PSICQUIC webservice and PSICQUIC-view release

[Marine]

Dear PSICQUIC community,

We are pleased to announce the official release of PSICQUIC-view and
PSICQUIC webservices supporting MITAB 2.6 and 2.7. Thanks again to all
the people who helped in the development of these new features, in
particular to all the participants of the PSICQUIC hackathon 2012.

Below is a list of all the changes that have been done :

PSICQUIC webservice

- Now the PSICQUIC webservice is based on a SOLR index
- It supports indexing of MITAB 2.5, MITAB 2.6 and MITAB 2.7 files
- It allows download of MITAB 2.5, MITAB 2.6, MITAB 2.7, PSI-XML 2.5,
RDF, Biopax, XGMML
- If the indexing was based on MITAB 2.5, exporting in MITAB 2.6
and 2.7 is possible and will return empty columns for the extanded
columns of MITAB 2.6 and 2.7
- The limitation of 5000 binary interactions which can be exported
in XGMML has been removed.
- It is not possible to download more than 500 binary interactions
in PSI-XML 2.5, RDF and Biopax in one query. If a user tries to do so, a
400 HTTP error will be thrown instead of truncating the results which
was confusing for the user exporting RDF or Biopax. If the user wants to
download more interactions in PSI-XML 2.5, Biopax and RDF, he has to use
pagination and merge the generated files. (needs some improvement there)
- Default format for download is tab25 for backward compatibility
with existing softwares and services.
- The webservice does not allow downloading negative interactions
in MITAB 2.5, XGMML, RDF and Biopax. They can only be exported in MITAB
2.6 and MITAB 2.7
- Negative interactions are always excluded by default. If a user wants
to include negative interactions in his results, it has to force the
webservice to do so by adding 'negative:(true OR false)' filter in the
query.
- For more information about how to index and install the new
webservice, look at
http://code.google.com/p/psicquic/wiki/HowToInstallPsicquicSolr.

=> next steps : supports statistics through faceting, improve
performances of XML download, indexing from XML, supports sorting, ...

PSICQUIC-view

- It is now possible to customize the columns in the results table.
MITAB 2.7 columns have been added.
- Download has been improved to support formats provided by each
PSICQUIC webservice (depending on the version of the webservice, you
will be able to download MITAB 2.6, MITAB 2.7, XGMML, RDF, Biopax, etc.)
- Download is done in the background instead of opening a new window.
- Documentation has been updated for MIQL 2.7.
- You cannot download more than 500 binary interactions in PSI-XML 2.5,
RDF and Biopax.
- A link to the original website of each PSICQUIC webservice has been added.
- Results are shown using MITAB 2.7 columns only if the webservice
supports it. The same goes for MITAB 2.6.
- The limitation of 500 interactions to visualize the network display
has been updated to 50000 interactions.
- If an interactor matches the user query, it will be displayed as first
interactor.
- Aliases 'display_short' and 'display_long' will always be shown by
default in alias columns when provided.
- In several columns, we added the possibility to hide/expand the results.
- Clustering is still based on MITAB 2.5 so clustered downloads are
available only in MITAB 2.5 and PSI-XML 2.5.
- Several bugs have been fixed (pagination problems, error handling,
mismatch in the number of results, ...).

=> next steps : adding a download all button (in MITAB only), default
table for all the results, better error handling when one service is
down while downloading results, clustering performances to be improved, ...

Don't hesitate to report any bugs or issues when using PSICQUIC view or
trying to install new PSICQUIC webservice by adding an issue at
http://code.google.com/p/psicquic/issues/list. You can also use the
PSICQUIC discussion group (http://groups.google.com/group/psicquic) if
you have more questions.
If you have feedback or new feature requests, don't hesitate to share
them at http://groups.google.com/group/psicquic.

Regards,

The PSICQUIC team