Changes and additions for phyloXML version 1.10
Originally published on Tuesday, October 27, 2009.
Changes
Sequence
Type ‘aa’ is changed to ‘protein’.
Id
Elements Sequence, Clade, and Phylogeny have an ‘id’ sub-element.
Currently, ‘id’ has a ‘type’ attribute, which is used to indicate the source, or database of the identifier.
‘type’ turned out to be an ill chosen name.
Hence, we rename ‘type’ into ‘provider’.
Date
Remove ‘range’ attribute, and replace it with ‘minimum’ and ‘maximum’ elements.
Taxonomy
Remove unnecessary ‘type’ attribute (‘type’ is part of ‘id’ and will be renamed there).
Additions
Sequence
Add ‘is_aligned’ attribute to ‘mol_seq’ sub-element.
This is used to indicated that the molecular sequence described by the mol_seq sub-element is aligned with all other sequences in the same tree for which ‘is aligned’ is true (which, in most cases, means that gaps were introduced, and that all sequences have the same length).
Taxonomy
Add elements for:
‘authority’
‘synonym’ (list)
Point
Add ‘alt_unit’ attribute. This is the unit for the altitude.