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Bioschemas Taxon profile specification

From: Franck Michel <fmichel@i3s.unice.fr>
Date: Wed, 27 Jun 2018 16:45:01 +0200
To: Leyla Garcia Castro <ljgarcia@ebi.ac.uk>, "Alasdair J.G. Gray" <a.j.g.gray@hw.ac.uk>
Cc: "public-bioschemas@w3.org" <public-bioschemas@w3.org>
Message-ID: <a92b433d-5218-8219-03ee-635f656c7dd0@i3s.unice.fr>
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",
    "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.

-- 
signature
	
Franck MICHEL
CNRS research engineer
	+33 (0)4 8915 4277
franck.michel@cnrs.fr <mailto: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 16:41:45 UTC

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