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

Seth_m55
Hi Everyone,

I'm trying to setup a Chado DB for some local testing before implementing changes to the webserver, however, I'm running into an odd error.  I make the chado database and prepare it for gmod_bulk_load_gff3.pl but I get a warning as soon as I start:

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.

Then it appears to continue loading the DB.  I tried Manually loading the ontologies and still got the warning.  I tried deleting the downloaded ontologies and reloading (automated and manual) and still got the warning.  Next, I hit google and read one issue is that the plant onotology now has a 'part_of' term as well, and the advice there was to delete the PO entry, which I did, but still got the warning.  I then manually reloaded the RO, but I still got the warning.

Any ideas?

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

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

Scott Cain
Hi Seth,

The query the loader is trying to execute is this:

select cvterm_id from cvterm where name = 'part_of' and cv_id in (
      SELECT cv_id FROM cv WHERE name='relationship')

(ugh, subselects).  If you run this in the psql shell, what do you get?  Assuming nothing, what do you get if you do this:

SELECT cv.name, cvterm.cvterm_id, cvterm.name FROM 
  cv JOIN cvterm ON (cv.cv_id = cvterm.cv_id) where cvterm.name='part_of'

Scott


On Wed, Apr 30, 2014 at 1:32 PM, Seth Munholland <[hidden email]> wrote:
>
> Hi Everyone,
>
> I'm trying to setup a Chado DB for some local testing before implementing changes to the webserver, however, I'm running into an odd error.  I make the chado database and prepare it for gmod_bulk_load_gff3.pl but I get a warning as soon as I start:
>
> 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.
>
> Then it appears to continue loading the DB.  I tried Manually loading the ontologies and still got the warning.  I tried deleting the downloaded ontologies and reloading (automated and manual) and still got the warning.  Next, I hit google and read one issue is that the plant onotology now has a 'part_of' term as well, and the advice there was to delete the PO entry, which I did, but still got the warning.  I then manually reloaded the RO, but I still got the warning.
>
> Any ideas?
>
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: (519) 253-3000 Ext: 4755
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> 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

------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
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Re: Unable to find a 'part_of' term in the relationship ontology

Seth_m55
Hi Scott,

From the first script I got the following:

 cvterm_id
-----------
      3652
(1 row)


Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Wed, Apr 30, 2014 at 2:10 PM, Scott Cain <[hidden email]> wrote:
Hi Seth,

The query the loader is trying to execute is this:

select cvterm_id from cvterm where name = 'part_of' and cv_id in (
      SELECT cv_id FROM cv WHERE name='relationship')

(ugh, subselects).  If you run this in the psql shell, what do you get?  Assuming nothing, what do you get if you do this:

SELECT cv.name, cvterm.cvterm_id, cvterm.name FROM 
  cv JOIN cvterm ON (cv.cv_id = cvterm.cv_id) where cvterm.name='part_of'

Scott


On Wed, Apr 30, 2014 at 1:32 PM, Seth Munholland <[hidden email]> wrote:
>
> Hi Everyone,
>
> I'm trying to setup a Chado DB for some local testing before implementing changes to the webserver, however, I'm running into an odd error.  I make the chado database and prepare it for gmod_bulk_load_gff3.pl but I get a warning as soon as I start:
>
> 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.
>
> Then it appears to continue loading the DB.  I tried Manually loading the ontologies and still got the warning.  I tried deleting the downloaded ontologies and reloading (automated and manual) and still got the warning.  Next, I hit google and read one issue is that the plant onotology now has a 'part_of' term as well, and the advice there was to delete the PO entry, which I did, but still got the warning.  I then manually reloaded the RO, but I still got the warning.
>
> Any ideas?
>
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> 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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
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Re: Unable to find a 'part_of' term in the relationship ontology

Scott Cain
Strange, it gets one result, which is exactly what it should get.  Is your Chado in the public schema, or something else?


On Wed, Apr 30, 2014 at 2:12 PM, Seth Munholland <[hidden email]> wrote:
Hi Scott,

From the first script I got the following:

 cvterm_id
-----------
      3652
(1 row)


Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Wed, Apr 30, 2014 at 2:10 PM, Scott Cain <[hidden email]> wrote:
Hi Seth,

The query the loader is trying to execute is this:

select cvterm_id from cvterm where name = 'part_of' and cv_id in (
      SELECT cv_id FROM cv WHERE name='relationship')

(ugh, subselects).  If you run this in the psql shell, what do you get?  Assuming nothing, what do you get if you do this:

SELECT cv.name, cvterm.cvterm_id, cvterm.name FROM 
  cv JOIN cvterm ON (cv.cv_id = cvterm.cv_id) where cvterm.name='part_of'

Scott


On Wed, Apr 30, 2014 at 1:32 PM, Seth Munholland <[hidden email]> wrote:
>
> Hi Everyone,
>
> I'm trying to setup a Chado DB for some local testing before implementing changes to the webserver, however, I'm running into an odd error.  I make the chado database and prepare it for gmod_bulk_load_gff3.pl but I get a warning as soon as I start:
>
> 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.
>
> Then it appears to continue loading the DB.  I tried Manually loading the ontologies and still got the warning.  I tried deleting the downloaded ontologies and reloading (automated and manual) and still got the warning.  Next, I hit google and read one issue is that the plant onotology now has a 'part_of' term as well, and the advice there was to delete the PO entry, which I did, but still got the warning.  I then manually reloaded the RO, but I still got the warning.
>
> Any ideas?
>
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> 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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




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

------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
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Re: Unable to find a 'part_of' term in the relationship ontology

Scott Cain
cc'ing schema list


On Wed, Apr 30, 2014 at 2:33 PM, Scott Cain <[hidden email]> wrote:
Hi Seth, 

Are you working from a svn checkout?  I just looked at the svn history of Adapter.pm where I added the code to give this warning, and much to my horror, I realized that there is no "if" statement attached to that warning, so it *always* prints out, regardless of what the status of finding part_of is.  

So, for now, you can ignore that message--sorry for the hassle.  I'll fix it in git as soon as there is a git repo.

Scott



On Wed, Apr 30, 2014 at 2:19 PM, Seth Munholland <[hidden email]> wrote:
It is public.  Just to see I ran the second script and got the following:

      name      | cvterm_id |  name  
----------------+-----------+---------
 relationship   |      3652 | part_of
 plant_ontology |        67 | part_of
(2 rows)

Apparently I didn't properly delete the PO entry.  I re-entered the delete command:

DELETE FROM cvterm WHERE cvterm_id = 67;

Then ran the second select script again to get:

     name     | cvterm_id |  name  
--------------+-----------+---------
 relationship |      3652 | part_of
(1 row)


Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Wed, Apr 30, 2014 at 2:15 PM, Scott Cain <[hidden email]> wrote:
Strange, it gets one result, which is exactly what it should get.  Is your Chado in the public schema, or something else?


