Unable to find a 'part_of' term in the relationship ontology

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Unable to find a 'part_of' term in the relationship ontology

Karl O. Pinc
Hi,

I tried loading a gff file for baboons and got the
error:

Unable to find a 'part_of' term in the relationship ontology

But there does seem to be such a term.  (See below.)

This is after setting up chado from HEAD
according to INSTALL.Chado and loading all the
ontologies except the plant ontology.

Any idea what's wrong?  How I can fix it?

(This is still in the testing stages so I could
always just delete the db and start over,
but it'd be nice to know more about what's
going on and how to fix things.)

Thanks.

Regards,

Karl

------------------<snip>--------------
export GMOD_ROOT=/usr/local/gmod ; \
        export CHADO_DB_NAME=chado_test ; \
        export CHADO_DB_USERNAME=babase_admin ; \
        export CHADO_DB_HOST=localhost ; \
        gmod_bulk_load_gff3.pl --organism baboon \
                               --gfffile
ref_Panu_2.0_top_level.sorted.gff3


WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the
database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the chado_test database
(This may take a while ...)
Unable to find srcfeature NC_018152.1 in the database.
Perhaps you need to rerun your data load with the '--recreate_cache'
option. at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 4603,
<GEN0> line 2.
        Bio::GMOD::DB::Adapter::src_second_chance
(Bio::GMOD::DB::Adapter=HASH(0x33fdb28),
Bio::SeqFeature::Annotated=HASH(0x36ef198)) called at /usr/local/bin/
gmod_bulk_load_gff3.pl line 854

Abnormal termination, trying to clean up...

Attempting to clean up the loader temp table (so that --recreate_cache
won't be needed)...
Trying to remove the run lock (so that --remove_lock won't be
needed)...
Exiting...
make: *** [panu] Error 1
[kop@papio gff]$ psql chado_test
psql (9.1.12)
Type "help" for help.

chado_test=> select * from cvterm where cvterm.name = 'part_of';
 cvterm_id | cv_id |  name   | definition | dbxref_id | is_obsolete |
is_relatio
nshiptype
-----------+-------+---------+------------+-----------+-------------
+-----------
----------
        66 |    13 | part_of |            |        68 |           0 |  
       
        1
       124 |    21 | part_of |            |       150 |           0 |  
       
        1
(2 rows)

chado_test=> Select cvterm.*,cv.name from cvterm join cv using (cv_id)
where cvterm.name = 'part_of';
 cvterm_id | cv_id |  name   | definition | dbxref_id | is_obsolete |
is_relatio
nshiptype |     name    
-----------+-------+---------+------------+-----------+-------------
+-----------
----------+--------------
        66 |    13 | part_of |            |        68 |           0 |  
       
        1 | relationship
       124 |    21 | part_of |            |       150 |           0 |  
       
        1 | external
(2 rows)
------------------<snip>--------------

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

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Re: Unable to find a 'part_of' term in the relationship ontology

Karl O. Pinc
Can somebody give me a clue here as to where the
'external' cv ontology is coming from and, perhaps,
how to get rid of it?

On 03/01/2014 09:15:57 PM, Karl O. Pinc wrote:

> Hi,
>
> I tried loading a gff file for baboons and got the
> error:
>
> Unable to find a 'part_of' term in the relationship ontology
>
> But there does seem to be such a term.  (See below.)
>
> This is after setting up chado from HEAD
> according to INSTALL.Chado and loading all the
> ontologies except the plant ontology.
>
> Any idea what's wrong?  How I can fix it?
>
> (This is still in the testing stages so I could
> always just delete the db and start over,
> but it'd be nice to know more about what's
> going on and how to fix things.)
>
> Thanks.
>
> Regards,
>
> Karl
>
> ------------------<snip>--------------
> export GMOD_ROOT=/usr/local/gmod ; \
> export CHADO_DB_NAME=chado_test ; \
> export CHADO_DB_USERNAME=babase_admin ; \
> export CHADO_DB_HOST=localhost ; \
> gmod_bulk_load_gff3.pl --organism baboon \
>                       --gfffile
> ref_Panu_2.0_top_level.sorted.gff3
>
>
> WARNING:
> Unable to find a 'part_of' term in the relationship ontology;
> It's absense indicates that there is something really wrong with the
> database.
> Consider stopping and checking the state of your cvterm table.
>
>
> Preparing data for inserting into the chado_test database
> (This may take a while ...)
> Unable to find srcfeature NC_018152.1 in the database.
> Perhaps you need to rerun your data load with the '--recreate_cache'
> option. at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 4603,
> <GEN0> line 2.
> Bio::GMOD::DB::Adapter::src_second_chance
> (Bio::GMOD::DB::Adapter=HASH(0x33fdb28),
> Bio::SeqFeature::Annotated=HASH(0x36ef198)) called at /usr/local/bin/
> gmod_bulk_load_gff3.pl line 854
>
> Abnormal termination, trying to clean up...
>
> Attempting to clean up the loader temp table (so that --
> recreate_cache
> won't be needed)...
> Trying to remove the run lock (so that --remove_lock won't be
> needed)...
> Exiting...
> make: *** [panu] Error 1
> [kop@papio gff]$ psql chado_test
> psql (9.1.12)
> Type "help" for help.
>
> chado_test=> select * from cvterm where cvterm.name = 'part_of';
>  cvterm_id | cv_id |  name   | definition | dbxref_id | is_obsolete |
> is_relatio
> nshiptype
> -----------+-------+---------+------------+-----------+-------------
> +-----------
> ----------
>         66 |    13 | part_of |            |        68 |           0 |
>  
>        
>         1
>        124 |    21 | part_of |            |       150 |           0 |
>  
>        
>         1
> (2 rows)
>
> chado_test=> Select cvterm.*,cv.name from cvterm join cv using
> (cv_id)
>
> where cvterm.name = 'part_of';
>  cvterm_id | cv_id |  name   | definition | dbxref_id | is_obsolete |
> is_relatio
> nshiptype |     name    
> -----------+-------+---------+------------+-----------+-------------
> +-----------
> ----------+--------------
>         66 |    13 | part_of |            |        68 |           0 |
>  
>        
>         1 | relationship
>        124 |    21 | part_of |            |       150 |           0 |
>  
>        
>         1 | external
> (2 rows)
> ------------------<snip>--------------
>
> Karl <[hidden email]>
> Free Software:  "You don't pay back, you pay forward."
>                  -- Robert A. Heinlein
>
> ------------------------------------------------------------------------------
> Flow-based real-time traffic analytics software. Cisco certified
> tool.
> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
> Customize your own dashboards, set traffic alerts and generate
> reports.
> Network behavioral analysis & security monitoring. All-in-one tool.
> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/
> ostg.clktrk
> _______________________________________________
> 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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With Perforce, you get hassle-free workflows. Merge that actually works.
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Re: Unable to find a 'part_of' term in the relationship ontology

Karl O. Pinc
On 03/04/2014 09:19:14 PM, Karl O. Pinc wrote:
> Can somebody give me a clue here as to where the
> 'external' cv ontology is coming from and, perhaps,
> how to get rid of it?

Seems to be part of
http://www.geneontology.org/ontology/gene_ontology.obo

And the readme
http://www.geneontology.org/ontology/README
says that it's deliberately included.

So, something's broken.  But I don't know
how to fix it.

My best guess is to filter ontologies by
namespace on load so as not to get any
surprises but I can imagine other possibilities.

Please advise.  Thanks.

