Difference between revisions of "Chado FAQ"

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: The best place to start would be the [[Chado_Manual#Modules|Chado Manual]] or [[GMOD_for_the_Biologist|GMOD for the Biologist]].
 
: The best place to start would be the [[Chado_Manual#Modules|Chado Manual]] or [[GMOD_for_the_Biologist|GMOD for the Biologist]].
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===Loading data into Chado===
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When I try to load data into Chado using the GFF bulk loader (gmod_bulk_load_gff3.pl), I get this error:
 +
 +
  DBD::Pg::db pg_endcopy failed: ERROR:  invalid input syntax for integer: ""
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 +
  CONTEXT:  COPY feature_relationship, line 1, column type_id: "" at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 2723, <$fh> line 64298.
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Why is that and what do I do?
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: Unfortunately there is a bug in one of the prerequisites for the Chado loader, a perl module called DBIx::DBStag, which does the actual writing of ontology data to the database.  When it loads the Gene Ontology (and possibly other ontologies), it destroys the 'part_of' cvterm that belongs to the relationship ontology and makes it part of GO instead.  This is the wrong behavior, but at the moment, there is nothing we can do about it.
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: Instead, you must run a SQL command to repair the database:
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<sql>
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update cvterm set cv_id = (select cv_id from cv where name = 'relationship')
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  where name = 'part_of'
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  and cv_id in (select cv_id from cv where name='gene_ontology');
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</sql>
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: Then, rerunning the loader with the --recreate_cache option should allow the database to load.  Sorry for the hassle.

Revision as of 21:44, 17 July 2008

About this FAQ

What is this FAQ?

It is the list of Frequently Asked Questions about Chado.

How is it maintained?

It is now maintained as a Wiki on this site. You can help maintain it by adding questions and answers.

Chado Questions

How do you pronounce chado?

Chado is usually pronounced like this.

How does one represent BLAST results in Chado? or alignments? or...

Questions about the best ways to represent a variety of observations are answered at the Chado Best Practices page. There is also a worked example for this at Load_BLAST_Into_Chado.

Where do I find a list of tables in Chado?

The Chado Tables page.

What are the modules in Chado?

They are listed in the Chado Manual page.

Is there a Chado for Beginners?

The best place to start would be the Chado Manual or GMOD for the Biologist.

Loading data into Chado

When I try to load data into Chado using the GFF bulk loader (gmod_bulk_load_gff3.pl), I get this error:

 DBD::Pg::db pg_endcopy failed: ERROR:  invalid input syntax for integer: ""
 
 CONTEXT:  COPY feature_relationship, line 1, column type_id: "" at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 2723, <$fh> line 64298.

Why is that and what do I do?

Unfortunately there is a bug in one of the prerequisites for the Chado loader, a perl module called DBIx::DBStag, which does the actual writing of ontology data to the database. When it loads the Gene Ontology (and possibly other ontologies), it destroys the 'part_of' cvterm that belongs to the relationship ontology and makes it part of GO instead. This is the wrong behavior, but at the moment, there is nothing we can do about it.
Instead, you must run a SQL command to repair the database:

<sql>

update cvterm set cv_id = (select cv_id from cv where name = 'relationship')
 where name = 'part_of'
  and cv_id in (select cv_id from cv where name='gene_ontology');

</sql>

Then, rerunning the loader with the --recreate_cache option should allow the database to load. Sorry for the hassle.