On Wed, Apr 30, 2014 at 2:12 PM, Seth Munholland <[hidden email]> wrote:
Hi Scott,

From the first script I got the following:

 cvterm_id
-----------
      3652
(1 row)


Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Wed, Apr 30, 2014 at 2:10 PM, Scott Cain <[hidden email]> wrote:
Hi Seth,

The query the loader is trying to execute is this:

select cvterm_id from cvterm where name = 'part_of' and cv_id in (
      SELECT cv_id FROM cv WHERE name='relationship')

(ugh, subselects).  If you run this in the psql shell, what do you get?  Assuming nothing, what do you get if you do this:

SELECT cv.name, cvterm.cvterm_id, cvterm.name FROM 
  cv JOIN cvterm ON (cv.cv_id = cvterm.cv_id) where cvterm.name='part_of'

Scott


On Wed, Apr 30, 2014 at 1:32 PM, Seth Munholland <[hidden email]> wrote:
>
> Hi Everyone,
>
> I'm trying to setup a Chado DB for some local testing before implementing changes to the webserver, however, I'm running into an odd error.  I make the chado database and prepare it for gmod_bulk_load_gff3.pl but I get a warning as soon as I start:
>
> 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.
>
> Then it appears to continue loading the DB.  I tried Manually loading the ontologies and still got the warning.  I tried deleting the downloaded ontologies and reloading (automated and manual) and still got the warning.  Next, I hit google and read one issue is that the plant onotology now has a 'part_of' term as well, and the advice there was to delete the PO entry, which I did, but still got the warning.  I then manually reloaded the RO, but I still got the warning.
>
> Any ideas?
>
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> 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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
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




--
------------------------------------------------------------------------
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



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

------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
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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 Seth_m55
On 04/30/2014 12:32:19 PM, Seth Munholland wrote:

> Hi Everyone,
>
> I'm trying to setup a Chado DB for some local testing before
> implementing
> changes to the webserver, however, I'm running into an odd error.  I
> make
> the chado database and prepare it for gmod_bulk_load_gff3.pl but I
> get
> a
> warning as soon as I start:
>
> 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.
>
> Then it appears to continue loading the DB.  I tried Manually loading
> the
> ontologies and still got the warning.  I tried deleting the
> downloaded
> ontologies and reloading (automated and manual) and still got the
> warning.
> Next, I hit google and read one issue is that the plant onotology now
> has a
> 'part_of' term as well, and the advice there was to delete the PO
> entry,
> which I did, but still got the warning.  I then manually reloaded the
> RO,
> but I still got the warning.

Loading the ontologies into some schema other than public
you need to change line 37 of
/usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm
(!?)

It's broken.



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

------------------------------------------------------------------------------
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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
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Re: Unable to find a 'part_of' term in the relationship ontology

Seth_m55
In reply to this post by Scott Cain
Hi Scott,

It looks like I might still have an error somewhere.  Trying to load the annotation file gave me a whole ton of the following message:

No feature found for scaffold_6830, org_id:13 when trying to add sequence at /usr/local/share/perl/5.14.2/Bio/GMOD/DB/Adapter.pm line 2566, <GEN0> line 350109.

Looking back there is a contig entry for scaffold_6830  (as well as all the other scaffolds I've checked so far).  Is this an error in uploading, or another issue with Adapter.pm from the missing if?

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Wed, Apr 30, 2014 at 2:44 PM, Seth Munholland <[hidden email]> wrote:
Hi Scott,

Yes, I did grab this chado bundle via svn.  Thanks for clarifying!

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Wed, Apr 30, 2014 at 2:33 PM, Scott Cain <[hidden email]> wrote:
cc'ing schema list


On Wed, Apr 30, 2014 at 2:33 PM, Scott Cain <[hidden email]> wrote:
Hi Seth, 

Are you working from a svn checkout?  I just looked at the svn history of Adapter.pm where I added the code to give this warning, and much to my horror, I realized that there is no "if" statement attached to that warning, so it *always* prints out, regardless of what the status of finding part_of is.  

So, for now, you can ignore that message--sorry for the hassle.  I'll fix it in git as soon as there is a git repo.

Scott



On Wed, Apr 30, 2014 at 2:19 PM, Seth Munholland <[hidden email]> wrote:
It is public.  Just to see I ran the second script and got the following:

      name      | cvterm_id |  name  
----------------+-----------+---------
 relationship   |      3652 | part_of
 plant_ontology |        67 | part_of
(2 rows)

Apparently I didn't properly delete the PO entry.  I re-entered the delete command:

DELETE FROM cvterm WHERE cvterm_id = 67;

Then ran the second select script again to get:

     name     | cvterm_id |  name  
--------------+-----------+---------
 relationship |      3652 | part_of
(1 row)


Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Wed, Apr 30, 2014 at 2:15 PM, Scott Cain <[hidden email]> wrote:
Strange, it gets one result, which is exactly what it should get.  Is your Chado in the public schema, or something else?


On Wed, Apr 30, 2014 at 2:12 PM, Seth Munholland <[hidden email]> wrote:
Hi Scott,

From the first script I got the following:

 cvterm_id
-----------
      3652
(1 row)


Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Wed, Apr 30, 2014 at 2:10 PM, Scott Cain <[hidden email]> wrote:
Hi Seth,

The query the loader is trying to execute is this:

select cvterm_id from cvterm where name = 'part_of' and cv_id in (
      SELECT cv_id FROM cv WHERE name='relationship')

(ugh, subselects).  If you run this in the psql shell, what do you get?  Assuming nothing, what do you get if you do this:

SELECT cv.name, cvterm.cvterm_id, cvterm.name FROM 
  cv JOIN cvterm ON (cv.cv_id = cvterm.cv_id) where cvterm.name='part_of'

Scott


On Wed, Apr 30, 2014 at 1:32 PM, Seth Munholland <[hidden email]> wrote:
>
> Hi Everyone,
>
> I'm trying to setup a Chado DB for some local testing before implementing changes to the webserver, however, I'm running into an odd error.  I make the chado database and prepare it for gmod_bulk_load_gff3.pl but I get a warning as soon as I start:
>
> 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.
>
> Then it appears to continue loading the DB.  I tried Manually loading the ontologies and still got the warning.  I tried deleting the downloaded ontologies and reloading (automated and manual) and still got the warning.  Next, I hit google and read one issue is that the plant onotology now has a 'part_of' term as well, and the advice there was to delete the PO entry, which I did, but still got the warning.  I then manually reloaded the RO, but I still got the warning.
>
> Any ideas?
>
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> 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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
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




--
------------------------------------------------------------------------
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



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

Seth_m55
Hi Scott,

Nevermind, I went through my command and the gff3 that was being loaded and I missed that there was a sequence at the end of it, as such my command was missing the --nosequence option.

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Thu, May 1, 2014 at 11:17 AM, Seth Munholland <[hidden email]> wrote:
Hi Scott,

It looks like I might still have an error somewhere.  Trying to load the annotation file gave me a whole ton of the following message:

No feature found for scaffold_6830, org_id:13 when trying to add sequence at /usr/local/share/perl/5.14.2/Bio/GMOD/DB/Adapter.pm line 2566, <GEN0> line 350109.

Looking back there is a contig entry for scaffold_6830  (as well as all the other scaffolds I've checked so far).  Is this an error in uploading, or another issue with Adapter.pm from the missing if?

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Wed, Apr 30, 2014 at 2:44 PM, Seth Munholland <[hidden email]> wrote:
Hi Scott,

Yes, I did grab this chado bundle via svn.  Thanks for clarifying!

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Wed, Apr 30, 2014 at 2:33 PM, Scott Cain <[hidden email]> wrote:
cc'ing schema list


On Wed, Apr 30, 2014 at 2:33 PM, Scott Cain <[hidden email]> wrote:
Hi Seth, 

Are you working from a svn checkout?  I just looked at the svn history of Adapter.pm where I added the code to give this warning, and much to my horror, I realized that there is no "if" statement attached to that warning, so it *always* prints out, regardless of what the status of finding part_of is.  

So, for now, you can ignore that message--sorry for the hassle.  I'll fix it in git as soon as there is a git repo.

