[BioSQL-l] Full text indexing/Searching in MySQL

[Richard Holland]

There's also Lucene, which is a Java-based full-text indexer which can
be attached to all kinds of data sources, including MySQL databases:

http://lucene.apache.org/java/docs/

cheers,
Richard

On Mon, 2009-05-18 at 18:37 +0100, Roy Chaudhuri wrote:
> 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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-- 
Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/