species-brainstorming

Species Brainstorming

Andy Mabbett

Proposal

There should, I believe, be a microformat for the markup of plant and animal names, to include their scientific names. Consider:

<abbr class="sci" title="Anas platyrhynchos">Mallard</abbr>

or

<span class="sci">Anas platyrhynchos</span>

The microformat would allow user agents to be configured to perform look-ups on on-line databases of species, according to user preferences. Specification of the taxonomic class would help user agents to know which such databases were applicable (i.e., use database A for plants, but database B for mammals and database C for insects.)

It would also allow for more specific searching (do I mean "crow" or do I mean "Corvus corone"?).

The specification should encourage, but not mandate, the correct capitalisation of scientific names, so "Anas platyrhynchos'" not "anas platyrhynchos" nor (except historically) "Anas Platyrhynchos". A reminder that such names should be styled with italics will also be included.

Straw man proposal

I'm tending towards this model, nested according to components of the microforamt, not taxonomically:

• sci (scientific name) (better: taxon)
  • domain (alternatively: "superregnum")
  • kingdom (alt: "regnum")
  • subkingdom (alt: "subregnum")
  • superphylum
  • phylum
  • subphylum
  • class (alt: "classis")
  • subclass (alt: "subclassis")
  • infraclass (alt: "infraclassis")
  • superorder (alt: "superordo")
  • order (alt: "ordo")
  • suborder (alt: "subordo")
  • infraorder (alt: "infraordo")
  • parvorder
  • superfamily (alt: "superfamilia")
  • family (alt: "familia")
  • subfamily (alt: "subfamilia")
  • bin ("binomial name")
    • genus
    • species (="specific epithet")
    • subsp ("subspecies")
    • var ("variety")
    • subvar ("subvariety")
    • form
    • subform
    • cult ("cultivar")
    • cultgp ("cultivar group")
    • cross (e.g. "F1")
    • strain
  • trade ("trade name")
  • breed (e.g. Bull Terrier)
  • sense (botanical - see examples)
  • authority
    • year (...of authority)
  • cname ("common name")

where all except "bin" are optional, and it is possible to infer from simply:

<abbr class="bin" title="Anas platyrhynchos">Mallard</abbr>

or

<span class="bin">Anas platyrhynchos</span>

that the genus is Anas and the species is platyrhynchos (and, thus, "bin" is to "sci"; as "adr" is to "hCard")

Examples

Extreme case (Pied Wagtail, a bird):

  <span class="sci">
    <span class="domain">Eukarya</span>
    <span class="kingdom">Animalia</span>
    <span class="subkingdom">Eumetazoa</span>
    <span class="superphylum">Deuterostomia</span>
    <span class="phylum">Chordata</span>
    <span class="subphylum">Vertebrata</span>
    <span class="class">Aves</span>
    <span class="subclass">Neognathae</span>
    <span class="order">Passeriformes</span>
    <span class="suborder">Passeri</span>
    <span class="parvordo">Passerida</span>
    <span class="superfamily">Passeroidea</span>
    <span class="family">Motacillidae</span>
    <span class="bin">
	<span class="genus">Motacilla</span>
	<span class="species">alba</span>
	<span class="subspecies">yarrellii</span>
    </span>
    <span class="cname">Pied Wagtail</span>
    <span class="authority">Linnaeus</span>
    <span class="year">1758</span>
  </span>

Simplified equivalent of the above:

    <span class="bin">
	<span class="genus">Motacilla</span>
	<span class="species">alba</span>
	<span class="subspecies">yarrellii</span>
    </span>

Sub-species (animal, common name displayed):

    <span class="sci">
        <span class="bin">Larus glaucoides</span>
        <span class="sub">kumlieni</span>
    </span>

Variety (plant):

  <span class="sci">
    <span class="bin">Pisum sativum</span>
    var. <span class="var">macrocarpon</span> 
  </span> 

Species (animal, common name displayed):

    <span class="sci">
        <abbr class="bin" title="Larus thayeri">
            <span class="common">Thayer's Gull</span>
        </abbr>
    </span> 

Species (animal, scientific name displayed):

    <span class="sci">
        <abbr class="common" title="Thayer's Gull"> 
            <span class="bin" Larus thayeri</span> 
        </abbr> 
    </span> 

Fungus, kingdom included:

    <span class="sci"> 
        <abbr class="kingdom" title="Fungi"> 
            <span class="bin">Amanita muscaria</span> 
        </abbr> 
    </span> 

Species (animal, with authority and year):

    <span class="sci"> 
        <span class="bin">Pica pica</span> 
        <span class="authority">Linnaeus</span>, 
        (<span class="year">1758</span>) 
    </span>

Re-classified species (animal):

    The species was classified as
    <span class="sci">
        <abbr class="bin" title="Bartramia longicauda">Tringa longicauda</abbr>
        by Johann Bechstein in 1812.
    </span>

Questions

• Is "sci" the best attribute name for the top-level?
  • No - Scott Reynen
    • What do you think would be better? - Andy Mabbett
      • Assuming "sci" is short for "scientific name", I propose "scientific-name".
        • It is. That's 12 extra characters! - Andy Mabbett
  • Taxon is a far better solution [1]. It's short, meaningful and in keeping with the other class types. - Andy Mabbett

• Should "bin", var", "cult", etc., be written in full? (I think not, to save bloating file sizes)
  • Yes - Scott Reynen

• Should other attribute names be abbreviated for brevity?
  • No, brevity is not one of the naming principles. "bin", "var", and "cult" all leave ambiguous meaning, which is a problem. We should "Use class names based on names from the original schema," e.g. full words or phrases where they aren't especially long. - Scott Reynen
    • Fair enough, though I worry about some of my pages, with tens or hundreds of species listed! Also, note that "var" "sub" and suchlike are the proper abbreviations to use, in botanical nomenclature (see the posted examples). - Andy Mabbett

• Is "class" a potentially confusing attribute name, and what should replace it ("taxoclass", perhaps? or "classis"?)

• What other attribute names are needed, if any (we could do with help from a taxonomist!)

• How to deal with: "Podiceps sp." (a grebe of unknown species)
  • How about the following, where we can infer an unknown species by the absence of that attribute?:

<span class="bin"><span class="genus">Podiceps</span></span>

• Should we allow divisions of "bin" with no parent "sci", such as:

<span class="bin">Larus glaucoides <span class="sub">kumlieni</span></span>

• Does "year of authority" need to be an hcal?

• Is the "fungus" example OK, given that Amanita muscaria is not an abbreviation of "funghi"?

• Do "authority" and "pair" need a joint wrapper?

• I first thought that "all except "bin" are optional"; now I'm not so sure. Should be be able to mark up:

An unidentified <abbr class="taxoclass" title="Sauropsida">reptile</abbr>

To add

• Animal hybrids

Embedding within other microformats

The proposed plant microformat (with care regime, supplier, etc.), hlisting or hReview (and possibly others) could contain a scientific name microformat, in the same way that an hCalendar can contain an hCard.

References

• Wikipedia: Scientific classification
• Wikipedia: Taxon
• International Commission on Zoological Nomenclature
• International Code of Botanical Nomenclature
• International Code of Nomenclature for Cultivated Plants
• Hortax - The Names of Garden Plants
• www.bgbm.fu-berlin.de/iapt/nomenclature/code/SaintLouis/0000St.Luistitle.htm
• WikiSpecies
  • Taxonomy

See also

• species-examples