Scott



On Wed, Apr 30, 2014 at 2:19 PM, Seth Munholland <[hidden email]> wrote:
It is public.  Just to see I ran the second script and got the following:

      name      | cvterm_id |  name  
----------------+-----------+---------
 relationship   |      3652 | part_of
 plant_ontology |        67 | part_of
(2 rows)

Apparently I didn't properly delete the PO entry.  I re-entered the delete command:

DELETE FROM cvterm WHERE cvterm_id = 67;

Then ran the second select script again to get:

     name     | cvterm_id |  name  
--------------+-----------+---------
 relationship |      3652 | part_of
(1 row)


Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Wed, Apr 30, 2014 at 2:15 PM, Scott Cain <[hidden email]> wrote:
Strange, it gets one result, which is exactly what it should get.  Is your Chado in the public schema, or something else?


On Wed, Apr 30, 2014 at 2:12 PM, Seth Munholland <[hidden email]> wrote:
Hi Scott,

From the first script I got the following:

 cvterm_id
-----------
      3652
(1 row)


Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Wed, Apr 30, 2014 at 2:10 PM, Scott Cain <[hidden email]> wrote:
Hi Seth,

The query the loader is trying to execute is this:

select cvterm_id from cvterm where name = 'part_of' and cv_id in (
      SELECT cv_id FROM cv WHERE name='relationship')

(ugh, subselects).  If you run this in the psql shell, what do you get?  Assuming nothing, what do you get if you do this:

SELECT cv.name, cvterm.cvterm_id, cvterm.name FROM 
  cv JOIN cvterm ON (cv.cv_id = cvterm.cv_id) where cvterm.name='part_of'

Scott


On Wed, Apr 30, 2014 at 1:32 PM, Seth Munholland <[hidden email]> wrote:
>
> Hi Everyone,
>
> I'm trying to setup a Chado DB for some local testing before implementing changes to the webserver, however, I'm running into an odd error.  I make the chado database and prepare it for gmod_bulk_load_gff3.pl but I get a warning as soon as I start:
>
> 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.
>
> Then it appears to continue loading the DB.  I tried Manually loading the ontologies and still got the warning.  I tried deleting the downloaded ontologies and reloading (automated and manual) and still got the warning.  Next, I hit google and read one issue is that the plant onotology now has a 'part_of' term as well, and the advice there was to delete the PO entry, which I did, but still got the warning.  I then manually reloaded the RO, but I still got the warning.
>
> Any ideas?
>
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> 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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
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




--
------------------------------------------------------------------------
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



--
------------------------------------------------------------------------
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




------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
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Re: Unable to find a 'part_of' term in the relationship ontology

Seth_m55
Hi Scott,

I'm running into some other issues in this same DB setup, they may be unrelated, but I am curious what is provided by the Plant Ontology that would be missing elsewhere?  My genomes are all plant oriented so it made the sense to include PO in my chado DBs, but if it's causing this large an issue I'm wondering can I get away without including it?

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Thu, May 1, 2014 at 11:34 AM, Seth Munholland <[hidden email]> wrote:
Hi Scott,

Nevermind, I went through my command and the gff3 that was being loaded and I missed that there was a sequence at the end of it, as such my command was missing the --nosequence option.

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Thu, May 1, 2014 at 11:17 AM, Seth Munholland <[hidden email]> wrote:
Hi Scott,

It looks like I might still have an error somewhere.  Trying to load the annotation file gave me a whole ton of the following message:

No feature found for scaffold_6830, org_id:13 when trying to add sequence at /usr/local/share/perl/5.14.2/Bio/GMOD/DB/Adapter.pm line 2566, <GEN0> line 350109.

Looking back there is a contig entry for scaffold_6830  (as well as all the other scaffolds I've checked so far).  Is this an error in uploading, or another issue with Adapter.pm from the missing if?

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Wed, Apr 30, 2014 at 2:44 PM, Seth Munholland <[hidden email]> wrote:
Hi Scott,

Yes, I did grab this chado bundle via svn.  Thanks for clarifying!

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Wed, Apr 30, 2014 at 2:33 PM, Scott Cain <[hidden email]> wrote:
cc'ing schema list


On Wed, Apr 30, 2014 at 2:33 PM, Scott Cain <[hidden email]> wrote:
Hi Seth, 

Are you working from a svn checkout?  I just looked at the svn history of Adapter.pm where I added the code to give this warning, and much to my horror, I realized that there is no "if" statement attached to that warning, so it *always* prints out, regardless of what the status of finding part_of is.  

So, for now, you can ignore that message--sorry for the hassle.  I'll fix it in git as soon as there is a git repo.

Scott



On Wed, Apr 30, 2014 at 2:19 PM, Seth Munholland <[hidden email]> wrote:
It is public.  Just to see I ran the second script and got the following:

      name      | cvterm_id |  name  
----------------+-----------+---------
 relationship   |      3652 | part_of
 plant_ontology |        67 | part_of
(2 rows)

Apparently I didn't properly delete the PO entry.  I re-entered the delete command:

DELETE FROM cvterm WHERE cvterm_id = 67;

Then ran the second select script again to get:

     name     | cvterm_id |  name  
--------------+-----------+---------
 relationship |      3652 | part_of
(1 row)


Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Wed, Apr 30, 2014 at 2:15 PM, Scott Cain <[hidden email]> wrote:
Strange, it gets one result, which is exactly what it should get.  Is your Chado in the public schema, or something else?


On Wed, Apr 30, 2014 at 2:12 PM, Seth Munholland <[hidden email]> wrote:
Hi Scott,

From the first script I got the following:

 cvterm_id
-----------
      3652
(1 row)


Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Wed, Apr 30, 2014 at 2:10 PM, Scott Cain <[hidden email]> wrote:
Hi Seth,

The query the loader is trying to execute is this:

select cvterm_id from cvterm where name = 'part_of' and cv_id in (
      SELECT cv_id FROM cv WHERE name='relationship')

(ugh, subselects).  If you run this in the psql shell, what do you get?  Assuming nothing, what do you get if you do this:

SELECT cv.name, cvterm.cvterm_id, cvterm.name FROM 
  cv JOIN cvterm ON (cv.cv_id = cvterm.cv_id) where cvterm.name='part_of'

Scott


On Wed, Apr 30, 2014 at 1:32 PM, Seth Munholland <[hidden email]> wrote:
>
> Hi Everyone,
>
> I'm trying to setup a Chado DB for some local testing before implementing changes to the webserver, however, I'm running into an odd error.  I make the chado database and prepare it for gmod_bulk_load_gff3.pl but I get a warning as soon as I start:
>
> 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.
>
> Then it appears to continue loading the DB.  I tried Manually loading the ontologies and still got the warning.  I tried deleting the downloaded ontologies and reloading (automated and manual) and still got the warning.  Next, I hit google and read one issue is that the plant onotology now has a 'part_of' term as well, and the advice there was to delete the PO entry, which I did, but still got the warning.  I then manually reloaded the RO, but I still got the warning.
>
> Any ideas?
>
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> 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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
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




--
------------------------------------------------------------------------
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



--
------------------------------------------------------------------------
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





------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
_______________________________________________
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Re: Unable to find a 'part_of' term in the relationship ontology

Scott Cain
Hi Seth,

Everything I know about PO I just copied from their website:

Plant Ontology project is a major international bioinformatics effort on standardizing the nomenclature, definitions, synonyms and relations of various terms/keywords/vocabularies that describe anatomical entities as well as the growth and developmental stages of plants

So, what I'm saying is, only you know if you'll want to use the PO.  What kind of data do you have?

