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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.