>
> On 03/01/2014 09:15:57 PM, Karl O. Pinc wrote:
> > Hi,
> >
> > I tried loading a gff file for baboons and got the
> > error:
> >
> > Unable to find a 'part_of' term in the relationship ontology
> >
> > But there does seem to be such a term.  (See below.)
> >
> > This is after setting up chado from HEAD
> > according to INSTALL.Chado and loading all the
> > ontologies except the plant ontology.
> >
> > Any idea what's wrong?  How I can fix it?
> >
> > (This is still in the testing stages so I could
> > always just delete the db and start over,
> > but it'd be nice to know more about what's
> > going on and how to fix things.)
> >
> > Thanks.
> >
> > Regards,
> >
> > Karl
> >
> > ------------------<snip>--------------
> > export GMOD_ROOT=/usr/local/gmod ; \
> > export CHADO_DB_NAME=chado_test ; \
> > export CHADO_DB_USERNAME=babase_admin ; \
> > export CHADO_DB_HOST=localhost ; \
> > gmod_bulk_load_gff3.pl --organism baboon \
> >                       --gfffile
> > ref_Panu_2.0_top_level.sorted.gff3
> >
> >
> > WARNING:
> > Unable to find a 'part_of' term in the relationship ontology;
> > It's absense indicates that there is something really wrong with
> the
>
> > database.
> > Consider stopping and checking the state of your cvterm table.
> >
> >
> > Preparing data for inserting into the chado_test database
> > (This may take a while ...)
> > Unable to find srcfeature NC_018152.1 in the database.
> > Perhaps you need to rerun your data load with the '--
> recreate_cache'
>
> > option. at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 4603,
> > <GEN0> line 2.
> > Bio::GMOD::DB::Adapter::src_second_chance
> > (Bio::GMOD::DB::Adapter=HASH(0x33fdb28),
> > Bio::SeqFeature::Annotated=HASH(0x36ef198)) called at
> /usr/local/bin/
> > gmod_bulk_load_gff3.pl line 854
> >
> > Abnormal termination, trying to clean up...
> >
> > Attempting to clean up the loader temp table (so that --
> > recreate_cache
> > won't be needed)...
> > Trying to remove the run lock (so that --remove_lock won't be
> > needed)...
> > Exiting...
> > make: *** [panu] Error 1
> > [kop@papio gff]$ psql chado_test
> > psql (9.1.12)
> > Type "help" for help.
> >
> > chado_test=> select * from cvterm where cvterm.name = 'part_of';
> >  cvterm_id | cv_id |  name   | definition | dbxref_id | is_obsolete
> |
> > is_relatio
> > nshiptype
> > -----------+-------+---------+------------+-----------
> +-------------
> > +-----------
> > ----------
> >         66 |    13 | part_of |            |        68 |           0
> |
> >  
> >        
> >         1
> >        124 |    21 | part_of |            |       150 |           0
> |
> >  
> >        
> >         1
> > (2 rows)
> >
> > chado_test=> Select cvterm.*,cv.name from cvterm join cv using
> > (cv_id)
> >
> > where cvterm.name = 'part_of';
> >  cvterm_id | cv_id |  name   | definition | dbxref_id | is_obsolete
> |
> > is_relatio
> > nshiptype |     name    
> > -----------+-------+---------+------------+-----------
> +-------------
> > +-----------
> > ----------+--------------
> >         66 |    13 | part_of |            |        68 |           0
> |
> >  
> >        
> >         1 | relationship
> >        124 |    21 | part_of |            |       150 |           0
> |
> >  
> >        
> >         1 | external
> > (2 rows)
> > ------------------<snip>--------------
> >
> > Karl <[hidden email]>
> > Free Software:  "You don't pay back, you pay forward."
> >                  -- Robert A. Heinlein
> >
> >
> ------------------------------------------------------------------------------
> > Flow-based real-time traffic analytics software. Cisco certified
> > tool.
> > Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow
> Analyzer
> > Customize your own dashboards, set traffic alerts and generate
> > reports.
> > Network behavioral analysis & security monitoring. All-in-one tool.
> > http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/
> > ostg.clktrk
> > _______________________________________________
> > 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
>
> ------------------------------------------------------------------------------
> Subversion Kills Productivity. Get off Subversion & Make the Move to
> Perforce.
> With Perforce, you get hassle-free workflows. Merge that actually
> works.
> Faster operations. Version large binaries.  Built-in WAN optimization
> and the
> freedom to use Git, Perforce or both. Make the move to Perforce.
> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/
> ostg.clktrk
> _______________________________________________
> 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

------------------------------------------------------------------------------
Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce.
With Perforce, you get hassle-free workflows. Merge that actually works.
Faster operations. Version large binaries.  Built-in WAN optimization and the
freedom to use Git, Perforce or both. Make the move to Perforce.
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Re: Unable to find a 'part_of' term in the relationship ontology

Hilmar Lapp-3
Normally part_of and other relations would come from RO, the Relations Ontology. However, I don't know how the Chado pre-population with ontologies is set up, and an ontology name of "external" certainly makes no sense to me, which just goes to show that I have no understanding of how this is set up to work, so my comment may be rather useless.

