Correction: Problem with gmod_bulk_load_gff3.pl

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Correction: Problem with gmod_bulk_load_gff3.pl

Hans Kraus
Hi,

A correction for my last mail (please disregard it); I stated the wrong
file/table name.

I have a problem with bulk loading a GFF into Chado. The error message
is:
--------------------------------START---------------------------------
Loading data into feature_relationship table ...
DBD::Pg::db pg_endcopy failed: FEHLER:  ungültige Eingabesyntax für
ganze Zahl: »«
KONTEXT:  COPY feature_relationship, Zeile 21043, Spalte type_id: »«
at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3258, <$fh>
line 47993.
---------------------------------END----------------------------------

After a bit of debugging (by the way: the argument '--save_files'
doesn't exist, at least in my version of gmod_bulk_load_gff3.pl) I found
the following:

About 21,000 features are (as I suppose) automatically generated. They
are all from two different types:
1) exon-auto<feature_id> (about 11,000)
2) polypeptide-auto<feature_id> (about 10,100)

The exon ones are processed without fault. But all entries in the
feature_relationship file for the polypeptide ones are missing the
value for the type_id.

The entries in the GFF look OK for me (one as example):
--------------------------------START---------------------------------
FN392320 GenBank gene 266 913 . - .
ID=PAS_chr2-1_0002;locus_tag=PAS_chr2-1_0002
FN392320 GenBank mRNA 266 913 . - .
ID=PAS_chr2-1_0002.t01;Parent=PAS_chr2-1_0002
FN392320 GenBank CDS 266 913 . - .
ID=PAS_chr2-1_0002.p01;Parent=PAS_chr2-1_0002.t01;Dbxref=GI:238030678,UniProtKB/TrEMBL:C4QZC7;codon_start=1;locus_tag=PAS_chr2-1_0002;product=Hypothetical
protein;protein_id=CAY68601.1;translation=length.215
FN392320 GenBank exon 266 913 . - . Parent=PAS_chr2-1_0002.t01
.
.
.
>PAS_chr2-1_0002.p01
MMASPTAGDHPAGDGPASGAQLGGEAGGATGEVSQVFQVRASASASPGGTVLEVEVSRED
---------------------------------END----------------------------------

As usual: any help appreciated,
Hans

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Re: Correction: Problem with gmod_bulk_load_gff3.pl

Scott Cain
Hi Hans,

The "save" option is called "--save_tmpfiles"; if you saw a reference
to "save_files" somewhere in the documentation, please let me know
where so I can fix it (it is correct in `perldoc
gmod_bulk_load_gff3.pl`).

Do you have an cvterm entry for the "derives_from" in you cvterm table
that belongs to the relationship ontology?  Try this query:

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

Scott


On Fri, Mar 2, 2012 at 4:14 AM, Hans Kraus <[hidden email]> wrote:

> Hi,
>
> A correction for my last mail (please disregard it); I stated the wrong
> file/table name.
>
> I have a problem with bulk loading a GFF into Chado. The error message
> is:
> --------------------------------START---------------------------------
> Loading data into feature_relationship table ...
> DBD::Pg::db pg_endcopy failed: FEHLER:  ungültige Eingabesyntax für
> ganze Zahl: »«
> KONTEXT:  COPY feature_relationship, Zeile 21043, Spalte type_id: »«
> at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3258, <$fh>
> line 47993.
> ---------------------------------END----------------------------------
>
> After a bit of debugging (by the way: the argument '--save_files'
> doesn't exist, at least in my version of gmod_bulk_load_gff3.pl) I found
> the following:
>
> About 21,000 features are (as I suppose) automatically generated. They
> are all from two different types:
> 1)      exon-auto<feature_id>           (about 11,000)
> 2)      polypeptide-auto<feature_id>    (about 10,100)
>
> The exon ones are processed without fault. But all entries in the
> feature_relationship file for the polypeptide ones are missing the
> value for the type_id.
>
> The entries in the GFF look OK for me (one as example):
> --------------------------------START---------------------------------
> FN392320        GenBank gene    266     913     .       -       .
> ID=PAS_chr2-1_0002;locus_tag=PAS_chr2-1_0002
> FN392320        GenBank mRNA    266     913     .       -       .
> ID=PAS_chr2-1_0002.t01;Parent=PAS_chr2-1_0002
> FN392320        GenBank CDS     266     913     .       -       .
> ID=PAS_chr2-1_0002.p01;Parent=PAS_chr2-1_0002.t01;Dbxref=GI:238030678,UniProtKB/TrEMBL:C4QZC7;codon_start=1;locus_tag=PAS_chr2-1_0002;product=Hypothetical
> protein;protein_id=CAY68601.1;translation=length.215
> FN392320        GenBank exon    266     913     .       -       .       Parent=PAS_chr2-1_0002.t01
> .
> .
> .
>>PAS_chr2-1_0002.p01
> MMASPTAGDHPAGDGPASGAQLGGEAGGATGEVSQVFQVRASASASPGGTVLEVEVSRED
> ---------------------------------END----------------------------------
>
> As usual: any help appreciated,
> Hans
>
> ------------------------------------------------------------------------------
> Virtualization & Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing
> also focuses on allowing computing to be delivered as a service.
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> _______________________________________________
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> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema



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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Correction: Problem with gmod_bulk_load_gff3.pl

Hans Kraus
Hi Scott,

I found "--save_tmpfiles" in an answer of you to the question of some
other guy in
<http://gmod.827538.n3.nabble.com/gmod-bulk-load-gff3-pl-error-DBD-Pg-db-pg-endcopy-failed-td3496791.htm>
and not in the documentation.

The query you proposed resulted in an empty result:
--------------------------------START---------------------------------
chado_pipa_GS115=# select * from cvterm where name = 'derives_from' and
cv_id in (
                                                        SELECT cv_id
FROM cv WHERE name='relationship'
 
                                 );
  cvterm_id | cv_id | name | definition | dbxref_id | is_obsolete |
is_relationshiptype
-----------+-------+------+------------+-----------+-------------+---------------------
(0 Zeilen)

---------------------------------END----------------------------------

Thanks for your help,
Hans

Am 02.03.2012 17:00, schrieb Scott Cain:

