[InterMine Dev] Logging messages from the rgd annotation parser

Julie Sullivan julie at flymine.org
Thu Oct 20 12:17:53 BST 2011


Andrew

I'm not trying to pretend I know what's going on at all, but here are the specs 
regarding column 12:

http://www.geneontology.org/GO.format.gaf-2_0.shtml#db_object_type
DB Object Type (column 12)

"    A description of the type of gene product being annotated. If a gene 
product form ID (column 17) is supplied, the DB object type will refer to that 
entity; if no gene product form ID is present, it will refer to the entity that 
the DB object symbol (column 2) is believed to produce and which actively 
carries out the function or localization described. "

I read that to be column 12 is not the type of the object being annotated but 
instead the type of gene product.

FlyBase's annotation files follow these rules, as do some others.  That's why I 
added the config to specify what is being annotated instead of depending on 
what's in column 12.  I would like to not use a config file and just use column 
12 though.  I'll email the GO helpdesk today and get some clarification.  I'd be 
interested to see what your curators say too.

In the meantime you can do this to annotate proteins instead:

	10116.identifier=primaryAccession
	10116.typeAnnotated=protein

If that doesn't work, send me your annotation file and I'll test it locally.

Cheers
Julie

On 19/10/11 22:05, Vallejos, Andrew wrote:
> Hi,
>
>
>
> I'm trying to get the annotation loader to use the 12th column to
> determine the type.  Unfortunately, the annotation loader just loads
> everything as a gene.  Also, I cannot get the annotation java file to
> log any messages.
>
>
>
> // LOG is the Logger object
>
> // type is a String value from array[11], or the 12th column of the data
> line being processed.
>
> LOG.info("TYPE " + type); yields no TYPE messages in my interine.log
> file or screen output.
>
>
>
> How do I send messages to the log file?
>
>
>
> Thanks,
>
>
>
> Andrew
>
>
>
> ======================
>
> Andrew Vallejos M.S.
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> avallejos at mcw.edu
>
>
>
>
>
>
>
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