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Re: [Proposal] CategoryCode as valid type for valueReference for any PropertyValue in Bioschemas/schema.org

From: Philippe <proccaserra@gmail.com>
Date: Mon, 19 Mar 2018 11:21:05 +0000
To: Luca Cherubin <cherubin@ebi.ac.uk>, public-bioschemas@w3.org
Message-ID: <cc316ac1-8a2d-272c-a886-a31869a444cb@gmail.com>
Hi Luca,

I am including a snippet from the notes so people can have a feel for 
how things could look like:

*

{

    "@context": "http://schema.org",

    "@type": ["DataRecord"],

    "additionalProperty": [

        {

            "@type": "PropertyValue",

            "name": "diagnosis_available",

            "value": "urn:miriam:icd:C00-C97",

            "valueReference": [

                {

                    "@type": "CategoryCode",

                    "name": "Malignant neoplasms",

                    "url": 
"http://purl.bioontology.org/ontology/ICD10/C00-C97.9",

                    "codeValue": "C00-C97.9"

                }

            ]

        },

        {

            "@type": "PropertyValue",

            "name": "diagnosis_available",

            "value": "urn:miriam:icd:D00-D09",

            "valueReference": [

                {

                    "@type": "CategoryCode",

                    "name": "In situ neoplasms",

                    "url": 
"http://purl.bioontology.org/ontology/ICD10/D00-D09.9",

                    "codeValue": "D00-D09.9"

                }

            ]

        },

*
I also include the link the schema.org CategoryCode:
https://pending.schema.org/CategoryCode and their JSON-LD snippet

 1. {
 2.   "@context": "http://schema.org/",
 3.   "@type": "CategoryCode",
 4.   "codeValue": "Man",
 5.   "inCodeSet": "http://id.loc.gov/vocabulary/resourceTypes"
 6. }



Question: Should 'inCodeSet' attribute be used instead ?

Best

Philippe

On 19/03/2018 11:10, Luca Cherubin wrote:
> Hi everybody,
>
> During the Hackathon event last week with various Biobanks 
> representatives we had the chance to use Bioschemas profiles and types 
> to support BioBanks use cases for metadata sharing.
>
> As you may know, in the Sample profile we proposed a solution for 
> linking ontology terms to a PropertyValue using CategoryCode as valid 
> type for the valueReference field. Note that CategoryCode is already a 
> proposed schema.org <http://schema.org> type but in the 
> bioschemas/samples specification we propose that it should be an 
> acceptable value for valueReference.
>
> To support BioBank use cases, we are using DataRecord and they need to 
> use the same CategoryCode strategy to describe all the PropertyValue 
> associated with a DataRecord.
>
> In our opinion this is a very strong use case for supporting the use 
> of CategoryCode as valid type for valueReference for any PropertyValue 
> in Bioschemas/schema.org <http://schema.org>, not only for the Sample 
> profile. We can see this being very useful in other areas where there 
> is a need for a flexible linking of ontology terms to values.
>
> We would like to get your feedback on this.
>
> Best regards,
>
> Luca and Matt 
Received on Monday, 19 March 2018 11:21:31 UTC

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