can gmod_load_cvterms.pl load any arbitrary relationshiptype?

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wyu
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can gmod_load_cvterms.pl load any arbitrary relationshiptype?

wyu
Hi Naama,

When I use your script gmod_load_cvterms.pl to load a obo file, I got a
warning: "Relationship ontology must be loaded first!!". So I download a
ro.obo file from http://www.obofoundry.org/ro/ro.obo.  After I ran  the
script for the ro.obo file, I got 6 relationshiptype are stored in
cvterm table:

cvterm_id | cv_id |         name         |                    
definition                     | dbxref_id | is_obsolete |
is_relationshiptype
-----------+-------+----------------------+----------------------------------------------------+-----------+-------------+---------------------
         1 |     1 | IS_A                 | IS_A relationship predicate
(type)                 |         1 |           0 |                   1
         2 |     1 | PART_OF              | PART_OF relationship
predicate (type)              |         2 |           0
|                   1
         3 |     1 | RELATED_TO           | RELATED_TO relationship
predicate (type)           |         3 |           0 |                   1
         4 |     1 | REGULATES            | REGULATES relationship
predicate (type)            |         4 |           0 |                   1
         5 |     1 | POSITIVELY_REGULATES | POSITIVELY_REGULATES
relationship predicate (type) |         5 |           0
|                   1
         6 |     1 | NEGATIVELY_REGULATES | NEGATIVELY_REGULATES
relationship predicate (type) |         6 |           0
|                   1
(6 rows)

I wan to know if your script can only load the 6 fixed relationshiptypes
rather than any other arbitrary relationshiptype.

Weixia

------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
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Re: can gmod_load_cvterms.pl load any arbitrary relationshiptype?

Naama Menda
I think one of the problem is that bioperl's obo parser does not handle 'typedefs'

Since RO has no 'Term' stanza, but just 'typedefs' , the loaded finds only the relationships, which is why you see 6 terms.

I'll have to look more into this and see where the parsing is happening, and how 'make ontologies' handles this.

-Naama



On Fri, Oct 22, 2010 at 11:47 PM, Naama Menda <[hidden email]> wrote:
could you send me the output of the loading script? (you can use the -o flag to write to an outfile) 

Thanks!
-Naama


Naama Menda
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca NY 14853
USA

(607) 254 3569
Sol Genomics Network
http://solgenomics.net/
[hidden email]



On Fri, Oct 22, 2010 at 6:11 PM, Weixia Yu <[hidden email]> wrote:
Hi Naama,

When I use your script gmod_load_cvterms.pl to load a obo file, I got a
warning: "Relationship ontology must be loaded first!!". So I download a
ro.obo file from http://www.obofoundry.org/ro/ro.obo.  After I ran  the
script for the ro.obo file, I got 6 relationshiptype are stored in
cvterm table:

cvterm_id | cv_id |         name         |
definition                     | dbxref_id | is_obsolete |
is_relationshiptype
-----------+-------+----------------------+----------------------------------------------------+-----------+-------------+---------------------
        1 |     1 | IS_A                 | IS_A relationship predicate
(type)                 |         1 |           0 |                   1
        2 |     1 | PART_OF              | PART_OF relationship
predicate (type)              |         2 |           0
|                   1
        3 |     1 | RELATED_TO           | RELATED_TO relationship
predicate (type)           |         3 |           0 |                   1
        4 |     1 | REGULATES            | REGULATES relationship
predicate (type)            |         4 |           0 |                   1
        5 |     1 | POSITIVELY_REGULATES | POSITIVELY_REGULATES
relationship predicate (type) |         5 |           0
|                   1
        6 |     1 | NEGATIVELY_REGULATES | NEGATIVELY_REGULATES
relationship predicate (type) |         6 |           0
|                   1
(6 rows)

I wan to know if your script can only load the 6 fixed relationshiptypes
rather than any other arbitrary relationshiptype.

Weixia

------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-schema



------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
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Re: can gmod_load_cvterms.pl load any arbitrary relationshiptype?