Scott



On Thu, May 1, 2014 at 3:32 PM, Seth Munholland <[hidden email]> wrote:
>
> Hi Scott,
>
> I'm running into some other issues in this same DB setup, they may be unrelated, but I am curious what is provided by the Plant Ontology that would be missing elsewhere?  My genomes are all plant oriented so it made the sense to include PO in my chado DBs, but if it's causing this large an issue I'm wondering can I get away without including it?
>
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: (519) 253-3000 Ext: 4755
>
>
> On Thu, May 1, 2014 at 11:34 AM, Seth Munholland <[hidden email]> wrote:
>>
>> Hi Scott,
>>
>> Nevermind, I went through my command and the gff3 that was being loaded and I missed that there was a sequence at the end of it, as such my command was missing the --nosequence option.
>>
>> Seth Munholland, B.Sc.
>> Department of Biological Sciences
>> Rm. 304 Biology Building
>> University of Windsor
>> 401 Sunset Ave. N9B 3P4
>> T: (519) 253-3000 Ext: 4755
>>
>>
>> On Thu, May 1, 2014 at 11:17 AM, Seth Munholland <[hidden email]> wrote:
>>>
>>> Hi Scott,
>>>
>>> It looks like I might still have an error somewhere.  Trying to load the annotation file gave me a whole ton of the following message:
>>>
>>> No feature found for scaffold_6830, org_id:13 when trying to add sequence at /usr/local/share/perl/5.14.2/Bio/GMOD/DB/Adapter.pm line 2566, <GEN0> line 350109.
>>>
>>> Looking back there is a contig entry for scaffold_6830  (as well as all the other scaffolds I've checked so far).  Is this an error in uploading, or another issue with Adapter.pm from the missing if?
>>>
>>> Seth Munholland, B.Sc.
>>> Department of Biological Sciences
>>> Rm. 304 Biology Building
>>> University of Windsor
>>> 401 Sunset Ave. N9B 3P4
>>> T: (519) 253-3000 Ext: 4755
>>>
>>>
>>> On Wed, Apr 30, 2014 at 2:44 PM, Seth Munholland <[hidden email]> wrote:
>>>>
>>>> Hi Scott,
>>>>
>>>> Yes, I did grab this chado bundle via svn.  Thanks for clarifying!
>>>>
>>>> Seth Munholland, B.Sc.
>>>> Department of Biological Sciences
>>>> Rm. 304 Biology Building
>>>> University of Windsor
>>>> 401 Sunset Ave. N9B 3P4
>>>> T: (519) 253-3000 Ext: 4755
>>>>
>>>>
>>>> On Wed, Apr 30, 2014 at 2:33 PM, Scott Cain <[hidden email]> wrote:
>>>>>
>>>>> cc'ing schema list
>>>>>
>>>>>
>>>>> On Wed, Apr 30, 2014 at 2:33 PM, Scott Cain <[hidden email]> wrote:
>>>>>>
>>>>>> Hi Seth,
>>>>>>
>>>>>> Are you working from a svn checkout?  I just looked at the svn history of Adapter.pm where I added the code to give this warning, and much to my horror, I realized that there is no "if" statement attached to that warning, so it *always* prints out, regardless of what the status of finding part_of is.  
>>>>>>
>>>>>> So, for now, you can ignore that message--sorry for the hassle.  I'll fix it in git as soon as there is a git repo.
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Apr 30, 2014 at 2:19 PM, Seth Munholland <[hidden email]> wrote:
>>>>>>>
>>>>>>> It is public.  Just to see I ran the second script and got the following:
>>>>>>>
>>>>>>>       name      | cvterm_id |  name  
>>>>>>> ----------------+-----------+---------
>>>>>>>  relationship   |      3652 | part_of
>>>>>>>  plant_ontology |        67 | part_of
>>>>>>> (2 rows)
>>>>>>>
>>>>>>> Apparently I didn't properly delete the PO entry.  I re-entered the delete command:
>>>>>>>
>>>>>>> DELETE FROM cvterm WHERE cvterm_id = 67;
>>>>>>>
>>>>>>> Then ran the second select script again to get:
>>>>>>>
>>>>>>>      name     | cvterm_id |  name  
>>>>>>> --------------+-----------+---------
>>>>>>>  relationship |      3652 | part_of
>>>>>>> (1 row)
>>>>>>>
>>>>>>>
>>>>>>> Seth Munholland, B.Sc.
>>>>>>> Department of Biological Sciences
>>>>>>> Rm. 304 Biology Building
>>>>>>> University of Windsor
>>>>>>> 401 Sunset Ave. N9B 3P4
>>>>>>> T: (519) 253-3000 Ext: 4755
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Apr 30, 2014 at 2:15 PM, Scott Cain <[hidden email]> wrote:
>>>>>>>>
>>>>>>>> Strange, it gets one result, which is exactly what it should get.  Is your Chado in the public schema, or something else?
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Apr 30, 2014 at 2:12 PM, Seth Munholland <[hidden email]> wrote:
>>>>>>>>>
>>>>>>>>> Hi Scott,
>>>>>>>>>
>>>>>>>>> From the first script I got the following:
>>>>>>>>>
>>>>>>>>>  cvterm_id
>>>>>>>>> -----------
>>>>>>>>>       3652
>>>>>>>>> (1 row)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Seth Munholland, B.Sc.
>>>>>>>>> Department of Biological Sciences
>>>>>>>>> Rm. 304 Biology Building
>>>>>>>>> University of Windsor
>>>>>>>>> 401 Sunset Ave. N9B 3P4
>>>>>>>>> T: (519) 253-3000 Ext: 4755
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Wed, Apr 30, 2014 at 2:10 PM, Scott Cain <[hidden email]> wrote:
>>>>>>>>>>
>>>>>>>>>> Hi Seth,
>>>>>>>>>>
>>>>>>>>>> The query the loader is trying to execute is this:
>>>>>>>>>>
>>>>>>>>>> select cvterm_id from cvterm where name = 'part_of' and cv_id in (
>>>>>>>>>>       SELECT cv_id FROM cv WHERE name='relationship')
>>>>>>>>>>
>>>>>>>>>> (ugh, subselects).  If you run this in the psql shell, what do you get?  Assuming nothing, what do you get if you do this:
>>>>>>>>>>
>>>>>>>>>> SELECT cv.name, cvterm.cvterm_id, cvterm.name FROM
>>>>>>>>>>   cv JOIN cvterm ON (cv.cv_id = cvterm.cv_id) where cvterm.name='part_of'
>>>>>>>>>>
>>>>>>>>>> Scott
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Wed, Apr 30, 2014 at 1:32 PM, Seth Munholland <[hidden email]> wrote:
>>>>>>>>>> >
>>>>>>>>>> > Hi Everyone,
>>>>>>>>>> >
>>>>>>>>>> > I'm trying to setup a Chado DB for some local testing before implementing changes to the webserver, however, I'm running into an odd error.  I make the chado database and prepare it for gmod_bulk_load_gff3.pl but I get a warning as soon as I start:
>>>>>>>>>> >
>>>>>>>>>> > 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.
>>>>>>>>>> >
>>>>>>>>>> > Then it appears to continue loading the DB.  I tried Manually loading the ontologies and still got the warning.  I tried deleting the downloaded ontologies and reloading (automated and manual) and still got the warning.  Next, I hit google and read one issue is that the plant onotology now has a 'part_of' term as well, and the advice there was to delete the PO entry, which I did, but still got the warning.  I then manually reloaded the RO, but I still got the warning.
>>>>>>>>>> >
>>>>>>>>>> > Any ideas?
>>>>>>>>>> >
>>>>>>>>>> > Seth Munholland, B.Sc.
>>>>>>>>>> > Department of Biological Sciences
>>>>>>>>>> > Rm. 304 Biology Building
>>>>>>>>>> > University of Windsor
>>>>>>>>>> > 401 Sunset Ave. N9B 3P4
>>>>>>>>>> > T: (519) 253-3000 Ext: 4755
>>>>>>>>>> >
>>>>>>>>>> > ------------------------------------------------------------------------------
>>>>>>>>>> > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>>>>>>>>> > Instantly run your Selenium tests across 300+ browser/OS combos.  Get
>>>>>>>>>> > unparalleled scalability from the best Selenium testing platform available.
>>>>>>>>>> > Simple to use. Nothing to install. Get started now for free."
>>>>>>>>>> > http://p.sf.net/sfu/SauceLabs
>>>>>>>>>> > _______________________________________________
>>>>>>>>>> > 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>>>>> Ontario Institute for Cancer Research
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> ------------------------------------------------------------------------
>>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>>> Ontario Institute for Cancer Research
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>>
>>>>
>>>
>>
>



