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obographs JSON

Chris Mungall

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!

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Re: obographs JSON

Scott Cain
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 <[hidden email]> 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!

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------------------------------------------------------------------------
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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Re: obographs JSON

Brian Repko-2
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 <[hidden email]>
To: Chris Mungall <[hidden email]>
Cc: gmod tripal devel <[hidden email]>, "GMOD Schema/Chado List" <[hidden email]>
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 <[hidden email]> 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:

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!

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--
------------------------------------------------------------------------
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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Re: obographs JSON

Chris Mungall
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 <[hidden email]> 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 <[hidden email]>
To: Chris Mungall <[hidden email]>
Cc: gmod tripal devel <[hidden email]>, "GMOD Schema/Chado List" <[hidden email]>
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 <[hidden email]> 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:

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!

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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
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Re: obographs JSON

Brian Repko-2
Hi Chris,

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

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. ;-)

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.

Cheers,
-brian

----- Original message -----
From: Chris Mungall <[hidden email]>
To: Brian Repko <[hidden email]>
Cc: "gmod-schema List" <[hidden email]>
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 <[hidden email]> 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 <[hidden email]>
To: Chris Mungall <[hidden email]>
Cc: gmod tripal devel <[hidden email]>, "GMOD Schema/Chado List" <[hidden email]>
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 <[hidden email]> 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:

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!

------------------------------------------------------------------------------
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) <a href="tel:216-392-3087">216-392-3087
Ontario Institute for Cancer Research


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Re: obographs JSON

Chris Mungall


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 <[hidden email]>
> To: Brian Repko <[hidden email]>
> Cc: "gmod-schema List" <[hidden email]>
> 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
> <[hidden email]> 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 <[hidden email]>
>> To: Chris Mungall <[hidden email]>
>> Cc: gmod tripal devel <[hidden email]>,
>> "GMOD
>> Schema/Chado List" <[hidden email]>
>> 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
>> <[hidden email]> 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
>>> [hidden email]
>>> 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
>>
>>
>> ----------------------------------------------------------------------
>> --------
>> _________________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>
>> ----------------------------------------------------------------------
>> --------
>>
>> _______________________________________________
>>  Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>



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