load human biopax level2 data from NCI

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load human biopax level2 data from NCI

wang su
Hi,
Now I have human and mouse biopax level2 pathway data downloaded from NCI ,Reactome and Wiki, I want to load these data to the database created by intermine, but nothing was showed on the web. Can you take Reactome human pathway data as an example to tell me which files it need to have or which file need to edit, I'm so confused of the difference between Biopax and Reactome directory under the bio/sources/

Thanks
Su
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Re: load human biopax level2 data from NCI

Julie Sullivan
Hi Su,


The Reactome converter processes Reactome's text files, you'll want to use the
BioPAX parser instead.

To load the BioPAX files into your InterMine, add the entry to your project XML
file.  Here is FlyMine's:

<source name="reactome" type="biopax">
   <property name="src.data.dir" location="/DATA/reactome"/>
   <property name="biopax.organisms" value="7227 9606"/>
   <property name="biopax.datasourcename" value="Reactome"/>
   <property name="biopax.datasetname" value="Reactome data set"/>
   <property name="biopax.curated" value="false"/>
</source>

See here for a details:

        http://intermine.org/wiki/Reactome

I've only ever used this parser with Reactome's BioPAX files.  BioPAX is
supposed to be a generic format though so hopefully it will work for your BioPAX
files from other sources.

So try the above and let me know how it goes?

Cheers
Julie

On 12/01/12 07:17, wang su wrote:
> Hi,
> Now I have human and mouse biopax level2 pathway data downloaded from NCI ,Reactome and Wiki, I want to load these data to the database created by intermine, but nothing was showed on the web. Can you take Reactome human pathway data

as an example to tell me which files it need to have or which file need to
edit, I'm so confused of the difference between Biopax and Reactome directory
under the bio/sources/
>
> Thanks
> Su
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

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[hidden email]
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