--
------------------------------------------------------------------------
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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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
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Re: Unable to find a 'part_of' term in the relationship ontology

Seth_m55
Hi Scott,

Just letting you know I was still having troubles with the Chado DB after getting everything worked out as above, so I went and grabbed the latest tar.gz instead and it worked first try.

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Thu, May 1, 2014 at 3:53 PM, Seth Munholland <[hidden email]> wrote:
I have fairly generic data at the moment; assembled scaffolds that have been annotated for predicted gene content, TE content, some RNAseq, and some SNPs.  I think I can get away with not including it for now, if it comes to that.

Thanks for your help!

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Thu, May 1, 2014 at 3:45 PM, Scott Cain <[hidden email]> wrote:
Hi Seth,

Everything I know about PO I just copied from their website:

Plant Ontology project is a major international bioinformatics effort on standardizing the nomenclature, definitions, synonyms and relations of various terms/keywords/vocabularies that describe anatomical entities as well as the growth and developmental stages of plants

So, what I'm saying is, only you know if you'll want to use the PO.  What kind of data do you have?

Scott




On Thu, May 1, 2014 at 3:32 PM, Seth Munholland <[hidden email]> wrote:
>
> Hi Scott,
>
> I'm running into some other issues in this same DB setup, they may be unrelated, but I am curious what is provided by the Plant Ontology that would be missing elsewhere?  My genomes are all plant oriented so it made the sense to include PO in my chado DBs, but if it's causing this large an issue I'm wondering can I get away without including it?
>
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>
>
> On Thu, May 1, 2014 at 11:34 AM, Seth Munholland <[hidden email]> wrote:
>>
>> Hi Scott,
>>
>> Nevermind, I went through my command and the gff3 that was being loaded and I missed that there was a sequence at the end of it, as such my command was missing the --nosequence option.
>>
>> Seth Munholland, B.Sc.
>> Department of Biological Sciences
>> Rm. 304 Biology Building
>> University of Windsor
>> 401 Sunset Ave. N9B 3P4
>> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>
>>
>> On Thu, May 1, 2014 at 11:17 AM, Seth Munholland <[hidden email]> wrote:
>>>
>>> Hi Scott,
>>>
>>> It looks like I might still have an error somewhere.  Trying to load the annotation file gave me a whole ton of the following message:
>>>
>>> No feature found for scaffold_6830, org_id:13 when trying to add sequence at /usr/local/share/perl/5.14.2/Bio/GMOD/DB/Adapter.pm line 2566, <GEN0> line 350109.
>>>
>>> Looking back there is a contig entry for scaffold_6830  (as well as all the other scaffolds I've checked so far).  Is this an error in uploading, or another issue with Adapter.pm from the missing if?
>>>
>>> Seth Munholland, B.Sc.
>>> Department of Biological Sciences
>>> Rm. 304 Biology Building
>>> University of Windsor
>>> 401 Sunset Ave. N9B 3P4
>>> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>>
>>>
>>> On Wed, Apr 30, 2014 at 2:44 PM, Seth Munholland <[hidden email]> wrote:
>>>>
>>>> Hi Scott,
>>>>
>>>> Yes, I did grab this chado bundle via svn.  Thanks for clarifying!
>>>>
>>>> Seth Munholland, B.Sc.
>>>> Department of Biological Sciences
>>>> Rm. 304 Biology Building
>>>> University of Windsor
>>>> 401 Sunset Ave. N9B 3P4
>>>> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>>>
>>>>
>>>> On Wed, Apr 30, 2014 at 2:33 PM, Scott Cain <[hidden email]> wrote:
>>>>>
>>>>> cc'ing schema list
>>>>>
>>>>>
>>>>> On Wed, Apr 30, 2014 at 2:33 PM, Scott Cain <[hidden email]> wrote:
>>>>>>
>>>>>> Hi Seth,
>>>>>>
>>>>>> Are you working from a svn checkout?  I just looked at the svn history of Adapter.pm where I added the code to give this warning, and much to my horror, I realized that there is no "if" statement attached to that warning, so it *always* prints out, regardless of what the status of finding part_of is.  
>>>>>>
>>>>>> So, for now, you can ignore that message--sorry for the hassle.  I'll fix it in git as soon as there is a git repo.
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Apr 30, 2014 at 2:19 PM, Seth Munholland <[hidden email]> wrote:
>>>>>>>
>>>>>>> It is public.  Just to see I ran the second script and got the following:
>>>>>>>
>>>>>>>       name      | cvterm_id |  name  
>>>>>>> ----------------+-----------+---------
>>>>>>>  relationship   |      3652 | part_of
>>>>>>>  plant_ontology |        67 | part_of
>>>>>>> (2 rows)
>>>>>>>
>>>>>>> Apparently I didn't properly delete the PO entry.  I re-entered the delete command:
>>>>>>>
>>>>>>> DELETE FROM cvterm WHERE cvterm_id = 67;
>>>>>>>
>>>>>>> Then ran the second select script again to get:
>>>>>>>
>>>>>>>      name     | cvterm_id |  name  
>>>>>>> --------------+-----------+---------
>>>>>>>  relationship |      3652 | part_of
>>>>>>> (1 row)
>>>>>>>
>>>>>>>
>>>>>>> Seth Munholland, B.Sc.
>>>>>>> Department of Biological Sciences
>>>>>>> Rm. 304 Biology Building
>>>>>>> University of Windsor
>>>>>>> 401 Sunset Ave. N9B 3P4
>>>>>>> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Apr 30, 2014 at 2:15 PM, Scott Cain <[hidden email]> wrote:
>>>>>>>>
>>>>>>>> Strange, it gets one result, which is exactly what it should get.  Is your Chado in the public schema, or something else?
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Apr 30, 2014 at 2:12 PM, Seth Munholland <[hidden email]> wrote:
>>>>>>>>>
>>>>>>>>> Hi Scott,
>>>>>>>>>
>>>>>>>>> From the first script I got the following:
>>>>>>>>>
>>>>>>>>>  cvterm_id
>>>>>>>>> -----------
>>>>>>>>>       3652
>>>>>>>>> (1 row)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Seth Munholland, B.Sc.
>>>>>>>>> Department of Biological Sciences
>>>>>>>>> Rm. 304 Biology Building
>>>>>>>>> University of Windsor
>>>>>>>>> 401 Sunset Ave. N9B 3P4
>>>>>>>>> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Wed, Apr 30, 2014 at 2:10 PM, Scott Cain <[hidden email]> wrote:
>>>>>>>>>>
>>>>>>>>>> Hi Seth,
>>>>>>>>>>
>>>>>>>>>> The query the loader is trying to execute is this:
>>>>>>>>>>
>>>>>>>>>> select cvterm_id from cvterm where name = 'part_of' and cv_id in (
>>>>>>>>>>       SELECT cv_id FROM cv WHERE name='relationship')
>>>>>>>>>>
>>>>>>>>>> (ugh, subselects).  If you run this in the psql shell, what do you get?  Assuming nothing, what do you get if you do this:
>>>>>>>>>>
>>>>>>>>>> SELECT cv.name, cvterm.cvterm_id, cvterm.name FROM
>>>>>>>>>>   cv JOIN cvterm ON (cv.cv_id = cvterm.cv_id) where cvterm.name='part_of'
>>>>>>>>>>
>>>>>>>>>> Scott
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Wed, Apr 30, 2014 at 1:32 PM, Seth Munholland <[hidden email]> wrote:
>>>>>>>>>> >
>>>>>>>>>> > Hi Everyone,
>>>>>>>>>> >
>>>>>>>>>> > I'm trying to setup a Chado DB for some local testing before implementing changes to the webserver, however, I'm running into an odd error.  I make the chado database and prepare it for gmod_bulk_load_gff3.pl but I get a warning as soon as I start:
>>>>>>>>>> >
>>>>>>>>>> > 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.
>>>>>>>>>> >
>>>>>>>>>> > Then it appears to continue loading the DB.  I tried Manually loading the ontologies and still got the warning.  I tried deleting the downloaded ontologies and reloading (automated and manual) and still got the warning.  Next, I hit google and read one issue is that the plant onotology now has a 'part_of' term as well, and the advice there was to delete the PO entry, which I did, but still got the warning.  I then manually reloaded the RO, but I still got the warning.
>>>>>>>>>> >
>>>>>>>>>> > Any ideas?
>>>>>>>>>> >
>>>>>>>>>> > Seth Munholland, B.Sc.
>>>>>>>>>> > Department of Biological Sciences
>>>>>>>>>> > Rm. 304 Biology Building
>>>>>>>>>> > University of Windsor
>>>>>>>>>> > 401 Sunset Ave. N9B 3P4
>>>>>>>>>> > T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>>>>>>>>> >
>>>>>>>>>> > ------------------------------------------------------------------------------
>>>>>>>>>> > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>>>>>>>>> > Instantly run your Selenium tests across 300+ browser/OS combos.  Get
>>>>>>>>>> > unparalleled scalability from the best Selenium testing platform available.
>>>>>>>>>> > Simple to use. Nothing to install. Get started now for free."
>>>>>>>>>> > http://p.sf.net/sfu/SauceLabs
>>>>>>>>>> > _______________________________________________
>>>>>>>>>> > 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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>>>>>>>>>> Ontario Institute for Cancer Research
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> ------------------------------------------------------------------------
>>>>>> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------------------
>>>>> 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
>>>>
>>>>
>>>
>>
>



