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. |
