Re: Bioschemas profiles refresh: recommendations for the @id property?

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> ---
>>
>>    1.
>>
>>    BioChemEntity
>>    <https://bioschemas.org/types/BioChemEntity/0.7-RELEASE-2019_06_19>
>>    0.7-RELEASE (14 June 2019)
>>    2.
>>
>>    ChemicalSubstance
>>    <https://bioschemas.org/profiles/ChemicalSubstance/0.4-RELEASE>
>>    0.4-RELEASE (7 April 2020)
>>    3.
>>
>>    MolecularEntity
>>    <https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE>
>>    0.5-RELEASE (7 April 2020)
>>    4.
>>
>>    Protein <https://bioschemas.org/profiles/Protein/0.11-RELEASE>
>>    0.11-RELEASE (7 April 2020)
>>    5.
>>
>>    Taxon <https://bioschemas.org/profiles/Taxon/0.6-RELEASE> 0.6-RELEASE
>>    (7 April 2020)
>>    6.
>>
>>    Gene <https://bioschemas.org/profiles/Gene/1.0-RELEASE> 1.0-RELEASE
>>    (7 April 2021)
>>
>>
>>    1.
>>
>>    Mandatory inclusion of a sitemap
>>    <https://bioschemas.org/tutorials/community/idp> file
>>    2.
>>
>>    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
>> <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
>>
>>
>>
>>