> Hi Hans,
>
> The "save" option is called "--save_tmpfiles"; if you saw a reference
> to "save_files" somewhere in the documentation, please let me know
> where so I can fix it (it is correct in `perldoc
> gmod_bulk_load_gff3.pl`).
>
> Do you have an cvterm entry for the "derives_from" in you cvterm table
> that belongs to the relationship ontology?  Try this query:
>
>    from cvterm where name = 'derives_from' and cv_id in (
>           SELECT cv_id FROM cv WHERE name='relationship'
>         )
>
> Scott
>
>
> On Fri, Mar 2, 2012 at 4:14 AM, Hans Kraus<[hidden email]>  wrote:
>> Hi,
>>
>> A correction for my last mail (please disregard it); I stated the wrong
>> file/table name.
>>
>> I have a problem with bulk loading a GFF into Chado. The error message
>> is:
>> --------------------------------START---------------------------------
>> Loading data into feature_relationship table ...
>> DBD::Pg::db pg_endcopy failed: FEHLER:  ungültige Eingabesyntax für
>> ganze Zahl: »«
>> KONTEXT:  COPY feature_relationship, Zeile 21043, Spalte type_id: »«
>> at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 3258,<$fh>
>> line 47993.
>> ---------------------------------END----------------------------------
>>
>> After a bit of debugging (by the way: the argument '--save_files'
>> doesn't exist, at least in my version of gmod_bulk_load_gff3.pl) I found
>> the following:
>>
>> About 21,000 features are (as I suppose) automatically generated. They
>> are all from two different types:
>> 1)      exon-auto<feature_id>             (about 11,000)
>> 2)      polypeptide-auto<feature_id>      (about 10,100)
>>
>> The exon ones are processed without fault. But all entries in the
>> feature_relationship file for the polypeptide ones are missing the
>> value for the type_id.
>>
>> The entries in the GFF look OK for me (one as example):
>> --------------------------------START---------------------------------
>> FN392320        GenBank gene    266     913     .       -       .
>> ID=PAS_chr2-1_0002;locus_tag=PAS_chr2-1_0002
>> FN392320        GenBank mRNA    266     913     .       -       .
>> ID=PAS_chr2-1_0002.t01;Parent=PAS_chr2-1_0002
>> FN392320        GenBank CDS     266     913     .       -       .
>> ID=PAS_chr2-1_0002.p01;Parent=PAS_chr2-1_0002.t01;Dbxref=GI:238030678,UniProtKB/TrEMBL:C4QZC7;codon_start=1;locus_tag=PAS_chr2-1_0002;product=Hypothetical
>> protein;protein_id=CAY68601.1;translation=length.215
>> FN392320        GenBank exon    266     913     .       -       .       Parent=PAS_chr2-1_0002.t01
>> .
>> .
>> .
>>> PAS_chr2-1_0002.p01
>> MMASPTAGDHPAGDGPASGAQLGGEAGGATGEVSQVFQVRASASASPGGTVLEVEVSRED
>> ---------------------------------END----------------------------------
>>
>> As usual: any help appreciated,
>> Hans
>>
>> ------------------------------------------------------------------------------
>> Virtualization&  Cloud Management Using Capacity Planning
>> Cloud computing makes use of virtualization - but cloud computing
>> also focuses on allowing computing to be delivered as a service.
>> http://www.accelacomm.com/jaw/sfnl/114/51521223/
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
>


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Re: Correction: Problem with gmod_bulk_load_gff3.pl - Addendum

Hans Kraus
In reply to this post by Scott Cain
Hi Scott,

in case it matters: I installed 'chado-1.2.tar.gz' in November 2011,
using '$Id: INSTALL.Chado,v 1.10 2008-11-04 20:36:20 scottcain Exp $'
as guide.

I experienced no errors. The steps (from my installing protocol):

$ perl Makefile.PL # take the default values, if proposed
$ make
$ sudo make install
$ make load_schema
$ make prepdb
$ make ontologies 1,2,3,4,5

Thanks,
Hans

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Re: Correction: Problem with gmod_bulk_load_gff3.pl - Addendum

Scott Cain
Hi Hans,

The fact that that query came up empty means there is something wrong with your ontologies.  Do you see "relationship" if you do a "SELECT * FROM cv"?  If so, what do you see if you do "SELECT count(*) FROM cvterm WHERE cv_id = ?" where you replace the cv_id of the relationship ontology from the cv table?

Scott

Sent from my iPad

On Mar 4, 2012, at 5:15 PM, Hans Kraus <[hidden email]> wrote:

> Hi Scott,
>
> in case it matters: I installed 'chado-1.2.tar.gz' in November 2011,
> using '$Id: INSTALL.Chado,v 1.10 2008-11-04 20:36:20 scottcain Exp $'
> as guide.
>
> I experienced no errors. The steps (from my installing protocol):
>
> $ perl Makefile.PL    # take the default values, if proposed
> $ make
> $ sudo make install
> $ make load_schema
> $ make prepdb
> $ make ontologies    1,2,3,4,5
>
> Thanks,
> Hans

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Re: Correction: Problem with gmod_bulk_load_gff3.pl - Addendum

Hans Kraus
Hi Scott,

 > The fact that that query came up empty means there is something wrong
 > with your ontologies.  Do you see "relationship" if you do a
 > "SELECT * FROM cv"?

Yes, I see 'relationship'.

 > If so, what do you see if you do
 > "SELECT count(*) FROM cvterm WHERE cv_id = ?"

The result is 3.

 > where you replace the cv_id of the relationship ontology from the cv
 > table?

Thanks,
Hans

chado_pipa_GS115=# SELECT * FROM cv;
  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
      6 | chado_properties     | Terms that are used in the chadoprop
     25 | relationship         |
     26 | synonym_type         |
     27 | cvterm_property_type |
     28 | anonymous            |
     29 | sequence             |
     30 | biological_process   |
     31 | molecular_function   |
     32 | cellular_component   |
     33 | gene_ontology        |
     34 | feature_property     |
(16 Zeilen)

chado_pipa_GS115=# SELECT count(*) FROM cvterm WHERE cv_id = 25;
  count
-------
      3
(1 Zeile)


chado_pipa_GS115=# select * FROM cvterm WHERE cv_id = 25;
  cvterm_id | cv_id |   name   | definition | dbxref_id | is_obsolete |
is_relationshiptype
-----------+-------+----------+------------+-----------+-------------+---------------------
        119 |    25 | is_a     |            |       119 |           0 |
                   1
       2236 |    25 | has_part |            |      2953 |           0 |
                   1
       2239 |    25 | part_of  |            |      2957 |           0 |
                   1
(3 Zeilen)



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Re: Correction: Problem with gmod_bulk_load_gff3.pl - Addendum

Scott Cain
Hi Hans,

That means that something went wrong when loading the relationship
ontology, but what exactly happened is hard for me to tell.  I am on
holiday this week, so I won't be able to do any testing right now; I
will take a look next week.

Scott


On Mon, Mar 5, 2012 at 5:25 PM, Hans Kraus <[hidden email]> wrote:

> Hi Scott,
>
>
>> The fact that that query came up empty means there is something wrong
>> with your ontologies.  Do you see "relationship" if you do a
>> "SELECT * FROM cv"?
>
> Yes, I see 'relationship'.
>
>
>> If so, what do you see if you do
>> "SELECT count(*) FROM cvterm WHERE cv_id = ?"
>
> The result is 3.
>
>
>> where you replace the cv_id of the relationship ontology from the cv
>> table?
>
> Thanks,
> Hans
>
> chado_pipa_GS115=# SELECT * FROM cv;
>  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
>     6 | chado_properties     | Terms that are used in the chadoprop
>    25 | relationship         |
>    26 | synonym_type         |
>    27 | cvterm_property_type |
>    28 | anonymous            |
>    29 | sequence             |
>    30 | biological_process   |
>    31 | molecular_function   |
>    32 | cellular_component   |
>    33 | gene_ontology        |
>    34 | feature_property     |
> (16 Zeilen)
>
> chado_pipa_GS115=# SELECT count(*) FROM cvterm WHERE cv_id = 25;
>  count
> -------
>     3
> (1 Zeile)
>
>
> chado_pipa_GS115=# select * FROM cvterm WHERE cv_id = 25;
>  cvterm_id | cv_id |   name   | definition | dbxref_id | is_obsolete |
> is_relationshiptype
> -----------+-------+----------+------------+-----------+-------------+---------------------
>       119 |    25 | is_a     |            |       119 |           0 |
>             1
>      2236 |    25 | has_part |            |      2953 |           0 |
>             1
>      2239 |    25 | part_of  |            |      2957 |           0 |
>             1
> (3 Zeilen)
>
>



--
------------------------------------------------------------------------
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: Correction: Problem with gmod_bulk_load_gff3.pl - Addendum

Hans Kraus
Hi Scott,

hopefully you enjoyed your vacation.

I set up a virtual machine and installed everything vom scratch again,
but got the same results.

I found an unrelated error in 'lib/Bio/Chado/Builder.pm', line 352. The
line should be changed:
-------------------------FROM-------------------------------------------
       $stag_string .= " --password $db_pass " if $db_pass;
--------------------------TO--------------------------------------------
       $stag_string .= " --password '$db_pass' " if $db_pass;
--------------------------END-------------------------------------------
Some passwords (with special characters in them) lead to errors
otherwise.

