1.0 Architecture

Overview

Sonya Lowry/Working group

Analytical pipeline

Sheldon McKay

Data model and scripts

Database Schema

The TR database stores gene tree reconciliations as a mapping of the nodes of the gene tree (guest tree) onto the nodes and edges of a species tree (host tree). The topology of the gene tree and species tree involved in the reconciliation are stored separate from the mapping itself. The attributes of the reconciliation mapping as well as the components of the gene trees and species trees can be labeled using a controlled vocabulary. The genes contributing to the gene trees are stored as 'members' within the database. 

The TR schema extends the preexisting Ensemble-Compara schema to include species trees, the mappings of reconciliations of gene trees onto these species trees, and a controlled vocabulary module to support the use of ontologies to tag attribute values within the database.The slides describing the initial thoughts on the development of the schema are available and would be helpful to view to see how the schema was designed.

Populating the Database

The tools to populate the database are written as Perl command line programs, and their use to populate the database are described in the populating the database section of the wiki.

Detailed Documentation

• Basic Model for Mapping Gene Trees to Species Tree
• Database Schema
• Populating the TR Database
• Example Queries Using TR Database   
  • Queries on singe tree topology
  • Queries on tree reconciliations
  • Queries on controlled vocabulary terms

Web API

Will be extracted as PerlDocs

Tree Visualization

https://pods.iplantcollaborative.org/wiki/display/iptol/Big+Tree+Viewer+Documentation

TR Standalone

Sonya Lowry

Viewer-Editor Integration Framework

Sonya Lowry