species

Species

Introduction

People use the vernacular AND taxonomic names of species in everyday speech and writing - just read or watch any populist gardening magazine or television programme.

Consider this list: "Blackbird", "poodle", "T Rex", "potato", "French Marigold", "Wisteria", "E. Coli", "HIV", "Rubella" and "human being".

"T Rex" is "Tyrannosaurus rex"; "E. Coli" is "Escherichia coli"; "HIV" is "Human immunodeficiency virus" and "Rubella" is "Rubella virus". All are the taxonomic (or scientific) names of unique species.

"Wisteria" is a taxonomic genus.

"Blackbird"; "poodle"; "potato"; "French Marigold" and "human being" (arguments about Neanderthals not withstanding) are vernacular (or common) names, but still refer to individual species.

Proposal

Imagine viewing a web page with a reference to a species - and being able to use an add-on to you browser to be taken directly to information about that species, on, say, Wikipedia, or Wikispecies, or Google Images, or another site, such as in an academic database, of your choosing.

Your software would automatically know to search site A of the scientific name referred to a moth, site B for a bird, and site C for a plant - and you could set your preferences as to which sites those were to be, and in which order two or more were to be searched (e.g. for moths, try UK Moths first, if not found try The Global Lepidoptera Names Index).

Or supposing someone writes a long, chronologically-ordered web page about all the birds, insects, mammals and plants they saw on a wildlife safari, with lots of prose description about the paces where they saw them and the people they were with, but you want to extract a list of species, sorted into alphabetical order within taxonomic class (birds first, then insects then...) or in taxonomic order.

Those are just two of the things a "species" microformat might do for you.

Existing taxonomies

The proposal respects all existing biological taxonomies, and is not intended to change or supplant any of them - it is intended merely to provide webmasters with a method of either:

1. marking-up a taxonomical name (or taxon-common name pair) in such a way that its components can be recognised by computers or
2. marking up a common name, so as to associative with it a taxonomical name, in such a way that the latter's components can be recognised by computers

Embedding within other microformats

The proposed plant microformat (with care regime, supplier, etc.), hlisting or hReview (and possibly others) could contain a scientific name microformat, in the same way that an hCalendar can contain an hCard.

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).

References

• Wikipedia: Scientific classification
  • Wikipedia: Binomial nomenclature
  • Wikipedia: Trinomial nomenclature
  • Wikipedia: Taxon
  • Wikipedia: Cultivars
  • Wikipedia: Varieties
  • Wikipedia: Sub-varieties
  • Wikipedia: forms
• http://www.iczn.org/ International Commission on Zoological Nomenclature
  • Wikipedia: International Commission on Zoological Nomenclature
• International Code of Botanical Nomenclature
• RHS Plant Finder: The naming of plants
• International Code of Nomenclature for Cultivated Plants
• Taxonomic Databases Working Group
• Hortax - The Names of Garden Plants
• www.bgbm.fu-berlin.de/iapt/nomenclature/code/SaintLouis/0000St.Luistitle.htm
• WikiSpecies
• Wiktionary: Taxonomy

Contributors

• Andy Mabbett (proponent)
• Roger Hyam (interested party?)

See also

Here's some work-in-progress:

• species-examples
• species-brainstorming