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

Obenchain, Valerie Valerie.Obenchain at roswellpark.org
Tue Apr 5 17:11:33 CEST 2016

Hi Karim,

I can help you put together an annotation package.

Here are the general 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.


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]]
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