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

Karim Mezhoud kmezhoud at gmail.com
Tue Apr 5 11:18:09 CEST 2016

Dear bioC developer,
I included in my bioCancer/inst/extdata a Reactome FI database (/

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?

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