[InterMine Dev] Error loading BioGRID data

Chen, Yian chenyian at nibiohn.go.jp
Mon Feb 15 00:52:54 GMT 2016


Hi Jeffrey,

Seems that you forgot to configure the settings in the 
"biogrid_config.properties" file
which is located at bio/sources/biogrid/main/resources/

Hope this helps.

Chen

On 2016/02/13 1:44, De Pons, Jeffrey wrote:
>
> Hello,
>
> I am attempting to load BioGRID data for rat, mouse, and human and am 
> getting an error.  Something is not configured correctly and I’m 
> hoping you can help.
>
> Here is the error
>
> -retrieve-tgt-from-custom-file:
>
> [integrate] Processing file: 
> /data/intermine/git_ratmine/ratmine_src_data_mod/biogrid/BIOGRID-ORGANISM-Homo_sapiens-3.4.133.psi25.xml
>
> [integrate] java.lang.RuntimeException: Entry in configuration file 
> for 9606 not found
>
> [integrate]     at 
> org.intermine.bio.dataconversion.BioGridConverter$BioGridHandler.startElement(BioGridConverter.java:334)
>
> [integrate]     at 
> org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
>
> My project.xml file is configured as follows
>
> <source name="rat-biogrid" type="biogrid">
>
>                 <property name="src.data.dir" 
> location="../../../ratmine_src_data_mod/biogrid"/>
>
>                 <property name="src.data.dir.includes" 
> value="*psi25.xml"/>
>
>                 <property name="biogrid.organisms" value="10116 10090 
> 9606"/>
>
> </source>
>
>
>
> _______________________________________________
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> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


-- 
Chen, Yian
chenyian at nibiohn.go.jp
Postdoctoral Fellow
Bioinformatics project
National Institutes of Biomedical Innovation, Health and Nutrition
7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan

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