--
------------------------------------------------------------------------
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



------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.
Get unparalleled scalability from the best Selenium testing platform available
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
_______________________________________________
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Re: Unable to find a 'part_of' term in the relationship ontology

Scott Cain
Hi Seth,

You mean the lastest tar of PO?

Scott



On Thu, May 15, 2014 at 10:57 AM, Seth Munholland <[hidden email]> wrote:
Hi Scott,

Just letting you know I was still having troubles with the Chado DB after getting everything worked out as above, so I went and grabbed the latest tar.gz instead and it worked first try.

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Thu, May 1, 2014 at 3:53 PM, Seth Munholland <[hidden email]> wrote:
I have fairly generic data at the moment; assembled scaffolds that have been annotated for predicted gene content, TE content, some RNAseq, and some SNPs.  I think I can get away with not including it for now, if it comes to that.

Thanks for your help!

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Thu, May 1, 2014 at 3:45 PM, Scott Cain <[hidden email]> wrote:
Hi Seth,

Everything I know about PO I just copied from their website:

Plant Ontology project is a major international bioinformatics effort on standardizing the nomenclature, definitions, synonyms and relations of various terms/keywords/vocabularies that describe anatomical entities as well as the growth and developmental stages of plants

So, what I'm saying is, only you know if you'll want to use the PO.  What kind of data do you have?

