species-brainstorming

Species Brainstorming

Andy Mabbett

Proposal

There should, I believe, be a "species" 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; aka botanical name) (better: taxon; also biota)
  • 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
    • ? morph
  • trade ("trade name")
  • breed (e.g. Bull Terrier)
  • sense (botanical - see examples)
  • authority
    • year (...of authority)
  • cname ("common name")
  • ? gender (useful for species exhibiting sexual dimorphism - "find me a picture of a male Pintail"; "I want to buy a female Holly bush" - a binary value, "m" or "f")- see Future development
  • ? age bracket (adult/ juvenile/ seed/ egg/ nymph/ nestling/ pup/ cub/ instar1/ instar2 etc. - needs more work) - see Future development
  • ? count (a number, or represenattion of some other value - none, unspecified, "present", etc) - see Future development

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
    • I think "taxonname" or "taxon-name" would be a better value for the class attribute. It is more descriptive of the data your trying to specify the format of. Taxon refers more to the classification grouping I thought. The class attribute is used frequently for the application of CSS styling so the top level class at least needs to be fairly distinctive I would have thought to avoid clashes with other class attribute values in the page and CSS files. - Tony Prichard
      • The OED defines taxon as "A taxonomic group". See also the URL cited, [2]. - 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
    • I think a balance will need to be achieved between brevity in the interests of avoiding bloated html in a page with many species names and giving a meaningful name - Tony Prichard

• Is "class" a potentially confusing attribute name, and what should replace it ("taxoclass", perhaps? or "classis"?)
  • Yes I would avoid class as it a frequent keyword in software languages - Tony Prichard

• 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>

• • There are also species aggregates and groups to be considered Grey/Dark Dagger sp., where it is one of two species but where the genus Acronicta cannot be used as there are more than the two species in the genus - Tony Prichard
    • Any suggestions? Or other examples? - Andy Mabbett

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

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

• Is the "fungus" example OK, given that Amanita muscaria is not an abbreviation of "funghi"?
  • I do not like the use of the abbr tag at all in the examples given. The abbr tag is for abbreviations with the suggestion that the title is used for the full name. The implication in the Mallard example is that Mallard is an abbreviation for the scientific name, it is not it is a different type of name - Tony Prichard

• Do the "authority" and "date" 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

Future development

Instead of including gender, age-bracket and count, we could allow for a furture microformat, called, perhpas, "sighting", which might have the components:

• sighting
  • species (a "species" microformat)
    • set (one or more)
      • count
      • age-bracket
      • gender
  • location (hCard or geo)
  • date-time

See West Midland Bird Club's Latest news from Ladywalk and In and around South Staffordshire 2006 (blog) for simple examples.

Bill Hull

My website has 17000+ photos of 4700+ bird species. There are also a handful of butterflies (organized very poorly as I am unaware of any published butterfly world taxonomies) and shortly will have a number of dragon/damselflies. The site is made up of static pages but is built from a database so it is easy for me to add it new HTML tags to the pages. If you are interested in some prototyping at some point I can probably build stuff into the pages. - Bill Hull

See also

• species-examples