- From: Vittorio Meloni <vittorio.meloni@crs4.it>
- Date: Thu, 8 Apr 2021 10:02:49 +0200
- To: jerven Bolleman <jerven.bolleman@sib.swiss>
- Cc: public-bioschemas@w3.org
- Message-ID: <CAFqAGsxnaqgnXGU_Nyihm4zuzYMxm0_zjdYka2BDxEpdE-+GiQ@mail.gmail.com>
Ok, I haven't considered it because it was an attribute of the DataRecord
I'll consider both the additionalProperty and the specialized context
solutions and try to decide which one to use
Thanks again,
Vittorio
Il giorno mer 7 apr 2021 alle ore 12:06 jerven Bolleman
<jerven.bolleman@sib.swiss> ha scritto:
> 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
>
>
--
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#>
Received on Thursday, 8 April 2021 08:03:21 UTC