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Re: DefinedTerm vs CategoryCode

From: LJ Garcia Castro <ljgarcia@ebi.ac.uk>
Date: Thu, 5 Jul 2018 09:32:38 +0100
To: Melanie Courtot <mcourtot@ebi.ac.uk>
Cc: Simon Jupp <jupp@ebi.ac.uk>, Melanie Courtot <courtot@ebi.ac.uk>, public-bioschemas@w3.org, Ricardo Arcila <arcila@ebi.ac.uk>
Message-ID: <1daecfe9-d6df-f0b4-ed01-f850a560ceae@ebi.ac.uk>
Hi Melanie,

I see now how this would not be the best approach for you.

Regarding the crawler, talk as well with Ricardo. I think he has already 
crawled BioSamples.

Regards,


On 05/07/2018 08:59, Melanie Courtot wrote:
> 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.
>
> Cheers,
> Melanie
>
>
>
>
>> 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 08:33:02 UTC

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