[Bioperl-l] Phyloxml parsing <clade_relation> <sequence_relation>

Chris Fields cjfields at uiuc.edu
Tue Jul 29 14:26:55 EDT 2008


+1 on Aaron's suggestion; though maybe with a shorter namespace ;>   
Though is it possible to have more than two nodes in a relationship,  
or is it just pairwise?

chris

On Jul 29, 2008, at 11:10 AM, Han, Mira wrote:

>
> Hi,
> I'd like to get some opinions on how to design the phyloxml parsing.
> There are a couple of tags in phyloxml that doesn't have obvious  
> bioperl
> implementations.
>
> 1. <clade_relation>
> This is for expressing network structures on the tree.
> <clade_relation id_ref_0="b" id_ref_1="c" type="network_connection"/>
> Will mean that c and b is connected even though they are not direct
> parent-daughters of each other.
>
> 2. <sequence_relation>
> Homology relationship between sequences.
> <sequence_relation id_ref_0="x" id_ref_1="y" type="paralogy"/>
>
>
> These tags are both used by the <phylogeny>.
> Right now I'm just saving the information in the tree as simple text  
> by
> tags.
> So that if the user wants to follow the information he can look up  
> the nodes
> by its id_src id by parsing the text.
> I was wondering if you would have any other ideas.
>
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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