Microformats Wiki - User contributions [en]

species-examples

2007-01-29T03:52:26Z

PeNGo: /* Contributors */

=Species Examples=

Examples of common and scientific names of living things, which could be marked up with a "'''[[species]]'''" (or similar) microformat. Note use of matching pairs of examples, where possible.

:'''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'''

'''If you find a link which is not working, please replace it with a suitable alternative, rather than simply deleting it. Thank you.'''

__TOC__

==Types of publishers==

There are, perhaps, three types of publisher of taxonomic information (with all the usual overlaps and exceptions one finds when generalising so much!):

#Those which publish a full or partial hierarchy, like [http://names.ubio.org/browser/classifications.php?conceptID=2463046 UBIO].
#Those which publish a binominal, or a binominal with a qualifier, like a subspecies, variety, breed, hybridisation - but still referring to a single type of living thing, with no higher- level taxonomy. e.g [http://www.westmidlandbirdclub.com/records/lists.htm the West Midland Bird Club's county lists]
#These which publish common (or "vernacular") names, but who would be interested in "aliasing" those to the scientific equivalent. e.g [http://www.westmidlandbirdclub.com/ladywalk/latest.htm the West Midland Bird Club's news from Ladywalk]

Interestingly, some sites (Wikipedia, for example) have pages which fall into each of the three categories!
#[http://en.wikipedia.org/wiki/Bar-tailed_Godwit Bar tailed Godwit]
#[http://en.wikipedia.org/wiki/Genetics_of_humans Genetics of humans]
#[http://en.wikipedia.org/wiki/Ladywalk Ladywalk]

[[User:AndyMabbett|AndyMabbett]] 12:05, 23 Oct 2006 (PDT)

==Binominals==

===Birds===

'''Black-tailed Godwit''' on [http://www.westmidlandbirdclub.com/ladywalk/latest.htm West Midland Bird Club's Ladywalk reserve latest news page]

<pre><nowiki>Black-tailed Godwit</nowiki></pre>

'''''Limosa limosa'''''
[http://www.westmidlandbirdclub.com/records/lists.htm West Midland Bird Club county lists]

<pre><nowiki>
<th scope="col">Common Name</th><th scope="col">Scientific Name</th>
[...]
<th scope="row" class="bird">Black-tailed Godwit</th><td class="sci">Limosa limosa</td>
</nowiki></pre>

'''''Eurasian Bittern'''''
[http://www.westmidlandbirdclub.com/ladywalk/BITTE.htm Bitterns at LAdywalk]

<pre><nowiki>
Eurasian Bitterns, (Botaurus stellaris)
</nowiki></pre>

===Mammal===
'''Wolf''' on [http://www.wolf.org/wolves/index.asp International Wolf Center]

'''''Canis_lupus''''' on [http://animaldiversity.ummz.umich.edu/site/accounts/information/Canis_lupus.html Animal Diversity Web]

===Fish===
'''Northern pike''' on [http://www.dnr.state.mn.us/fish/northern/index.html Minnesota Department of Natural Resources]

'''''Esox lucius''''' on [http://www.pikezander.co.uk/pike.htm Pike & Zander]

===Insect===
'''Death’s Head Hawkmoth''' on [http://funkman.org/animal/insect/deathheadmoth.html Animal Teachers]

'''''Acherontia atropos''''' on [http://ukmoths.org.uk/show.php?id=2540 UK Moths]

'''Migrant Hawker''' (''Aeshna mixta'') on [http://www.sxbrc.org.uk/news/friston-forest-recording-day Sussex Biodiversity Record Centre]

===Arachnid===
'''Rose Trantula''' on [http://www.practical-pet-care.com/spider_question.php?ID=1.2006100416232172 Pet Care Forum]

'''''Araneus angulatus''''' on [http://www.sxbrc.org.uk/news/friston-forest-recording-day Sussex Biodiversity Record Centre] (this is a duplicate. [[User:BenWest|BenWest]] 21:56, 21 Oct 2006 (PDT))

===Plant===
'''Bog Pimpernel''' on [http://www.map-reading.co.uk/wildflowers/HTML%20files/f0219.htm Map Reading's Wildflower Images]

'''''Anagallis tenella''''' on [http://www.bioimages.org.uk/HTML/T47624.HTM BioImages]

'''''Persicaria campanulatum''''' on [http://www.record-lrc.co.uk/?Mod=Forum&Do=ViewThread&ForumID=6&ThreadID=75 rECOrd - The Biodiversity Information Centre for the Cheshire region]

'''''Galeopsis tetrahit s.s.'''''
[http://www.westmidlandbirdclub.com/blithfield/plants20060815.htm West Midland Bird Club]
<pre><nowiki>
Galeopsis tetrahit <abbr lang="la" title="sensu stricto">s.s.</abbr> (Common Hemp-nettle)
</nowiki></pre>

===Fungi===

'''''Amanita muscaria''''' on [http://www.mykoweb.com/CAF/species/Amanita_muscaria.html California Fungi]
* as '''''Amanita muscaria'' (L. per Fr.) Hooker'''
* as '''''Amanita muscaria var. flavivolvata'''''