Scott Cain
Hi Naama,

The make ontologies command is using go-perl under the hood,
converting obo files to chadoxml.  I'm reasonably sure it does see
typedefs; the relationship ontology loaded with it has 26 rows.

Scott


On Mon, Oct 25, 2010 at 12:21 PM, Naama Menda <[hidden email]> wrote:

> I think one of the problem is that bioperl's obo parser does not handle
> 'typedefs'
>
> Since RO has no 'Term' stanza, but just 'typedefs' , the loaded finds only
> the relationships, which is why you see 6 terms.
>
> I'll have to look more into this and see where the parsing is happening, and
> how 'make ontologies' handles this.
>
> -Naama
>
>
>
> On Fri, Oct 22, 2010 at 11:47 PM, Naama Menda <[hidden email]> wrote:
>>
>> could you send me the output of the loading script? (you can use the -o
>> flag to write to an outfile)
>> Thanks!
>> -Naama
>>
>> Naama Menda
>> Boyce Thompson Institute for Plant Research
>> Tower Rd
>> Ithaca NY 14853
>> USA
>>
>> (607) 254 3569
>> Sol Genomics Network
>> http://solgenomics.net/
>> [hidden email]
>>
>>
>> On Fri, Oct 22, 2010 at 6:11 PM, Weixia Yu <[hidden email]> wrote:
>>>
>>> Hi Naama,
>>>
>>> When I use your script gmod_load_cvterms.pl to load a obo file, I got a
>>> warning: "Relationship ontology must be loaded first!!". So I download a
>>> ro.obo file from http://www.obofoundry.org/ro/ro.obo.  After I ran  the
>>> script for the ro.obo file, I got 6 relationshiptype are stored in
>>> cvterm table:
>>>
>>> cvterm_id | cv_id |         name         |
>>> definition                     | dbxref_id | is_obsolete |
>>> is_relationshiptype
>>>
>>> -----------+-------+----------------------+----------------------------------------------------+-----------+-------------+---------------------
>>>         1 |     1 | IS_A                 | IS_A relationship predicate
>>> (type)                 |         1 |           0 |                   1
>>>         2 |     1 | PART_OF              | PART_OF relationship
>>> predicate (type)              |         2 |           0
>>> |                   1
>>>         3 |     1 | RELATED_TO           | RELATED_TO relationship
>>> predicate (type)           |         3 |           0 |
>>> 1
>>>         4 |     1 | REGULATES            | REGULATES relationship
>>> predicate (type)            |         4 |           0 |
>>> 1
>>>         5 |     1 | POSITIVELY_REGULATES | POSITIVELY_REGULATES
>>> relationship predicate (type) |         5 |           0
>>> |                   1
>>>         6 |     1 | NEGATIVELY_REGULATES | NEGATIVELY_REGULATES
>>> relationship predicate (type) |         6 |           0
>>> |                   1
>>> (6 rows)
>>>
>>> I wan to know if your script can only load the 6 fixed relationshiptypes
>>> rather than any other arbitrary relationshiptype.
>>>
>>> Weixia
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Nokia and AT&T present the 2010 Calling All Innovators-North America
>>> contest
>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and
>>> Canada
>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in
>>> marketing
>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>> http://p.sf.net/sfu/nokia-dev2dev
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> 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

------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
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Re: can gmod_load_cvterms.pl load any arbitrary relationshiptype?

Daniel Quest
I have no idea if this is helpful or even interesting...  I was having
some trouble figuring out how to get OWL ontologies loaded into Chado.
 So I wrote a java-jena based ontology loader into chado.  It still is
lacking some features, but it is obvious how I could include those
given time.  Hope this is interesting to people.  I probably should
have asked the GMODSchema group how to deal with this before I wrote
the tool, but It really helped me understand what goes into what
table.

