[Bioc-devel] big file ReactomeFI --> bioC annotate package

[Karim Mezhoud]

Thank you Valerie,
TxDb uses sqlite format. Maybe I need to know how to convert reactomeFI.txt
to reactomeFI.sqlite.

I found from    bioC workshop 2006 a  Lab: How to use SQLite
<http://master.bioconductor.org/help/course-materials/2006/rforbioinformatics/labs/thurs/SQLite-R-howto.pdf>
.
Is it a good starting tutorial?
Any tutorial is welcome.
Thanks
Karim




On Tue, Apr 5, 2016 at 4:11 PM, Obenchain, Valerie <
Valerie.Obenchain at roswellpark.org> wrote:

> Hi Karim,
>
> I can help you put together an annotation package.
>
> Here are the general guidelines:
>
> http://www.bioconductor.org/developers/package-guidelines/
>
> We ask that annotations packages implement the select() interface from
> AnnotationDbi (eg, keys(), columns(), keytypes(), etc.). You can see how
> select() works with the TxDb and OrgDb packages. Once you've got that
> working you can open a new ticket on the package tracker.
>
> Feel free to write me at valerie.obenchain at roswellpark.org if you have
> other questions.
>
> Valerie
>
>
>
>
> On 04/05/2016 02:18 AM, Karim Mezhoud wrote:
> > Dear bioC developer,
> > I included in my bioCancer/inst/extdata a Reactome FI database (/
> >
> http://reactomews.oicr.on.ca:8080/caBigR3WebApp2015/FIsInGene_031516_with_annotations.txt.zip
> > )
> >
> > Gene1    Gene2    Annotation    Direction    Score
> > 16-5-5    CDC42    predicted    -    0.82
> > 16-5-5    RHOJ    predicted    -    0.82
> > 16-5-5    RHOQ    predicted    -    0.82
> > <DELTA>FAS/APO-1/CD95    BID    activate    ->    1.00
> > <DELTA>FAS/APO-1/CD95    CASP10    complex    -    1.00
> > <DELTA>FAS/APO-1/CD95    DAXX    complex; reaction    -    1.00
> > <DELTA>FAS/APO-1/CD95    DKFZP686N0154    activate    ->    1.00
> > <DELTA>FAS/APO-1/CD95    FADD    complex    -    1.00
> > <DELTA>FAS/APO-1/CD95    FASLG    complex; input    -    1.00
> > <DELTA>FAS/APO-1/CD95    HSPB1    reaction    -    1.00
> > <DELTA>FAS/APO-1/CD95    MAP2K3    activate    ->    1.00
> > <DELTA>FAS/APO-1/CD95    MAP2K4    activate    ->    1.00
> >
> > bioCancer uses this file to extract the Direction/arrowhead of gene-gene
> > interaction (activates, inhibits, predicted, complexe.....).
> > This kind of data is not available in Reactome.db package nor by Reactome
> > API service (to my knowledge).
> >
> > I have to remove this file from my new package and may get annotate
> package
> > for ReactomeFI database.
> > How to?
> > Karim
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
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