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. |