The output of 'make ontologies':
-------------------------START------------------------------------------
gbrowse@Kauz:~/Work/Chado/chado-1.2$ make ontologies
./Build ontologies
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4,5
fetching files for Relationship Ontology
   +http://www.obofoundry.org/ro/ro.obo
     ./tmp/obo/OBO_REL/ro.obo is up to date
fetching files for Sequence Ontology
   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
     updated
     loading...done!
fetching files for Gene Ontology
   +http://www.geneontology.org/ontology/gene_ontology.obo
     updated
     loading...done!
fetching files for Chado Feature Properties
   +load/etc/feature_property.obo
     loading...done!
fetching files for Plant Ontology
 
+http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co
     updated
     loading...done!
--------------------------END-------------------------------------------

Thanks, Hans

Am 06.03.2012 05:29, schrieb Scott Cain:

> Hi Hans,
>
> That means that something went wrong when loading the relationship
> ontology, but what exactly happened is hard for me to tell.  I am on
> holiday this week, so I won't be able to do any testing right now; I
> will take a look next week.
>
> Scott
>
>
> On Mon, Mar 5, 2012 at 5:25 PM, Hans Kraus<[hidden email]>  wrote:
>> Hi Scott,
>>
>>
>>> The fact that that query came up empty means there is something wrong
>>> with your ontologies.  Do you see "relationship" if you do a
>>> "SELECT * FROM cv"?
>>
>> Yes, I see 'relationship'.
>>
>>
>>> If so, what do you see if you do
>>> "SELECT count(*) FROM cvterm WHERE cv_id = ?"
>>
>> The result is 3.
>>
>>
>>> where you replace the cv_id of the relationship ontology from the cv
>>> table?
>>
>> Thanks,
>> Hans
>>
>> chado_pipa_GS115=# SELECT * FROM cv;
>>   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
>>      6 | chado_properties     | Terms that are used in the chadoprop
>>     25 | relationship         |
>>     26 | synonym_type         |
>>     27 | cvterm_property_type |
>>     28 | anonymous            |
>>     29 | sequence             |
>>     30 | biological_process   |
>>     31 | molecular_function   |
>>     32 | cellular_component   |
>>     33 | gene_ontology        |
>>     34 | feature_property     |
>> (16 Zeilen)
>>
>> chado_pipa_GS115=# SELECT count(*) FROM cvterm WHERE cv_id = 25;
>>   count
>> -------
>>      3
>> (1 Zeile)
>>
>>
>> chado_pipa_GS115=# select * FROM cvterm WHERE cv_id = 25;
>>   cvterm_id | cv_id |   name   | definition | dbxref_id | is_obsolete |
>> is_relationshiptype
>> -----------+-------+----------+------------+-----------+-------------+---------------------
>>        119 |    25 | is_a     |            |       119 |           0 |
>>              1
>>       2236 |    25 | has_part |            |      2953 |           0 |
>>              1
>>       2239 |    25 | part_of  |            |      2957 |           0 |
>>              1
>> (3 Zeilen)
>>
>>
>
>
>


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Re: Correction: Problem with gmod_bulk_load_gff3.pl - Addendum

Scott Cain
Hello Hans,

That is very strange indeed.  I just tried a fresh database, and all
of RO loaded.  Can you find ro.obo and ro.oboxml and send them to me?
The are probably in tmp/obo/OBO_REL/ (where "tmp" is the directory
where you said to store downloaded ontology files, the default being a
directory named tmp in your working directory).  If those look OK, I
may ask you to let me have your VM (to save me time setting up a new
one) so I can test on it, but lets not go crazy throwing around
gigabytes when kilobytes might do the trick :-)

Scott


On Mon, Mar 12, 2012 at 4:38 AM, Hans Kraus <[hidden email]> wrote:

> Hi Scott,
>
> hopefully you enjoyed your vacation.
>
> I set up a virtual machine and installed everything vom scratch again,
> but got the same results.
>
> I found an unrelated error in 'lib/Bio/Chado/Builder.pm', line 352. The
> line should be changed:
> -------------------------FROM-------------------------------------------
>      $stag_string .= " --password $db_pass " if $db_pass;
> --------------------------TO--------------------------------------------
>      $stag_string .= " --password '$db_pass' " if $db_pass;
> --------------------------END-------------------------------------------
> Some passwords (with special characters in them) lead to errors
> otherwise.
>
> The output of 'make ontologies':
> -------------------------START------------------------------------------
> gbrowse@Kauz:~/Work/Chado/chado-1.2$ make ontologies
> ./Build ontologies
> Available ontologies:
> [1] Relationship Ontology
> [2] Sequence Ontology
> [3] Gene Ontology
> [4] Chado Feature Properties
> [5] Plant Ontology
>
> Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4,5
> fetching files for Relationship Ontology
>  +http://www.obofoundry.org/ro/ro.obo
>    ./tmp/obo/OBO_REL/ro.obo is up to date
> fetching files for Sequence Ontology
>  +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>    updated
>    loading...done!
> fetching files for Gene Ontology
>  +http://www.geneontology.org/ontology/gene_ontology.obo
>    updated
>    loading...done!
> fetching files for Chado Feature Properties
>  +load/etc/feature_property.obo
>    loading...done!
> fetching files for Plant Ontology
>
> +http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co
>    updated
>    loading...done!
> --------------------------END-------------------------------------------
>
> Thanks, Hans
>
> Am 06.03.2012 05:29, schrieb Scott Cain:
>
>> Hi Hans,
>>
>> That means that something went wrong when loading the relationship
>> ontology, but what exactly happened is hard for me to tell.  I am on
>> holiday this week, so I won't be able to do any testing right now; I
>> will take a look next week.
>>
>> Scott
>>
>>
>> On Mon, Mar 5, 2012 at 5:25 PM, Hans Kraus<[hidden email]>  wrote:
>>>
>>> Hi Scott,
>>>
>>>
>>>> The fact that that query came up empty means there is something wrong
>>>> with your ontologies.  Do you see "relationship" if you do a
>>>> "SELECT * FROM cv"?
>>>
>>>
>>> Yes, I see 'relationship'.
>>>
>>>
>>>> If so, what do you see if you do
>>>> "SELECT count(*) FROM cvterm WHERE cv_id = ?"
>>>
>>>
>>> The result is 3.
>>>
>>>
>>>> where you replace the cv_id of the relationship ontology from the cv
>>>> table?
>>>
>>>
>>> Thanks,
>>> Hans
>>>
>>> chado_pipa_GS115=# SELECT * FROM cv;
>>>  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
>>>     6 | chado_properties     | Terms that are used in the chadoprop
>>>    25 | relationship         |
>>>    26 | synonym_type         |
>>>    27 | cvterm_property_type |
>>>    28 | anonymous            |
>>>    29 | sequence             |
>>>    30 | biological_process   |
>>>    31 | molecular_function   |
>>>    32 | cellular_component   |
>>>    33 | gene_ontology        |
>>>    34 | feature_property     |
>>> (16 Zeilen)
>>>
>>> chado_pipa_GS115=# SELECT count(*) FROM cvterm WHERE cv_id = 25;
>>>  count
>>> -------
>>>     3
>>> (1 Zeile)
>>>
>>>
>>> chado_pipa_GS115=# select * FROM cvterm WHERE cv_id = 25;
>>>  cvterm_id | cv_id |   name   | definition | dbxref_id | is_obsolete |
>>> is_relationshiptype
>>>
>>> -----------+-------+----------+------------+-----------+-------------+---------------------
>>>       119 |    25 | is_a     |            |       119 |           0 |
>>>             1
>>>      2236 |    25 | has_part |            |      2953 |           0 |
>>>             1
>>>      2239 |    25 | part_of  |            |      2957 |           0 |
>>>             1
>>> (3 Zeilen)
>>>
>>>
>>
>>
>>
>



--
------------------------------------------------------------------------
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: Correction: Problem with gmod_bulk_load_gff3.pl - Addendum

Hans Kraus
Hello Scott,

the compressed files are appended.

