species

Species

For the latest ideas, and to make comments, please see species-brainstorming.

Note: the original name of the proposed microformat, "species", is likely to change, probably to "biota" or "taxon". The former has been retained here, to avoid having to make many repetitive and perhaps redundant edits

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.

The scientific naming of organisms is a part of biodiversity informatics - "the application of information technology to the domain of biodiversity".

Also, for interest, see Note 4, on Robert Rothenburg's April 1998 paper on Dictionaries. It's interesting that microformats have given us the first three missing items - and were now debating the fourth!

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 if 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 (from personal hobby sites to major academic databases; from news outlets to retail organisations) 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 associate 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, recipe or hReview (and possibly others) could contain a scientific name microformat, in the same way that an hCalendar can contain an hCard.

See also: species-brainstorming#Future development

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
• Biodiversity Informatics: Taxonomic names, metadata, and the Semantic Web

Contributors & Supporters

• Andy Mabbett (proponent)
• Roger Hyam (interested party?)
• Charles Roper, Sussex Biodiversity Record Centre (proponent)
• Steve McWilliam, rECOrd - The Biodiversity Information System for the Cheshire region (supporter)
• Kieren Pitts, ILRT - Institute for Learning and Research Technology and the Amateur Entomologists' Society (supporter)
• Cyndy Parr, Spire project (interested party)
• Animal Diversity Web, [1] (interested party)

See also

Here's some work-in-progress:

• species-examples
• species-brainstorming
• Biobar - A customisable Firefox Extension providing a toolbar and content menu options for browsing biological data and databases, which shows what a user-agent could do, with data extracted from a species microformat

Implementations (pending)

• Taxon Checker - a software tool which, given a common name, searches for the relevant taxonomic data and outputs the selected species' details as (among other options) an HTML fragment. It is intended to provide templates for outputting such fragments with "species" microformat markup, once this proposal is implemented.