'''Fly Agaric''' on [http://www.treesforlife.org.uk/forest/mythfolk/flyagaric.html Trees for Life]

'''''Rhodocollybia maculata'' (Albertini & Schweinitz: Fries) Singer''' on [http://www.ilmyco.gen.chicago.il.us/Taxa/Rhodomacul540.html]
*also written as '''''Rhodocollybia maculata'' (Albertini & Schweinitz ex Fries) Singer'''
*(This is where a post-Linnean author is given special rights (because his descriptions were comparatively complete - i.e. recognisable) so his interpretation of earlier names is taken as the sense meant by the original author. Think these used to be "apud" and are now "ex" although a colon has also been used. There are only a few sanctioning authors, the main one being Elias Fries.(Fr.) )

==More than binominals==

===Authority===
'''''Pica pica'' Linnaeus, (1758)''' on [http://en.wikipedia.org/wiki/European_Magpie Wikipedia: European Magpie]
:(i.e. named by Linnaeus in 1758)

===Unspecified species===
'''''Podiceps sp.''''' on [http://www.birdlife.org/datazone/species/index.html?action=SpcHTMDetails.asp&sid=3644&m=0 Bird Life] <pre><nowiki>Podiceps sp.</nowiki></pre>

'''Psyllid plant hopper''' [http://ramblingsofanaturalist.blogspot.com/2006/07/bay-sucker-gall-trioza-alacris.html on Ramblings of a Naturalist blog]

===Sub-species===

====Animal====
'''''Larus glaucoides kumlieni''' on [http://www.birdguides.com/html/vidlib/species/Larus_glaucoides_kumlieni.htm BirdGuides]

'''Kumlien's Gull''' on [http://www.birdsireland.com/pages/rare_bird_news/2005/january_photos.html Birds Ireland]

====Plant====
'''''Pisum sativum L. subsp. sativum''''' on [http://www.plantnames.unimelb.edu.au/Sorting/Pisum.html] (also has other examples; note lack of required italics)
<pre><nowiki>Pisum sativum L. subsp. sativum</nowiki></pre>

===Cultivars (plant)===
'''''Chamaecyparis lawsoniana 'Aureomarginata'''''' on [http://en.wikipedia.org/wiki/Cultivar Wikipedia: Cultivar]

<pre><nowiki><dd>Chamaecyparis lawsoniana 'Aureomarginata'</dd></nowiki></pre>

'''''Chamaecyparis lawsoniana'' 'Golden Wonder'''' on [http://www.plantago.nl/plantindex/c/Chamaecyparis/Chamaecyparis_4.htm plantago.nl]

====Cultivar groups (plant)====
'''''Brassica oleracea'' Botrytis Group''' on [http://en.wikipedia.org/wiki/Cultivar Wikipedia: Cultivar]

===Trade names (plant)===

'''''Rosa'' Peace''' on [http://en.wikipedia.org/wiki/Cultivar Wikipedia: Cultivar]
:("Peace" is a trade designation or "selling name" for the cultivar R. 'Madame A. Meilland' and should therefore be printed in a different typeface from the rest of the name, without any quote marks)

'''Sunflower 'Giant Single'''' on [http://cgi.www.johnsons-seeds.com/cgi-bin/www.johnsons-seeds.com/detail/azlist/S-1 Johnsons Seeds]

'''Sunflower 'Infrared' F1''' on [http://cgi.www.johnsons-seeds.com/cgi-bin/www.johnsons-seeds.com/detail/azlist/S-1 Johnsons Seeds]
:(Note "F1" cross designation)

===Variety (plant)===
'''''Pisum sativum var. macrocarpon''''' on [http://davesgarden.com/pf/go/8/index.html Dave's Garden]

====Sub-variety (plant)====

'''''Betula ermani var. genuina subvar. brevidentata''''' on [http://www.nccpg.com/gloucestershire/wilson1.html National Council for the Conservation of Plants and Gardens, Gloucestershire Group] (plus many other examples)

===Form (plant)===

'''''Acanthocalycium spiniflorum f. klimpelianum''''' on [http://en.wikipedia.org/wiki/Form_%28botany%29 Wikipedia: form (botany)]
*aka '''''Acanthocalycium spiniflorum forma klimpelianum'''''

===Sense (plant)===
'''''Ranunculus aquatilis s.l.''''' and '''''R. aquatilis s.s'''''; on [http://www.westmidlandbirdclub.com/blithfield/plants20060815.htm Blithfield Reservoir: Survey of Flowering Plants...] (see also footnotes on that page)

===Cross (plant)===
'''''Digitalis x mertonensis''''' on [http://www.hortax.org.uk/gardenplantsnames.html Hortax]
:The hybrid name for all plants derived from the cross between '''D. purpurea''' and '''D. grandiflora'''. The "x" indicates the hybrid status.

