ContentMine / phylotree

A repository for ami-phylotree development
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NeXML validation issue #39

Open rossmounce opened 9 years ago

rossmounce commented 9 years ago

All our NeXML files aren't quite valid at the moment. As validated against: http://www.nexml.org/nexml/phylows/validator

we currently have:

...
<otus label="RootTaxaBlock" xmlns:cmphy="http://contentmine.org/phylotree">
 <otu id="otu1">Marinobacler hydrocarbonoclasticus ATCC 49840T (ABO19148)</otu>
  <otu id="otu2">Microbulbifer hydrolyticus DSM 11525T (U5813138)</otu>
...
 </otus>
 <trees>
  <tree id="T1">
   <node id="NT1.1" label="NT1.1" x="119.0" y="292.0"/>
...

Instead, we need a reference from trees to the otus tag e.g.:

...
<otus about="#Tls34455" id="Tls34455" label="Taxa" xml:base="http://purl.org/phylo/treebase/phylows/taxon/TB2:" label="RootTaxaBlock" xmlns:cmphy="http://contentmine.org/phylotree">
 <otu id="otu1">Marinobacler hydrocarbonoclasticus ATCC 49840T (ABO19148)</otu>
  <otu id="otu2">Microbulbifer hydrolyticus DSM 11525T (U5813138)</otu>
...
 </otus>
 <trees otus="Tls34455">
  <tree id="T1">
   <node id="NT1.1" label="NT1.1" x="119.0" y="292.0"/>
...