species-strawman-01

(Difference between revisions)

Jump to: navigation, search
(to-do: fix heading level)
m (headings)
Line 6: Line 6:
[Note: in taxonomy, levels such as "subphylum", "class" or "order" are known as a "rank"].
[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|hCard]].]
[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|hCard]].]
Line 52: Line 54:
**? age bracket (adult/ juvenile/ seed/ egg/ nymph/ nestling/ pup/ cub/ instar1/ instar2 etc. - '''needs more work''') - see [[#Future development|Future development]]
**? age bracket (adult/ juvenile/ seed/ egg/ nymph/ nestling/ pup/ cub/ instar1/ instar2 etc. - '''needs more work''') - see [[#Future development|Future development]]
**? count (a number, or represenattion of some other value - none, unspecified, "present", etc) - see [[#Future development|Future development]]
**? count (a number, or represenattion of some other value - none, unspecified, "present", etc) - see [[#Future development|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?]
+
** [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 commnuity, for these distinctions?]
-
 
+
where are optional, and it is possible to infer from simply:
where are optional, and it is possible to infer from simply:
Line 188: Line 189:
</nowiki></pre>
</nowiki></pre>
-
=====Expressing a species with a GUID=====
+
===Expressing a species with a GUID===
Work is currently underway, through [http://www.nhm.ac.uk/hosted_sites/tdwg/ TDWG] to develop a [http://wiki.gbif.org/guidwiki/wikka.php?wakka=HomePage truly global GUID system] based on [http://wiki.gbif.org/guidwiki/wikka.php?wakka=LSID LSID]s. [http://xml.coverpages.org/lsid.html More on LSIDs].
Work is currently underway, through [http://www.nhm.ac.uk/hosted_sites/tdwg/ TDWG] to develop a [http://wiki.gbif.org/guidwiki/wikka.php?wakka=HomePage truly global GUID system] based on [http://wiki.gbif.org/guidwiki/wikka.php?wakka=LSID LSID]s. [http://xml.coverpages.org/lsid.html More on LSIDs].
Line 223: Line 224:
uBio has a publicly available [http://www.ubio.org/index.php?pagename=soap_tools SOAP web services interface] which makes mining for taxonomic intelligence relatively easy.
uBio has a publicly available [http://www.ubio.org/index.php?pagename=soap_tools SOAP web services interface] which makes mining for taxonomic intelligence relatively easy.
-
====Questions====
+
===Questions===
* Is "sci" the best attribute name for the top-level?  
* Is "sci" the best attribute name for the top-level?  
Line 291: Line 292:
:<blockquote>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).</blockquote>
:<blockquote>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).</blockquote>
-
====To add====
+
===To add===
* Animal hybrids
* Animal hybrids
* GUID (Globally Unique Identifier). When referencing to a taxon name, there is also often the need to provide a GUID which relates to a taxonomic concept database (such as the [http://nbn.nhm.ac.uk/nhm/ NHM Species Dictionary]). By providing a GUID, ambiguity is removed. - Charles Roper
* GUID (Globally Unique Identifier). When referencing to a taxon name, there is also often the need to provide a GUID which relates to a taxonomic concept database (such as the [http://nbn.nhm.ac.uk/nhm/ NHM Species Dictionary]). By providing a GUID, ambiguity is removed. - Charles Roper
** Thank you. [[User:AndyMabbett|AndyMabbett]] 11:55, 26 Sep 2006 (PDT)
** Thank you. [[User:AndyMabbett|AndyMabbett]] 11:55, 26 Sep 2006 (PDT)
-
====Future development====
+
==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:
+
Instead of including gender, age-bracket and count, we could allow for a future microformat, called, perhaps, "sighting", which might have the components:
*sighting
*sighting
Line 311: Line 312:
==See also==
==See also==
-
{[species-related-pages}}
+
{{species-related-pages}}

Revision as of 10:50, 17 January 2008

Contents

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

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 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.

See also

Template:species-related-pages

species-strawman-01 was last modified: Wednesday, December 31st, 1969

Views