'''''× Fatshedera lizei''''' on [http://oregonstate.edu/dept/ldplants/sci-names.htm Scientific Plant Names, Oregon State Univ., Landscape Plants]

===Strain (bacteria)===
'''''Escherichia coli O157:H7''''' on [http://www.cfsan.fda.gov/~mow/chap15.html FDA.gov]

'''''E.Coli''''' on [http://news.bbc.co.uk/1/hi/england/southern_counties/5346842.stm BBC news]

==Misc==
===Superseded names===
'''''Tringa bartramia''''' superseded by '''''Bartramia longicauda''''' on [http://www.westmidlandbirdclub.com/firsts/UPLSA.htm West Midland Bird Club's Upland Sandpiper article]

===GUID===
'''NBN Taxon Key''' for European Otter, ''Lutra lutra'', on [http://nbn.nhm.ac.uk/nhm/bin/nbntaxa.dll/taxon_details?taxon_key=NBNSYS0000005133 NBN Species Dictionary]: '''NBNSYS0000005133'''

'''LSID ([http://lsid.sourceforge.net/#whatislsid Life Science Indicator])''' for ''Popillia japonica'' on [http://names.ubio.org/browser/details2.php?names=on&authors=on&sci=on&vern=on&conceptID=&expand=&namebankID=3377001 uBio]: '''urn:lsid:ubio.org:namebank:3377001'''

===Wikipedia===
'''Black-tailed Godwit''' on [http://en.wikipedia.org/wiki/Black-tailed_Godwit Wikipedia: Black-tailed Godwit]

Wikipedia uses several sets of markup, e.g. (in-line styles and links, plus some other markup, removed, for clarity):

<pre><nowiki>The Black-tailed Godwit, Limosa limosa</nowiki></pre>

====Linking====
Wikipedia uses the standard convention of having species italicised. Internal links to species may be to the common name or scientific name depending on which is used as the article's title (usually common for animals, scientific for plants, although there are exceptions). Links to scientific names work regardless:

<pre><nowiki>''[[Limosa limosa]]''</nowiki></pre>

Link to common name:

<pre><nowiki>[[Black-tailed Godwit]]</nowiki></pre>

Link to common name, but displaying scientific name:

<pre><nowiki>''[[Black-tailed Godwit|Limosa limosa]]''</nowiki></pre>

These types of links are not used in the Black-tailed Godwit article itself, but in others related to it. e.g. [http://en.wikipedia.org/wiki/British_avifauna British avifauna]

====Taxobox====

Wiki markup for the taxobox (taxonomy infobox) on the English Wikipedia, as used on the Black-tailed Godwit article, with irrelevant fields removed:

<pre><nowiki>
{{Taxobox
| name = Black-tailed Godwit
| regnum = [[Animal]]ia
| phylum = [[Chordate|Chordata]]
| classis = [[bird|Aves]]
| ordo = [[Charadriiformes]]
| familia = [[Scolopacidae]]
| genus = ''[[Godwit|Limosa]]''
| species = '''''L. limosa'''''
| binomial = ''Limosa limosa''
| binomial_authority = ([[Carolus Linnaeus|Linnaeus]], 1758)
}}
</nowiki></pre>

Above is vaguely displayed in an HTML table as (with formatting and links removed):

<pre><nowiki>
<tr>
<td>Kingdom:</td>
<td>Animalia</td>
</tr>
<tr>
<td>Phylum:</td>
<td>Chordata</td>
</tr>
<tr>
<td>Class:</td>
<td>Aves</td>
</tr>
<tr>
<td>Order:</td>
<td>Charadriiformes</td>
</tr>
<tr>
<td>Family:</td>
<td>Scolopacidae</td>
</tr>
<tr>
<td>Genus:</td>
<td>Limosa</td>
</tr>
<tr>
<td>Species:</td>
<td>L. limosa</td>
</tr>

<tr>
<th>binominal name</th>
</tr>
<tr>
<td>Limosa limosa
<td>(Linnaeus, 1758)</td>
</tr>
</nowiki></pre>

Also allows for other levels of taxonomy (e.g. genus or subspecies), and synonyms.

==Quantitative evidence==

For evidence of quantitative, rather than qualitative, use of species' and other taxonomic names, see [http://microformats.org/discuss/mail/microformats-discuss/2006-September/005790.html] and [http://microformats.org/discuss/mail/microformats-discuss/2006-September/005791.html]. Furthermore:

*Wikipedia:
** '''All''' species articles, e.g. [http://en.wikipedia.org/wiki/Little_Ringed_Plover Little Ringed Plover] (see [[species-examples#Wikipedia|above]])
** '''All''' genera articles, e.g. [http://en.wikipedia.org/wiki/Plover Charadrius (Plover)] (e.g [http://en.wikipedia.org/wiki/Category:Genera_of_birds '''200''' pages, for birds] alone)
** '''All''' higher classes, e.g. [http://en.wikipedia.org/wiki/Charadriidae Charadriidae]
** '''All''' regional lists, e.g. [http://en.wikipedia.org/wiki/List_of_British_birds:_non-passerines List of British birds]
** '''All''' dedicatees, e.g. [http://en.wikipedia.org/wiki/Alexander_Wilson Alexander Wilson]
** '''All''' authorities, e.g. [http://en.wikipedia.org/wiki/Giovanni_Antonio_Scopoli Giovanni Antonio Scopoli]
** '''All''' images of living things, e.g. [http://en.wikipedia.org/wiki/Image:Charadrius_dubius_4_%28Marek_Szczepanek%29.jpg Charadrius dubius 4 (Marek Szczepanek).jpg]
** Many reserves, lakes, and other places of interest, e.g. [http://en.wikipedia.org/wiki/Belvide Belvide]
** Many biological authors and illustrators, e.g. [http://en.wikipedia.org/wiki/John_Audubon John Audubon]; [http://en.wikipedia.org/wiki/Gilbert_White Gilbert White]
** Random articles on other topics, e.g. [http://en.wikipedia.org/wiki/Balancing_lake Balancing lake}]
** Wines. E/g/ [http://en.wikipedia.org/wiki/Cabernet_Sauvignon Cabernet Sauvignon]
** '''All the above, again''', for each alternative language e.g. [http://cy.wikipedia.org/wiki/Cwtiad_Torchog_Bach Welsh]; [http://fr.wikipedia.org/wiki/Petit_gravelot French]; [http://zh.wikipedia.org/wiki/%E9%87%91%E7%9C%B6%E9%B8%BB Chinese]

*Wikimedia Commons
** '''All''' species indexes, e.g. [http://commons.wikimedia.org/wiki/Charadrius_dubius Charadrius dubius]
** '''Each individual''' image, e.g. [http://commons.wikimedia.org/wiki/Image:Charadrius_dubius_1_%28Marek_Szczepanek%29.jpg Charadrius dubius 1 (Marek Szczepanek).jpg]
** '''Each family''' list [http://commons.wikimedia.org/wiki/Charadriidae Charadriidae]

*Wiktionary
** '''All''' species articles, e.g. [http://en.wiktionary.org/wiki/american_golden_plover American Golden Plover]
** '''All''' family articles, e.g. [http://en.wiktionary.org/wiki/plover Plover]
** '''Many of the above, in other langauges''' e.g. [http://en.wiktionary.org/wiki/aquila_reale Italian]; [http://en.wiktionary.org/wiki/%D0%B1%D0%B5%D1%80%D0%BA%D1%83%D1%82 Russian]

*Wikispecies
** '''Every''' speices, e.g. [http://species.wikimedia.org/wiki/Charadrius_dubius Charadrius dubius]
** '''Every''' genus, e.g. [http://species.wikimedia.org/wiki/Charadrius Charadrius]
** '''Every''' sub-family, e.g. [http://species.wikimedia.org/wiki/Charadriinae Charadriinae]
** '''Every''' family, e.g. [http://species.wikimedia.org/wiki/Charadriidae Charadriidae]
** and so on, for '''every other rank'''
** '''Every''' image (e.g. [http://species.wikimedia.org/wiki/Image:Charadrius_hiaticula_He.jpg Charadrius hiaticula He.jpg]

*Wikibooks
** [http://en.wikibooks.org/wiki/Dichotomous_Key Dichotomous Key]

*Google
**[http://www.google.co.uk/search?hl=en&hs=dBU&client=firefox-a&rls=org.mozilla:en-US:official&sa=X&oi=spell&resnum=0&ct=result&cd=1&q=%22E+coli%22&spell=1 Google finds about '''37,600,000''' for "E coli"].
***[http://www.google.co.uk/search?hs=Apo&hl=en&client=firefox-a&rls=org.mozilla%3Aen-US%3Aofficial&q=%22Escherichia+coli%22&btnG=Search&meta= Google finds about '''19,500,000''' for "Escherichia coli"]
***[http://www.google.co.uk/search?hs=zqo&hl=en&client=firefox-a&rls=org.mozilla%3Aen-US%3Aofficial&q=%22Ecoli%22&btnG=Search&meta= Google finds about '''722,000''' for "Ecoli"].
**[http://www.google.co.uk/search?hs=vWC&hl=en&client=firefox-a&rls=org.mozilla%3Aen-US%3Aofficial&q=%22Homo+sapiens%22&btnG=Search&meta= Google finds about '''14,200,000''' for "Homo sapiens"]
***[http://www.google.co.uk/search?hs=vWC&hl=en&client=firefox-a&rls=org.mozilla%3Aen-US%3Aofficial&q=%22Homo+sapien%22+-sapiens&btnG=Search&meta= Google finds about '''273,000''' for the mis-spelling "Homo sapien" -sapiens.]
**[http://www.google.co.uk/search?q=%22%22Homo+erectus%22%22&start=0&ie=utf-8&oe=utf-8&client=firefox-a&rls=org.mozilla:en-US:official Google finds about '''1,260,000''' for ""Homo erectus"]
**[http://www.google.com/search?svnum=10&as_scoring=r&hl=en&edition=us&as_drrb=q&as_qdr=&as_mind=1&as_minm=9&as_maxd=1&as_maxm=10&q=%22Clostridium+difficile%22&ie=UTF-8&sa=N&tab=nw Google finds about '''1,380,000''' for "Clostridium difficile"].
**[http://www.google.com/search?hl=en&lr=&edition=us&q=%22Passer+domesticus%22&btnG=Search Google finds about '''841,000''' for "Passer domesticus"].
***[http://images.google.com/images?hl=en&lr=&edition=us&q=%22Passer%20domesticus%22&btnG=Search&sa=N&tab=wi Google images finds about '''3,140''' for "Passer domesticus"].
**[http://www.google.co.uk/search?hl=en&hs=oEU&client=firefox-a&rls=org.mozilla:en-US:official&sa=X&oi=spell&resnum=0&ct=result&cd=1&q=%22Acer+palmatum%22&spell=1 Google finds about '''602,000''' for "Acer palmatum"]
** At the time of writing, '''every single one''' of the first 20 [http://www.google.com/search?q=%22Noctule+bat%22 Google results for "Noctule Bat"] also includes the scientific name ''Nyctalus noctula''.

*[http://www.arkive.org/ ARKive] - '''2000''' species ("It is ARKive's current aim to compile audio-visual records, where such media exists, for the 15,000-plus species currently threatened with extinction, according to the World Conservation Union's (IUCN) Red List of Threatened Species.")

*[http://www.rhs.org.uk/rhsplantfinder/plantfinder.asp Royal Horticultural Society - RHS Plant Finder] - '''70,000''' plants

*[http://www.bacterio.net List of Prokaryotic Names (formerly List of Bacterial Names)] - 2,032 *files*; '''10,268''' published names (to 2006-09-07)

*[http://nbn.nhm.ac.uk/nhm/ UK National Biodiversity Network's Species Dictionary]

*[http://www.searchnbn.net/ UK National Biodiversity Network Gateway] - '''20 million+''' species records

*[http://www.sp2000.org/ Species 2000] - '''450,000 species'''

*[http://www.bioimages.org.uk/index.html BioImages - Virtual Fieldguide] - '''53,000''' images depicting 4,600 species (see [[species-brainstorming#Malcolm_Storey|Wiki comments from site owner]])

*[http://animaldiversity.ummz.umich.edu/ Animal Diversity Web] - "'''Thousands''' of species accounts ['''plus'''] descriptions of levels of organization above the species level, especially phyla, classes, and in some cases, orders and families. Hundreds of hyperlinked pages and images illustrate the traits and general biology of these groups"

* [http://www.ubio.org/index.php?pagename=home uBio]
**NameBank is a repository of '''millions''' of recorded biological names and facts that link those names together.
**ClassificationBank stores multiple classifications and taxonomic concepts that are the result of expert opinions. It extends the functionality of NameBank.
**Over '''500,000''' common names are catalogued.

*[http://www.birdlife.org/datazone/species/ BirdLife International] - all birds of the world (~'''10,000''')

*[http://bugguide.net/ Bug Guide] - all insects, spiders, and allies, of the USA and Canada (most with more than one page).
** e.g. [http://bugguide.net/node/view/70875 Arge pectoralis - Birch Sawfly]

*[http://www.bto.org/birdtrack/ BirdTrack]
**[http://blx1.bto.org/bt-dailyresults/results/s171-20-06.html Lapwing]

*[http://www.discoverlife.org/ Discover Life] - "contains '''306,553''' species. The Polistes Foundation and its scientific partners plan to add high-quality identification guides, maps, images, and text for '''a million species''' by 2012. [...] Each month Discover Life serves approximately 3 million pages and images to 70,000 IP addresses"

*[http://www.record-lrc.co.uk/ rECOrd] (the Local Biological Records Centre serving the Cheshire region of England) - '''1.6 million''' species records available online for the public to search and map

*[http://www.dnabarcoding.ca/ Canadian Centre for DNA Barcoding ] multiple sites, covering over '''11,000''' species ('''134,990''' records; target 55,000+ species.
**[http://www.barcodinglife.org/ Barcode of Life Data Systems] "BOLD-ECS provides web developers and bioinformaticians the ability to build tools and workflows that can be integrated with the BOLD framework. We welcome the addition of new analytical modules."

* [http://hbs.bishopmuseum.org/fiji/checklists.html Fiji Arthropod Survey] - (insects, arachnids, crustaceans, and others) > '''7,000''' Families, Genera and Species

*[http://simile.mit.edu/timeline/examples/dinosaurs/dinosaurs2.html Simile Dinosaur Timeline] '''all''' dinosaurs genus - potential hCalendar mash-up.

*PhotoPic
**[http://community.fotopic.net/search/simple.php?txt=bird&action.x=0&action.y=0&action=Go galleries for "bird"] = '''929'''
*** e.g. [http://parentphoto.fotopic.net/c1119884.html Ryan Parent's pictures]
**[http://community.fotopic.net/search/simple.php?txt=insect&action.x=0&action.y=0&action=Go galleries for "insect"] = '''194'''
***e.g. [http://foto-fountain.fotopic.net/ Foto Fountain]
**[http://community.fotopic.net/search/simple.php?txt=wildlife&action.x=0&action.y=0&action=Go galleries for "wildlife"] = '''458'''
***e.g. [http://johnmartin.photos.gb.com/c1113758.html Martin's Photo Images]
**etc.

===Planned sites===
*[http://herbariaunited.org/atHome/ Herbaria United] (part of The website of the Botanical Collection Managers Group (BCMG), a specialist group of the Linnean Society of London) - "The UK has the world's largest and oldest collections of herbarium specimens held in trust by museums and universities. A new project is just getting underway to put all this online."

==Notable websites==
These high-profile websites use species names

*Amazon
**[http://www.amazon.co.uk/s/?url=search-alias%3Daps&field-keywords=%22house+sparrow%22 search for "House Sparrow"]

*BBC News
**[http://news.bbc.co.uk/1/hi/uk/4835208.stm Fewer birds spotted in UK gardens]
**[http://news.bbc.co.uk/1/hi/england/london/4743250.stm Study to solve sparrow's decline riddle]

*Encyclopaedia Britannica - all species, e.g.
**[http://concise.britannica.com/ebc/article-9379473/starling Starling]

*Flickr
**[http://www.flickr.com/photos/tags/citheronia/ Tag for moth genera 'citheronia']
***[http://www.flickr.com/photos/30268343@N00/152101772/ Sample result from that search]
**[http://www.flickr.com/groups/birdguide/ Field Guide: Birds of the World] 23,073 tagged photos, as at 2006-10-21

*CNN
**[http://archives.cnn.com/2001/NATURE/01/24/dying.eagles/ Disease threatens bald eagle population]

*eBay
**[http://search.ebay.com/house-sparrow search for "House Sparrow"]

*The Guardian
**[http://environment.guardian.co.uk/conservation/story/0,,1878956,00.html The call of the wildlife]
**[http://education.guardian.co.uk/higher/news/story/0,,1665396,00.html Sparrow joins 'raped' duck in Dutch museum] (note improper capitalisation "''passer domesticus''")

*The Internet Movie Database
**[http://www.imdb.com/title/tt0029443/ Private Life of the Gannets]
***[http://www.imdb.com/title/tt0029443/trivia Private Life of the Gannets trivia page with binominal]
**[http://www.imdb.com/title/tt0133318/ The Trials of Life]
**[http://www.imdb.com/title/tt0227812/ Whooping Crane]
***[http://www.imdb.com/title/tt0227812/trivia Whooping Crane trivia page with binominal]
**[http://www.imdb.com/title/tt0301727/ Winged Migration]

*London Zoo
**[http://www.zsl.org/london-zoo/animals/birds/tawny-frogmouth,99,AN.html Tawny frogmouth]

*Microsoft
**[http://www.microsoft.com/games/zootycoon/zoo2/zoo2_ymi_animals1.asp Zoo Tycoon]

*MSN-Encarta - all species, e.g.
**[http://encarta.msn.com/encnet/refpages/search.aspx?q=vulgaris&Submit2=Go Search for "vulgaris"]

*MySpace
**[http://blog.myspace.com/index.cfm?fuseaction=blog.view&friendID=47134278&blogID=79591637]

*Nature
**[http://www.nature.com/nature/focus/avianflu/index.html Avian flu web focus]

*Nature Network, Boston
**[http://network.nature.com/boston/news/archive/2006/06/13/the-student-and-the-squid The student and the squid] '''N.B.''' site already supports rel-tag, hCard for user profiles and hCalendar for marking up events across the site.

*NASA
**[http://history.nasa.gov/SP-401/ch3.htm SP-401 Skylab, Classroom in Space. Part II - Student Experiments] ("The common Cross spider (Araneus diadematus)")

*New York Times
**[http://query.nytimes.com/gst/fullpage.html?sec=travel&res=9D04E4DE1131F93BA25751C0A9669C8B63 Where the Eagles Fly: Seeing the National Symbol]

*Snopes (Urban Legends Reference Pages)
**[http://www.snopes.com/photos/animals/fishfly.asp Fish Fly]

*United Kingdom Government
**[http://www.defra.gov.uk/wildlife-countryside/vertebrates/gen-licence.htm DEFRA: General licences under the Wildlife & Countryside Act 1981]

*United States of America Government
**ITIS, e.g. [http://www.itis.usda.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=179628 Passer Domesticus] - "authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world"

*W3C
**[http://dev.w3.org/cvsweb/2000/10/swap/test/ferrell/biology.n3?rev=1.4 An Ontology of Biology]
**[http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/Reagents/Status_Reports/2006-05-04 BioRDF Sub-group Status Report, 4 May 2006]

*Yahoo Groups
**[http://tech.groups.yahoo.com/group/passerdomesticus/ passerdomesticus] species as group name!

*YouTube
**[http://www.youtube.com/results?search_query=starling&search=Search YouTube search for 'starling']]

==Breaking news==
In under two weeks, the BBC News website carried the following stories, all including the scientific names of species:
*[http://news.bbc.co.uk/1/shared/spl/hi/pop_ups/06/sci_nat_orchid_spectacular/html/1.stm BBC News: Stunning new orchids from Asia's rainforest] - 2006-10-16
*[http://news.bbc.co.uk/1/hi/sci/tech/6045802.stm BBC News: Winter home find cheers twitchers] (winter home of the northern bald ibis found) - 2006-10-13
*[http://news.bbc.co.uk/1/hi/sci/tech/6043648.stm BBC News: New mouse find is 'living fossil'] - 2006-10-12
*[http://news.bbc.co.uk/1/hi/sci/tech/6035113.stm BBC News: Giant camel fossil found in Syria] - 2006-10-10
*[http://news.bbc.co.uk/1/hi/sci/tech/5414410.stm BBC News: Sharks swim into political waters] - 2006-10-06
*[http://news.bbc.co.uk/1/hi/sci/tech/5403570.stm BBC News: 'Monster' fossil find in Arctic] - 2006-10-05

==Use in blogs==
*[http://technorati.com/search/%22passer%20domesticus%22 Technorati search for "Passer domesticus"] (367 found, as at 2006-09-25)
*[http://technorati.com/search/%22acer%20palmatum%22 Technorati search for "Acer palmatum"] (682 found, as at 2006-09-25)
*[http://technorati.com/search/%22Homo%20sapiens%22 Technorati search for "Homo sapiens"] (40,932 found, as at 2006-09-25)
*[http://technorati.com/search/birding Technorati search for "birding"] (26,472 found, as at 2006-09-25)
*[http://ramblingsofanaturalist.blogspot.com/ Ramblings of a Naturalist]
*[http://squaremetre1.blogspot.com/ The Square Metre]
*[http://windowboxwildlife.blogspot.com/index.html Windowbox Wildlife]
*[http://www.rxwildlife.org.uk/ RXWildlife]
*[http://newsbou.blogspot.com/ British Ornithologists' Union news]
*[http://fieldmarking.reger.com/ FieldMarking] - An experiment to see how people can collaborate to record wildlife observations in blogs.

==And finally...==
Gary Larson, in his book ''The Far Side Gallery'' (Warner Books, 1980, ISBN 0751502367) has a cartoon, showing two entomologists sitting down to eat dinner in a jungle. One says to the other "Hey! What's this ''Drosophila melanogaster'' doing in my soup?"

==Contributors==
*[[User:AndyMabbett|Andy Mabbett]] (proponent)
*Malcolm Storey (per e-mail)
*[[User:SXBRC|Charles Roper]], [http://www.sxbrc.org.uk/ Sussex Biodiversity Record Centre] (proponent)
*[[User:SteveMcBill|Steve McWilliam]], [http://www.rECOrd-LRC.co.uk/ rECOrd - The Biodiversity Information System for the Cheshire region] (proponent)
*[[User:PeNGo|Peter Halasz]], Wikipedia Admin.

==See also==
{{species}}

User:PeNGo

2007-01-29T03:52:02Z

PeNGo:

I am User:Pengo from English Wikipedia. Leave me a [http://en.wikipedia.org/wiki/User_talk:Pengo message] there.

species-brainstorming

2007-01-29T03:49:04Z

PeNGo: my own comments

=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'''

==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:

:<pre><nowiki><abbr class="species" title="Anas platyrhynchos">Mallard</abbr></nowiki></pre>
or
:<pre><nowiki>Anas platyrhynchos</nowiki></pre>

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:

[Note: in taxonomy, levels such as "subphylum", "class" or "order" are known as a "rank"].

[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]].]

*species (scientific name; aka botanical name) (better: '''taxon'''; or '''biota''')
**domain (alternatively: "superregnum")
**kingdom (alt: "regnum")
**subkingdom (alt: "subregnum")
**superphylum
**phylum
**subphylum
**taxoclass (alt: "taxo-class ", "taxonclass", "taxon-class", "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")
**rank (alt: "taxorank", "taxon-rank", et al) - "unranked". See [http://names.ubio.org/browser/classifications.php?conceptID=2463046]; might also be used where the level of a rank is disputed, or the author simply has no ability or wish to declare the rank more explicitly.
**binominal ("binominal name" alt: "binomial")
***genus
***specific (="''specific epithet''")
**subsp ("subspecies")
**variety
**subvar ("subvariety")
**form
**subform
**cultivar
**cultgp ("cultivar group")
**cross (e.g. "F1")
**strain
**? morph (or phase) (e.g "Gyrfalcons, for example, have a grey morph and a white morph" [http://www.peregrine-foundation.ca/info/dictionary.html]; "the Lesser Snow Goose (C. c. caerulescens), commonly occurs in two plumage variants. White-phase birds are white except for black wing tips, but blue-phase geese have bluish-grey plumage replacing most of the white except on the head, neck and tail tip." [http://en.wikipedia.org/wiki/Snow_goose])
**trade ("trade name")
**breed (e.g. Bull Terrier)
**sense (botanical - see [[species-examples#Sense (plant)|examples]])
**authority
***year (...of authority)
**cname ("common name" - should this be "common" or "vernacular"?)
**guid
**vgroup ("vernacular group" (alt: "vernacular-group") - there is possibly a better term for this. Often, a genus or family doesn't encapsulate a particular group of species in a practical or useful fashion. For example, it is difficult to seperate fungi species and lichen species as they are taxonomically intermingled. Thus, within taxonomic databases, a vernacular group of "fungi" and "lichen" is often applied to species falling into either of these groups. A vernacular group could be considered similar to a common name, but for groups of species. See the [http://www.searchnbn.net/directory/browseTGLevel1.jsp NBN Gateway] for an example of vernacular groups in use; these group names are also used in the [http://www.recordersoftware.org/ Recorder] biological recording software.
**? 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'''ale or '''f'''emale; or including '''n'''ueter, '''h'''ermaphoradite, '''u'''nspecified and/ or '''m'''ixed?)- 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]]
** [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?]

