Species element

[nschorgh]

Dedicated elements for species found in a cave would be a welcome addition to the CaveXML data exchange standard.
Here are some thoughts.

1. One possibility is a hierarchy, similar to fields proposed in the draft UISIC exchange standard:

   <species> - maxOccurs=unbounded
      <species-scientific-name> - binomial nomenclature (genus + species epithet), maxOccurs=1 or more?
      <species-genus> - Not needed since genus is already contained in scientific name
      <species-family>  
      <species-order>
      <species-class>
      <species-phylum> 
      <species-kingdom> - needed? how many kingdoms?
      <species-common-name> - maxOccurs=unbounded
      <species-reference> - bibliographical reference or URI
   <species>
   

   In most cases the higher ranks can be automatically looked up from the genus in scientific-name.
   Hemihomonyms can lead to ambiguities, but these are rare.

   Another possibility is a flat arrangement, with fewer elements:
   <species-scientific-name>
<species-common-name>
<species-reference> (applied collectively for species entries in the record)

   Or an even more concise format:
   <species> scientific name (common name) </species>

2. Scientific names use binomial nomenclature (genus + species epithet) appropriate in zoology and for plants, algae, and fungi. But will these elements also work for bacteria, archaea, and viruses?
   See:
   International Code of Zoological Nomenclature (ICZN)
   International Code of Nomenclature for algae, fungi, and plants (ICNafp) (including cyanobacteria)
   International Code of Nomenclature of Bacteria (ICNB) (including Archaea).
   International Committee on Taxonomy of Viruses (ICTV)

3. How to distinguish between extant and extinct species?
   Evidence for extinct species can be in a variety of forms.
   What if it is not known whether a fossil belongs to an extinct or extant species?
   Biologists and paleontologist must have thought about this.

4. How should links to genome sequences or other systematic data be organized?
   With a dedicated element that accepts a URI?

5. The organization of species data entries is not specific to cave sites, and it might be better to implement this as a second namespace rather than as part of CaveXML. Has such a namespace been designed?

Potential examples:

<species>
  <species-name> Oliarus polyphemus </species-name>
  <species-family> cixiidae </species-family>
  <species-superfamily> fulgoroidea </species-superfamily>
  <species-suborder> homptera </species-suborder>
  <species-order> hemiptera </species-order>
  <species-class> insecta </species-class>
  <species-phylum> arthropoda </species-phylum>
  <species-kingdom> animalia </species-kingdom>
</species>

<species>
   <scientific-name> homo naledi </scientific-name>
   <species-family> Hominidae </species>
   <type> extinct </type>
   <type> fossil </type>
</species>

Footnote:
UISIC = Informatics Commission of the International Speleological Union