Scott




On Thu, May 1, 2014 at 3:32 PM, Seth Munholland <[hidden email]> wrote:
>
> Hi Scott,
>
> I'm running into some other issues in this same DB setup, they may be unrelated, but I am curious what is provided by the Plant Ontology that would be missing elsewhere?  My genomes are all plant oriented so it made the sense to include PO in my chado DBs, but if it's causing this large an issue I'm wondering can I get away without including it?
>
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>
>
> On Thu, May 1, 2014 at 11:34 AM, Seth Munholland <[hidden email]> wrote:
>>
>> Hi Scott,
>>
>> Nevermind, I went through my command and the gff3 that was being loaded and I missed that there was a sequence at the end of it, as such my command was missing the --nosequence option.
>>
>> Seth Munholland, B.Sc.
>> Department of Biological Sciences
>> Rm. 304 Biology Building
>> University of Windsor
>> 401 Sunset Ave. N9B 3P4
>> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>
>>
>> On Thu, May 1, 2014 at 11:17 AM, Seth Munholland <[hidden email]> wrote:
>>>
>>> Hi Scott,
>>>
>>> It looks like I might still have an error somewhere.  Trying to load the annotation file gave me a whole ton of the following message:
>>>
>>> No feature found for scaffold_6830, org_id:13 when trying to add sequence at /usr/local/share/perl/5.14.2/Bio/GMOD/DB/Adapter.pm line 2566, <GEN0> line 350109.
>>>
>>> Looking back there is a contig entry for scaffold_6830  (as well as all the other scaffolds I've checked so far).  Is this an error in uploading, or another issue with Adapter.pm from the missing if?
>>>
>>> Seth Munholland, B.Sc.
>>> Department of Biological Sciences
>>> Rm. 304 Biology Building
>>> University of Windsor
>>> 401 Sunset Ave. N9B 3P4
>>> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>>
>>>
>>> On Wed, Apr 30, 2014 at 2:44 PM, Seth Munholland <[hidden email]> wrote:
>>>>
>>>> Hi Scott,
>>>>
>>>> Yes, I did grab this chado bundle via svn.  Thanks for clarifying!
>>>>
>>>> Seth Munholland, B.Sc.
>>>> Department of Biological Sciences
>>>> Rm. 304 Biology Building
>>>> University of Windsor
>>>> 401 Sunset Ave. N9B 3P4
>>>> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>>>
>>>>
>>>> On Wed, Apr 30, 2014 at 2:33 PM, Scott Cain <[hidden email]> wrote:
>>>>>
>>>>> cc'ing schema list
>>>>>
>>>>>
>>>>> On Wed, Apr 30, 2014 at 2:33 PM, Scott Cain <[hidden email]> wrote:
>>>>>>
>>>>>> Hi Seth,
>>>>>>
>>>>>> Are you working from a svn checkout?  I just looked at the svn history of Adapter.pm where I added the code to give this warning, and much to my horror, I realized that there is no "if" statement attached to that warning, so it *always* prints out, regardless of what the status of finding part_of is.  
>>>>>>
>>>>>> So, for now, you can ignore that message--sorry for the hassle.  I'll fix it in git as soon as there is a git repo.
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Apr 30, 2014 at 2:19 PM, Seth Munholland <[hidden email]> wrote:
>>>>>>>
>>>>>>> It is public.  Just to see I ran the second script and got the following:
>>>>>>>
>>>>>>>       name      | cvterm_id |  name  
>>>>>>> ----------------+-----------+---------
>>>>>>>  relationship   |      3652 | part_of
>>>>>>>  plant_ontology |        67 | part_of
>>>>>>> (2 rows)
>>>>>>>
>>>>>>> Apparently I didn't properly delete the PO entry.  I re-entered the delete command:
>>>>>>>
>>>>>>> DELETE FROM cvterm WHERE cvterm_id = 67;
>>>>>>>
>>>>>>> Then ran the second select script again to get:
>>>>>>>
>>>>>>>      name     | cvterm_id |  name  
>>>>>>> --------------+-----------+---------
>>>>>>>  relationship |      3652 | part_of
>>>>>>> (1 row)
>>>>>>>
>>>>>>>
>>>>>>> Seth Munholland, B.Sc.
>>>>>>> Department of Biological Sciences
>>>>>>> Rm. 304 Biology Building
>>>>>>> University of Windsor
>>>>>>> 401 Sunset Ave. N9B 3P4
>>>>>>> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Apr 30, 2014 at 2:15 PM, Scott Cain <[hidden email]> wrote:
>>>>>>>>
>>>>>>>> Strange, it gets one result, which is exactly what it should get.  Is your Chado in the public schema, or something else?
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Apr 30, 2014 at 2:12 PM, Seth Munholland <[hidden email]> wrote:
>>>>>>>>>
>>>>>>>>> Hi Scott,
>>>>>>>>>
>>>>>>>>> From the first script I got the following:
>>>>>>>>>
>>>>>>>>>  cvterm_id
>>>>>>>>> -----------
>>>>>>>>>       3652
>>>>>>>>> (1 row)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Seth Munholland, B.Sc.
>>>>>>>>> Department of Biological Sciences
>>>>>>>>> Rm. 304 Biology Building
>>>>>>>>> University of Windsor
>>>>>>>>> 401 Sunset Ave. N9B 3P4
>>>>>>>>> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Wed, Apr 30, 2014 at 2:10 PM, Scott Cain <[hidden email]> wrote:
>>>>>>>>>>
>>>>>>>>>> Hi Seth,
>>>>>>>>>>
>>>>>>>>>> The query the loader is trying to execute is this:
>>>>>>>>>>
>>>>>>>>>> select cvterm_id from cvterm where name = 'part_of' and cv_id in (
>>>>>>>>>>       SELECT cv_id FROM cv WHERE name='relationship')
>>>>>>>>>>
>>>>>>>>>> (ugh, subselects).  If you run this in the psql shell, what do you get?  Assuming nothing, what do you get if you do this:
>>>>>>>>>>
>>>>>>>>>> SELECT cv.name, cvterm.cvterm_id, cvterm.name FROM
>>>>>>>>>>   cv JOIN cvterm ON (cv.cv_id = cvterm.cv_id) where cvterm.name='part_of'
>>>>>>>>>>
>>>>>>>>>> Scott
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Wed, Apr 30, 2014 at 1:32 PM, Seth Munholland <[hidden email]> wrote:
>>>>>>>>>> >
>>>>>>>>>> > Hi Everyone,
>>>>>>>>>> >
>>>>>>>>>> > I'm trying to setup a Chado DB for some local testing before implementing changes to the webserver, however, I'm running into an odd error.  I make the chado database and prepare it for gmod_bulk_load_gff3.pl but I get a warning as soon as I start:
>>>>>>>>>> >
>>>>>>>>>> > 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.
>>>>>>>>>> >
>>>>>>>>>> > Then it appears to continue loading the DB.  I tried Manually loading the ontologies and still got the warning.  I tried deleting the downloaded ontologies and reloading (automated and manual) and still got the warning.  Next, I hit google and read one issue is that the plant onotology now has a 'part_of' term as well, and the advice there was to delete the PO entry, which I did, but still got the warning.  I then manually reloaded the RO, but I still got the warning.
>>>>>>>>>> >
>>>>>>>>>> > Any ideas?
>>>>>>>>>> >
>>>>>>>>>> > Seth Munholland, B.Sc.
>>>>>>>>>> > Department of Biological Sciences
>>>>>>>>>> > Rm. 304 Biology Building
>>>>>>>>>> > University of Windsor
>>>>>>>>>> > 401 Sunset Ave. N9B 3P4
>>>>>>>>>> > T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>>>>>>>>> >
>>>>>>>>>> > ------------------------------------------------------------------------------
>>>>>>>>>> > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>>>>>>>>> > Instantly run your Selenium tests across 300+ browser/OS combos.  Get
>>>>>>>>>> > unparalleled scalability from the best Selenium testing platform available.
>>>>>>>>>> > Simple to use. Nothing to install. Get started now for free."
>>>>>>>>>> > http://p.sf.net/sfu/SauceLabs
>>>>>>>>>> > _______________________________________________
>>>>>>>>>> > 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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>>>>>>>>>> Ontario Institute for Cancer Research
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> ------------------------------------------------------------------------
>>>>>> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------------------
>>>>> 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
>>>>
>>>>
>>>
>>
>



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

Seth_m55
Hi Scott,

I got all the latest ontology tars when I tried loading them manually, in this case I mean chado-1.23.tar.gz.

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Thu, May 15, 2014 at 11:00 AM, Scott Cain <[hidden email]> wrote:
Hi Seth,

You mean the lastest tar of PO?

Scott



On Thu, May 15, 2014 at 10:57 AM, Seth Munholland <[hidden email]> wrote:
Hi Scott,

Just letting you know I was still having troubles with the Chado DB after getting everything worked out as above, so I went and grabbed the latest tar.gz instead and it worked first try.

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Thu, May 1, 2014 at 3:53 PM, Seth Munholland <[hidden email]> wrote:
I have fairly generic data at the moment; assembled scaffolds that have been annotated for predicted gene content, TE content, some RNAseq, and some SNPs.  I think I can get away with not including it for now, if it comes to that.

Thanks for your help!

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755


On Thu, May 1, 2014 at 3:45 PM, Scott Cain <[hidden email]> wrote:
Hi Seth,

Everything I know about PO I just copied from their website:

Plant Ontology project is a major international bioinformatics effort on standardizing the nomenclature, definitions, synonyms and relations of various terms/keywords/vocabularies that describe anatomical entities as well as the growth and developmental stages of plants

So, what I'm saying is, only you know if you'll want to use the PO.  What kind of data do you have?