Thanks
-Daniel

On Mon, Oct 25, 2010 at 1:44 PM, Scott Cain <[hidden email]> wrote:

> Hi Naama,
>
> The make ontologies command is using go-perl under the hood,
> converting obo files to chadoxml.  I'm reasonably sure it does see
> typedefs; the relationship ontology loaded with it has 26 rows.
>
> Scott
>
>
> On Mon, Oct 25, 2010 at 12:21 PM, Naama Menda <[hidden email]> wrote:
>> I think one of the problem is that bioperl's obo parser does not handle
>> 'typedefs'
>>
>> Since RO has no 'Term' stanza, but just 'typedefs' , the loaded finds only
>> the relationships, which is why you see 6 terms.
>>
>> I'll have to look more into this and see where the parsing is happening, and
>> how 'make ontologies' handles this.
>>
>> -Naama
>>
>>
>>
>> On Fri, Oct 22, 2010 at 11:47 PM, Naama Menda <[hidden email]> wrote:
>>>
>>> could you send me the output of the loading script? (you can use the -o
>>> flag to write to an outfile)
>>> Thanks!
>>> -Naama
>>>
>>> Naama Menda
>>> Boyce Thompson Institute for Plant Research
>>> Tower Rd
>>> Ithaca NY 14853
>>> USA
>>>
>>> (607) 254 3569
>>> Sol Genomics Network
>>> http://solgenomics.net/
>>> [hidden email]
>>>
>>>
>>> On Fri, Oct 22, 2010 at 6:11 PM, Weixia Yu <[hidden email]> wrote:
>>>>
>>>> Hi Naama,
>>>>
>>>> When I use your script gmod_load_cvterms.pl to load a obo file, I got a
>>>> warning: "Relationship ontology must be loaded first!!". So I download a
>>>> ro.obo file from http://www.obofoundry.org/ro/ro.obo.  After I ran  the
>>>> script for the ro.obo file, I got 6 relationshiptype are stored in
>>>> cvterm table:
>>>>
>>>> cvterm_id | cv_id |         name         |
>>>> definition                     | dbxref_id | is_obsolete |
>>>> is_relationshiptype
>>>>
>>>> -----------+-------+----------------------+----------------------------------------------------+-----------+-------------+---------------------
>>>>         1 |     1 | IS_A                 | IS_A relationship predicate
>>>> (type)                 |         1 |           0 |                   1
>>>>         2 |     1 | PART_OF              | PART_OF relationship
>>>> predicate (type)              |         2 |           0
>>>> |                   1
>>>>         3 |     1 | RELATED_TO           | RELATED_TO relationship
>>>> predicate (type)           |         3 |           0 |
>>>> 1
>>>>         4 |     1 | REGULATES            | REGULATES relationship
>>>> predicate (type)            |         4 |           0 |
>>>> 1
>>>>         5 |     1 | POSITIVELY_REGULATES | POSITIVELY_REGULATES
>>>> relationship predicate (type) |         5 |           0
>>>> |                   1
>>>>         6 |     1 | NEGATIVELY_REGULATES | NEGATIVELY_REGULATES
>>>> relationship predicate (type) |         6 |           0
>>>> |                   1
>>>> (6 rows)
>>>>
>>>> I wan to know if your script can only load the 6 fixed relationshiptypes
>>>> rather than any other arbitrary relationshiptype.
>>>>
>>>> Weixia
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America
>>>> contest
>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and
>>>> Canada
>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in
>>>> marketing
>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>>> http://p.sf.net/sfu/nokia-dev2dev
>>>> _______________________________________________
>>>> Gmod-schema mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> http://p.sf.net/sfu/nokia-dev2dev
>> _______________________________________________
>> 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
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>

------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
wyu
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Re: can gmod_load_cvterms.pl load any arbitrary relationshiptype?

wyu
My problem is not only to load an ontology, but to update it. Before I
used stag-storenode.pl to load a custom ontology, it works fine. But I
got a trouble to update it. So I changed to use gmod_load_cvterms.pl
script.