  -hilmar  


On Wed, Mar 5, 2014 at 12:16 AM, Karl O. Pinc <[hidden email]> wrote:
On 03/04/2014 09:19:14 PM, Karl O. Pinc wrote:
> Can somebody give me a clue here as to where the
> 'external' cv ontology is coming from and, perhaps,
> how to get rid of it?

Seems to be part of
http://www.geneontology.org/ontology/gene_ontology.obo

And the readme
http://www.geneontology.org/ontology/README
says that it's deliberately included.

So, something's broken.  But I don't know
how to fix it.

My best guess is to filter ontologies by
namespace on load so as not to get any
surprises but I can imagine other possibilities.

Please advise.  Thanks.

>
> On 03/01/2014 09:15:57 PM, Karl O. Pinc wrote:
> > Hi,
> >
> > I tried loading a gff file for baboons and got the
> > error:
> >
> > Unable to find a 'part_of' term in the relationship ontology
> >
> > But there does seem to be such a term.  (See below.)
> >
> > This is after setting up chado from HEAD
> > according to INSTALL.Chado and loading all the
> > ontologies except the plant ontology.
> >
> > Any idea what's wrong?  How I can fix it?
> >
> > (This is still in the testing stages so I could
> > always just delete the db and start over,
> > but it'd be nice to know more about what's
> > going on and how to fix things.)
> >
> > Thanks.
> >
> > Regards,
> >
> > Karl
> >
> > ------------------<snip>--------------
> > export GMOD_ROOT=/usr/local/gmod ; \
> >     export CHADO_DB_NAME=chado_test ; \
> >     export CHADO_DB_USERNAME=babase_admin ; \
> >     export CHADO_DB_HOST=localhost ; \
> >     gmod_bulk_load_gff3.pl --organism baboon \
> >                            --gfffile
> > ref_Panu_2.0_top_level.sorted.gff3
> >
> >
> > WARNING:
> > Unable to find a 'part_of' term in the relationship ontology;
> > It's absense indicates that there is something really wrong with
> the
>
> > database.
> > Consider stopping and checking the state of your cvterm table.
> >
> >
> > Preparing data for inserting into the chado_test database
> > (This may take a while ...)
> > Unable to find srcfeature NC_018152.1 in the database.
> > Perhaps you need to rerun your data load with the '--
> recreate_cache'
>
> > option. at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 4603,
> > <GEN0> line 2.
> >     Bio::GMOD::DB::Adapter::src_second_chance
> > (Bio::GMOD::DB::Adapter=HASH(0x33fdb28),
> > Bio::SeqFeature::Annotated=HASH(0x36ef198)) called at
> /usr/local/bin/
> > gmod_bulk_load_gff3.pl line 854
> >
> > Abnormal termination, trying to clean up...
> >
> > Attempting to clean up the loader temp table (so that --
> > recreate_cache
> > won't be needed)...
> > Trying to remove the run lock (so that --remove_lock won't be
> > needed)...
> > Exiting...
> > make: *** [panu] Error 1
> > [kop@papio gff]$ psql chado_test
> > psql (9.1.12)
> > Type "help" for help.
> >
> > chado_test=> select * from cvterm where cvterm.name = 'part_of';
> >  cvterm_id | cv_id |  name   | definition | dbxref_id | is_obsolete
> |
> > is_relatio
> > nshiptype
> > -----------+-------+---------+------------+-----------
> +-------------
> > +-----------
> > ----------
> >         66 |    13 | part_of |            |        68 |           0
> |
> >
> >
> >         1
> >        124 |    21 | part_of |            |       150 |           0
> |
> >
> >
> >         1
> > (2 rows)
> >
> > chado_test=> Select cvterm.*,cv.name from cvterm join cv using
> > (cv_id)
> >
> > where cvterm.name = 'part_of';
> >  cvterm_id | cv_id |  name   | definition | dbxref_id | is_obsolete
> |
> > is_relatio
> > nshiptype |     name
> > -----------+-------+---------+------------+-----------
> +-------------
> > +-----------
> > ----------+--------------
> >         66 |    13 | part_of |            |        68 |           0
> |
> >
> >
> >         1 | relationship
> >        124 |    21 | part_of |            |       150 |           0
> |
> >
> >
> >         1 | external
> > (2 rows)
> > ------------------<snip>--------------
> >
> > Karl <[hidden email]>
> > Free Software:  "You don't pay back, you pay forward."
> >                  -- Robert A. Heinlein
> >
> >
> ------------------------------------------------------------------------------
> > Flow-based real-time traffic analytics software. Cisco certified
> > tool.
> > Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow
> Analyzer
> > Customize your own dashboards, set traffic alerts and generate
> > reports.
> > Network behavioral analysis & security monitoring. All-in-one tool.
> > http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/
> > ostg.clktrk
> > _______________________________________________
> > 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
>
> ------------------------------------------------------------------------------
> Subversion Kills Productivity. Get off Subversion & Make the Move to
> Perforce.
> With Perforce, you get hassle-free workflows. Merge that actually
> works.
> Faster operations. Version large binaries.  Built-in WAN optimization
> and the
> freedom to use Git, Perforce or both. Make the move to Perforce.
> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/
> ostg.clktrk
> _______________________________________________
> 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

