Taxonomy

[Melissa37]

This is on the priority list. Not sure what the issue is, please add your thoughts!

[hubgit]

The standard for marking up taxonomic descriptions is TaxPub, implemented by Pensoft in Zookeys.

• JATS-Con 2010: http://www.ncbi.nlm.nih.gov/books/NBK100351/
• JATS-Con 2012: http://www.ncbi.nlm.nih.gov/books/NBK47081/
• Sourceforge: http://sourceforge.net/projects/taxpub/
• Documentation: http://taxpub.sourceforge.net/taxpub-doc/
• XML schemas and mark-up practices of taxonomic literature
• Taxonomic treatments
• Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples
• Definition: http://terms.tdwg.org/wiki/TaxPub
• GitHub: https://github.com/tcatapano/TaxPub
• Namespace: http://purl.net/taxpub/ (404)

Unfortunately it's not as simple as adding a taxpub-namespaced taxon-treatment element to a JATS document, as the JATS DTD has to be extended to specify where that element is allowed to appear.

[hubgit]

Example:

<tp:nomenclature xmlns:tp="http://purl.net/taxpub/">
   <tp:taxon-name>
      <tp:taxon-name-part taxon-name-part-type="genus">Spigelia</tp:taxon-name-part>
      <tp:taxon-name-part taxon-name-part-type="species">genuflexa</tp:taxon-name-part>
      <object-id xlink:type="simple">urn:lsid:ipni.org:names:77114017-1</object-id>
      <object-id xlink:type="simple">http://species-id.net/wiki/Spigelia_genuflexa</object-id>
   </tp:taxon-name>
   <tp:taxon-authority>Popovkin &amp; Struwe</tp:taxon-authority>
   <tp:taxon-status>sp. nov.</tp:taxon-status>
   <xref ref-type="fig" rid="F1">Figs 1</xref>
   <xref ref-type="fig" rid="F2">2</xref>
</tp:nomenclature>