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Table 1 phyloXML elements and attributes summary

From: phyloXML: XML for evolutionary biology and comparative genomics

Element/Attribute

Description and Sub-elements

phylogeny

Represents a phylogeny, contains clades.

clade

Used recursively to represent node of a phylogeny.

taxonomy

Represents taxonomic information.

 

id

 

code

 

scientific_name

 

common_name

 

synonym

 

authority

sequence

A gene or protein associated with a clade.

 

symbol

 

accession

 

name

 

location

 

mol_seq

 

uri

 

annotation

 

domain_architecture

events

Events at a clade.

 

type

 

duplications

 

speciations

 

losses

 

confidence

annotation

Annotation of sequence.

 

desc

 

confidence

 

property

 

uri

property

Typed and referenced mixed (free text) content.

uri

Uniform resource identifier (e.g. a URL).

confidence

Statistical confidence.

distribution

Geographic distribution of the items of a clade.

date

Date associated with a clade.

sequence_relation

Typed relationship between two sequences.

clade_relation

Typed relationship between two clades.

id_ref

Attribute, used together with id_source to describe relations between various elements.

id_source

Attribute, used together with id_ref to describe relations between various elements.

  1. Representative elements and attributes of phyloXML (version 1.10) are shown. XML element/attribute names are in bold letters.