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Re: JSON-LD and context questions (plus no additionalType and I don't like DataRecord)

From: Jerven Bolleman <jerven.bolleman@sib.swiss>
Date: Wed, 21 Nov 2018 17:27:36 +0100
To: Melanie Courtot <mcourtot@ebi.ac.uk>
Cc: ljgarcia <ljgarcia@ebi.ac.uk>, public-bioschemas@w3.org
Message-ID: <1b15abe3-bceb-9eca-bd33-537bbaf3dd41@sib.swiss>
On 11/21/2018 04:54 PM, Melanie Courtot wrote:
> Thanks both, that looks much more straighforward. I see that the 
> identifier property from bioschema in my original snippet, 
>   "identifier": "biosample:SAMEA100000”, as also been rewritten using 
> @id - shouldn’t we expand the biosample prefix in the context as well 
> then? The final version would then be:
> 
> {
>   "@context": [ "http://schema.org",
>   {
>     "OBI" :"http://purl.obolibrary.org/obo/OBI_”
>     “biosample":”http://identifiers.org/biosample"
>   }],
>   "@type": "DataRecord",
>   "@id": "biosample:SAMEA100000",
>   "mainEntity": {
>     "@type" : ["Sample","OBI:0000747"]
>   }
> }
Yes :)
> 
> 
> I’m still unclear about the notation  "@context": "http://schema.org” - 
> is that the default context for anything not otherwise bound to a prefix?
> 
> Is there a difference between @context": "http://schema.org” and
> "@context":{
>          "@base": "http://schema.org",
>      }
The first imports the schema.org context as it is provided by the 
schema.org community. The second states that if something can be 
identified as an IRI without a curie then it will be schema.org/...


> As said I couldn’t find an explanation for the syntax "@context": 
> "http://schema.org” in the json-ld spec at 
> https://www.w3.org/TR/json-ld/#the-context
> 
> 
> 
> Finally  (and that’s maybe Jerven feels about strongly as well, given 
> the edits to the subject line ;)): we now have a DataRecord with ID as 
> well as the mainEntity of the page with the same ID.
> 
>    "mainEntity": {
>      "@id": ""biosample:SAMEA100000",
That is off. Either the datarecord has that id or the mainEntity. else 
you end up doing the equivalent of owl:sameAs between the Sample and the 
DataRecord.>
> 
> Should we use @id in the data Record as the actual URL of the biosamples 
> page we are referring to, i.e., 
> https://www.ebi.ac.uk/biosamples/samples/SAMEA100000, and the the ID of 
> the mainEntity is the identifiers.org 
> <http://identifiers.org> “canonical” IRI for this sample?  
No because the data record is something different then the webpage 
right? the webpage is a representation but you have the same record in
multiple formats.
> It seems a 
> little bit circular to be honest. We may be better off saying this is a 
> dataRecord with  "@id": "biosample:SAMEA100000” and then not have an ID 
> for the mainEntity? Or is the circularity not a problem?
Not having an ID for the mainEntity is an option. However, it's the 
thing you want to talk about so it not having an ID is not ideal.
My preference is not to have a DataRecord and just go from webpage to 
Sample in one step.

Regards,
Jerven

> 
> Thanks again for the help,
> Melanie
> 
> 
> 
> 
> 
>> On 21 Nov 2018, at 15:26, Jerven Bolleman <jerven.bolleman@sib.swiss 
>> <mailto:jerven.bolleman@sib.swiss>> wrote:
>>
>> Hi Melanie, Leyla,
>>
>> I see the error in my reply.
>>
>> You want to say the anonymous mainEntity is a schema:Sample and a 
>> OBI:0000747 at the same time.
>> Then you want to use this
>> {
>>  "@context": [ "http://schema.org",
>>  {
>>    "OBI" :"http://purl.obolibrary.org/obo/OBI_"
>>  }],
>>  "@type": "DataRecord",
>>  "@id": "biosample:SAMEA100000",
>>  "mainEntity": {
>>    "@type" : ["Sample","OBI:0000747"]
>>  }
>> }
>>
>> There may be or may not be a file somewhere that relates the 
>> schema;Sample to OBI:0000747 in some way in the future but this is not 
>> expressible in a context in JSON-LD (not now in 1.0 nor in 1.1)
>>
>> Regards,
>> Jerven
>> On 11/21/2018 03:45 PM, ljgarcia wrote:
>>> Hi Melanie,
>>> I do not see why you would need the second local context in your example.
>>> Now, regarding http://purl.obolibrary.org/obo/OBI_0000747. Are you 
>>> trying to express that schema:Sample is somehow "inspired/based" on 
>>> http://purl.obolibrary.org/obo/OBI_0000747? If yes, you do not need 
>>> to add it here. That will be expressed somehow as part of the Sample 
>>> definition is schema.org <http://schema.org>. The "somehow" way to 
>>> express it, I think has not been agreed yet, it would be a property 
>>> such as "baseOn", "equivalentTo" or so.
>>> Kind regards,
>>> On 2018-11-21 14:00, Jerven Bolleman wrote:
>>>> Hi Melanie,
>>>>
>>>> I think you want to do this.
>>>>
>>>> {
>>>>   "@context": [ "http://schema.org",
>>>>               {
>>>>                 "OBI" :"http://purl.obolibrary.org/obo/OBI_"
>>>>               }
>>>>   ],
>>>>   "@type": "DataRecord",
>>>>   "@id": "biosample:SAMEA100000",
>>>>   "mainEntity": {
>>>>     "@type" : "OBI:0000747"
>>>>   }
>>>> }
>>>>
>>>> Here we start with merging two contexts. The standard schema.org 
>>>> <http://schema.org> and
>>>> one just for your file. Here trying to make the OBI one easier to
>>>> read.
>>>>
>>>> So your top level is a DataRecord linked via schema:mainEntity to
>>>> something with type "OBI:0000747".
>>>>
>>>> You can see what a JSON-LD snipit means in RDF at
>>>> https://json-ld.org/playground/ e.g. http://tinyurl.com/y9ccen2j
>>>>
>>>>
>>>> I am repeating myself here but in additionalType is only for the
>>>> MicroData serialization which no one in the bioschema space seems to
>>>> use.
>>>>
>>>> If you have more than one type just do
>>>>
>>>> {
>>>>   "@context": [ "http://schema.org",
>>>>               {
>>>>                 "OBI" :"http://purl.obolibrary.org/obo/OBI_"
>>>>               }
>>>>   ],
>>>>   "@type": [ "DataRecord", "Thing", "WebPage" ],
>>>>   "@id": "biosample:SAMEA100000",
>>>>   "mainEntity": {
>>>>     "@type" : "OBI:0000747"
>>>>   }
>>>> }
>>>>
>>>> To be honest I don't like the DataRecord at all and am still
>>>> advocating it's removal from bioschema. Mostly because schema.org 
>>>> <http://schema.org>
>>>> doesn't have StoreRecord, just Store.
>>>>
>>>> Regards,
>>>> Jerven
>>>>
>>>> PS Alasdair, Leyla maybe remove additionalType considering the
>>>> confusion it has generated and we have no Microdata examples.
>>>>
>>>> On 11/21/2018 02:40 PM, Melanie Courtot wrote:
>>>>> Hi,
>>>>>
>>>>> Hi - following up discussions at the BioHackathon we’re looking at 
>>>>> updating our sample serialisation. We are running into some 
>>>>> questions with respect to the context usage and are hoping someone 
>>>>> can help.
>>>>>
>>>>> Specifically, I’m trying to understand the usage of contexts and 