------------------------------------------------------------------------------
Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce.
With Perforce, you get hassle-free workflows. Merge that actually works.
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freedom to use Git, Perforce or both. Make the move to Perforce.
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--
Hilmar Lapp -:- lappland.io


------------------------------------------------------------------------------
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Re: Unable to find a 'part_of' term in the relationship ontology

Karl O. Pinc
On 03/05/2014 08:29:25 AM, Hilmar Lapp wrote:
> Normally part_of and other relations would come from RO, the
> Relations
> Ontology. However, I don't know how the Chado pre-population with
> ontologies is set up, and an ontology name of "external" certainly
> makes no
> sense to me, which just goes to show that I have no understanding of
> how
> this is set up to work, so my comment may be rather useless.

Thanks for the reply anyway.  I eventually figured out enough
about perl packaging to determine the cause,
although I don't know the right fix.  (See my previous message
in this thread.)  Either the gene ontology project is
distributing brokenness or chado hasn't kept up, ... or
something else.


Karl <[hidden email]>
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Re: Unable to find a 'part_of' term in the relationship ontology

Siddhartha Basu
On Wed, 05 Mar 2014, Karl O. Pinc wrote:

> On 03/05/2014 08:29:25 AM, Hilmar Lapp wrote:
> > Normally part_of and other relations would come from RO, the
> > Relations
> > Ontology. However, I don't know how the Chado pre-population with
> > ontologies is set up, and an ontology name of "external" certainly
> > makes no
> > sense to me, which just goes to show that I have no understanding of
> > how
> > this is set up to work, so my comment may be rather useless.
>
> Thanks for the reply anyway.  I eventually figured out enough
> about perl packaging to determine the cause,
> although I don't know the right fix.  (See my previous message
> in this thread.)  Either the gene ontology project is
> distributing brokenness or chado hasn't kept up, ... or
> something else.

Just wondering if have you loaded the sequence ontology(SO) before the gff3
bulk load. The bulk loader might be looking for part_of under sequence
namespace.

>
>
> Karl <[hidden email]>
> Free Software:  "You don't pay back, you pay forward."
>                  -- Robert A. Heinlein
>
> ------------------------------------------------------------------------------
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Re: Unable to find a 'part_of' term in the relationship ontology

Scott Cain
No, it looks in RO (I was thinking maybe there was a bug where it didn't specify what cv to looking, but it does specify "relationship").

Karl,

In your database can you do a select * from cv?  I'm wondering what the names of the ontologies are?  Given Chris's comment about changing what cv.name means, I'm wondering if some OBO files have changed what is in that space.

Scott


Sent from my iPhone

> On Mar 5, 2014, at 12:33 PM, Siddhartha Basu <[hidden email]> wrote:
>
>> On Wed, 05 Mar 2014, Karl O. Pinc wrote:
>>
>>> On 03/05/2014 08:29:25 AM, Hilmar Lapp wrote:
>>> Normally part_of and other relations would come from RO, the
>>> Relations
>>> Ontology. However, I don't know how the Chado pre-population with
>>> ontologies is set up, and an ontology name of "external" certainly
>>> makes no
>>> sense to me, which just goes to show that I have no understanding of
>>> how
>>> this is set up to work, so my comment may be rather useless.
>>
>> Thanks for the reply anyway.  I eventually figured out enough
>> about perl packaging to determine the cause,
>> although I don't know the right fix.  (See my previous message
>> in this thread.)  Either the gene ontology project is
>> distributing brokenness or chado hasn't kept up, ... or
>> something else.
>
> Just wondering if have you loaded the sequence ontology(SO) before the gff3
> bulk load. The bulk loader might be looking for part_of under sequence
> namespace.
>
>>
>>
>> Karl <[hidden email]>
>> Free Software:  "You don't pay back, you pay forward."
>>                 -- Robert A. Heinlein
>>
>> ------------------------------------------------------------------------------
>> Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce.
>> With Perforce, you get hassle-free workflows. Merge that actually works.
>> Faster operations. Version large binaries.  Built-in WAN optimization and the
>> freedom to use Git, Perforce or both. Make the move to Perforce.
>> http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk
>> _______________________________________________
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>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
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Re: Unable to find a 'part_of' term in the relationship ontology

Karl O. Pinc
On 03/05/2014 11:45:26 AM, Scott Cain wrote:
> No, it looks in RO (I was thinking maybe there was a bug where it
> didn't specify what cv to looking, but it does specify
> "relationship").

I was wondering about that.  Since you've got "namespaces"
it would make sense to use them.

>
> Karl,
>
> In your database can you do a select * from cv?  I'm wondering what
> the names of the ontologies are?  Given Chris's comment about
> changing
> what cv.name means, I'm wondering if some OBO files have changed what
> is in that space.


chado_test=> select * from cv order by cv_id;
 cv_id |         name         |                                    
definition  
                                 
-------+----------------------
+-------------------------------------------------
---------------------------------
     1 | null                 |
     2 | local                | Locally created terms
     3 | Statistical Terms    | Locally created terms for statistics
     4 | developmental stages |
     5 | autocreated          | Terms that are automatically inserted
by loading
 software
     6 | chado_properties     | Terms that are used in the chadoprop
table to de
scribe the state of the database
    13 | relationship         |
    14 | synonym_type         |
    15 | cvterm_property_type |
    16 | anonymous            |
    17 | sequence             |
    18 | biological_process   |
    19 | molecular_function   |
    20 | cellular_component   |
    21 | external             |
    22 | feature_property     |
(16 rows)


Siddhartha,

FYI.  I did a "make ontologies", loading everything but
the plant ontology (probably by typing the numbers 1,2,3, <whatever>
in order but I've forgotten if this is really true).

Then I followed the wiki gff loading instructions,
first sorting and then loading.


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

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Re: Unable to find a 'part_of' term in the relationship ontology

Scott Cain
Karl,

Is chado in the public schema or another one? (The most typical other would be a schema named 'chado'). If it's not in the public schema, is there an entry in the db conf in /usr/local/gmod/conf that points to that schema?

Scott


Sent from my iPhone

> On Mar 5, 2014, at 1:06 PM, "Karl O. Pinc" <[hidden email]> wrote:
>
>> On 03/05/2014 11:45:26 AM, Scott Cain wrote:
>> No, it looks in RO (I was thinking maybe there was a bug where it
>> didn't specify what cv to looking, but it does specify
>> "relationship").
>
> I was wondering about that.  Since you've got "namespaces"
> it would make sense to use them.
>
>>
>> Karl,
>>
>> In your database can you do a select * from cv?  I'm wondering what
>> the names of the ontologies are?  Given Chris's comment about
>> changing
>> what cv.name means, I'm wondering if some OBO files have changed what
>> is in that space.
>
>
> chado_test=> select * from cv order by cv_id;
> cv_id |         name         |                                    
> definition  
>
> -------+----------------------
> +-------------------------------------------------
> ---------------------------------
>     1 | null                 |
>     2 | local                | Locally created terms
>     3 | Statistical Terms    | Locally created terms for statistics
>     4 | developmental stages |
>     5 | autocreated          | Terms that are automatically inserted
> by loading
> software
>     6 | chado_properties     | Terms that are used in the chadoprop
> table to de
> scribe the state of the database
>    13 | relationship         |
>    14 | synonym_type         |
>    15 | cvterm_property_type |
>    16 | anonymous            |
>    17 | sequence             |
>    18 | biological_process   |
>    19 | molecular_function   |
>    20 | cellular_component   |
>    21 | external             |
>    22 | feature_property     |
> (16 rows)
>
>
> Siddhartha,
>
> FYI.  I did a "make ontologies", loading everything but
> the plant ontology (probably by typing the numbers 1,2,3, <whatever>
> in order but I've forgotten if this is really true).
>
> Then I followed the wiki gff loading instructions,
> first sorting and then loading.
>
>
> Karl <[hidden email]>
> Free Software:  "You don't pay back, you pay forward."
>                 -- Robert A. Heinlein

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Re: Unable to find a 'part_of' term in the relationship ontology

Karl O. Pinc
On 03/05/2014 12:12:31 PM, Scott Cain wrote:
> Karl,
>
> Is chado in the public schema or another one? (The most typical other
> would be a schema named 'chado'). If it's not in the public schema,
> is
> there an entry in the db conf in /usr/local/gmod/conf that points to
> that schema?

Chado is in the public schema.  (I've yet to figure out how to put
it in it's own schema.)   This is (AFAIK) a "default" install.
(It is off of HEAD....)



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

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Re: Unable to find a 'part_of' term in the relationship ontology

Karl O. Pinc
On 03/05/2014 12:27:09 PM, Karl O. Pinc wrote:
> On 03/05/2014 12:12:31 PM, Scott Cain wrote:
> > Karl,
> >
> > Is chado in the public schema or another one?

chado_test=> \dn
       List of schemas
     Name     |    Owner    
--------------+--------------
 frange       | babase_admin
 genetic_code | babase_admin
 public       | babase_admin
 so           | babase_admin
(4 rows)

chado_test=> show search_path;
  search_path  
----------------
 "$user",public
(1 row)




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

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Re: Unable to find a 'part_of' term in the relationship ontology

Karl O. Pinc
In reply to this post by Scott Cain
On 03/05/2014 12:12:31 PM, Scott Cain wrote:
> Is chado in the public schema or another one? (The most typical other
> would be a schema named 'chado'). If it's not in the public schema,
> is
> there an entry in the db conf in /usr/local/gmod/conf that points to
> that schema?

Scott,

FYI

I do have 2 conf files in /usr/local/gmod/conf (plus a default.conf
symlink and a gmod.conf).  They are for different dbs, chado_test.conf
and babase_copy.conf.  Both chado__test.conf and babase_copy.conf
have "DEFAULT=y" in them.  (I tried getting chado into it's own
schema in the babase_copy db and gave up and went to a "default"
install in a new db, chado_test.)  The default.conf symlink points to
chado_test.conf.

I've now changed babase_copy.conf to DEFAULT=n and the problem
remains....

Would it help to get you a Unix login?  I'll have to check
with my overlords first but don't imagine they'll be
a problem.


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

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Re: Unable to find a 'part_of' term in the relationship ontology

Scott Cain
Hi Karl,

I would be willing to take a look; that can certainly be a lot faster than emails back and forth.

Scott


Sent from my iPhone

> On Mar 5, 2014, at 1:51 PM, "Karl O. Pinc" <[hidden email]> wrote:
>
>> On 03/05/2014 12:12:31 PM, Scott Cain wrote:
>> Is chado in the public schema or another one? (The most typical other
>> would be a schema named 'chado'). If it's not in the public schema,
>> is
>> there an entry in the db conf in /usr/local/gmod/conf that points to
>> that schema?
>
> Scott,
>
> FYI
>
> I do have 2 conf files in /usr/local/gmod/conf (plus a default.conf
> symlink and a gmod.conf).  They are for different dbs, chado_test.conf
> and babase_copy.conf.  Both chado__test.conf and babase_copy.conf
> have "DEFAULT=y" in them.  (I tried getting chado into it's own
> schema in the babase_copy db and gave up and went to a "default"
> install in a new db, chado_test.)  The default.conf symlink points to
> chado_test.conf.
>
> I've now changed babase_copy.conf to DEFAULT=n and the problem
> remains....
>
> Would it help to get you a Unix login?  I'll have to check
> with my overlords first but don't imagine they'll be
> a problem.
>
>
> Karl <[hidden email]>
> Free Software:  "You don't pay back, you pay forward."
>                 -- Robert A. Heinlein

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