Re: [irefindex] Digest for irefindex@googlegroups.com - 2 Messages in 1 Topic
Hufeng Zhou
Thanks very much for your rely.
I understand that more clearly now, and I will first filter out the
OPHID before using the iRefindex data.
Thanks again.
Best Regards,
Hufeng
On Fri, Apr 20, 2012 at 1:19 PM, <iref...@googlegroups.com> wrote:
> Today's Topic Summary
>
> Group: http://groups.google.com/group/irefindex/topics
>
> About datasource of iRefindex [2 Updates]
>
> About datasource of iRefindex
>
> Hufeng Zhou <zhouh...@gmail.com> Apr 18 06:12PM -0700
>
> Dear All:
> I am a little bit puzzled about the datasource of iRefindex, as it extract
> PPI from following databases, BIND, BioGRID, CORUM, DIP, HPRD, InnateDB,
> IntAct, MatrixDB, MINT, MPact, MPIDB, MPPI and OPHID.
> The fist 9 databases contains all the manually curated data, whereas, OPHID
> contains also the prediction data, I am wondering why iRefindex also
> include data from a PPI prediction database like OPHID?
> So after I delete the data source form OPHID in the iRefindex then it will
> be come a whole comprehensive manually curated PPI dataset?
> Thanks very much for your help.
>
>
>
> <i.m.do...@biotek.uio.no> Apr 19 10:58AM +0200
>
> Dear Hufeng
>
> Yes. That is true. We made the decision to include OPHID for comparison
> purposes with curated data.
> It can be easily filtered out leaving only "curated" data. These data
> should all have references back to the primary literature and methods -
> although in practice this is not completely true.
>
> OPHID is very out of date and should be replaced with I2D. We never did
> this because we had problems tracing the origins of the predicted
> interactions.
>
> In future, I would like to remove OPHID and make a separate collection just
> for predicted data. However, I don't have any immediate plans to do this.
>
> Best regards
> Ian
>
>>Subject: [irefindex] About datasource of iRefindex
>
>>Dear All:
>>I am a little bit puzzled about the datasource of iRefindex, as it extract
> PPI
>>IntAct, MatrixDB, MINT, MPact, MPIDB, MPPI and OPHID.
>>The fist 9 databases contains all the manually curated data, whereas, OPHID
>>contains also the prediction data, I am wondering why iRefindex also
> include
>>data from a PPI prediction database like OPHID?
>>So after I delete the data source form OPHID in the iRefindex then it will
> be
>
>
>
> You received this message because you are subscribed to the Google Group
> irefindex.
> You can post via email.
> To unsubscribe from this group, send an empty message.
> For more options, visit this group.
>
> --
> You received this message because you are subscribed to the Google Groups
> "irefindex" group.
> To post to this group, send email to iref...@googlegroups.com.
> To unsubscribe from this group, send email to
> irefindex+...@googlegroups.com.
> For more options, visit this group at
> http://groups.google.com/group/irefindex?hl=en.