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Re: Bioschemas Taxon profile specification

From: Justin Clark-Casey <justinccdev@gmail.com>
Date: Wed, 27 Jun 2018 19:19:34 +0100
Message-ID: <CAME9NR-w0fkgB0+cCKD+b3ycMBJR-jHUa_nFoyzO8p6TRKF_fA@mail.gmail.com>
To: fmichel@i3s.unice.fr
Cc: ljgarcia@ebi.ac.uk, a.j.g.gray@hw.ac.uk, public-bioschemas@w3.org
I think we should have mandatory known @types and properties.  In my view,
Bioschemas should be as easy as possible to write and consume.  Multiple
options will increase cognitive load on writers (which one do I choose?
Why are these 2 examples using these different terms?) and open the door to
greater inconsistency.  Non-mandatory types will also raise the barriers
for writing Bioschemas software that will have to be aware of equivalent
mappings.

I would go one step further and say that Bioschemas should provide an
http://bioschemas.org context that will define types such as Taxon, rather
than blessing particular ontology terms.  This context can also document
equivalent terms in different ontologies.

On Wed, 27 Jun 2018 at 17:42, Franck Michel <fmichel@i3s.unice.fr> wrote:

> Dear all,
>
> As we start discussing the Taxon profile specification
> <https://drive.google.com/drive/folders/1Fp2AKbb07So7rVvUhnQIjpl8HLPSwpbP>,
> a question strikingly comes up for each and every term that we discuss:
> what to do when equivalent terms are available from several well known
> ontologies?
>
> In the taxon case, this question occurs with respect to the main entity
> type as well as properties such as the taxon rank, scientific name, parent
> taxon etc. For all of these cases, we have candidate terms in DarwinCore,
> TDWG ontologies, NCBITaxon, Wikidata and possibly others. So what to do?
>
> Main type:
> - should we pick up one type as the preferred/mandatory type (in the
> @type), and optionally add other types in an additionalType property?
>
> Example:
>     "@type" : [ "BioChemEntity", "dwc:Taxon" ],
>     "additionalType": [ "wd:Q16521", "tdwg:TaxonConcept" ],
>
> - or should we propose several alternatives and leave it up to the data
> provider to decide which one to use?
>
> Example:
>     "@type" : [ "BioChemEntity", "wd:Q16521" ],
>
>
> Properties - almost the same questions:
> - should we pick up one property as the preferred one, and allow optional
> other properties? And if so, do we denote the others directly or using a
> PropertyValue?
>
> Example:
>     "wdt:P105": { "@id": "http://www.wikidata.org/entity/Q7432" },
>     "dwc:taxonRank": "species",
>     "tdwg:rank": { "@id": "
> http://rs.tdwg.org/ontology/voc/TaxonRank#Species" },
>     "ncbi:has_rank":  { "@id": "
> http://purl.obolibrary.org/obo/NCBITaxon_species" },
>
> PropertyValue alternative:
>     "wdt:P105": "http://www.wikidata.org/entity/Q7432"
> <http://www.wikidata.org/entity/Q7432>,
>     "additionalProperty" : {
>         "propertyID": { "@id": "dwc:taxonRank" },
>         "value": "species",
>     },
>     "additionalProperty" : {
>         "propertyID": { "@id": "tdwg:rank" },
>         "value": { "@id": "
> http://rs.tdwg.org/ontology/voc/TaxonRank#Species" }
>     },
>     "additionalProperty" : {
>         "propertyID": { "@id": "ncbi:has_rank" },
>         "value": { "@id": "
> http://purl.obolibrary.org/obo/NCBITaxon_species" }
>     },
>
> - or should we propose several alternatives and leave it up to the data
> provider to decide which one to use?
>
>
> Feedback and advices are most welcome.
>
> Regards,
>     Franck.
>
> --
>
> Franck MICHEL
> CNRS research engineer
> +33 (0)4 8915 4277
> franck.michel@cnrs.fr
>
>
>
> Université Côte d’Azur, CNRS - I3S - UMR 7271
> 930 route des Colles - Bât. Les Templiers
> BP 145 - 06903 Sophia Antipolis CEDEX - France
> Tel. +33 (0)4 9294 2680
>
Received on Wednesday, 27 June 2018 18:20:33 UTC

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