Hi Inna,
First, if you're using PDF articles, make sure that the text extraction tools in config.inc.php are properly configured; see the index[application/pdf] directive.
You can then re-generate the index using the tools/rebuildSearchIndex.php script.
Regards,
Alec Smecher
Open Journal Systems Team
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Don't miss the First International PKP Scholarly Publishing Conference
July 11 - 13, 2007, Vancouver, BC, Canada
http://ocs.sfu.ca/pkp2007/