Changes to iRefindex psicquic service

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Sabry

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Oct 14, 2010, 9:35:41 AM10/14/10
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Dear iRefindex psicquic users,

The iRefIndex psicquic web service is now updated to version 1.1.6 and
there
are some changes to the returned results.

In 1.1.5 the results returned were interaction centric: each line in
the
results represented a collection of evidences that all support an
interaction between a given pair of proteins or a protein's membership
in
some complex. This is the so-called "clustered" view of the data.

From 1.1.6 onwards the results will be experimental centric: one line
per
evidence per source. Users can still cluster multiple MITAB lines from
this
output themselves using the rigid checksum provided in column 14.


The new extended PSI MI-TAB (version 2.6) is used in the
implementation but
only the first 15 columns will be available at the moment in order to
maintain cross compatibility. For further details on the returned
results
please refer to the following WIKI pages:

http://irefindex.uio.no/wiki/README_PSICQUIC_web_services_for_iRefIndex
http://irefindex.uio.no/wiki/README_MITAB2.6_for_iRefIndex_7.0

The second major change is the usage of UniProt and RefSeq identifiers
as
uidA and uidB when ever that is possible. In 1.1.5 all uidA and uidB
columns
used ROGIDs, but now we have replaced this with UniProt identifiers
whenever
possible and with RefSeq identifiers when UniProt identifiers are not
available. However, ROGID may be used for some proteins as uid as
UniProt or
RefSeq identifiers were not available for those.
ROGIDs and RIGIDs (identifiers for each distinct protein and distinct
interaction) are still made available inside the first 15 columns of
the
MITAB. See the README for details.

Please contact us if you face face any problems or if you have any
comments
about the new version.

Regards,

Sabry & Ian
(http://irefindex.uio.no)
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