Thanks, Hans

Am 13.03.2012 18:56, schrieb Scott Cain:

> Hello Hans,
>
> That is very strange indeed.  I just tried a fresh database, and all
> of RO loaded.  Can you find ro.obo and ro.oboxml and send them to me?
> The are probably in tmp/obo/OBO_REL/ (where "tmp" is the directory
> where you said to store downloaded ontology files, the default being a
> directory named tmp in your working directory).  If those look OK, I
> may ask you to let me have your VM (to save me time setting up a new
> one) so I can test on it, but lets not go crazy throwing around
> gigabytes when kilobytes might do the trick :-)
>
> Scott
>
>
> On Mon, Mar 12, 2012 at 4:38 AM, Hans Kraus<[hidden email]>  wrote:
>> Hi Scott,
>>
>> hopefully you enjoyed your vacation.
>>
>> I set up a virtual machine and installed everything vom scratch again,
>> but got the same results.
>>
>> I found an unrelated error in 'lib/Bio/Chado/Builder.pm', line 352. The
>> line should be changed:
>> -------------------------FROM-------------------------------------------
>>       $stag_string .= " --password $db_pass " if $db_pass;
>> --------------------------TO--------------------------------------------
>>       $stag_string .= " --password '$db_pass' " if $db_pass;
>> --------------------------END-------------------------------------------
>> Some passwords (with special characters in them) lead to errors
>> otherwise.
>>
>> The output of 'make ontologies':
>> -------------------------START------------------------------------------
>> gbrowse@Kauz:~/Work/Chado/chado-1.2$ make ontologies
>> ./Build ontologies
>> Available ontologies:
>> [1] Relationship Ontology
>> [2] Sequence Ontology
>> [3] Gene Ontology
>> [4] Chado Feature Properties
>> [5] Plant Ontology
>>
>> Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4,5
>> fetching files for Relationship Ontology
>>   +http://www.obofoundry.org/ro/ro.obo
>>     ./tmp/obo/OBO_REL/ro.obo is up to date
>> fetching files for Sequence Ontology
>>   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>>     updated
>>     loading...done!
>> fetching files for Gene Ontology
>>   +http://www.geneontology.org/ontology/gene_ontology.obo
>>     updated
>>     loading...done!
>> fetching files for Chado Feature Properties
>>   +load/etc/feature_property.obo
>>     loading...done!
>> fetching files for Plant Ontology
>>
>> +http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co
>>     updated
>>     loading...done!
>> --------------------------END-------------------------------------------
>>
>> Thanks, Hans
>>
>> Am 06.03.2012 05:29, schrieb Scott Cain:
>>
>>> Hi Hans,
>>>
>>> That means that something went wrong when loading the relationship
>>> ontology, but what exactly happened is hard for me to tell.  I am on
>>> holiday this week, so I won't be able to do any testing right now; I
>>> will take a look next week.
>>>
>>> Scott
>>>
>>>
>>> On Mon, Mar 5, 2012 at 5:25 PM, Hans Kraus<[hidden email]>    wrote:
>>>>
>>>> Hi Scott,
>>>>
>>>>
>>>>> The fact that that query came up empty means there is something wrong
>>>>> with your ontologies.  Do you see "relationship" if you do a
>>>>> "SELECT * FROM cv"?
>>>>
>>>>
>>>> Yes, I see 'relationship'.
>>>>
>>>>
>>>>> If so, what do you see if you do
>>>>> "SELECT count(*) FROM cvterm WHERE cv_id = ?"
>>>>
>>>>
>>>> The result is 3.
>>>>
>>>>
>>>>> where you replace the cv_id of the relationship ontology from the cv
>>>>> table?
>>>>
>>>>
>>>> Thanks,
>>>> Hans
>>>>
>>>> chado_pipa_GS115=# SELECT * FROM cv;
>>>>   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
>>>>      6 | chado_properties     | Terms that are used in the chadoprop
>>>>     25 | relationship         |
>>>>     26 | synonym_type         |
>>>>     27 | cvterm_property_type |
>>>>     28 | anonymous            |
>>>>     29 | sequence             |
>>>>     30 | biological_process   |
>>>>     31 | molecular_function   |
>>>>     32 | cellular_component   |
>>>>     33 | gene_ontology        |
>>>>     34 | feature_property     |
>>>> (16 Zeilen)
>>>>
>>>> chado_pipa_GS115=# SELECT count(*) FROM cvterm WHERE cv_id = 25;
>>>>   count
>>>> -------
>>>>      3
>>>> (1 Zeile)
>>>>
>>>>
>>>> chado_pipa_GS115=# select * FROM cvterm WHERE cv_id = 25;
>>>>   cvterm_id | cv_id |   name   | definition | dbxref_id | is_obsolete |
>>>> is_relationshiptype
>>>>
>>>> -----------+-------+----------+------------+-----------+-------------+---------------------
>>>>        119 |    25 | is_a     |            |       119 |           0 |
>>>>              1
>>>>       2236 |    25 | has_part |            |      2953 |           0 |
>>>>              1
>>>>       2239 |    25 | part_of  |            |      2957 |           0 |
>>>>              1
>>>> (3 Zeilen)
>>>>
>>>>
>>>
>>>
>>>
>>
>
>
>

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Re: Correction: Problem with gmod_bulk_load_gff3.pl - Addendum

Scott Cain
Hi Hans,

If you know of somewhere that you could upload your compressed virtual
machine to, I'd like to get a copy of it to do some testing (assuming
it's a vmware image).  If not, I'll create a AWS machine and do some
testing on it.  What OS/distro are you using?

One thing you can try in the meantime is this: create a fresh database
through the "make prepdb" step.  Then you can run the loading step
manually to see if you get any more useful output.  The reason I
suggest this is that the oboxml file you sent me is functionally the
same as the one I have that worked (there were only minor differences
in formatting, probably due to a difference in the version of
xsltproc).  To load the ro.oboxml file manual, run this command:

  stag-storenode.pl -d
'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT'
\
     --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD ro.oboxml

(you can leave out the things that don't matter like host and port if
the database is running on the local machine using the default port).
It appears to be terminating early when loading this file, and I'm
hoping that you'll get some sort of useful error message when that
happens.

Scott


On Tue, Mar 13, 2012 at 2:18 PM, Hans Kraus <[hidden email]> wrote:

