GMOD

XORT Presentation

This Wiki section is an edited version of Josh Goodman and Pinglei Zhou’s presentation.

Contents

Introduction
Chado XML
Components
Highlights of Chado XML Specification
Putting it together: New FlyBase dataflow Part 1

There are three Flybase sites, and most curation is done at Harvard and Cambridge. Proforma is the curation format at Cambridge and Harvard, but Harvard also curates with Apollo and ChadoXML.

Once in Chado, the reporting instance, there’s a denormalization step in moving data to a read-only database. Once in the read-only database there are dumps, for reporting purposes, using XORT to create ChadoXML. Once ChadoXML is created version 2 of XSLT is used to create HTML and GFF. HTML reports are for human-readable reports, GFF for GBrowse and for various power users.

1.a. Proforma (FlyBase Cambridge) is converted to ChadoXML

1.b. ChadoXML is created by Apollo (Harvard)

1.c. ChadoXML is created by Java SEAN (Harvard)

2. All ChadoXML is loaded into Chado by XORT

Putting it together: New FlyBase dataflow Part 2

3. Chado (Harvard) is denormalized and loaded into Chado (Indiana)

4. ChadoXML is created from Chado using XORT

5.a. GFF and Fasta is created from ChadoXML

5.b. HTML is created from Chado XML

Data & Report Generation
Hibernate & XORT
Support for complex transactions using XORT

For example:

Step 1. Dump all data use simple dumpspec

 <chado>
  <feature dump=“all”>
   <uniquename test=“eq”>x</uniquename>
  </feature>
 </chado>

Step 2 Delete feature x from DB, with triggers to clean orphan records, if necessary

Step 3. Edit the output xml, change uniquename x to y, then load the edited file back to DB

CHIA (Chado Interface Application)

A Java application that organizes SQL and XORT functionality for internal users, e.g.:

CHIA is being designed to be extensible for adding new functionality as needed.

Documentation
Acknowledgements

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