SDD proposal:
xml code to define tree, cyclical, and graph ordering of character states

TDWG working group: Structure of Descriptive Data (SDD)

Introduction

Most descriptive language packages aimed at interactive identification offer only the choice between unordered (nominal) and linearly ordered categorical character states. In many cases more complex ordering options for states are desirable. DELTA 2 proposed an additional character type "cyclical" and for phylogenetic analysis (esp. using the NEXUS format) tree ordering is frequently requested.

Proposal

The following types of ordered character state arrangements will be discussed:

order state arrangements

The following xml code using keyref references to the character state definitions is proposed to define these topologies:

Tree

<tree>
  <node keyref="c1">
    <node keyref="c2"/>
    <node keyref="c3">
      <node keyref="c5"/>
    </node>
    <node keyref="c4"/>
  </node>
</tree>

Cycle

<cycle>
  <node keyref="c11"/>
  <node keyref="c12"/>
  <node keyref="c13"/>
  <node keyref="c14"/>
</cycle>

     

Graph

<digraph>
  <node keyref="c21">
    <edges>
      <edge keyref="c22"/>
      <edge keyref="c23"/>
      <edge keyref="c24"/>
    </edges>
  </node>
  <node keyref="c23">
    <edges>
      <edge keyref="c24"/>
      <edge keyref="c25"/>
    </edges>
  </node>
  <node keyref="c25">
    <edges>
      <edge keyref="c24"/>
      <edge keyref="c22"/>
    </edges>
  </node>
  <node keyref="c22"/>
  <node keyref="c24"/>
</digraph>

Click here to download the xml example file and the corresponding xml-schema.

Request for discussion

Please send your criticism or suggestions to the sdd mailing list.

R. A. Morris (UMASS-Boston); Vers. 1; 18. Oct. 2002


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First published 2002-10-18, last update: 2002-10-18.

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