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Re: DefinedTerm vs CategoryCode

From: Melanie Courtot <mcourtot@ebi.ac.uk>
Date: Thu, 5 Jul 2018 08:59:28 +0100
Cc: Simon Jupp <jupp@ebi.ac.uk>, Melanie Courtot <courtot@ebi.ac.uk>, public-bioschemas@w3.org
Message-Id: <C393A442-4EE9-4017-A770-C8E06642AA99@ebi.ac.uk>
To: ljgarcia <ljgarcia@ebi.ac.uk>
HI Leyla,

Thanks for the note. I understand defined terms to be a mechanism to provide a finite list of terms to be used in our profiles - which is why I thought they’d be a good way to define “protein” “samples” “gene” etc - the 20 or so entities we are using throughout. I don’t think they’d be suitable for a list of unknown terms as we obviously wouldn’t want to have a dictionary of millions of terms (in addition to them already being hosted by OLS for example)

I would love to hear your thoughts if you can think of a way it could work better for the samples representation. We have deployed the bioschemas markup on the BioSamples samples, and are now adding a context to link the sample entity to the corresponding OBI term - similar to what was done for protein and PRO. It seems to be working fine at the moment.

We are about to try and crawl the resources and extract all ontology terms (which was one of our use cases) - @Justin we’ll try your crawler but this is an early notice that may come back with requests for help/modifications.


> On 4 Jul 2018, at 21:29, ljgarcia <ljgarcia@ebi.ac.uk> wrote:
> Hi Melanie, Simon, all,
> I think you are using CategoryCode in Samples to refer to ontology terms. Would it not be more appropriate to use DefinedTerm in that case? I am wondering about it, any thoughts? If Samples mark up is already in use and tools are working fine with CategoryCode, I guess it would be better to stick to it.
> Regards,
Received on Thursday, 5 July 2018 07:59:32 UTC

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