[BioSQL-l] Full text indexing/Searching in MySQL
Roy Chaudhuri
roy.chaudhuri at gmail.com
Mon May 18 17:37:39 UTC 2009
Hi Mick,
> Has anyone implemented full text indexing/searching for BioSQL in MySQL,
> either using MySQL's full text features or any other solution?
I've kind of done this. The trouble is that full text is only
implemented on the non-transactional MyISAM tables, not InnoDB (it has
long been promised for InnoDB, but no sign yet). My hack solution was to
parse out the fields I was interested in (feature tags such as gene and
product) and include them in a separate MyISAM table, cross-referenced
to BioSQL using seqfeature_id. This involves duplicating data (which is
a bad thing), but should be okay if database updates are infrequent. I
mimic atomic changes by building an updated version of the MyISAM table
separately, then switching to use the new version at the same time as I
commit the BioSQL updates.
There's also Sphinx (http://www.sphinxsearch.com), which is a plug-in
that can implement full-text searches in InnoDB, but I haven't
experimented with that so have no idea how well it works.
Cheers.
Roy.
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