species-strawman-01

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Species straw-man proposal

This page is a sub-page of species-brainstorming

I (Andy Mabbett) am 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"].

Strawman

[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.]

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

In the following example case an NBN GUID is provided. This GUID would be usable on the NBN Gateway, The NHM Species Dictionary, in Recorder 2002 and Recorder 6, and in the forthcoming OpenRecorder online recording toolkit. As there are different GUIDs for different databases, the type of GUID can be indicated with a code followed by a hyphen followed by the GUID (e.g. nbn-NBNSYS0000005133).

    <span class="sci nbn-NBNSYS0000005133">
        <span class="binominal">Lutra lutra</span>
    </span>

Alternatively, the GUID could be expressed as an element in its own right, with the GUID type being expressed as a secondary class name:

    <span class="species">
        <span class="binominal">Lutra lutra</span>
        <span class="uid nbn">NBNSYS0000005133</span>
    </span>

As a further alternative, the abbr-design-pattern could potentially be used, although this is semantically questionable:

    <span class="species">
        <abbr class="binominal" title="NBNSYS0000005133">Lutra lutra</abbr>
    </span>

Yet another alternative, using a uBio LSID as the GUID:

    <span class="species urn:lsid:ubio.org:namebank:8341384">
      <span class="cname">Green Sandpiper</span>
      <span class="binominal">Tringa ochropus</span>
    </span>

uBio has a publicly available SOAP web services interface which makes mining for taxonomic intelligence relatively easy.

Questions

<span class="bin"><span class="genus">Podiceps</span></span>
<span class="bin"><span class="genus">Podiceps</span><span class="species">unknown</span></span>
<span class="bin">Phylloscopus trochilus/Phylloscopus collybita</span>
<span class="bin"><span class="genus">Anser</span>/<span class="genus">Branta</span></span>
<span class="group.or"><span class="bin">Phylloscopus trochilus</span><span>Phylloscopus collybita</span></span>
<span class="group.and"><span class="bin">Phylloscopus trochilus</span><span>Phylloscopus collybita</span></span>
<span class="binominal">Larus glaucoides <span class="sub">kumlieni</span></span>
Salmonella enterica (ex Kauffmann & Edwards 1952) Le Minor & Popoff 1987

in which the parentheses are significant (see Wikipedia Taxobox usage and Wikipedia's article on zoological authority citations for further examples). Should we therefore allow "authority" to be a text string, and omit a separate year field? Andy Mabbett 03:17, 27 Jun 2007 (PDT)

I definitely prefer "superregnum" over "superkingdom". Using the Latin forms of the taxon names makes the format less language-dependent and more international. It probably also reduces ambiguity somewhat (a biological "kingdom" is also called an "empire" in English).

To add

Future development

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

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

Implementations

This proposal has been implemented approximately in Cognition and Operator (user script). Both are roughly compatible, but more work is required fleshing out the details of this spec so that full compatibility can be achieved, and more implementors can jump on board.

See also

Template:species-related-pages

species-strawman-01 was last modified: Wednesday, July 21st, 2010

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