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This page is pulled directly from the README.Apollo documentation in the Chado code repository and is converted to text and dynamically loaded in this page. The README was most recently changed on Thursday 21st of September 2006 01:26:42 PM
Reading and Writing to a Chado database with Apollo This needs to be better documented, but here is a start: In order to use Apollo read/write with chado, here are things that need to be done: Grant privileges to users to several tables (list here) In the absense of a complete list of tables, you can grant access to all tables using sqlt and the perl Template::Toolkit template, bin/privileges.tmpl sqlt -f PostgreSQL -t TTSchema --template bin/privileges.tmpl modules/nofuncs.sql | psql You can edit the template to grant privileges to just specific users instead of PUBLIC, which of course would be a lot more secure. Insert several ad hoc cv terms found in modules/sequence/apollo-bridge/cv_inserts.sql. This file contains sql commands to insert several controlled vocabulary terms that Apollo expects to be in the database. This file can be recreated with additional terms as needed by editing the file modules/sequence/apollo-bridge/ad_hoc_cv and running the perl script modules/sequence/apollo-bridge/insert_ad_doc_cv.pl. The resulting sql file can be inserted into the database with this command: $ psql $DBNAME < modules/sequence/apollo-bridge/cv_inserts.sql Insert a few misc items like those found in modules/sequence/apollo-bridge/apollo.inserts Essentially, Apollo and chado have to agree about what the names of the programs in the analysis table are, and there needs to be a few terms in the cv table. About naming analysis results: there are no restrictions on what you name them, however the GFF3 bulk loader will insert them typically one of two ways: 1 If you specify the -a (--analysis) flag with an argument, the loader will look for an entry in the analysis table where analysis.name is equal to the argument supplied with -a. 2 If you don't give an argument with -a, the loader will look for analysis.name that is equal to the GFF source and type concatentated with and underscore between them, ie 'source_type', eg, 'Rice_cDNA_match'. The inserts into the db table are there so that dbxref entries in GFF files I typically process. They can be ignored unless you are loading GFF files with Dbxref entries. Then there is the uniquename_id_generator sequence, for which integers for building uniquenames are used. Then there are two interts in to cvtermprop for the suffix and prefix for uniquename generation. Generated uniquenames with be of the form: $prefix . (int from uniquename_id sequence) . $suffix For exmple, if you insert 'RICE' for the prefix and 'X' for the suffix, the resulting name of the first feature will be 'RICE000001X'; Add the functions and triggers to chado. Use the perl script: % /usr/local/bin/gmod_apollo_triggers.pl create Note that this script can also be used to drop and add the triggers in case you want to do some bulk loading and want to disactivate the triggers for that. Modify the Apollo configuration file, chado-adapter.xml. IS THERE DOCUMENTATION FOR DOING THAT IN APOLLO'S DOCS? Yes, there is a section for connecteding directly to flybase chado in the apollo doc directory: doc/html/userguide.html but it is somewhat out of date. I need to work with Mark to update it (it will probably need me to write it and have Mark proof it). I understand that these directions are somewhat vague. Getting Apollo to work with chado requires a little hands on tinkering. If you find yourself having difficulties, please contact me. Scott Cain firstname.lastname@example.org 4/29/05