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What sequence ontology to get?

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What sequence ontology to get?

Karl O. Pinc
Hi,

Looks like the sequence ontology has moved from sourceforge
to github.  The url in chado/load/tt2/load.conf.tt2
no longer works.

What is the corresponding url on github?
Is it the first so download link of:
https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp-simple.obo

?

The various choices are at:
https://github.com/The-Sequence-Ontology/SO-Ontologies

Thanks.

Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Re: What sequence ontology to get?

Chris Mungall-5
I recommend using purls for all ontologies

E.g.

http://purl.obolibrary.org/obo/so.obo

These should remain stable allowing the underlying delivery system to
change

On 22 Jul 2015, at 16:04, Karl O. Pinc wrote:

> Hi,
>
> Looks like the sequence ontology has moved from sourceforge
> to github.  The url in chado/load/tt2/load.conf.tt2
> no longer works.
>
> What is the corresponding url on github?
> Is it the first so download link of:
> https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp-simple.obo
>
> ?
>
> The various choices are at:
> https://github.com/The-Sequence-Ontology/SO-Ontologies
>
> Thanks.
>
> Karl <[hidden email]>
> Free Software:  "You don't pay back, you pay forward."
>               -- Robert A. Heinlein
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

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Re: What sequence ontology to get?

Scott Cain
Hi Chris, 

I hadn't heard about the purl urls.  Is a list of them published somewhere?

Thanks,
Scott


On Wed, Jul 22, 2015 at 7:50 PM, Chris Mungall <[hidden email]> wrote:
I recommend using purls for all ontologies

E.g.

http://purl.obolibrary.org/obo/so.obo

These should remain stable allowing the underlying delivery system to
change

On 22 Jul 2015, at 16:04, Karl O. Pinc wrote:

> Hi,
>
> Looks like the sequence ontology has moved from sourceforge
> to github.  The url in chado/load/tt2/load.conf.tt2
> no longer works.
>
> What is the corresponding url on github?
> Is it the first so download link of:
> https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp-simple.obo
>
> ?
>
> The various choices are at:
> https://github.com/The-Sequence-Ontology/SO-Ontologies
>
> Thanks.
>
> Karl <[hidden email]>
> Free Software:  "You don't pay back, you pay forward."
>               -- Robert A. Heinlein
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

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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: What sequence ontology to get?

Chris Mungall-5
Yes and no.

The PURL for an OBO always follows the form documented here:
http://www.obofoundry.org/id-policy.shtml

So you can generate a list by taking the 'namespace' field here and
lowercasing:
http://obo-registry.googlecode.com/svn/trunk/metadata/ontologies.txt

Yes, that is a google code url and we do know it's shutting down. We're
going to move the OBO registry to a node server driven from a yaml file
but this is just volunteer work at the moment. When it's done, the
global metadata file will look like this:
https://github.com/OBOFoundry/omb/blob/master/data/repository.yaml



On 22 Jul 2015, at 17:05, Scott Cain wrote:

> Hi Chris,
>
> I hadn't heard about the purl urls.  Is a list of them published
> somewhere?
>
> Thanks,
> Scott
>
>
> On Wed, Jul 22, 2015 at 7:50 PM, Chris Mungall <[hidden email]>
> wrote:
>
>> I recommend using purls for all ontologies
>>
>> E.g.
>>
>> http://purl.obolibrary.org/obo/so.obo
>>
>> These should remain stable allowing the underlying delivery system to
>> change
>>
>> On 22 Jul 2015, at 16:04, Karl O. Pinc wrote:
>>
>>> Hi,
>>>
>>> Looks like the sequence ontology has moved from sourceforge
>>> to github.  The url in chado/load/tt2/load.conf.tt2
>>> no longer works.
>>>
>>> What is the corresponding url on github?
>>> Is it the first so download link of:
>>>
>> https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp-simple.obo
>>>
>>> ?
>>>
>>> The various choices are at:
>>> https://github.com/The-Sequence-Ontology/SO-Ontologies
>>>
>>> Thanks.
>>>
>>> Karl <[hidden email]>
>>> Free Software:  "You don't pay back, you pay forward."
>>>            -- Robert A. Heinlein
>>>
>>>
>> ------------------------------------------------------------------------------
>>> _______________________________________________
>>> 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
>>
>
>
>
> --
> ------------------------------------------------------------------------
> 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: What sequence ontology to get?

Karl O. Pinc
In reply to this post by Chris Mungall-5
On Wed, 22 Jul 2015 16:50:56 -0700
"Chris Mungall" <[hidden email]> wrote:

> I recommend using purls for all ontologies
>
> E.g.
>
> http://purl.obolibrary.org/obo/so.obo
>
> These should remain stable allowing the underlying delivery system to
> change

Ok.  Thanks.

So the correct SO to download is the so-xp.obo, right?
(That's what the prul points to.)

>
> On 22 Jul 2015, at 16:04, Karl O. Pinc wrote:
>
> > Hi,
> >
> > Looks like the sequence ontology has moved from sourceforge
> > to github.  The url in chado/load/tt2/load.conf.tt2
> > no longer works.
> >
> > What is the corresponding url on github?
> > Is it the first so download link of:
> > https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp-simple.obo
> >
> > ?
> >
> > The various choices are at:
> > https://github.com/The-Sequence-Ontology/SO-Ontologies
> >
> > Thanks.
> >
> > Karl <[hidden email]>
> > Free Software:  "You don't pay back, you pay forward."
> >               -- Robert A. Heinlein
> >
> > ------------------------------------------------------------------------------
> > _______________________________________________
> > Gmod-schema mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>





Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Re: What sequence ontology to get?

Chris Mungall-5
Yes, that's right (it may point to something else in the future, it shouldn't really be exposing the 'so-xp' filename, but this shouldn't affect anything)

On Wed, Jul 22, 2015 at 5:21 PM, Karl O. Pinc <[hidden email]> wrote:
On Wed, 22 Jul 2015 16:50:56 -0700
"Chris Mungall" <[hidden email]> wrote:

> I recommend using purls for all ontologies
>
> E.g.
>
> http://purl.obolibrary.org/obo/so.obo
>
> These should remain stable allowing the underlying delivery system to
> change

Ok.  Thanks.

So the correct SO to download is the so-xp.obo, right?
(That's what the prul points to.)

>
> On 22 Jul 2015, at 16:04, Karl O. Pinc wrote:
>
> > Hi,
> >
> > Looks like the sequence ontology has moved from sourceforge
> > to github.  The url in chado/load/tt2/load.conf.tt2
> > no longer works.
> >
> > What is the corresponding url on github?
> > Is it the first so download link of:
> > https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp-simple.obo
> >
> > ?
> >
> > The various choices are at:
> > https://github.com/The-Sequence-Ontology/SO-Ontologies
> >
> > Thanks.
> >
> > Karl <[hidden email]>
> > Free Software:  "You don't pay back, you pay forward."
> >               -- Robert A. Heinlein
> >
> > ------------------------------------------------------------------------------
> > _______________________________________________
> > Gmod-schema mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>





Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein


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Re: What sequence ontology to get?

Karl O. Pinc
On Mon, 27 Jul 2015 13:44:36 -0700
Chris Mungall <[hidden email]> wrote:

> Yes, that's right (it may point to something else in the future, it
> shouldn't really be exposing the 'so-xp' filename, but this shouldn't
> affect anything)
>
> On Wed, Jul 22, 2015 at 5:21 PM, Karl O. Pinc <[hidden email]> wrote:

> > So the correct SO to download is the so-xp.obo, right?

Thanks!





Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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