About datasource of iRefindex

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Hufeng Zhou

Apr 18, 2012, 9:12:27 PM4/18/12
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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.


Apr 19, 2012, 4:58:17 AM4/19/12
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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OPHID is very out of date and should be replaced with I2D.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

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

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