> > Yesterday, Greg suggested using the BioSQL database schema for the Seq > object-to-SQL Database interface Nico and I were discussing. > > Initial reaction: Whoa, it's simply overwhelming! But if Greg or > anyone here would volunteer to relate the pertinent table/columns to > what I have at http://genephp.sf.net/mysql_dbscripts.html, it would > certainly be a big help. > > Nonetheless, I proceeded to write some PHP code that generates SQL > INSERTs from data displayed on web forms. You can find them at: > > http://genephp.sf.net/parse_na_gb_par.html [1] > http://genephp.sf.net/parse_na_gb_res.php [2] > http://genephp.sf.net/insert_na_gb_res.php [3] Do these scripts work with the BioSQL database or with the tables you wrote? I suggest to stick to the BioSQL layout and write the scripts necessary to insert a (biophp) seq object into this structure and to read them back out again. No need to reinvent the wheel. > Nico has graciously offered to help out in the MySQL-to-ADODB > conversion (so the SQL scripts could be used for other RDBMs). > > If anyone would like to work on a MySQL-to-PearDB conversion of the > CREATEs in http://genephp.sf.net/mysql_dbscripts.html, > or the INSERTs at insert_na_gb_res.php, you're mighty welcome! PEAR and adodb basically do the same thing. Since you really do not need to 'install' anything to get either PEAR or adodb to work (you simply have to download one or the other) and I don't think we are ready to spread our resources by using both of them, it makes sense to choose one or the other. Sean's argument for using PEAR is that is standard (since it is distributed with php). My two arguments for adodb are: 1. I have experience working with making it a lot of easier to develop quickly with adodb, and 2. it appears to be twice as fast as PEAR (at least according to php.weblog.com. Maybe the choice should come down to the people who are going to write the code... > If anyone would also like to work on a DATABASE SCHEMA for data > extracted by the various parser scripts (there are 30 formats > supported fully/partially at http://genephp.sf.net/io_set.html), well, > that would be swell... All great and nice, but I don't see any of the code... What are you parsing into? Are you using the seqIOimport (http://bioinformatics.org/cgi-bin/cvsweb.cgi/biophp/genephp/ seqIOimport.inc.php) class are something completely different? Sometimes I have the feeling we are not really working together here... Best, Nico