Re: [Gmod-schema] obographs JSON

[Chris M. <cjm...@lb...>]

On 12 Sep 2016, at 5:26, Brian Repko wrote:

> Hi Chris,
>
> My understanding is that JSON is a representation of an object tree,
> adding JSON Pointer gets you an object graph.

Yes, technically it's a graph layered on a tree (json) representation

> I guess what I'm asking is - what are the objects being represented?
> Will they be nodes and edges or will they be terms and typedefs?

In Chado terms, the nodes are terms and typedefs

> If nodes and edges, then the model is some form of a graph model and
> there probably isn't a need for a JSON Schema.
> But if the objects modeled are terms and typedefs then you could also
> make use of JSON Schema for that as well.
> It's almost like GMOD Chado (cv module) is obo-relational-database -
> which could be represented in JSON (tables/columns).
> You have a obo-graph-model - represented in JSON. Perhaps, I'm what 
> I'm
> thinking of is an obo-json project. ;-)

Yes, that would have been equally good a name for it (though there is a 
structurally equivalent YAML if you want it)

> I don't have super deep knowledge of the OBO model itself so please
> forgive me if I'm missing something.
> Didn't mean to criticize the project, I am just trying to understand
> it's goals/vision.

No worries, thanks

> Cheers,
> -brian
>
> ----- Original message -----
> From: Chris Mungall <cjm...@lb...>
> To: Brian Repko <bri...@le...>
> Cc: "gmod-schema List" <gmo...@li...>
> Subject: Re: [Gmod-schema] obographs JSON
> Date: Sun, 11 Sep 2016 16:20:12 -0700
>
> Yes, it could. The oboformat library is a very direct translation of 
> OBO
> syntax - it's not very convenient, but probably not too bad for the
> purposes of writing a chado loader. And if what you have works there 
> is
> no reason to rewrite it.
> Although not sure I understand the last part: obographs give you the
> convenience of JSON (no need for a special parser) but at the same 
> time,
> it's graph oriented, in the way the cvterm_relationship table is.
>
> On Mon, Sep 5, 2016 at 12:03 PM, Brian Repko 
> <bri...@le...> wrote:
>> __
>> Our use case is also a bit different as well since we have GMOD Chado
>> as converted to Java / Liquibase (for mulitiple database support). We
>> load obo files with BBOP's oboformat library. This gives us access to
>> Term and Typedef objects directly and the data within them. Could
>> obograph support that kind of model but in JSON vs a graph-oriented
>> node/edge model?
>>
>> -brian
>>
>> ----- Original message -----
>> From: Scott Cain <sc...@sc...>
>> To: Chris Mungall <cjm...@lb...>
>> Cc: gmod tripal devel <gmo...@li...>, 
>> "GMOD
>> Schema/Chado List" <gmo...@li...>
>> Subject: Re: [Gmod-schema] obographs JSON
>> Date: Fri, 2 Sep 2016 11:05:39 -0400
>>
>> I think there a probably some people (besides me) using stag-
>> storenode, but probably not many.  The majority of Chado users these
>> days are using Tripal, so we'd want to see the current Tripal 
>> ontology
>> loader updated as well.  I cc'ed the dev list to make sure they're
>> aware of it too (though I imagine they're all on the Chado list too).
>>
>>
>> On Fri, Sep 2, 2016 at 7:38 AM, Chris Mungall
>> <cjm...@lb...> wrote:
>>>
>>> For a while there has been a need of a developer-friendly 
>>> replacement
>>> for OBO format. While advanced applications should target OWL,
>>> there a
>>> number of things that make direct OWL consumption developer-
>>> unfriendly
>>> (especially perl and python developers)
>>>
>>> We have come up with a proposed JSON representation that is
>>> intended to
>>> have the simplicity of OBO, with optional extensions for advanced 
>>> OWL
>>> axioms - in JSON or YAML:
>>> https://github.com/geneontology/obographs
>>>
>>> The intent is for any replacements for stage-storenode.pl to
>>> target this
>>> (I'm not up to date on what people are currently using)
>>>
>>> It shouldn't be regarded as stable yet - I'd like feedback from
>>> the GMOD
>>> community first. Please email here or use the issue tracker with any
>>> comments, thanks!
>>>
>>> ---------------------------------------------------------------------
>>> ---------
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>
>>
>>
>>
>> --
>> ----------------------------------------------------------------
>> --------
>> Scott Cain, Ph. D.                                   scott at
>> scottcain dot net
>> GMOD Coordinator (http://gmod.org/) 216-392-3087
>> Ontario Institute for Cancer Research
>>
>>
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