Re: Orthodb configuration

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Re: Orthodb configuration

Julie Sullivan

> /Does the parser for orthodb data automatically updates its lookup table
> depending on the organism?

No, we use a file we generated to look up organism names. If you add
your organism to it, Orthodb will load correctly. Here is what worked
for me:

https://github.com/intermine/intermine/commit/330309caac713ceb950f5e6efa6a4fdd53ced1ac

I've made a ticket to do this automatically:

https://github.com/intermine/intermine/issues/814


On 17/11/14 20:04, Tayal, Aditi wrote:

> Hi Julie,
> I am trying to load orthodb data for “Pogonomyrmex barbatus/” //Taxonomy
> ID: /144034/ in intermine. The gene id for this organism is present in
> the gff. However, the data is from the orthodb file is not loading  and
> the database is empty. I tried doing this with and without the ID
> resolver. /
> /Does the parser for orthodb data automatically updates its lookup table
> depending on the organism? Or is there some modifications we have to do
> to the parser / gene info table.?/
> /
> /
> /
> /
> / Following is a snip of the orthodb and the gff /
> /
> /
> /
> /
> /orthodb file(/OrthoDB7_ALL_METAZOA_tabtext)
> /
> /
> 286EOG72K577PB22745-PA*PB22745*Pogonomyrmex
> barbatus9HYMENULLNULLIPR000608 IPR016135
> /
> /
> gff file
>
> scf71pbar1.7gene24356122436860.-.*ID=PB22745;Name=PB22745*;Alias=PB22745;
> scf71pbar1.7mRNA24356122436860.-.ID=PB22745-RA;Name=PB22745-RA;Alias=PB22745-RA
>
>
> Orthodb_config file
>
> 144034.geneid=primaryIdentifier
>
> Orthodb_keys file
>
> Gene.key_primaryidentifier=primaryIdentifier
>
>
> Gff keys file
>
> Gene.key_primaryidentifier=primaryIdentifier
>
>
> Thank you



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