Go Loader Fail

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Go Loader Fail

Vallejos, Andrew

The GO OBO loader failed during itegration with the following error:

 

-retrieve-from-obo:

[integrate] Error: Expected :.

[integrate] on line: 348543 of file:/home/intermine/build/ratmine_src_data/go/gene_ontology.1_2.obo

[integrate] charnum: 0

[integrate] line: Term]

 

I am assuming that the data file is bad some maybe?  I need to check the OBO file, but I figured I would let you know in case that this is not the case.

 

======================

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

[hidden email]

 


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Re: Go Loader Fail

Richard Smith
Thanks, that looks like an error from the OBOEdit parser we use to
generate transitive closure.  And it does indeed appear to be an error
of some sort in the .obo file.

Cheers,
Richard.




Vallejos, Andrew wrote:

> The GO OBO loader failed during itegration with the following error:
>
>  
>
> -retrieve-from-obo:
>
> [integrate] Error: Expected :.
>
> [integrate] on line: 348543 of
> file:/home/intermine/build/ratmine_src_data/go/gene_ontology.1_2.obo
>
> [integrate] charnum: 0
>
> [integrate] line: Term]
>
>  
>
> I am assuming that the data file is bad some maybe?  I need to check the
> OBO file, but I figured I would let you know in case that this is not
> the case.
>
>  
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>  
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


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Re: Go Loader Fail

Vallejos, Andrew
Yup...the error was actually on line 348543.  The OBO line read Term]
instead of [Term].  Pretty easy fix.

-Andrew

-----Original Message-----
From: Richard Smith [mailto:[hidden email]]
Sent: Friday, August 06, 2010 4:27 AM
To: Vallejos, Andrew
Cc: [hidden email]
Subject: Re: [InterMine Dev] Go Loader Fail

Thanks, that looks like an error from the OBOEdit parser we use to
generate transitive closure.  And it does indeed appear to be an error
of some sort in the .obo file.

Cheers,
Richard.




Vallejos, Andrew wrote:

> The GO OBO loader failed during itegration with the following error:
>
>  
>
> -retrieve-from-obo:
>
> [integrate] Error: Expected :.
>
> [integrate] on line: 348543 of
> file:/home/intermine/build/ratmine_src_data/go/gene_ontology.1_2.obo
>
> [integrate] charnum: 0
>
> [integrate] line: Term]
>
>  
>
> I am assuming that the data file is bad some maybe?  I need to check
the

> OBO file, but I figured I would let you know in case that this is not
> the case.
>
>  
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>  
>
>
>
>
>
------------------------------------------------------------------------
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev