[SO-devel] The latest version of SO in cvs

[Karen E. <ei...@fr...>]

Hi,
I just wanted to let you all know that I just checked in a version of 
SO that is slightly different from what we are used to. It is called 
so-xp.obo
It uses OBO_1_2 format, and captures cross product terms.
*warning*
This new SO still has kinks to be worked out, and the cross products 
are not for the faint hearted.


I have added several attributes of features:

engineered, foreign, fragment, fusion, natural, predicted, rescue, 
transgenic and wild_type

These are general properties that can be used to describe many types of 
feature. My hope is that we will be able to use these properties in 
combination with features to make cross product terms in a controlled 
way.

These cross product terms are different to other terms in the ontology 
in that they have logical definitions.

Example:

[Term]
id: SO:0000819
name: mitochondrial_chromosome
namespace: sequence
intersection_of: SO:0000340 ! chromosome
intersection_of: has_origin SO:0000737 ! mitochondrial_sequence

I have used this technique of term generation to solve 3 problems, each 
addressed in a separate email (following shortly):
1. Types of chromosomes
2. engineered terms for FB via Gillian Milburn
3. Some terms relating to reagents and TE's via Lynn Crosby also at FB.

This is very much a work in progress, and is just the beginning of 
making the attributes in SO useful.

--Karen