> Hello Scott,
>
> the compressed files are appended.
>
> Thanks, Hans
>
> Am 13.03.2012 18:56, schrieb Scott Cain:
>
>> Hello Hans,
>>
>> That is very strange indeed.  I just tried a fresh database, and all
>> of RO loaded.  Can you find ro.obo and ro.oboxml and send them to me?
>> The are probably in tmp/obo/OBO_REL/ (where "tmp" is the directory
>> where you said to store downloaded ontology files, the default being a
>> directory named tmp in your working directory).  If those look OK, I
>> may ask you to let me have your VM (to save me time setting up a new
>> one) so I can test on it, but lets not go crazy throwing around
>> gigabytes when kilobytes might do the trick :-)
>>
>> Scott
>>
>>
>> On Mon, Mar 12, 2012 at 4:38 AM, Hans Kraus<[hidden email]>  wrote:
>>>
>>> Hi Scott,
>>>
>>> hopefully you enjoyed your vacation.
>>>
>>> I set up a virtual machine and installed everything vom scratch again,
>>> but got the same results.
>>>
>>> I found an unrelated error in 'lib/Bio/Chado/Builder.pm', line 352. The
>>> line should be changed:
>>> -------------------------FROM-------------------------------------------
>>>      $stag_string .= " --password $db_pass " if $db_pass;
>>> --------------------------TO--------------------------------------------
>>>      $stag_string .= " --password '$db_pass' " if $db_pass;
>>> --------------------------END-------------------------------------------
>>> Some passwords (with special characters in them) lead to errors
>>> otherwise.
>>>
>>> The output of 'make ontologies':
>>> -------------------------START------------------------------------------
>>> gbrowse@Kauz:~/Work/Chado/chado-1.2$ make ontologies
>>> ./Build ontologies
>>> Available ontologies:
>>> [1] Relationship Ontology
>>> [2] Sequence Ontology
>>> [3] Gene Ontology
>>> [4] Chado Feature Properties
>>> [5] Plant Ontology
>>>
>>> Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4,5
>>> fetching files for Relationship Ontology
>>>  +http://www.obofoundry.org/ro/ro.obo
>>>    ./tmp/obo/OBO_REL/ro.obo is up to date
>>> fetching files for Sequence Ontology
>>>  +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>>>    updated
>>>    loading...done!
>>> fetching files for Gene Ontology
>>>  +http://www.geneontology.org/ontology/gene_ontology.obo
>>>    updated
>>>    loading...done!
>>> fetching files for Chado Feature Properties
>>>  +load/etc/feature_property.obo
>>>    loading...done!
>>> fetching files for Plant Ontology
>>>
>>>
>>> +http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co
>>>    updated
>>>    loading...done!
>>> --------------------------END-------------------------------------------
>>>
>>> Thanks, Hans
>>>
>>> Am 06.03.2012 05:29, schrieb Scott Cain:
>>>
>>>> Hi Hans,
>>>>
>>>> That means that something went wrong when loading the relationship
>>>> ontology, but what exactly happened is hard for me to tell.  I am on
>>>> holiday this week, so I won't be able to do any testing right now; I
>>>> will take a look next week.
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Mon, Mar 5, 2012 at 5:25 PM, Hans Kraus<[hidden email]>
>>>>  wrote:
>>>>>
>>>>>
>>>>> Hi Scott,
>>>>>
>>>>>
>>>>>> The fact that that query came up empty means there is something wrong
>>>>>> with your ontologies.  Do you see "relationship" if you do a
>>>>>> "SELECT * FROM cv"?
>>>>>
>>>>>
>>>>>
>>>>> Yes, I see 'relationship'.
>>>>>
>>>>>
>>>>>> If so, what do you see if you do
>>>>>> "SELECT count(*) FROM cvterm WHERE cv_id = ?"
>>>>>
>>>>>
>>>>>
>>>>> The result is 3.
>>>>>
>>>>>
>>>>>> where you replace the cv_id of the relationship ontology from the cv
>>>>>> table?
>>>>>
>>>>>
>>>>>
>>>>> Thanks,
>>>>> Hans
>>>>>
>>>>> chado_pipa_GS115=# SELECT * FROM cv;
>>>>>  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
>>>>>     6 | chado_properties     | Terms that are used in the chadoprop
>>>>>    25 | relationship         |
>>>>>    26 | synonym_type         |
>>>>>    27 | cvterm_property_type |
>>>>>    28 | anonymous            |
>>>>>    29 | sequence             |
>>>>>    30 | biological_process   |
>>>>>    31 | molecular_function   |
>>>>>    32 | cellular_component   |
>>>>>    33 | gene_ontology        |
>>>>>    34 | feature_property     |
>>>>> (16 Zeilen)
>>>>>
>>>>> chado_pipa_GS115=# SELECT count(*) FROM cvterm WHERE cv_id = 25;
>>>>>  count
>>>>> -------
>>>>>     3
>>>>> (1 Zeile)
>>>>>
>>>>>
>>>>> chado_pipa_GS115=# select * FROM cvterm WHERE cv_id = 25;
>>>>>  cvterm_id | cv_id |   name   | definition | dbxref_id | is_obsolete |
>>>>> is_relationshiptype
>>>>>
>>>>>
>>>>> -----------+-------+----------+------------+-----------+-------------+---------------------
>>>>>       119 |    25 | is_a     |            |       119 |           0 |
>>>>>             1
>>>>>      2236 |    25 | has_part |            |      2953 |           0 |
>>>>>             1
>>>>>      2239 |    25 | part_of  |            |      2957 |           0 |
>>>>>             1
>>>>> (3 Zeilen)
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>>
>



--
------------------------------------------------------------------------
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: Correction: Problem with gmod_bulk_load_gff3.pl - Addendum

Scott Cain
Hi Hans,

I had an Ubuntu 11.10 VM lying around that I tried Pg 9.1 with and had
no problems loading the relationship ontology or other ontologies and
was able to load the SGD yeast GFF3 file (though there are some GO
terms in the SGD file that weren't in GO, but that's not my fault :-)

Any progress on your end?

Scott


On Tue, Mar 13, 2012 at 10:44 PM, Scott Cain <[hidden email]> wrote:

> Hi Hans,
>
> If you know of somewhere that you could upload your compressed virtual
> machine to, I'd like to get a copy of it to do some testing (assuming
> it's a vmware image).  If not, I'll create a AWS machine and do some
> testing on it.  What OS/distro are you using?
>
> One thing you can try in the meantime is this: create a fresh database
> through the "make prepdb" step.  Then you can run the loading step
> manually to see if you get any more useful output.  The reason I
> suggest this is that the oboxml file you sent me is functionally the
> same as the one I have that worked (there were only minor differences
> in formatting, probably due to a difference in the version of
> xsltproc).  To load the ro.oboxml file manual, run this command:
>
>  stag-storenode.pl -d
> 'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT'
> \
>     --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD ro.oboxml
>
> (you can leave out the things that don't matter like host and port if
> the database is running on the local machine using the default port).
> It appears to be terminating early when loading this file, and I'm
> hoping that you'll get some sort of useful error message when that
> happens.
>
> Scott
>
>
> On Tue, Mar 13, 2012 at 2:18 PM, Hans Kraus <[hidden email]> wrote:
>> Hello Scott,
>>
>> the compressed files are appended.
>>
>> Thanks, Hans
>>
>> Am 13.03.2012 18:56, schrieb Scott Cain:
>>
>>> Hello Hans,
>>>
>>> That is very strange indeed.  I just tried a fresh database, and all
>>> of RO loaded.  Can you find ro.obo and ro.oboxml and send them to me?
>>> The are probably in tmp/obo/OBO_REL/ (where "tmp" is the directory
>>> where you said to store downloaded ontology files, the default being a
>>> directory named tmp in your working directory).  If those look OK, I
>>> may ask you to let me have your VM (to save me time setting up a new
>>> one) so I can test on it, but lets not go crazy throwing around
>>> gigabytes when kilobytes might do the trick :-)
>>>
>>> Scott
>>>
>>>
>>> On Mon, Mar 12, 2012 at 4:38 AM, Hans Kraus<[hidden email]>  wrote:
>>>>
>>>> Hi Scott,
>>>>
>>>> hopefully you enjoyed your vacation.
>>>>
>>>> I set up a virtual machine and installed everything vom scratch again,
>>>> but got the same results.
>>>>
>>>> I found an unrelated error in 'lib/Bio/Chado/Builder.pm', line 352. The
>>>> line should be changed:
>>>> -------------------------FROM-------------------------------------------
>>>>      $stag_string .= " --password $db_pass " if $db_pass;
>>>> --------------------------TO--------------------------------------------
>>>>      $stag_string .= " --password '$db_pass' " if $db_pass;
>>>> --------------------------END-------------------------------------------
>>>> Some passwords (with special characters in them) lead to errors
>>>> otherwise.
>>>>
>>>> The output of 'make ontologies':
>>>> -------------------------START------------------------------------------
>>>> gbrowse@Kauz:~/Work/Chado/chado-1.2$ make ontologies
>>>> ./Build ontologies
>>>> Available ontologies:
>>>> [1] Relationship Ontology
>>>> [2] Sequence Ontology
>>>> [3] Gene Ontology
>>>> [4] Chado Feature Properties
>>>> [5] Plant Ontology
>>>>
>>>> Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4,5
>>>> fetching files for Relationship Ontology
>>>>  +http://www.obofoundry.org/ro/ro.obo
>>>>    ./tmp/obo/OBO_REL/ro.obo is up to date
>>>> fetching files for Sequence Ontology
>>>>  +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>>>>    updated
>>>>    loading...done!
>>>> fetching files for Gene Ontology
>>>>  +http://www.geneontology.org/ontology/gene_ontology.obo
>>>>    updated
>>>>    loading...done!
>>>> fetching files for Chado Feature Properties
>>>>  +load/etc/feature_property.obo
>>>>    loading...done!
>>>> fetching files for Plant Ontology
>>>>
>>>>
>>>> +http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co
>>>>    updated
>>>>    loading...done!
>>>> --------------------------END-------------------------------------------
>>>>
>>>> Thanks, Hans
>>>>
>>>> Am 06.03.2012 05:29, schrieb Scott Cain:
>>>>
>>>>> Hi Hans,
>>>>>
>>>>> That means that something went wrong when loading the relationship
>>>>> ontology, but what exactly happened is hard for me to tell.  I am on
>>>>> holiday this week, so I won't be able to do any testing right now; I
>>>>> will take a look next week.
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Mon, Mar 5, 2012 at 5:25 PM, Hans Kraus<[hidden email]>
>>>>>  wrote:
>>>>>>
>>>>>>
>>>>>> Hi Scott,
>>>>>>
>>>>>>
>>>>>>> The fact that that query came up empty means there is something wrong
>>>>>>> with your ontologies.  Do you see "relationship" if you do a
>>>>>>> "SELECT * FROM cv"?
>>>>>>
>>>>>>
>>>>>>
>>>>>> Yes, I see 'relationship'.
>>>>>>
>>>>>>
>>>>>>> If so, what do you see if you do
>>>>>>> "SELECT count(*) FROM cvterm WHERE cv_id = ?"
>>>>>>
>>>>>>
>>>>>>
>>>>>> The result is 3.
>>>>>>
>>>>>>
>>>>>>> where you replace the cv_id of the relationship ontology from the cv
>>>>>>> table?
>>>>>>
>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>> Hans
>>>>>>
>>>>>> chado_pipa_GS115=# SELECT * FROM cv;
>>>>>>  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
>>>>>>     6 | chado_properties     | Terms that are used in the chadoprop
>>>>>>    25 | relationship         |
>>>>>>    26 | synonym_type         |
>>>>>>    27 | cvterm_property_type |
>>>>>>    28 | anonymous            |
>>>>>>    29 | sequence             |
>>>>>>    30 | biological_process   |
>>>>>>    31 | molecular_function   |
>>>>>>    32 | cellular_component   |
>>>>>>    33 | gene_ontology        |
>>>>>>    34 | feature_property     |
>>>>>> (16 Zeilen)
>>>>>>
>>>>>> chado_pipa_GS115=# SELECT count(*) FROM cvterm WHERE cv_id = 25;
>>>>>>  count
>>>>>> -------
>>>>>>     3
>>>>>> (1 Zeile)
>>>>>>
>>>>>>
>>>>>> chado_pipa_GS115=# select * FROM cvterm WHERE cv_id = 25;
>>>>>>  cvterm_id | cv_id |   name   | definition | dbxref_id | is_obsolete |
>>>>>> is_relationshiptype
>>>>>>
>>>>>>
>>>>>> -----------+-------+----------+------------+-----------+-------------+---------------------
>>>>>>       119 |    25 | is_a     |            |       119 |           0 |
>>>>>>             1
>>>>>>      2236 |    25 | has_part |            |      2953 |           0 |
>>>>>>             1
>>>>>>      2239 |    25 | part_of  |            |      2957 |           0 |
>>>>>>             1
>>>>>> (3 Zeilen)
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> 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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Re: Correction: Problem with gmod_bulk_load_gff3.pl - Addendum

Hans Kraus
Hi Scott,

I'm back with some weird results.

After setting up the DB wich 'make load_schema' and 'make prepdb'
I called:
stag-storenode.pl -d 'dbi:Pg:dbname=dev_chado_pp_01' --user gbrowse
--password '<pwd>' ro.oboxml
No errors, there were 26 rows in the cvterm table for the
relationship entries.

I called 'make load_schema', 'make prepdb' and 'make ontologies'
again and got 26 rows too. The same result on my server.

I set up a new virtual machine, Debian 6.0.4 64Bit on Oracle Virtual
Box, like the old one. All steps to install Chado are protocolled in
ni.txt.

With the new virtual machine I got 3 rows in the cvterm table for the
relationship entries. I called 'make load_schema', 'make prepdb' and
'make ontologies' again and got 1 row in the cvterm table for the
relationship entries.

'make load_schema', 'make prepdb' and 'stag-storenode.pl .....' gave 26
rows.

'make load_schema', 'make prepdb' and 'make ontologies' gave 1 row.

2. round of the commands above, same results.

The good thing is that I have now a working DB on my server.

Thanks, Hans

Am 15.03.2012 03:38, schrieb Scott Cain:

