Difference between revisions of "species-brainstorming"

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'''Expressing a species with a GUID'''. In the following case it is an NBN GUID and 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, 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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'''Expressing a species with a GUID'''. 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, 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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     <span class="sci nbn-NBNSYS0000005133">
 
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         <span class="bin">Lutra lutra</span>
 
         <span class="bin">Lutra lutra</span>
 
         <span class="uid nbn">NBNSYS0000005133</span>
 
         <span class="uid nbn">NBNSYS0000005133</span>
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As a further alternative, the [[abbr-design-pattern]] could potentially be used, although this is semantically questionable:
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    <span class="sci">
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        <abbr class="bin" title="NBNSYS0000005133">Lutra lutra</abbr>
 
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Revision as of 15:00, 27 September 2006

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 1.0")

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. 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, 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

  • 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
          • I agree that taxon would be the most suitable name. It could be considered as a shortening of TaxonConcept (or TaxonName), which is the term used by the TCS - Charles Roper
    • or Biota - 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
        • Would bloating really be an issue? Many, if not most, servers (including this one) now gzip,deflate content and thus transfer time aren't so much of an issue. The front page of the microformats site states "Designed for humans first and machines second[...]", so unabbreviated terms would be more consistent with this aim. - Charles Roper
  • 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
      • "bin" and "var" are also extremely common terms using in programming languages - Charles Roper
  • 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>
  • Is "bin" (short for binomial) the most appropriate term for a taxon name? When subspecies, var, subvar, etc. are nested, then surely it becomes trinomial? Would simply name or TaxonName not be more flexible? - Charles Roper

To add

  • 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 NHM Species Dictionary). By providing a GUID, ambiguity is removed. - Charles Roper

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

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).

  • Thanks, Roger - it's good to have the involvement of such an august body, especially just before such a fortuitously-scheduled event. Is there any chance (and I realise that this is rather late in the day) that this proposal could be on the agenda in St Louis (even if only through a note in the papers/ programme); or that someone from the microformat community could attend/ speak there? Or that the TDWG and/or conference websites could link to http://microformats.org/wiki/species? - Andy Mabbett

See also