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Re: Advice for applying Bioschemas to BBMRI Directory

From: jerven Bolleman <jerven.bolleman@sib.swiss>
Date: Tue, 6 Apr 2021 15:37:58 +0200
To: public-bioschemas@w3.org
Message-ID: <e7f3c906-1b14-42ff-9ce7-bba7f1c2fb83@sib.swiss>
Hi Vittorio,

Take this as suggestions, as I do expect that some people would model 
things differently than I would here.


You reuse a number of ontologies, where the url is the ID.
e.g.
{
	"@type": "CategoryCode",
         "codeValue": "OBI_0000922",
         "name": "frozen specimen",
         "url": "http://purl.obolibrary.org/obo/OBI_0000922",
->>>>   "@id": "http://purl.obolibrary.org/obo/OBI_0000922"
}


You are inconsistent with ICD 10 references

   "value": "urn:miriam:icd:C34.9",
in one place.
    "http://identifiers.org/icd/C34.9"
in another
should really be
    "https://id.who.int/icd/release/10/C34.9"

Which is not free, but is the IRI of the thing in the official
ICD repositories. In any case pick one and be consistent about it.
If you want to use identifiers.org use it for everything, not 
identifiers.org for some things and obolibrary for other things.
An option here is

{
   "@id" : "https://id.who.int/icd/release/10/C34.9",
   "url" : "https://icd.who.int/browse10/2010/en#/C34.9"
}

My personal opinion here is to also stop with schema.org and start with
domain specific ontologies. For example the schema:diagnosis property 
looks enticing but would be wrong to use. I also don't think the 
schema:variableMeasured is correct.

The diagnosis is not a measured variable of the dataset but of the 
original patient around the time the tissue sample was taken. If I was
staying within (bio)schema.org I would use schema:additionalProperty 
even if it is not preferred, because being specialist I don't think 
there is a good generic solution.

To be honest adding a bit of context so that you can use specialist 
ontologies seems better to me. Something in the spirit of this "wrong"
modeling.


"@context": [ "https://schema.org",
                { "diagnosis" : { "@id": 
"http://purl.obolibrary.org/obo/OGMS_0000073"},
                 "icd10":"https://id.who.int/icd/release/10/"
                }
	],
   "@type": "Dataset",
   "@id": "bbmri-eric:ID:UK_GBR-1-56:collection:162-526",
->>>>  "diagnosis": "icd10:C34.9",
    "name": "Neoplastic pathways",

Diagnosis is a owl:class abused as a property here, which is not "good"
but I unfortunately don't have time to look for an existing property 
which accurately expresses your needs.