Weixia
Daniel Quest wrote:

> I have no idea if this is helpful or even interesting...  I was having
> some trouble figuring out how to get OWL ontologies loaded into Chado.
>  So I wrote a java-jena based ontology loader into chado.  It still is
> lacking some features, but it is obvious how I could include those
> given time.  Hope this is interesting to people.  I probably should
> have asked the GMODSchema group how to deal with this before I wrote
> the tool, but It really helped me understand what goes into what
> table.
>
> Thanks
> -Daniel
>
> On Mon, Oct 25, 2010 at 1:44 PM, Scott Cain <[hidden email]> wrote:
>  
>> Hi Naama,
>>
>> The make ontologies command is using go-perl under the hood,
>> converting obo files to chadoxml.  I'm reasonably sure it does see
>> typedefs; the relationship ontology loaded with it has 26 rows.
>>
>> Scott
>>
>>
>> On Mon, Oct 25, 2010 at 12:21 PM, Naama Menda <[hidden email]> wrote:
>>    
>>> I think one of the problem is that bioperl's obo parser does not handle
>>> 'typedefs'
>>>
>>> Since RO has no 'Term' stanza, but just 'typedefs' , the loaded finds only
>>> the relationships, which is why you see 6 terms.
>>>
>>> I'll have to look more into this and see where the parsing is happening, and
>>> how 'make ontologies' handles this.
>>>
>>> -Naama
>>>
>>>
>>>
>>> On Fri, Oct 22, 2010 at 11:47 PM, Naama Menda <[hidden email]> wrote:
>>>      
>>>> could you send me the output of the loading script? (you can use the -o
>>>> flag to write to an outfile)
>>>> Thanks!
>>>> -Naama
>>>>
>>>> Naama Menda
>>>> Boyce Thompson Institute for Plant Research
>>>> Tower Rd
>>>> Ithaca NY 14853
>>>> USA
>>>>
>>>> (607) 254 3569
>>>> Sol Genomics Network
>>>> http://solgenomics.net/
>>>> [hidden email]
>>>>
>>>>
>>>> On Fri, Oct 22, 2010 at 6:11 PM, Weixia Yu <[hidden email]> wrote:
>>>>        
>>>>> Hi Naama,
>>>>>
>>>>> When I use your script gmod_load_cvterms.pl to load a obo file, I got a
>>>>> warning: "Relationship ontology must be loaded first!!". So I download a
>>>>> ro.obo file from http://www.obofoundry.org/ro/ro.obo.  After I ran  the
>>>>> script for the ro.obo file, I got 6 relationshiptype are stored in
>>>>> cvterm table:
>>>>>
>>>>> cvterm_id | cv_id |         name         |
>>>>> definition                     | dbxref_id | is_obsolete |
>>>>> is_relationshiptype
>>>>>
>>>>> -----------+-------+----------------------+----------------------------------------------------+-----------+-------------+---------------------
>>>>>         1 |     1 | IS_A                 | IS_A relationship predicate
>>>>> (type)                 |         1 |           0 |                   1
>>>>>         2 |     1 | PART_OF              | PART_OF relationship
>>>>> predicate (type)              |         2 |           0
>>>>> |                   1
>>>>>         3 |     1 | RELATED_TO           | RELATED_TO relationship
>>>>> predicate (type)           |         3 |           0 |
>>>>> 1
>>>>>         4 |     1 | REGULATES            | REGULATES relationship
>>>>> predicate (type)            |         4 |           0 |
>>>>> 1
>>>>>         5 |     1 | POSITIVELY_REGULATES | POSITIVELY_REGULATES
>>>>> relationship predicate (type) |         5 |           0
>>>>> |                   1
>>>>>         6 |     1 | NEGATIVELY_REGULATES | NEGATIVELY_REGULATES
>>>>> relationship predicate (type) |         6 |           0
>>>>> |                   1
>>>>> (6 rows)
>>>>>
>>>>> I wan to know if your script can only load the 6 fixed relationshiptypes
>>>>> rather than any other arbitrary relationshiptype.
>>>>>
>>>>> Weixia
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America
>>>>> contest
>>>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and
>>>>> Canada
>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in
>>>>> marketing
>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>>>> http://p.sf.net/sfu/nokia-dev2dev
>>>>> _______________________________________________
>>>>> Gmod-schema mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>          
>>> ------------------------------------------------------------------------------
>>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>>> http://p.sf.net/sfu/nokia-dev2dev
>>> _______________________________________________
>>> 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
>>
>> ------------------------------------------------------------------------------
>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> http://p.sf.net/sfu/nokia-dev2dev
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>    
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>  


------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema