Re: OWL2 serialized as JSON?

On 4 Oct 2016, at 10:25, Ignazio Palmisano wrote:

> On 4 Oct 2016 18:17, "Chris Mungall" <cjmungall@lbl.gov> wrote:
>>
>> Hi Michael,
>>
>> Yes I agree, this is what Bijan and I were circling around in the
> original discussion. There were questions as to how "S-expressiony" 
> the
> mapping would be (like OWL-XML) vs having named parameters. I think 
> the
> latter makes sense.
>>
>> The additional JSON format I am proposing would be structurally 
>> different
> but semantically equivalent or a well-defined subset, and it would be 
> aimed
> at a different use case (e.g. bioinformatics programmers who was 
> simple
> access to graph-representations of the existential graph of a T-Box)
>>
>
> Having read your explanation post but before seeing the proof of 
> concept
> implementation: this could be wrapped easily as a pluggable format for 
> owl
> api for easy experiments (we intended to have a way to add/remove 
> parsers
> and storers without the need to rebuild the owl api, but this has had 
> only
> limited testing with real implementations).

This would be useful

> This does little for your needs except removing one obstacle to 
> adoption:
> if all works out as it's supposed to, you don't have to wait for 
> Protégé or
> owl api to catch up with your work for people to start using it - it 
> would
> work on the current protégé build.

Well, there are other advantages in having it be better integrated with 
the owlapi

I'm not sure there is such a use case for saving from within Protege. 
The use of obographs is less during the ontology development cycle and 
more part of the publish-release cycle. But nevertheless it might be 
nice to have.

> Cheers,
> I.
>
>> On Tue, Oct 4, 2016 at 12:13 AM, Michael Schneider <m_schnei@gmx.de>
> wrote:
>>>
>>> Hi Chris,
>>>
>>> I don't know if anyone has been working on an OWL 2 JSON 
>>> serialization
> yet, but I would expect this to be relatively straightforward, if one 
> would
> create it along the lines of the OWL 2 Functional Syntax [1], in a 
> similar
> way as it has already been done for the OWL 2 XML Serialization [2].
>>>
>>> [1] <https://www.w3.org/2007/OWL/wiki/Syntax>
>>> [2] <https://www.w3.org/2007/OWL/wiki/XML_Serialization>
>>>
>>> Michael
>>>
>>> Am 04.10.2016 um 07:12 schrieb Chris Mungall:
>>>>
>>>> Sorry, I can't just let the OWL-as-JSON thing go.
>>>> We've previously discussed the need for a JSON serialization 
>>>> independent
>>>> of RDF, and most of us who work with OWL agree this would be a 
>>>> useful
>>>> thing. I'm not sure there is any general uptake of this - I think 
>>>> there
>>>> has been a whittling down effect where anyone doing anything heavy 
>>>> duty
>>>> with OWL by now uses Java or a JVM language.
>>>> I still think the idea of a standard context for serializing OWL as
>>>> JSON-LD (below) is a good one, for a subset of users, but it 
>>>> exposes too
>>>> much of the RDF mapping of OWL.
>>>> In the bioinformatics community there is a need for something that 
>>>> is at
>>>> the same level of abstraction as OBO-format, but less broken, with
>>>> better OWL support, and serialized in JSON and/or YAML.
>>>> Here is what we have so far:
>>>> https://github.com/geneontology/obographs
>>>> And a post describing the motivation here:
>>>>
> https://douroucouli.wordpress.com/2016/10/04/a-developer-friendly-json-exchange-format-for-ontologies/
>>>>
>>>> On 6 Aug 2013, at 15:45, Chris Mungall wrote:
>>>>
>>>>     Remember this thread?
>>>>
>>>>     It stirred a bit of discussion regarding the relative merits of 
>>>> a
>>>>     direct serialization of OWL2 into JSON vs indirect via RDF. 
>>>> Probably
>>>>     somewhat academic, as here we are some time later and there 
>>>> don't
>>>>     seem to be many people publicly shunting around OWL as JSON. I 
>>>> have
>>>>     a translation I have been using for internal purposes but would 
>>>> like
>>>>     to abandon it in favor of something more standard.
>>>>
>>>>     I have shifted somewhat in the direction of an RDF-oriented
>>>>     solution. IMany of the OWL class axioms I work with tend to 
>>>> generate
>>>>     fairly verbose RDF (and consequently JSON derived from this).
>>>>     However, it's likely that *any* translation to JSON will likely 
>>>> be
>>>>     ugly for my axioms.
>>>>
>>>>     It seems JSON-LD has been gaining traction, and has nice 
>>>> features
>>>>     for avoid verbosity. Is there any move to have a standard 
>>>> @context
>>>>     (perhaps served from a standard URL) for OWL 2? Rather than 
>>>> having
>>>>     an abstract discussion about relative merits it might help to 
>>>> see
>>>>     some concrete examples of ontologies of varying levels of 
>>>> complexity
>>>>     translated to JSON and compacted as JSON-LD. I'm particularly
>>>>     interested in any JSON-LD tricks could be used for a more 
>>>> compact
>>>>     encoding of axiom annotations.
>>>>
>>>>
>>>>
>>>>     On Thu, Dec 1, 2011 at 10:17 AM, Chris Mungall 
>>>> <cjmungall@lbl.gov
>>>>     <mailto:cjmungall@lbl.gov>> wrote:
>>>>
>>>>
>>>>         On Apr 7, 2011, at 5:54 AM, Bijan Parsia wrote:
>>>>
>>>>         > On 7 Apr 2011, at 08:33, Jerven Bolleman wrote:
>>>>         >
>>>>         >> Hi Chris, All,
>>>>         >>
>>>>         >> I have the feeling that you are going about this the 
>>>> wrong
>>>>         way round.
>>>>         >> I would first write a compelling JS api to deal with OWL
>>>>         concepts. And later if necessary design an optimized
>>>>         serialization format.
>>>>         >
>>>>         > Actually this is pretty close to what I proposed to do.
>>>>         >
>>>>         > The structure spec defines a quite nice API for OWL
> ontologies:
>>>>         >       http://www.w3.org/TR/2009/REC-owl2-syntax-20091027/
>>>>         > (The Manchester OWL API adheres to this.)
>>>>         >
>>>>         > The XML Serialization mirrors this closely:
>>>>         >
>>>>         http://www.w3.org/TR/2009/REC-owl2-xml-serialization-20091027/
>>>>         >
>>>>         > All other serializations (Manchester Syntax, RDF syntax) 
>>>> have
>>>>         a mapping to the abstract model.
>>>>         >
>>>>         > Although there are some issues with things for 
>>>> serialization
>>>>         (e.g., prefixes). I'll try to separate these out (as I'm
>>>>         currently doing for XML).
>>>>         >
>>>>         > Thus, the idea is to produce something close to this 
>>>> (with
>>>>         perhaps a few tweaks) so that, e.g., the structural spec 
>>>> serves
>>>>         as documentation for the API.
>>>>         >
>>>>         > I would generally recommend this as the preferred way to
>>>>         handle additional mappings and concrete formats. That was
>>>>         certainly the intent of the design.
>>>>
>>>>         Hi Bijan. How is this progressing?
>>>>
>>>>         I've written some code on top of the OWL API that generates 
>>>> json
>>>>         from either expressions or axioms. The resulting json is 
>>>> fairly
>>>>         generic and loosely corresponds to OWL-XML. Anything that 
>>>> is not
>>>>         a URI or a literal is translated to a hash with a "type" 
>>>> key
>>>>         that maps to the axiom or expression type, and an "args" 
>>>> arr.
>>>>         This is mostly for internal purposes write now - I'd like 
>>>> to
>>>>         adopt whatever de facto standard there is out there.
>>>>
>>>>
>>>>         > Cheers,
>>>>         > Bijan.
>>>>         >
>>>>
>>>>
>>>
>>

Received on Tuesday, 4 October 2016 18:22:51 UTC