> Hi Hans,
>
> I had an Ubuntu 11.10 VM lying around that I tried Pg 9.1 with and had
> no problems loading the relationship ontology or other ontologies and
> was able to load the SGD yeast GFF3 file (though there are some GO
> terms in the SGD file that weren't in GO, but that's not my fault :-)
>
> Any progress on your end?
>
> Scott
>
>
> On Tue, Mar 13, 2012 at 10:44 PM, Scott Cain<[hidden email]>  wrote:
>> Hi Hans,
>>
>> If you know of somewhere that you could upload your compressed virtual
>> machine to, I'd like to get a copy of it to do some testing (assuming
>> it's a vmware image).  If not, I'll create a AWS machine and do some
>> testing on it.  What OS/distro are you using?
>>
>> One thing you can try in the meantime is this: create a fresh database
>> through the "make prepdb" step.  Then you can run the loading step
>> manually to see if you get any more useful output.  The reason I
>> suggest this is that the oboxml file you sent me is functionally the
>> same as the one I have that worked (there were only minor differences
>> in formatting, probably due to a difference in the version of
>> xsltproc).  To load the ro.oboxml file manual, run this command:
>>
>>   stag-storenode.pl -d
>> 'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT'
>> \
>>      --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD ro.oboxml
>>
>> (you can leave out the things that don't matter like host and port if
>> the database is running on the local machine using the default port).
>> It appears to be terminating early when loading this file, and I'm
>> hoping that you'll get some sort of useful error message when that
>> happens.
>>
>> Scott
>>
>>
>> On Tue, Mar 13, 2012 at 2:18 PM, Hans Kraus<[hidden email]>  wrote:
>>> Hello Scott,
>>>
>>> the compressed files are appended.
>>>
>>> Thanks, Hans
>>>
>>> Am 13.03.2012 18:56, schrieb Scott Cain:
>>>
>>>> Hello Hans,
>>>>
>>>> That is very strange indeed.  I just tried a fresh database, and all
>>>> of RO loaded.  Can you find ro.obo and ro.oboxml and send them to me?
>>>> The are probably in tmp/obo/OBO_REL/ (where "tmp" is the directory
>>>> where you said to store downloaded ontology files, the default being a
>>>> directory named tmp in your working directory).  If those look OK, I
>>>> may ask you to let me have your VM (to save me time setting up a new
>>>> one) so I can test on it, but lets not go crazy throwing around
>>>> gigabytes when kilobytes might do the trick :-)
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Mon, Mar 12, 2012 at 4:38 AM, Hans Kraus<[hidden email]>    wrote:
>>>>>
>>>>> Hi Scott,
>>>>>
>>>>> hopefully you enjoyed your vacation.
>>>>>
>>>>> I set up a virtual machine and installed everything vom scratch again,
>>>>> but got the same results.
>>>>>
>>>>> I found an unrelated error in 'lib/Bio/Chado/Builder.pm', line 352. The
>>>>> line should be changed:
>>>>> -------------------------FROM-------------------------------------------
>>>>>       $stag_string .= " --password $db_pass " if $db_pass;
>>>>> --------------------------TO--------------------------------------------
>>>>>       $stag_string .= " --password '$db_pass' " if $db_pass;
>>>>> --------------------------END-------------------------------------------
>>>>> Some passwords (with special characters in them) lead to errors
>>>>> otherwise.
>>>>>
>>>>> The output of 'make ontologies':
>>>>> -------------------------START------------------------------------------
>>>>> gbrowse@Kauz:~/Work/Chado/chado-1.2$ make ontologies
>>>>> ./Build ontologies
>>>>> Available ontologies:
>>>>> [1] Relationship Ontology
>>>>> [2] Sequence Ontology
>>>>> [3] Gene Ontology
>>>>> [4] Chado Feature Properties
>>>>> [5] Plant Ontology
>>>>>
>>>>> Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4,5
>>>>> fetching files for Relationship Ontology
>>>>>   +http://www.obofoundry.org/ro/ro.obo
>>>>>     ./tmp/obo/OBO_REL/ro.obo is up to date
>>>>> fetching files for Sequence Ontology
>>>>>   +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>>>>>     updated
>>>>>     loading...done!
>>>>> fetching files for Gene Ontology
>>>>>   +http://www.geneontology.org/ontology/gene_ontology.obo
>>>>>     updated
>>>>>     loading...done!
>>>>> fetching files for Chado Feature Properties
>>>>>   +load/etc/feature_property.obo
>>>>>     loading...done!
>>>>> fetching files for Plant Ontology
>>>>>
>>>>>
>>>>> +http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co
>>>>>     updated
>>>>>     loading...done!
>>>>> --------------------------END-------------------------------------------
>>>>>
>>>>> Thanks, Hans
>>>>>
>>>>> Am 06.03.2012 05:29, schrieb Scott Cain:
>>>>>
>>>>>> Hi Hans,
>>>>>>
>>>>>> That means that something went wrong when loading the relationship
>>>>>> ontology, but what exactly happened is hard for me to tell.  I am on
>>>>>> holiday this week, so I won't be able to do any testing right now; I
>>>>>> will take a look next week.
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> On Mon, Mar 5, 2012 at 5:25 PM, Hans Kraus<[hidden email]>
>>>>>>   wrote:
>>>>>>>
>>>>>>>
>>>>>>> Hi Scott,
>>>>>>>
>>>>>>>
>>>>>>>> The fact that that query came up empty means there is something wrong
>>>>>>>> with your ontologies.  Do you see "relationship" if you do a
>>>>>>>> "SELECT * FROM cv"?
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Yes, I see 'relationship'.
>>>>>>>
>>>>>>>
>>>>>>>> If so, what do you see if you do
>>>>>>>> "SELECT count(*) FROM cvterm WHERE cv_id = ?"
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> The result is 3.
>>>>>>>
>>>>>>>
>>>>>>>> where you replace the cv_id of the relationship ontology from the cv
>>>>>>>> table?
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Hans
>>>>>>>
>>>>>>> chado_pipa_GS115=# SELECT * FROM cv;
>>>>>>>   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
>>>>>>>      6 | chado_properties     | Terms that are used in the chadoprop
>>>>>>>     25 | relationship         |
>>>>>>>     26 | synonym_type         |
>>>>>>>     27 | cvterm_property_type |
>>>>>>>     28 | anonymous            |
>>>>>>>     29 | sequence             |
>>>>>>>     30 | biological_process   |
>>>>>>>     31 | molecular_function   |
>>>>>>>     32 | cellular_component   |
>>>>>>>     33 | gene_ontology        |
>>>>>>>     34 | feature_property     |
>>>>>>> (16 Zeilen)
>>>>>>>
>>>>>>> chado_pipa_GS115=# SELECT count(*) FROM cvterm WHERE cv_id = 25;
>>>>>>>   count
>>>>>>> -------
>>>>>>>      3
>>>>>>> (1 Zeile)
>>>>>>>
>>>>>>>
>>>>>>> chado_pipa_GS115=# select * FROM cvterm WHERE cv_id = 25;
>>>>>>>   cvterm_id | cv_id |   name   | definition | dbxref_id | is_obsolete |
>>>>>>> is_relationshiptype
>>>>>>>
>>>>>>>
>>>>>>> -----------+-------+----------+------------+-----------+-------------+---------------------
>>>>>>>        119 |    25 | is_a     |            |       119 |           0 |
>>>>>>>              1
>>>>>>>       2236 |    25 | has_part |            |      2953 |           0 |
>>>>>>>              1
>>>>>>>       2239 |    25 | part_of  |            |      2957 |           0 |
>>>>>>>              1
>>>>>>> (3 Zeilen)
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> 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: Correction: Problem with gmod_bulk_load_gff3.pl - Addendum

Scott Cain
Hi Hans,

I agree, that is really weird.  I'll have to try setting up a Debian
64bit box to see if I can reproduce.  As an aside, there is a debian
package for Chado (called libchado-perl I think), though I can't
remember where it is; "untested" maybe?  I haven't worked with it yet,
so I'm still a little unclear on the specifics.

Scott


On Thu, Mar 15, 2012 at 12:34 PM, Hans Kraus <[hidden email]> wrote:

