- From: Franck Michel <fmichel@i3s.unice.fr>
- Date: Wed, 21 Dec 2022 17:21:09 +0100
- To: "LJ.Garcia" <lj.garcia.co@gmail.com>, "Garcia-Castro, Leyla Jael" <ljgarcia@zbmed.de>
- Cc: Ivan Micetic <ivan.micetic@unipd.it>, Bioschemas Steering Council <steering@bioschemas.org>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
- Message-ID: <5150946f-48c1-9f4a-5426-724014867e32@i3s.unice.fr>
Hi Leyla,
Yes indeed we have also linked to other portals using a schema:sameAs to
their webpage URLs.
So in my example, we have GBIF id as a schema:identifier and GBIF URL as
a schema:sameAs:
"@type": "Taxon",
"dct:conformsTo": { "@id":
"https://bioschemas.org/profiles/Taxon/0.7-DRAFT"
<https://bioschemas.org/profiles/Taxon/0.7-DRAFT> },
* "@id": "http://taxref.mnhn.fr/lod/taxon/60932"
<http://taxref.mnhn.fr/lod/taxon/60932>,*
"*identifier*": [{
"@type": "PropertyValue",
"name": "GBIF id",
"propertyID": "http://www.wikidata.org/prop/direct/P846"
<http://www.wikidata.org/prop/direct/P846>,
"value": "5220003"
}],
"sameAs": "https://www.gbif.org/species/5220003",
...
Coming back to my initial question, any recommendations wrt. the value
of the @id annotation?
I'm asking because it is part of the mandatory properties, and Ivan's
email was warning that "Non-compliant markup will result in your
resource being ignored by services such as Google’s Dataset Search,
ELIXIR endorsed services (TeSS, Bioschemas-live deploys) and OpenAIRE
Research Graph."
Regards,
Franck.
Le 20/12/2022 à 19:13, LJ.Garcia a écrit :
> Re-adding mailing list to the loop
>
> On Tue, Dec 20, 2022 at 7:10 PM Garcia-Castro, Leyla Jael
> <ljgarcia@zbmed.de> wrote:
>
> Hi Franck,
>
>
> One more comment. Will you also add the identifier URLs to the
> sameAs? I think it would be good to do so. Any thoughts?
>
>
> Kind regards,
>
>
> -----
>
> Dr. Leyla Jael Castro | ljgarcia@zbmed.de | @lj_garcia
> Semantic Retrieval team leader (part of the Knowledge Management
> group)
>
>
> ZB MED – Information Centre for Life Sciences | www.zbmed.de
> <https://www.zbmed.de/en/>
> Gleueler Straße 60. 50931 Cologne. Germany
>
>
> INFORMATION. KNOWLEDGE. LIFE.
> ------------------------------------------------------------------------
> *From:* LJ.Garcia <lj.garcia.co@gmail.com>
> *Sent:* Tuesday, December 13, 2022 8:32 PM
> *To:* Franck Michel
> *Cc:* Ivan Micetic; Bioschemas Steering Council;
> public-bioschemas@w3.org
> *Subject:* Re: Bioschemas profiles refresh: recommendations for
> the @id property?
> Hi Franck, all,
>
> It all looks good to me. Nice way to use the PropertyValue, I have
> not seen an example using propertyID. This usage reminds me of
> DefinedTerm but as DefinedTerm is not within the range of
> identifier, I would say the alternative with PropertyValue is
> quite good, I like it.
>
> Any other thoughts?
>
> Kind regards,
>
> On Tue, Dec 13, 2022 at 4:48 PM Franck Michel
> <fmichel@i3s.unice.fr> wrote:
>
> Hi Ivan and all,
>
> Ivan, following your email below, I'm having a look at the
> markup data we have on NMNH Paris's website, and I wonder what
> to do with the @id annotation.
>
> BSC's howto
> <https://bioschemas.org/tutorials/howto/howto_add_markup> says
> "@id: so it is clear what the identifier of the thing you are
> describing is". Yet figuring out the right id is not always
> obvious. Commonly, we deal with websites where people may not
> have come up with a URI uniquely identifying the resource that
> is described on a webpage, apart from the webpage URL itself.
> I'm considering using the URIs from TAXREF-LD which is the RDF
> knowledge graph representing the NMNH Paris's taxonomy.
>
> Besides, Schema.org also has a schema:identifier property. In
> BSC, have we recommended using this one too, and what for?
> On NMNH Paris's website, I've used it with a
> schema:PropertyValue object to cross-reference the "internal"
> identifiers of other portals (as well as NMNH Paris's
> identifier itself btw).
>
> So in the end, here is what would be on page
> https://inpn.mnhn.fr/espece/cd_nom/60932:
>
> "@type": "Taxon",
> "dct:conformsTo": { "@id":
> "https://bioschemas.org/profiles/Taxon/0.7-DRAFT"
> <https://bioschemas.org/profiles/Taxon/0.7-DRAFT> },
> * "@id": "http://taxref.mnhn.fr/lod/taxon/60932"
> <http://taxref.mnhn.fr/lod/taxon/60932>,*
> "*identifier*": [
> {
> "@type": "PropertyValue",
> "name": "TAXREF id",
> "propertyID": "https://www.wikidata.org/entity/P3186"
> <https://www.wikidata.org/entity/P3186>,
> "value": "60932"
> },{
> "@type": "PropertyValue",
> "name": "GBIF id",
> "propertyID": "http://www.wikidata.org/prop/direct/P846"
> <http://www.wikidata.org/prop/direct/P846>,
> "value": "5220003"
> }],
> ...
>
> What do you think? Are these good practices? Any other
> suggestions wrt. to the @id and identifier ?
