NeXML Test Files

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Purposes

These files are for experimenting with representation schemes, and to provide instances for tests.

Representation scheme

  • to understand the syntax for metadata, see the metadata representation page (note: what the standard says on referencing blank nodes)
  • in the example below, we wish to assign a bootstrap value to an edge in a tree; since nexml does not have a bootstrap attribute, we can use the cdao:has_Support_Value concept like this

<xml> 

     <edge id="edge22" about="foo">
       <meta property="cdao:has_Support_Value">0.425</meta>
     </edge>

</xml>

Tools

Test files from the nexml web site

http://nexml-dev.nescent.org/nexml/examples/

Test files from the hackathon code repository


Bootstrap values test files

  • uses: test ability to display or process branch support values such as bootstraps
  • comment: The newick tree looks like this:
(otuA:4,(((otuB:1,otuC:1):1[0.35],otuD:2):1[0.425],(otuE:1,otuF:1):2[0.65]):1);
  • this image (from nexplorer) shows the values mapped to the tree image bootstraps on this tree

Bootstraps represented using the "meta" tag

<xml> 

 <trees>
   <tree>
     <edge id="edge22" about="this_edge22" length="1" source="node21" target="node22">
       <meta typeof="cdao:Edge" property="cdao:has_Support_Value" datatype="xsd:float">0.425</meta>
     </edge>
     <edge id="edge27" about="this_edge27" length="2" source="node21" target="node27">
       <meta typeof="cdao:Edge" property="cdao:has_Support_Value" datatype="xsd:float">0.65</meta>
     </edge>
     <edge id="edge23" about="this_edge23" length="1" source="node22" target="node23">
       <meta typeof="cdao:Edge" property="cdao:has_Support_Value" datatype="xsd:float">0.35</meta>
     </edge>
   </tree>
 <trees>

</xml>

Bootstraps represented without new tags or elements

<xml> 

 <trees>
   <tree>
     <edge id="edge22" length="1" source="node21" target="node22"
         typeof="cdao:Edge" property="cdao:has_Support_Value" datatype="xsd:float" content="0.425" />
     <edge id="edge27" length="2" source="node21" target="node27"
         typeof="cdao:Edge" property="cdao:has_Support_Value" datatype="xsd:float" content="0.65" />
     <edge id="edge23" length="1" source="node22" target="node23"
         typeof="cdao:Edge" property="cdao:has_Support_Value" datatype="xsd:float" content="0.35" />
   </tree>
 <trees>

</xml>

Labels for internal nodes

  • uses: test ability to display or process labels for ancestral (internal) nodes
  • comment: the Newick standard allows internal node labels like this:
(otuA:4,(((otuB:1,otuC:1)inodeBC:1,otuD:2)inodeBCD:1,(otuE:1,otuF:1)inodeEF:2)inodeBCDEF:1)inodeABCDEF;
  • comment: here is what it looks like

image of trees showing internal node labels

<xml> 

 <trees>
   <tree>
     <node id="node19" label="inodeABCDEF" root="true"/>
     <node id="node20" label="otuA" otu="otu2"/>
     <node id="node21" label="inodeBCDEF"/>
     <node id="node22" label="inodeBCD"/>
     <node id="node27" label="inodeEF"/>
     <node id="node23" label="inodeBC"/>
     <node id="node26" label="otuD" otu="otu5"/>
   </tree>
 <trees>

</xml>

Ancestral states test files

  • uses: test ability to display or process ancestral state data
  • comment:

Ancestral states represented RDFa style using meta tags

<xml> 

 <trees>
   <tree>
     <node id="node19" label="inodeABCDEF" root="true" about="uniquely_this_node19">
       <meta property="cdao:has_Datum">
         <meta typeof="cdao:CharacterStateDatum" rel="cdao:has_State" resource="#s1"/>
       </meta>
     </node>
     <node id="node20" label="otuA" otu="otu2"/>
     <node id="node21" label="inodeBCDEF" about="uniquely_this_node21">
       <meta property="cdao:has_Datum">
         <meta typeof="cdao:CharacterStateDatum" rel="cdao:has_State" resource="#s1"/>
       </meta>
     </node>
     <node id="node22" label="inodeBCD" about="uniquely_this_node22">
       <meta property="cdao:has_Datum">
         <meta typeof="cdao:CharacterStateDatum" rel="cdao:has_State" resource="#s1"/>
       </meta>
     </node>
     <node id="node27" label="inodeEF" about="uniquely_this_node27">
       <meta property="cdao:has_Datum">
         <meta typeof="cdao:CharacterStateDatum" rel="cdao:has_State" resource="#s3"/>
       </meta>
     </node>
     <node id="node23" label="inodeBC" about="uniquely_this_node23">
       <meta property="cdao:has_Datum">
         <meta typeof="cdao:CharacterStateDatum" rel="cdao:has_State" resource="#s1"/>
       </meta>
     </node>
   </tree>
 <trees>

