species-brainstorming

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=====Expressing a species with a GUID=====
=====Expressing a species with a GUID=====
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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].
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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%20lutra&spKey=NBNSYS0000005133 NBN Gateway], [http://nbn.nhm.ac.uk/nhm/bin/nbntaxa.dll/taxon_details?taxon_key=NBNSYS0000005133 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).
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%20lutra&spKey=NBNSYS0000005133 NBN Gateway], [http://nbn.nhm.ac.uk/nhm/bin/nbntaxa.dll/taxon_details?taxon_key=NBNSYS0000005133 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).
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Revision as of 16:20, 29 September 2006

Contents

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:

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>
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="bin">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="sci">
        <span class="bin">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="sci">
        <abbr class="bin" title="NBNSYS0000005133">Lutra lutra</abbr>
    </span>

Questions

<span class="bin"><span class="genus">Podiceps</span></span>
<span class="bin">Larus glaucoides <span class="sub">kumlieni</span></span>
An unidentified <abbr class="taxoclass" title="Sauropsida">reptile</abbr>

To add

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:

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

Roger Hyam

Taxonomic Databases Working Group

TDWG is the organisation for standardisation in exchange of biodiversity data. The organisation is currently undergoing a degree of re-organisation and is developing an architecture to integrate the different standards it produces with each other and with those in use in the semantic web and geospatial communities. Part of this architecture will be a central ontology for things like scientific biological names.

Because of its role in bridging technologies the application that manages the ontology will need to be able to express the same basic semantics in multiple formats (e.g. RDFS, OWL, Geography Mark Up, OBO etc). It seems logical that this application should also generate basic microformat definitions for each of the classes it contains. If we have an ontology defining 'Taxon Name' and 'specific epithet' for example the same notion should be mapped to as many technologies as possible.

TDWG is also supporting a system for Globally Unique Identifiers based on Life Science Identifiers for biodiveristy objects such as taxon names, specimens, herbaria etc which it would be cool to integrate into any microformat.

There is a meeting in St Louis, USA, October 2006 where the way forward for the ontology will be discussed. Decisions made at the meeting will govern what is possible. It is difficult to take this further without concensus from that meeting.

If it is after October 2006 and you are interested in learning more please contact me (Roger Hyam).

Malcolm Storey

(extracted from e-mails to Andy Mabbett, by kind permission)

ICZN, ICBN et al

You don't cover the full set of levels of taxonomic hierarchy defined by the relevant body ICZN or ICBN (plus the others - one each for garden plant varieties, bacteria, viruses. Don't know about mycoplasmas, diseases, BSE factors etc.

ICBN Ranks listed [5], [6]

AIUI ICBN only goes down to species.

ICZN isn't so easy: [7]

1.2.2. The Code regulates the names of taxa in the family group, genus group, and species group. Articles 1-4, 7-10, 11.1-11.3, 14, 27, 28 and 32.5.2.5 also regulate names of taxa at ranks above the family group. (But none of the above articles list the taxonomic ranks.)

ICZN Only goes down to subspecies (art 1.3.4)

Note also:

1.4. Independence. Zoological nomenclature is independent of other systems of nomenclature in that the name of an animal taxon is not to be rejected merely because it is identical with the name of a taxon that is not animal (see Article 1.1.1)

(eg Trichia, Oenanthe, Melanotus)

DNA

You may want to consider refs to DNA sequences. They're not part of taxonomy, but they can be considered the bottom rung of the taxonomic hierarchy and they will be of increasing significance.

See also

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

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