some questions about dataConverter java script

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some questions about dataConverter java script

wang su
Hi,

I'm confused that 1, If I want to load other database's biopax leve2 pathway data, do I need to build a new source and write the dataconverter.java instead of just modify some key worlds of ReactomeConverter.java?
                                  2.  Dose org.intermine.bio.dataconversion.FlyBaseIdResolverFactory;  only write for loading flybase's data?
                                  3.  Can BioPax level3 data be loaded into my database which build by InterMine?

Thank you very much!

Su



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Re: some questions about dataConverter java script

Julie Sullivan


On 06/12/11 07:34, wang su wrote:
> Hi,
>
> I'm confused that 1, If I want to load other database's biopax leve2 pathway data, do I need to build a new source and write the dataconverter.java instead of just modify some key worlds of ReactomeConverter.java?

In theory, you should be able to load any BioPAX file with InterMine's BioPAX
converter.  However I've only used the converter to process Reactome's files so
I'm not totally certain.

Try it and see how it works?  You will probably have some issues with
identifiers.  Reactome's look like REACT_12345 so the parser looks for "REACT_".
  You can set this value (which prefix to use) in the config file:
       
        # bio/sources/biopax/main/resources
        xrefPrefix = REACT_

You can also set which database to get the bioentity identifiers from, they are
set to be UniProt now.

>                                    2.  Dose org.intermine.bio.dataconversion.FlyBaseIdResolverFactory;  only write for loading flybase's data?

Yes.  It queries the flybase chado database for all of the valid fly identifiers
and creates a big index for lookup.  We also have one for worms (from wormbase
chado) and human (from entrez gene flat file).

>                                    3.  Can BioPax level3 data be loaded into my database which build by InterMine?

No, not yet.  I've never worked with level 3 files, I'm not sure what the
difference is actually.  Is that something you would be interested in loading?

> Thank you very much!
>
> Su
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
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