>
> Thx in advance,
> Franck.
>
>
> Le 28/11/2022 à 11:30, Ivan Micetic a écrit :
>>
>> Dear Bioschemas user,
>>
>> We are contacting you as a developer of a resource which
>> publishes Bioschemas markup. We kindly request that you check
>> the compliance of the Bioschemas markup in your
>> resource/service with respect to the latest updates to
>> Bioschemas/Schema.org. Non-compliant markup will result in
>> your resource being ignored by services such as Google’s
>> Dataset Search <https://datasetsearch.research.google.com/>,
>> ELIXIR endorsed services (TeSS
>> <https://tess.elixir-europe.org/>, Bioschemas-live deploys
>> <https://bioschemas.org/developer/liveDeploys>) and OpenAIRE
>> Research Graph <https://graph.openaire.eu/>.
>>
>> To assist you, we have come up with the following checklist,
>> which summarises key points for a successful implementation
>> of Bioschemas markup:
>>
>> 1.
>>
>> Mandatory inclusion of standard properties: @context,
>> @type, @id, dct:conformsTo
>> <https://bioschemas.org/tutorials/howto/howto_add_markup>
>>
>> 2.
>>
>> Obsoletion of DataRecord profile
>> <https://bioschemas.org/tutorials/howto/howto_right_profile>
>>
>> 3.
>>
>> Update markup to latest profile releases:
>>
>> 1.
>>
>> TrainingMaterial
>> <https://bioschemas.org/profiles/TrainingMaterial/1.0-RELEASE>1.0-RELEASE
>> (1 June 2022)
>>
>> 2.
>>
>> Dataset
>> <https://bioschemas.org/profiles/Dataset/1.0-RELEASE>1.0-RELEASE
>> (12 July 2022)
>>
>> 3.
>>
>> Course
>> <https://bioschemas.org/profiles/Course/1.0-RELEASE>and
>> CourseInstance
>> <https://bioschemas.org/profiles/CourseInstance/1.0-RELEASE>1.0-RELEASE
>> (13 September 2022)
>>
>> ---- profiles included in Schema.org 13.0
>> <https://schema.org/docs/releases.html#v13.0>---
>>
>> 4.
>>
>> BioChemEntity
>> <https://bioschemas.org/types/BioChemEntity/0.7-RELEASE-2019_06_19>0.7-RELEASE
>> (14 June 2019)
>>
>> 5.
>>
>> ChemicalSubstance
>> <https://bioschemas.org/profiles/ChemicalSubstance/0.4-RELEASE>0.4-RELEASE
>> (7 April 2020)
>>
>> 6.
>>
>> MolecularEntity
>> <https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE>0.5-RELEASE
>> (7 April 2020)
>>
>> 7.
>>
>> Protein
>> <https://bioschemas.org/profiles/Protein/0.11-RELEASE>0.11-RELEASE
>> (7 April 2020)
>>
>> 8.
>>
>> Taxon
>> <https://bioschemas.org/profiles/Taxon/0.6-RELEASE>0.6-RELEASE
>> (7 April 2020)
>>
>> 9.
>>
>> Gene
>> <https://bioschemas.org/profiles/Gene/1.0-RELEASE>1.0-RELEASE
>> (7 April 2021)
>>
>> 4.
>>
>> Mandatory inclusion of a sitemap
>> <https://bioschemas.org/tutorials/community/idp>file
>>
>> 5.
>>
>> Generation of Bioschemas metadata data dumps
>> <https://bioschemas.org/developer/liveDeploys#nav-datadump>
>>
>>
>> If your Bioschemas markup complies with all the latest
>> profiles, but you still have an uncovered need or issue, we
>> are working on several updates and improvements to the
>> Bioschemas ecosystem:
>>
>> *
>>
>> Help us update the draft versions of profiles
>> <https://bioschemas.org/profiles#nav-draft>, or propose a
>> new profile
>> <https://bioschemas.org/tutorials/howto/howto_create_new_profile>[started
>> at BioHackathon22, #5
>> <https://github.com/elixir-europe/biohackathon-projects-2022/tree/main/5>]
>>
>> *
>>
>> Contribute to new profiles for Data/Software Management
>> Plans and Machine learning
>> <https://github.com/elixir-europe/biohackathon-projects-2022/tree/main/17>[started
>> at BioHackathon22, #17
>> <https://github.com/elixir-europe/biohackathon-projects-2022/tree/main/17>]
>>
>> *
>>
>> Efficient consumption of Bioschemas metadata
>> <https://github.com/elixir-europe/biohackathon-projects-2022/tree/main/23>via
>> Data Dumps [started at BioHackathon22, #23
>> <https://github.com/elixir-europe/biohackathon-projects-2022/tree/main/23>]
>>
>>
>> Please let us know of any changes and improvements of
>> published Bioschemas markup in your resource/service and feel
>> free to reach us by subscribing to the public Bioschemas
>> mailing list <mailto:public-bioschemas-request@w3.org>or
>> participate in the discussions on GitHub
>> <https://github.com/Bioschemas/specifications/issues>.
>>
>>
>> Kind regards,
>>
>> Ivan Mičetić
>>
>> on behalf of the Bioschemas Steering Council
>>
>>
>> --
>> Ivan Mičetić, PhD(he/him/his)
>> Department of Biomedical Sciences
>> University of Padua
>> Viale G. Colombo 3
>> 35131 Padova
>> Italy
>> Tel: +39-049-827 6269
>> Fax: +39-049-827 6363
>> mailto:ivan.micetic@unipd.it
>> biocomputingup.it <https://biocomputingup.it>
>>
>>
>
Received on Wednesday, 21 December 2022 16:21:27 UTC