[Biopython-dev] [Wg-phyloinformatics] BioGeography update

Eric Talevich eric.talevich at gmail.com
Wed Jul 8 04:45:16 UTC 2009

On Tue, Jul 7, 2009 at 11:12 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> Perhaps some specific examples of the "enhancements" would help?
Sure. Here are the special phyloXML element types listed at phyloxml.org,
with comments:

Annotation -- attached to Sequence; has metadata
BinaryCharacters -- "names and/or counts of binary characters present,
gained, and lost at the root of a clade"
BranchColor -- RGB, for graphics support
CladeRelation -- typed relationship between two clades, e.g. multiple
Date -- e.g. #mya, or name of period ("Silurian")
Distribution, Point, Polygon -- geographic distribution of the items of a
clade (species, sequences)
DomainArchitecture, ProteinDomain -- like SeqFeature for a protein sequence
Events -- e.g. one gene duplication on the current clade
Property -- attach external references to a node, kind of meta
Reference -- literature reference: doi or text description
Sequence -- like SeqRecord; more specific annotation fields
SequenceRelation -- typed relationship between two sequences, e.g. orthology
Taxonomy -- with scientific name, common names, rank, id, code, URI

Some of these could be adapted into generally useful Biopython objects, such
as Taxonomy and Reference. A few are metadata related to the structure or
interpretation of the tree, and a few are small classes that could be
converted to dictionaries if necessary. The conversion between Sequence and
SeqRecord could probably be made lossless, or close to it, and then it would
be safe to just plug the Biopython object directly into the tree instead of
using a PhyloXML-specific class.


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