Regards and good luck,

Jerven


On 06/04/2021 14:33, Vittorio Meloni wrote:
> Hi Jerven,
> yes of course. You can find attached an example of a Biobank and a 
> Collection one.
> 
> Thanks,
> Vittorio
> 
> Il giorno mar 6 apr 2021 alle ore 14:12 jerven Bolleman 
> <jerven.bolleman@sib.swiss> ha scritto:
> 
>     Hi Petr, Vittorio,
> 
>     Would you mind sharing some markup/json-ld so that we have a concrete
>     example to work with. For me at least a concrete example helps a lot.
> 
>     Regards,
>     Jerven
> 
>     On 06/04/2021 14:07, Petr Holub wrote:
>      > Dear all,
>      >
>      > could you please review Vittorio's proposal below? We are
>     implementing
>      > the BioSchemas into production in the BBMRI-ERIC Directory and the
>      > initial mapping we have done almost 3 years back are no longer
>     usable -
>      > and thus Vittorio has created the proposal below and we would
>     like to
>      > confirm it before continuing.
>      >
>      > Thanks,
>      > Petr
>      >
>      >
>      >
>      > **Assoc. Prof. *RNDr. Petr Holub, Ph.D.
>      > *Senior IT/Data Protection Manager*
>      >
>      > BBMRI-ERIC*  | Neue Stiftingtalstrasse 2/B/6 |  8010 Graz | AUSTRIA
>      > Phone: +43 316 34 99 17-18  | Fax: +43 316 34 99 17-99 | Mobile:
>     +43 664
>      > 88 72 18 77
>      > Skype:holubp | petr.holub@bbmri-eric.eu
>     <mailto:petr.holub@bbmri-eric.eu>
>      > <mailto:petr.holub@bbmri-eric.eu
>     <mailto:petr.holub@bbmri-eric.eu>> | www.bbmri-eric.eu
>     <http://www.bbmri-eric.eu>
>      > <http://www.bbmri-eric.eu
>     <http://www.bbmri-eric.eu>><https://mail.acpcloud.de/owa/redir.aspx?C=tQtD-G9C_kuPP8hViFQ4hgNjuhtf_dEI0JIE-vC5gXhf36JcThZMI5N8J9ocveR1mgFita1orqo.&URL=http%3a%2f%2fwww.bbmri-eric.eu%2f
>     <https://mail.acpcloud.de/owa/redir.aspx?C=tQtD-G9C_kuPP8hViFQ4hgNjuhtf_dEI0JIE-vC5gXhf36JcThZMI5N8J9ocveR1mgFita1orqo.&URL=http%3a%2f%2fwww.bbmri-eric.eu%2f>>
>      >
>      >
>     ------------------------------------------------------------------------
>      > *From:* Vittorio Meloni <vittorio.meloni@crs4.it
>     <mailto:vittorio.meloni@crs4.it>>
>      > *Sent:* Tuesday, March 30, 2021 14:09
>      > *To:* public-bioschemas@w3.org <mailto:public-bioschemas@w3.org>
>     <public-bioschemas@w3.org <mailto:public-bioschemas@w3.org>>
>      > *Subject:* Advice for applying Bioschemas to BBMRI Directory
>      > Dear Bioschemas Members,
>      > I am Vittorio Meloni and I'm collaborating with BBMRI to add
>     Bioschemas
>      > into the Biobanks' Directory. In particular, I need to represent
>      > Biobanks and Collections concepts, which are compliant with the
>     MIABIS
>      > 2.0 model: the Biobank is the organization that stores samples
>     and data
>      > related to the samples while a Collection is the set of samples.
>      > According to these definitions, I mapped the Biobank to DataCatalog,
>      > using the "provider" attribute to describe the organization and the
>      > "dataset" attribute for the list of Collections, and the
>     Collection to a
>      > Dataset. Do you think this mapping would be correct?
>      > Another issue I have is how to add additional properties to a
>      > Collection: for example, how can I express that a Collection
>     collects
>      > materials as DNA? With the DataRecord I could use
>     additionalProperty,
>      > but it is Deprecated now. I've found the variableMeasured
>     property but
>      > I'm not sure it fits correctly. Do you think that's the right way
>     to go?
>      >
>      > Any suggestion or comment would be appreciated.
>      > Thank you,
>      > Vittorio
>      >
>      > --
>      > Vittorio Meloni
>      > Data Intensive Computing - Digital Health Group
>      > CRS4 - Centro di Ricerche, Sviluppo e Studi Superiori della Sardegna
>      > POLARIS, Edificio 1, 09010 PULA (CA - Italy)
>      >
>      > Email: vittorio.meloni@crs4.it <mailto:vittorio.meloni@crs4.it>
>      > <https://webmail.crs4.it/imp/message.php?index=221#
>     <https://webmail.crs4.it/imp/message.php?index=221#>>
> 
>     -- 
> 
>              *Jerven Tjalling Bolleman*
>     Principal Software Developer
>     *SIB | Swiss Institute of Bioinformatics*
>     1, rue Michel Servet - CH 1211 Geneva 4 - Switzerland
>     t +41 22 379 58 85
>     Jerven.Bolleman@sib.swiss - www.sib.swiss
> 
> 
> 
> 
> -- 
> Vittorio Meloni
> Data Intensive Computing - Digital Health Group
> CRS4 - Centro di Ricerche, Sviluppo e Studi Superiori della Sardegna
> POLARIS, Edificio 1, 09010 PULA (CA - Italy)
> 
> Email: vittorio.meloni@crs4.it 
> <https://webmail.crs4.it/imp/message.php?index=221#>

-- 

	*Jerven Tjalling Bolleman*
Principal Software Developer
*SIB | Swiss Institute of Bioinformatics*
1, rue Michel Servet - CH 1211 Geneva 4 - Switzerland
t +41 22 379 58 85
Jerven.Bolleman@sib.swiss - www.sib.swiss
Received on Tuesday, 6 April 2021 13:38:17 UTC

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