[Bioc-devel] big file ReactomeFI --> bioC annotate package
kmezhoud at gmail.com
Wed Apr 6 16:16:08 CEST 2016
Thank you Valerie,
TxDb uses sqlite format. Maybe I need to know how to convert reactomeFI.txt
I found from bioC workshop 2006 a Lab: How to use SQLite
Is it a good starting tutorial?
Any tutorial is welcome.
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:
> 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 (/
> > )
> > 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
> > 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
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]
More information about the Bioc-devel