From peili at morgan.harvard.edu Tue Jun 17 12:49:54 2003 From: peili at morgan.harvard.edu (Peili Zhang) Date: Tue Jun 17 12:03:02 2003 Subject: [Bioperl-announce-l] an extension to Bio::SeqIO Message-ID: <3EEF38A2.21547C70@morgan.harvard.edu> Hi, here at FlyBase, we implement chado database schema to store sequence, annotation, genetic, controlled vocabulary, publication and other types of data (for detailed information about chado schema, please visit http://www.gmod.org and read the schema documentations and scripts in its CVS). we have developed tools to dump FlyBase data into chadoxml and load data in chadoxml format into FlyBase (for chadoxml dtd, please see http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/gmod/schema/chado/dat/chado.dtd), to facilitate data communication among the different sites of FlyBase and between FlyBase and the rest of the world. need arises for a tool to convert external data in other formats into chadoxml. I'm coding a perl module chadoxml.pm to write out a Bio::Seq object into chadoxml. we'd like to get your feedback on whether it's useful to add this module into bioperl as an extension to the Bio::SeqIO package. if you already have working code for the same purpose, maybe we can discuss how to merge our code to produce a better version. thanks for your input. regards, Peili Zhang FlyBase-Harvard