</xml>

Ancestral states represented some other way

<xml> 

 <trees>
   <tree>
   </tree>
 <trees>

</xml>

Taxonomy references test files

  • Description: These are pairs of files. Each file has 6 OTUs, one of which is labeled "S. glaucus". In one file, this is supposed to mean "Scomber glaucus", the Derbio (related to mackerels and tunas), and in the other file it is supposed to mean "Squalus glaucus", the blue shark.
  • uses:
    • the pair of files together can be used to address the super-tree case of finding matching OTUs
    • either file can serve for a visualization case
    • either file can serve for a taxonomy resolution case
    • either file can be used to resolve synonyms. According to fishbase, both S. glaucus names are junior synonyms: the preferred name for Scomber glaucus is Trachinotus ovatus (English common name is Derbio or Pompano); the preferred name for Squalus glaucus is Prionace glauca (common name "blue shark").

OTUs with no taxrefs

  • description: two files that share the OTU label "S. glaucus" and have no external tax refs by which to disambiguate


OTUs with tax refs via the TDWG taxon concept

  • description: two files that share the OTU label "S. glaucus" and have tax refs that could be used to disambiguate
  • file(s):
  • comment: THESE FILES FAIL THE NEXML VALIDATOR AT NEXML.ORG!!
  • comment: this has the tax refs in RDFa syntax that Roger suggests to assign an LSID value TDWG taxon concept

<xml> 

 <otu id="otu3" label="S. glaucus" about="foo" typeof="tc:TaxonConcept" xmlns:tc="http://rs.tdwg.org/ontology/voc/TaxonConcept#" xmlns:tn="http://rs.tdwg.org/ontology/voc/TaxonName#">
   <meta rel="tc:hasName">
     <meta typeof="tn:TaxonName" about="urn:lsid:zoobank.org:act:A6AD1B85-C65C-4079-B425-56828418620C">
       <meta property="tn:genusPart">Scomber</meta>
       <meta property="tn:specificEpithet">glaucus</meta>
     </meta>
   </meta>
 </otu>

</xml>

OTUs with tax refs in alternative RDFa syntax

  • description: two files that share the OTU label "S. glaucus" and have tax refs that could be used to disambiguate
  • file(s):
  • comment: these files are valid nexml according to the validator
  • comment: this syntax may be more consistent with the use of RDFa, but it is not extendable to having multiple triples with the same implicit subject; this is why there is a value to have an "annotation" or "any" tag (used like "span" in html docs)

<xml> 

 <otus id="otus1" xmlns:cdao="http://www.evolutionaryontology.org/cdao/1.0/cdao.owl">
   <otu id="otu3" label="S. glaucus" about="[_:this_otu3]" typeof="cdao:TU" property="cdao:has_Taxonomy_Reference"
      resource="http://www.zoobank.org/?urn:lsid:zoobank.org:act:A6AD1B85-C65C-4079-B425-56828418620C" />
 </otus>

</xml>

OTUs with tax refs in deprecated "dict" syntax

  • description: two files that share the OTU label "S. glaucus" and have taxrefs that could allow disambiguation
  • file(s):
  • comment: this will validate at nexml-dev.nescent.org (if 'any' element has ' xmlns="" ')
  • comment: this has the tax refs in nexml "dict" syntax to assign an LSID value via CDAO property

<xml> 

 <otu id="otu5" label="S. glaucus">
   <dict xmlns:cdao="http://evolutionaryontology.org/cdao/1.0/cdao.owl" id="dict1">
     <any id="bar" xmlns="">
       <cdao:TU rdf:id="baz">
         <cdao:has_Taxonomy_Reference rdf:resource="http://www.zoobank.org/?lsid=urn:lsid:zoobank.org:act:2CD1E27B-D572-447C-BD0F-2AA998447FBF"/>
       </cdao:TU>
     </any>
   </dict>
 </otu>

</xml>

OTUs with tax refs in other syntax

  • description: planned, in progress
  • file(s):
    • dogfish (genus Squalus):
    • mackerel (genus Scomber):
  • comment:

notes for dict references

Prunella

Oenanthe ZooBank record (urn:lsid:zoobank.org:act:5E78566E-FE5B-4135-ABC0-B70AA36396EF)

Pavonia** Ubio LSID: urn:lsid:ubio.org:namebank:798505 Nemphalid genus Pavonia Godart 1824 and swampmallow

Anacharis

Morus

Pieris

Mallotus

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