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Re: Advice for applying Bioschemas to BBMRI Directory

From: jerven Bolleman <jerven.bolleman@sib.swiss>
Date: Wed, 7 Apr 2021 12:06:11 +0200
To: Vittorio Meloni <vittorio.meloni@crs4.it>
Cc: public-bioschemas@w3.org
Message-ID: <f351560e-a15c-5979-a85e-b09eb03b84af@sib.swiss>
Hi Vittorio,

additionalProperty is not deprecated at schema.org so valid to use I 
would think. Of course it trends towards making your sample a Product,
but somehow that seems reasonable enough to me. As in, I suspect your 
biobank offfers tissue samples to researchers to work with (if the right 
conditions are met)

Regards,
Jerven

On 07/04/2021 09:29, Vittorio Meloni wrote:
> Hi Jerven,
> thank you very much for the feedback and suggestions.
> The use of variableMeasured to express additional attributes not 
> provided by the model was actually one of the major doubts I had.
> I've adopted it because it is the only one I've found for Dataset in 
> Bioschema profile.
> I agree that additionalProperty seems to fit better but I've found it 
> only in the deprecated DataRecord type.
> I'll consider also the "specialist" way.
> 
> Thanks again,
> Vittorio
> 
> Il giorno mar 6 apr 2021 alle ore 15:39 jerven Bolleman 
> <jerven.bolleman@sib.swiss> ha scritto:
> 
>     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
>     <http://purl.obolibrary.org/obo/OBI_0000922>",
>     ->>>>   "@id": "http://purl.obolibrary.org/obo/OBI_0000922
>     <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
>     <http://identifiers.org/icd/C34.9>"
>     in another
>     should really be
>          "https://id.who.int/icd/release/10/C34.9
>     <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 <http://identifiers.org> use it
>     for everything, not
>     identifiers.org <http://identifiers.org> for some things and
>     obolibrary for other things.
>     An option here is
> 
>     {
>         "@id" : "https://id.who.int/icd/release/10/C34.9
>     <https://id.who.int/icd/release/10/C34.9>",
>         "url" : "https://icd.who.int/browse10/2010/en#/C34.9
>     <https://icd.who.int/browse10/2010/en#/C34.9>"
>     }
> 
>     My personal opinion here is to also stop with schema.org
>     <http://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 <http://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 <https://schema.org>",
>                      { "diagnosis" : { "@id":
>     "http://purl.obolibrary.org/obo/OGMS_0000073
>     <http://purl.obolibrary.org/obo/OGMS_0000073>"},
>                       "icd10":"https://id.who.int/icd/release/10/
>     <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>>
>      >      > <mailto: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>>
>      >      > <http://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>
>      >   
>       <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>
>      >     <mailto: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> <mailto:public-bioschemas@w3.org
>     <mailto:public-bioschemas@w3.org>>
>      >     <public-bioschemas@w3.org <mailto:public-bioschemas@w3.org>
>     <mailto: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> <mailto: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#>
>      >     <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 <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 Wednesday, 7 April 2021 10:06:32 UTC

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