> Hi Scott,
>
> I'm back with some weird results.
>
> After setting up the DB wich 'make load_schema' and 'make prepdb'
> I called:
> stag-storenode.pl -d 'dbi:Pg:dbname=dev_chado_pp_01' --user gbrowse
> --password '<pwd>' ro.oboxml
> No errors, there were 26 rows in the cvterm table for the
> relationship entries.
>
> I called 'make load_schema', 'make prepdb' and 'make ontologies'
> again and got 26 rows too. The same result on my server.
>
> I set up a new virtual machine, Debian 6.0.4 64Bit on Oracle Virtual
> Box, like the old one. All steps to install Chado are protocolled in
> ni.txt.
>
> With the new virtual machine I got 3 rows in the cvterm table for the
> relationship entries. I called 'make load_schema', 'make prepdb' and
> 'make ontologies' again and got 1 row in the cvterm table for the
> relationship entries.
>
> 'make load_schema', 'make prepdb' and 'stag-storenode.pl .....' gave 26
> rows.
>
> 'make load_schema', 'make prepdb' and 'make ontologies' gave 1 row.
>
> 2. round of the commands above, same results.
>
> The good thing is that I have now a working DB on my server.
>
> Thanks, Hans
>
> Am 15.03.2012 03:38, schrieb Scott Cain:
>
>> Hi Hans,
>>
>> I had an Ubuntu 11.10 VM lying around that I tried Pg 9.1 with and had
>> no problems loading the relationship ontology or other ontologies and
>> was able to load the SGD yeast GFF3 file (though there are some GO
>> terms in the SGD file that weren't in GO, but that's not my fault :-)
>>
>> Any progress on your end?
>>
>> Scott
>>
>>
>> On Tue, Mar 13, 2012 at 10:44 PM, Scott Cain<[hidden email]>  wrote:
>>>
>>> Hi Hans,
>>>
>>> If you know of somewhere that you could upload your compressed virtual
>>> machine to, I'd like to get a copy of it to do some testing (assuming
>>> it's a vmware image).  If not, I'll create a AWS machine and do some
>>> testing on it.  What OS/distro are you using?
>>>
>>> One thing you can try in the meantime is this: create a fresh database
>>> through the "make prepdb" step.  Then you can run the loading step
>>> manually to see if you get any more useful output.  The reason I
>>> suggest this is that the oboxml file you sent me is functionally the
>>> same as the one I have that worked (there were only minor differences
>>> in formatting, probably due to a difference in the version of
>>> xsltproc).  To load the ro.oboxml file manual, run this command:
>>>
>>>  stag-storenode.pl -d
>>> 'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT'
>>> \
>>>     --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD ro.oboxml
>>>
>>> (you can leave out the things that don't matter like host and port if
>>> the database is running on the local machine using the default port).
>>> It appears to be terminating early when loading this file, and I'm
>>> hoping that you'll get some sort of useful error message when that
>>> happens.
>>>
>>> Scott
>>>
>>>
>>> On Tue, Mar 13, 2012 at 2:18 PM, Hans Kraus<[hidden email]>  wrote:
>>>>
>>>> Hello Scott,
>>>>
>>>> the compressed files are appended.
>>>>
>>>> Thanks, Hans
>>>>
>>>> Am 13.03.2012 18:56, schrieb Scott Cain:
>>>>
>>>>> Hello Hans,
>>>>>
>>>>> That is very strange indeed.  I just tried a fresh database, and all
>>>>> of RO loaded.  Can you find ro.obo and ro.oboxml and send them to me?
>>>>> The are probably in tmp/obo/OBO_REL/ (where "tmp" is the directory
>>>>> where you said to store downloaded ontology files, the default being a
>>>>> directory named tmp in your working directory).  If those look OK, I
>>>>> may ask you to let me have your VM (to save me time setting up a new
>>>>> one) so I can test on it, but lets not go crazy throwing around
>>>>> gigabytes when kilobytes might do the trick :-)
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Mon, Mar 12, 2012 at 4:38 AM, Hans Kraus<[hidden email]>
>>>>>  wrote:
>>>>>>
>>>>>>
>>>>>> Hi Scott,
>>>>>>
>>>>>> hopefully you enjoyed your vacation.
>>>>>>
>>>>>> I set up a virtual machine and installed everything vom scratch again,
>>>>>> but got the same results.
>>>>>>
>>>>>> I found an unrelated error in 'lib/Bio/Chado/Builder.pm', line 352.
>>>>>> The
>>>>>> line should be changed:
>>>>>>
>>>>>> -------------------------FROM-------------------------------------------
>>>>>>      $stag_string .= " --password $db_pass " if $db_pass;
>>>>>>
>>>>>> --------------------------TO--------------------------------------------
>>>>>>      $stag_string .= " --password '$db_pass' " if $db_pass;
>>>>>>
>>>>>> --------------------------END-------------------------------------------
>>>>>> Some passwords (with special characters in them) lead to errors
>>>>>> otherwise.
>>>>>>
>>>>>> The output of 'make ontologies':
>>>>>>
>>>>>> -------------------------START------------------------------------------
>>>>>> gbrowse@Kauz:~/Work/Chado/chado-1.2$ make ontologies
>>>>>> ./Build ontologies
>>>>>> Available ontologies:
>>>>>> [1] Relationship Ontology
>>>>>> [2] Sequence Ontology
>>>>>> [3] Gene Ontology
>>>>>> [4] Chado Feature Properties
>>>>>> [5] Plant Ontology
>>>>>>
>>>>>> Which ontologies would you like to load (Comma delimited)? [0]
>>>>>>  1,2,3,4,5
>>>>>> fetching files for Relationship Ontology
>>>>>>  +http://www.obofoundry.org/ro/ro.obo
>>>>>>    ./tmp/obo/OBO_REL/ro.obo is up to date
>>>>>> fetching files for Sequence Ontology
>>>>>>  +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>>>>>>    updated
>>>>>>    loading...done!
>>>>>> fetching files for Gene Ontology
>>>>>>  +http://www.geneontology.org/ontology/gene_ontology.obo
>>>>>>    updated
>>>>>>    loading...done!
>>>>>> fetching files for Chado Feature Properties
>>>>>>  +load/etc/feature_property.obo
>>>>>>    loading...done!
>>>>>> fetching files for Plant Ontology
>>>>>>
>>>>>>
>>>>>>
>>>>>> +http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co
>>>>>>    updated
>>>>>>    loading...done!
>>>>>>
>>>>>> --------------------------END-------------------------------------------
>>>>>>
>>>>>> Thanks, Hans
>>>>>>
>>>>>> Am 06.03.2012 05:29, schrieb Scott Cain:
>>>>>>
>>>>>>> Hi Hans,
>>>>>>>
>>>>>>> That means that something went wrong when loading the relationship
>>>>>>> ontology, but what exactly happened is hard for me to tell.  I am on
>>>>>>> holiday this week, so I won't be able to do any testing right now; I
>>>>>>> will take a look next week.
>>>>>>>
>>>>>>> Scott
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Mar 5, 2012 at 5:25 PM, Hans Kraus<[hidden email]>
>>>>>>>  wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Hi Scott,
>>>>>>>>
>>>>>>>>
>>>>>>>>> The fact that that query came up empty means there is something
>>>>>>>>> wrong
>>>>>>>>> with your ontologies.  Do you see "relationship" if you do a
>>>>>>>>> "SELECT * FROM cv"?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Yes, I see 'relationship'.
>>>>>>>>
>>>>>>>>
>>>>>>>>> If so, what do you see if you do
>>>>>>>>> "SELECT count(*) FROM cvterm WHERE cv_id = ?"
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> The result is 3.
>>>>>>>>
>>>>>>>>
>>>>>>>>> where you replace the cv_id of the relationship ontology from the
>>>>>>>>> cv
>>>>>>>>> table?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Hans
>>>>>>>>
>>>>>>>> chado_pipa_GS115=# SELECT * FROM cv;
>>>>>>>>  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
>>>>>>>>     6 | chado_properties     | Terms that are used in the chadoprop
>>>>>>>>    25 | relationship         |
>>>>>>>>    26 | synonym_type         |
>>>>>>>>    27 | cvterm_property_type |
>>>>>>>>    28 | anonymous            |
>>>>>>>>    29 | sequence             |
>>>>>>>>    30 | biological_process   |
>>>>>>>>    31 | molecular_function   |
>>>>>>>>    32 | cellular_component   |
>>>>>>>>    33 | gene_ontology        |
>>>>>>>>    34 | feature_property     |
>>>>>>>> (16 Zeilen)
>>>>>>>>
>>>>>>>> chado_pipa_GS115=# SELECT count(*) FROM cvterm WHERE cv_id = 25;
>>>>>>>>  count
>>>>>>>> -------
>>>>>>>>     3
>>>>>>>> (1 Zeile)
>>>>>>>>
>>>>>>>>
>>>>>>>> chado_pipa_GS115=# select * FROM cvterm WHERE cv_id = 25;
>>>>>>>>  cvterm_id | cv_id |   name   | definition | dbxref_id | is_obsolete
>>>>>>>> |
>>>>>>>> is_relationshiptype
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> -----------+-------+----------+------------+-----------+-------------+---------------------
>>>>>>>>       119 |    25 | is_a     |            |       119 |           0
>>>>>>>> |
>>>>>>>>             1
>>>>>>>>      2236 |    25 | has_part |            |      2953 |           0
>>>>>>>> |
>>>>>>>>             1
>>>>>>>>      2239 |    25 | part_of  |            |      2957 |           0
>>>>>>>> |
>>>>>>>>             1
>>>>>>>> (3 Zeilen)
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> 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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