Scott




On Thu, May 1, 2014 at 3:32 PM, Seth Munholland <[hidden email]> wrote:
>
> Hi Scott,
>
> I'm running into some other issues in this same DB setup, they may be unrelated, but I am curious what is provided by the Plant Ontology that would be missing elsewhere?  My genomes are all plant oriented so it made the sense to include PO in my chado DBs, but if it's causing this large an issue I'm wondering can I get away without including it?
>
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>
>
> On Thu, May 1, 2014 at 11:34 AM, Seth Munholland <[hidden email]> wrote:
>>
>> Hi Scott,
>>
>> Nevermind, I went through my command and the gff3 that was being loaded and I missed that there was a sequence at the end of it, as such my command was missing the --nosequence option.
>>
>> Seth Munholland, B.Sc.
>> Department of Biological Sciences
>> Rm. 304 Biology Building
>> University of Windsor
>> 401 Sunset Ave. N9B 3P4
>> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>
>>
>> On Thu, May 1, 2014 at 11:17 AM, Seth Munholland <[hidden email]> wrote:
>>>
>>> Hi Scott,
>>>
>>> It looks like I might still have an error somewhere.  Trying to load the annotation file gave me a whole ton of the following message:
>>>
>>> No feature found for scaffold_6830, org_id:13 when trying to add sequence at /usr/local/share/perl/5.14.2/Bio/GMOD/DB/Adapter.pm line 2566, <GEN0> line 350109.
>>>
>>> Looking back there is a contig entry for scaffold_6830  (as well as all the other scaffolds I've checked so far).  Is this an error in uploading, or another issue with Adapter.pm from the missing if?
>>>
>>> Seth Munholland, B.Sc.
>>> Department of Biological Sciences
>>> Rm. 304 Biology Building
>>> University of Windsor
>>> 401 Sunset Ave. N9B 3P4
>>> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>>
>>>
>>> On Wed, Apr 30, 2014 at 2:44 PM, Seth Munholland <[hidden email]> wrote:
>>>>
>>>> Hi Scott,
>>>>
>>>> Yes, I did grab this chado bundle via svn.  Thanks for clarifying!
>>>>
>>>> Seth Munholland, B.Sc.
>>>> Department of Biological Sciences
>>>> Rm. 304 Biology Building
>>>> University of Windsor
>>>> 401 Sunset Ave. N9B 3P4
>>>> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>>>
>>>>
>>>> On Wed, Apr 30, 2014 at 2:33 PM, Scott Cain <[hidden email]> wrote:
>>>>>
>>>>> cc'ing schema list
>>>>>
>>>>>
>>>>> On Wed, Apr 30, 2014 at 2:33 PM, Scott Cain <[hidden email]> wrote:
>>>>>>
>>>>>> Hi Seth,
>>>>>>
>>>>>> Are you working from a svn checkout?  I just looked at the svn history of Adapter.pm where I added the code to give this warning, and much to my horror, I realized that there is no "if" statement attached to that warning, so it *always* prints out, regardless of what the status of finding part_of is.  
>>>>>>
>>>>>> So, for now, you can ignore that message--sorry for the hassle.  I'll fix it in git as soon as there is a git repo.
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Apr 30, 2014 at 2:19 PM, Seth Munholland <[hidden email]> wrote:
>>>>>>>
>>>>>>> It is public.  Just to see I ran the second script and got the following:
>>>>>>>
>>>>>>>       name      | cvterm_id |  name  
>>>>>>> ----------------+-----------+---------
>>>>>>>  relationship   |      3652 | part_of
>>>>>>>  plant_ontology |        67 | part_of
>>>>>>> (2 rows)
>>>>>>>
>>>>>>> Apparently I didn't properly delete the PO entry.  I re-entered the delete command:
>>>>>>>
>>>>>>> DELETE FROM cvterm WHERE cvterm_id = 67;
>>>>>>>
>>>>>>> Then ran the second select script again to get:
>>>>>>>
>>>>>>>      name     | cvterm_id |  name  
>>>>>>> --------------+-----------+---------
>>>>>>>  relationship |      3652 | part_of
>>>>>>> (1 row)
>>>>>>>
>>>>>>>
>>>>>>> Seth Munholland, B.Sc.
>>>>>>> Department of Biological Sciences
>>>>>>> Rm. 304 Biology Building
>>>>>>> University of Windsor
>>>>>>> 401 Sunset Ave. N9B 3P4
>>>>>>> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Apr 30, 2014 at 2:15 PM, Scott Cain <[hidden email]> wrote:
>>>>>>>>
>>>>>>>> Strange, it gets one result, which is exactly what it should get.  Is your Chado in the public schema, or something else?
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Apr 30, 2014 at 2:12 PM, Seth Munholland <[hidden email]> wrote:
>>>>>>>>>
>>>>>>>>> Hi Scott,
>>>>>>>>>
>>>>>>>>> From the first script I got the following:
>>>>>>>>>
>>>>>>>>>  cvterm_id
>>>>>>>>> -----------
>>>>>>>>>       3652
>>>>>>>>> (1 row)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Seth Munholland, B.Sc.
>>>>>>>>> Department of Biological Sciences
>>>>>>>>> Rm. 304 Biology Building
>>>>>>>>> University of Windsor
>>>>>>>>> 401 Sunset Ave. N9B 3P4
>>>>>>>>> T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Wed, Apr 30, 2014 at 2:10 PM, Scott Cain <[hidden email]> wrote:
>>>>>>>>>>
>>>>>>>>>> Hi Seth,
>>>>>>>>>>
>>>>>>>>>> The query the loader is trying to execute is this:
>>>>>>>>>>
>>>>>>>>>> select cvterm_id from cvterm where name = 'part_of' and cv_id in (
>>>>>>>>>>       SELECT cv_id FROM cv WHERE name='relationship')
>>>>>>>>>>
>>>>>>>>>> (ugh, subselects).  If you run this in the psql shell, what do you get?  Assuming nothing, what do you get if you do this:
>>>>>>>>>>
>>>>>>>>>> SELECT cv.name, cvterm.cvterm_id, cvterm.name FROM
>>>>>>>>>>   cv JOIN cvterm ON (cv.cv_id = cvterm.cv_id) where cvterm.name='part_of'
>>>>>>>>>>
>>>>>>>>>> Scott
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Wed, Apr 30, 2014 at 1:32 PM, Seth Munholland <[hidden email]> wrote:
>>>>>>>>>> >
>>>>>>>>>> > Hi Everyone,
>>>>>>>>>> >
>>>>>>>>>> > I'm trying to setup a Chado DB for some local testing before implementing changes to the webserver, however, I'm running into an odd error.  I make the chado database and prepare it for gmod_bulk_load_gff3.pl but I get a warning as soon as I start:
>>>>>>>>>> >
>>>>>>>>>> > 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.
>>>>>>>>>> >
>>>>>>>>>> > Then it appears to continue loading the DB.  I tried Manually loading the ontologies and still got the warning.  I tried deleting the downloaded ontologies and reloading (automated and manual) and still got the warning.  Next, I hit google and read one issue is that the plant onotology now has a 'part_of' term as well, and the advice there was to delete the PO entry, which I did, but still got the warning.  I then manually reloaded the RO, but I still got the warning.
>>>>>>>>>> >
>>>>>>>>>> > Any ideas?
>>>>>>>>>> >
>>>>>>>>>> > Seth Munholland, B.Sc.
>>>>>>>>>> > Department of Biological Sciences
>>>>>>>>>> > Rm. 304 Biology Building
>>>>>>>>>> > University of Windsor
>>>>>>>>>> > 401 Sunset Ave. N9B 3P4
>>>>>>>>>> > T: <a href="tel:%28519%29%20253-3000%20Ext%3A%204755" value="+15192533000" target="_blank">(519) 253-3000 Ext: 4755
>>>>>>>>>> >
>>>>>>>>>> > ------------------------------------------------------------------------------
>>>>>>>>>> > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>>>>>>>>> > Instantly run your Selenium tests across 300+ browser/OS combos.  Get
>>>>>>>>>> > unparalleled scalability from the best Selenium testing platform available.
>>>>>>>>>> > Simple to use. Nothing to install. Get started now for free."
>>>>>>>>>> > http://p.sf.net/sfu/SauceLabs
>>>>>>>>>> > _______________________________________________
>>>>>>>>>> > 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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
>>>>>>>>>> Ontario Institute for Cancer Research
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> ------------------------------------------------------------------------
>>>>>> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------------------
>>>>> 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
>>>>
>>>>
>>>
>>
>



--
------------------------------------------------------------------------
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





--
------------------------------------------------------------------------
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


------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.
Get unparalleled scalability from the best Selenium testing platform available
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema