Re: New property for BioChemEntity (and types vs. profiles)

Hi Dominique,

A type in Bioschemas is the same as a type in schema.org. The 
BioChemEntity is flexible and extensible thanks to generic properties 
such as additionalType, additionalProperty and contains/isContainedBy. 
This generic approach was selected because new profiles  can be easily 
incorporated in Bioschemas without going into schema.org (which requires 
some sort of process).

You can see a profile as a customization where additionalType is fixed 
(or limited to a predefined set) and specific uses of additionalProperty 
(like "transcribed-from-gene") and isContainedIn/contains (like 
"in-organism-XYZ"). So, validators and tools will need access to the 
profile specifications, including all these customization I just 
mentioned. We have not yet fully defined how that customization should 
be specified.

I am wondering how this customization will work for validators and 
tools. So I was wondering if having the profile name in this new 
property preferredLabel would help at all.

Regards,


On 16/10/2017 17:22, BATISTA Dominique wrote:
> Leyla,
> Adding a new property to select a profile is good for me. I wonder how 
> it would look like though.
>
> {
>     "@type" : "object_type",
>     "PrefferedLabel" : "object_profile"
>     ...
> }
>
> Would we then have one spec file per profile with common properties in 
> the corresponding type spec file? I'm not really sure to have fully 
> understand that whole profile thing. What's the difference between a 
> profile and inheritance and why did you guys choose one over an other?
>
> Thanks :)
>
> Cheers,
>
> Dominique Batista
> Ingénieur Web IFB Core
> CNRS - UMS3601
> Tel: 01.69.82.46.92
> Site: http://www.france-bioinformatique.fr
> ------------------------------------------------------------------------
> *From:* Leyla Garcia [ljgarcia@ebi.ac.uk]
> *Sent:* Monday, October 16, 2017 6:13 PM
> *To:* public-bioschemas@w3.org; BATISTA Dominique
> *Subject:* Re: New property for BioChemEntity
>
> Hello,
>
> It is in addition to additionalType. additionalType links to ontology 
> terms, preferredLabel would point to a plain text. Having just one 
> preferred label in English (any other language would be optional) 
> would make things easier for validation (I think but Dominique can 
> tell better).
>
> Regards,
>
> On 16/10/2017 17:08, Stephen Anyango wrote:
>>
>> Hello Leyla,
>>
>> Is this in addition to additionalType which is also meant to be an 
>> enumeration of ontological terms labelling the profile? An example 
>> would suffice for clarity.
>>
>> kind regards,
>>
>> Stephen Anyango
>> PDBe
>> EMBL-EBI
>> On 16-Oct-17 4:40 PM, Leyla Garcia wrote:
>>> Hi all,
>>>
>>> I have discussed with Rafael the need of a way to refer to a 
>>> particular profile from a type specification. I think adding a new 
>>> property could work. Please see below.
>>>
>>> Type: BioChemEntity
>>> Property: PreferredLabel
>>> Expected type: Text
>>> schema.org description: Preferred label in plain text for this entity
>>> Bioschemas description: The preferred label corresponds to the 
>>> Bioschemas profile. Please refer to the Bioschemas profile 
>>> enumeration to find the available labels <some link will go here>. 
>>> Although multiple languages are allowed, a label in English should 
>>> always be provided. If the label you are looking for does not exist, 
>>> please contact Bioschemas.org <some link will go here>.
>>> Bioschemas restrictions: Minimum, Many (at least one in English), 
>>> Enumeration.
>>>
>>> Validators could use this label to "know" better what the minimum, 
>>> recommended and so really are as they change from profile to profile.
>>>
>>> I do not think at this point that such property would be 
>>> needed/useful for Record. If you think it is, then we could propose 
>>> it for Thing rather than BioChemEntity. Please share your thoughts.
>>>
>>> Regards,
>>>
>>>
>>
>