MySQL SELECT query with joins takes too long - mysql

Question

I have the following SELECT query with table joins and it taking about a minute to return 6 records:
SELECT * FROM specimen, topography_index, morphology, specimen_image_lookup, image
WHERE
SUBSTRING(specimen.topography_index, 2, 2) = topography_index.topography_index_code
AND
morphology.morphology_code = specimen.snop_code
AND
specimen_image_lookup.specimen_fk = specimen.specimen_pk
AND
image.image_pk = specimen_image_lookup.image_fk
AND
specimen.topography_index, 2, 2) IN('".implode("','",$system)."')
Any ideas what I should here?
Table structures are:
CREATE TABLE `specimen` (
`specimen_pk` int(4) NOT NULL AUTO_INCREMENT,
`number` varchar(20) NOT NULL,
`unit_number` varchar(10) NOT NULL,
`topography_index` varchar(5) NOT NULL DEFAULT '',
`snop_axis` char(1) NOT NULL,
`snop_code` varchar(4) NOT NULL,
`example` int(2) NOT NULL,
`gender` char(1) NOT NULL,
`age` varchar(3) NOT NULL DEFAULT 'NA',
`clinical_history` text NOT NULL,
`specimen` text NOT NULL,
`macroscopic` text NOT NULL,
`microscopic` text NOT NULL,
`conclusion` text NOT NULL,
`comment` text NOT NULL,
`room` char(1) NOT NULL,
`position` varchar(8) NOT NULL,
`created` datetime NOT NULL,
`created_by` int(3) NOT NULL,
`updated` datetime NOT NULL,
`updated_by` int(3) NOT NULL,
PRIMARY KEY (`specimen_pk`),
FULLTEXT KEY `clinical_history` (`clinical_history`),
FULLTEXT KEY `specimen` (`specimen`),
FULLTEXT KEY `macroscopic` (`macroscopic`),
FULLTEXT KEY `microscopic` (`microscopic`),
FULLTEXT KEY `conclusion` (`conclusion`),
FULLTEXT KEY `comment` (`comment`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 AUTO_INCREMENT=500 ;
CREATE TABLE `topography_index` (
`topography_index_pk` int(3) NOT NULL AUTO_INCREMENT,
`topography_index_code` varchar(2) DEFAULT NULL,
`topography_index_nomen` text,
PRIMARY KEY (`topography_index_pk`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 AUTO_INCREMENT=138 ;
CREATE TABLE `specimen_image_lookup` (
`specimen_image_lookup_pk` int(8) NOT NULL AUTO_INCREMENT,
`specimen_fk` int(4) NOT NULL,
`image_fk` int(4) NOT NULL,
PRIMARY KEY (`specimen_image_lookup_pk`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 AUTO_INCREMENT=141 ;
CREATE TABLE `morphology` (
`morphology_pk` int(6) NOT NULL AUTO_INCREMENT,
`morphology_code` varchar(4) NOT NULL,
`morphology_nomen` varchar(120) NOT NULL,
PRIMARY KEY (`morphology_pk`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 AUTO_INCREMENT=2295 ;
CREATE TABLE `image` (
`image_pk` int(4) NOT NULL AUTO_INCREMENT,
`image_title` varchar(80) NOT NULL,
`image_description` text NOT NULL,
`image_thumbnail` varchar(100) NOT NULL,
`image_small` varchar(100) NOT NULL,
`image_large` varchar(100) NOT NULL,
`created` datetime NOT NULL,
`created_by` int(3) NOT NULL,
`updated` datetime NOT NULL,
`updated_by` int(3) NOT NULL,
PRIMARY KEY (`image_pk`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 AUTO_INCREMENT=138 ;

Answer 1

By performing a substring on specimen.topography_index, you're asking the database to perform that calculation on every row in the specimen table before finding if the value exists in topography_index. One way to address this is to store the actual integer value that will match with topography_index, rather than a string with that value embedded.