Table 1 |
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phyloXML elements and attributes summary |
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Element/Attribute |
Description and Sub-elements |
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phylogeny |
Represents a phylogeny, contains clades. |
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clade |
Used recursively to represent node of a phylogeny. |
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taxonomy |
Represents taxonomic information. |
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id |
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code |
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scientific_name |
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common_name |
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synonym |
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authority |
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sequence |
A gene or protein associated with a clade. |
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symbol |
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accession |
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name |
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location |
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mol_seq |
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uri |
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annotation |
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domain_architecture |
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events |
Events at a clade. |
|
type |
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duplications |
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speciations |
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losses |
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confidence |
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annotation |
Annotation of sequence. |
|
desc |
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confidence |
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property |
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uri |
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property |
Typed and referenced mixed (free text) content. |
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uri |
Uniform resource identifier (e.g. a URL). |
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confidence |
Statistical confidence. |
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distribution |
Geographic distribution of the items of a clade. |
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date |
Date associated with a clade. |
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sequence_relation |
Typed relationship between two sequences. |
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clade_relation |
Typed relationship between two clades. |
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id_ref |
Attribute, used together with id_source to describe relations between various elements. |
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id_source |
Attribute, used together with id_ref to describe relations between various elements. |
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Representative elements and attributes of phyloXML (version 1.10) are shown. XML element/attribute names are in bold letters. |
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Han and Zmasek BMC Bioinformatics 2009 10:356 doi:10.1186/1471-2105-10-356 |
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