species-brainstorming

Species Brainstorming

Note: the original name of the proposed microformat, "species", is likely to change, probably to "biota" or "taxon". The former has been retained here, to avoid having to make many repetitive and perhaps redundant edits

updated! The new beta of Operator detects Species. A test page is available. Work on both continues!

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="species" title="Anas platyrhynchos">Mallard</abbr>

or

<span class="species">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 microformat, not taxonomically:

[Note: in taxonomy, levels such as "subphylum", "class" or "order" are known as a "rank"].

[Note: It is intended that all these (X)HTML classes be optionally' available to publishers, but they need use only those which apply to their particular needs. Compare, for instance, with all the classes and types available in hCard.]

• species (scientific name; aka botanical name) (better: taxon; or biota)
  • domain (alternatively: "superregnum")
  • kingdom (alt: "regnum")
  • subkingdom (alt: "subregnum")
  • superphylum
  • phylum
  • subphylum
  • taxoclass (alt: "taxo-class ", "taxonclass", "taxon-class", "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")
  • rank (alt: "taxorank", "taxon-rank", et al) - "unranked". See [1]; might also be used where the level of a rank is disputed, or the author simply has no ability or wish to declare the rank more explicitly.
  • binominal ("binominal name" alt: "binomial")
    • genus
    • specific (="specific epithet")
  • subsp ("subspecies")
  • variety
  • subvar ("subvariety")
  • form
  • subform
  • cultivar
  • cultgp ("cultivar group")
  • cross (e.g. "F1")
  • strain
  • ? morph (or phase) (e.g "Gyrfalcons, for example, have a grey morph and a white morph" [2]; "the Lesser Snow Goose (C. c. caerulescens), commonly occurs in two plumage variants. White-phase birds are white except for black wing tips, but blue-phase geese have bluish-grey plumage replacing most of the white except on the head, neck and tail tip." [3])
  • trade ("trade name")
  • breed (e.g. Bull Terrier)
  • sense (botanical - see examples)
  • authority
    • year (...of authority)
  • cname ("common name" - should this be "common" or "vernacular"?)
  • guid
  • vgroup ("vernacular group" (alt: "vernacular-group") - there is possibly a better term for this. Often, a genus or family doesn't encapsulate a particular group of species in a practical or useful fashion. For example, it is difficult to seperate fungi species and lichen species as they are taxonomically intermingled. Thus, within taxonomic databases, a vernacular group of "fungi" and "lichen" is often applied to species falling into either of these groups. A vernacular group could be considered similar to a common name, but for groups of species. See the NBN Gateway for an example of vernacular groups in use; these group names are also used in the Recorder biological recording software.
  • ? 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, male or female; or including nueter, hermaphoradite, unspecified and/ or mixed?)- 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
  • [name to be suggested ("type", "role"?)] an indicator of type, e.g. for bees, "queen" or "worker" [Q: Is there a proper name, in the scientific cmmnuity, for thes edistinctions?]

where are optional, and it is possible to infer from simply:

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

or

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

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

A species (Citrine Wagtail, a bird):

    <span class="species">
	<span class="binominal">Motacilla citreola</span>
    </span>

Sub-species (animal):

    <span class="species">
        <span class="binominal">Larus glaucoides</span>
        <span class="subsp">kumlieni</span>
    </span>

Variety (plant):

  <span class="species">
    <span class="binominal">Pisum sativum</span>
    var. <span class="variety">macrocarpon</span> 
  </span> 

Species (animal, common name displayed):

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

Species (animal, scientific name displayed):

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

Fungus, kingdom included:

    <span class="species"> 
        <abbr class="kingdom" title="Fungi"> 
            <span class="binominal">Amanita muscaria</span> 
        </abbr> 
    </span> 

Same name for different Genera:

    <p class="species">
        An unidentified
         <abbr class="taxoclass" title="Aves"> 
         <abbr class="genus" title="Oenanthe">
         <span class="common">
            Wheatear
         </span>
         </abbr>
         </abbr>
    </p>

and :

    <p class="species">
        An unidentified
         <abbr class="taxoclass" title="Magnoliopsida"> 
         <abbr class="genus" title="Oenanthe">
         <span class="common">
            Water Dropwort
         </span>
         </abbr>
         </abbr>
        sp.
    </p>

Species (animal, with authority and year):

    <span class="species"> 
        <span class="binominal">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="species">
        <abbr class="binominal" title="Bartramia longicauda">Tringa longicauda</abbr>
        by Johann Bechstein in 1812.
    </span>

A more extreme example, where there is a need to describe the full taxonomic hierarchy:

  <span class="species">
    <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="taxoclass">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="binominal">
	<span class="genus">Motacilla</span>
	<span class="specific">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>

Expressing a species with a GUID

Work is currently underway, through TDWG to develop a truly global GUID system based on LSIDs. More on LSIDs.

In the following example case an NBN GUID is provided. This GUID would be usable on the [http://www.searchnbn.net/speciesInfo/taxonomy.jsp?searchTerm=lutra lutra