>>>>> base IRIS - I’m familiar with XML base and namespaces as well as 
>>>>> RDF, but I was looking at some schema.org <http://schema.org> 
>>>>> <http://schema.org> JSON-LD and trying to understand nuances based 
>>>>> on the official spec at https://www.w3.org/TR/json-ld/#the-context
>>>>>
>>>>> Here is the relevant excerpt from our serialisation:
>>>>>
>>>>> {
>>>>>    "@context": "http://schema.org",
>>>>>    "@type": "DataRecord",
>>>>>    "identifier": "biosample:SAMEA100000",
>>>>>    "mainEntity": {
>>>>>      "@context": [
>>>>>        "http://schema.org",
>>>>>        {
>>>>>          "@base": "http://schema.org"
>>>>>        },
>>>>>        {
>>>>>          "Sample": {
>>>>>            "@id": "http://purl.obolibrary.org/obo/OBI_0000747"
>>>>>          }
>>>>>        }
>>>>>      ],
>>>>> ….
>>>>>
>>>>>
>>>>> As you can see there is a repetition of contexts and base that I 
>>>>> don’t think is needed.
>>>>>
>>>>> 1. The first context, which is at the top level in our sample page, 
>>>>> seems to match example 4 from the spec, and would actually be a 
>>>>> reference to another json-ld context? Though it doesn’t point to a 
>>>>> json-ld file. I couldn’t find this specific notation anywhere else 
>>>>> in the JSON-LD spec, but this is what is used throughout on 
>>>>> schema.org <http://schema.org> <http://schema.org>, eg 
>>>>> https://schema.org/Person, example 1 in json-ld.
>>>>>
>>>>> 2. The whole page is a DataRecord (where DataRecord is a new type 
>>>>> we are proposing to schema.org <http://schema.org> 
>>>>> <http://schema.org>, so should expand to 
>>>>> http://schema.org/DataRecord) - which is expected as we want to 
>>>>> describe a data record in our resource, and we then describe the 
>>>>> mainEntity in that DataRecord.
>>>>> As you can see, the context is redefined in mainEntity - my 
>>>>> understanding is that this means this specific context declaration 
>>>>> will be valid only within the scope of that mainEntity. This 
>>>>> context reads
>>>>>
>>>>>      "@context": [
>>>>>        "http://schema.org",
>>>>>        {
>>>>>          "@base": "http://schema.org"
>>>>>        },
>>>>>
>>>>> I don’t understand what the first "http://schema.org” means, and 
>>>>> whether it’s needed as we explicitly define the base. Also this 
>>>>> seems redundant with the global page context we have defined at the 
>>>>> page level, so I’d be tempted to just have
>>>>>
>>>>>      "@context": {
>>>>>          "@base": "http://schema.org"
>>>>>        },
>>>>>
>>>>> At the top level.
>>>>>
>>>>> 3. Finally, we are trying to say that 
>>>>> http://schema.org/Sample (which is a new type we’re proposing) also 
>>>>> has the IRI "http://purl.obolibrary.org/obo/OBI_0000747”. I’m not 
>>>>> sure adding
>>>>>
>>>>>        {
>>>>>          "Sample": {
>>>>>            "@id": "http://purl.obolibrary.org/obo/OBI_0000747"
>>>>>          }
>>>>>
>>>>> In the context is the right way of doing it, or whether we should 
>>>>> just add an additionalType 
>>>>> <https://schema.org/additionalType> property on the sample object 
>>>>> later on - or should we do both?
>>>>>
>>>>> Apologies for the rather long email, but I hope we have a JSON-LD 
>>>>> specialist on this list that can provide some guidance as to how we 
>>>>> should best use those. Thanks in advance for any help!
>>>>>
>>>>> Cheers,
>>>>> Melanie
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -- Mélanie Courtot, PhD
>>>>> GA4GH/BioSamples Project lead
>>>>> European Bioinformatics Institute (EMBL-EBI)
>>>>>
>>
>>
> 
Received on Wednesday, 21 November 2018 16:28:13 UTC

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