema.org>, 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 <mailto: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" <http://semanticscience.org/resource/is-transcribed-from>and 
>> some use "http://purl.obolibrary.org/obo/RO_0002510 <http://purl.obolibrary.org/obo/RO_0002510>" (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 <mailto: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 Tuesday, 7 November 2017 18:41:06 UTC

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