where are optional, and it is possible to infer from simply:
:<pre><nowiki><abbr class="binominal" title="Anas platyrhynchos">Mallard</abbr></nowiki></pre>
or
:<pre><nowiki>Anas platyrhynchos</nowiki></pre>
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):

<pre><nowiki>

Motacilla citreola

</nowiki></pre>

Sub-species (animal):
<pre><nowiki>

Larus glaucoides
kumlieni

</nowiki></pre>

Variety (plant):
<pre><nowiki>

Pisum sativum
var. macrocarpon

</nowiki></pre>

Species (animal, common name displayed):
<pre><nowiki>

<abbr class="binominal" title="Larus thayeri">
Thayer's Gull
</abbr>

</nowiki></pre>

Species (animal, scientific name displayed):
<pre><nowiki>

<abbr class="common" title="Thayer's Gull">

</abbr>

</nowiki></pre>

Fungus, kingdom included:
<pre><nowiki>

<abbr class="kingdom" title="Fungi">
Amanita muscaria
</abbr>

</nowiki></pre>

Same name for different Genera:

<pre><nowiki>

An unidentified
<abbr class="taxoclass" title="Aves">
<abbr class="genus" title="Oenanthe">

Wheatear

</abbr>
</abbr>

</nowiki></pre>

and :

<pre><nowiki>

An unidentified
<abbr class="taxoclass" title="Magnoliopsida">
<abbr class="genus" title="Oenanthe">

Water Dropwort

</abbr>
</abbr>
sp.
</nowiki></pre>

Species (animal, with authority and year):
<pre><nowiki>

Pica pica
Linnaeus,
(1758)

</nowiki></pre>

Re-classified species (animal):
<pre><nowiki>
The species was classified as

<abbr class="binominal" title="Bartramia longicauda">Tringa longicauda</abbr>
by Johann Bechstein in 1812.

</nowiki></pre>

A more extreme example, where there is a need to describe the full taxonomic hierarchy:

<pre><nowiki>

Eukarya
Animalia
Eumetazoa
Deuterostomia
Chordata
Vertebrata
Aves
Neognathae
Passeriformes
Passeri
Passerida
Passeroidea
Motacillidae

Motacilla
alba
yarrellii

Pied Wagtail
Linnaeus
1758

</nowiki></pre>

=====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].

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).
<pre><nowiki>

Lutra lutra

</nowiki>
</pre>
Alternatively, the GUID could be expressed as an element in its own right, with the GUID type being expressed as a secondary class name:
<pre><nowiki>

Lutra lutra
NBNSYS0000005133

</nowiki>
</pre>
As a further alternative, the [[abbr-design-pattern]] could potentially be used, although this is semantically questionable:
<pre><nowiki>

<abbr class="binominal" title="NBNSYS0000005133">Lutra lutra</abbr>

</nowiki>
</pre>
Yet another alternative, using a [http://www.ubio.org/index.php?pagename=home uBio] LSID as the GUID:
<pre><nowiki>

Green Sandpiper
Tringa ochropus

</nowiki>
</pre>
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====

* 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 [http://en.wiktionary.org/wiki/taxon]. 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, [http://en.wiktionary.org/wiki/taxon]. - 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 [http://tdwg.napier.ac.uk/index.php?pagename=VotingDraftIntroduction TCS] - Charles Roper
** or '''Biota''' - Andy Mabbett
*'''Species''' is used in the above, for the sake of having one name to use, but "biota" or "taxon" are likely to be used in the final version. [[User:AndyMabbett|AndyMabbett]] 09:15, 22 Oct 2006 (PDT)

* Should "bin", var", "cult", etc., be written in full? (I think not, to save bloating file sizes)
** Yes - Scott Reynen
***'''Conceded''', and applied to the above. What about "subsp", etc? [[User:AndyMabbett|AndyMabbett]] 09:15, 22 Oct 2006 (PDT)

* Should other attribute names be abbreviated for brevity?
** No, brevity is not one of the [[naming-principles|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
*****[http://www.westmidlandbirdclub.com/records/lists.htm 341 species, 58Kb]. 'Nuff said? [[User:AndyMabbett|AndyMabbett]] 11:53, 26 Sep 2006 (PDT)
******Your bird list page can be [http://snipurl.com/zfmj compressed by 79%], i.e. it would go down from 58KB to 12KB by enabling output compression on your server. It would also make the page load faster and save you bandwidth. No doubt compression technologies will improve over time, as will connection speeds and server speeds, so the technical solution to reducing page size would seem to me to be preferable over the "manual compression" method, i.e. using abbreviated, less clear, less readable class names. While it is easy to improve the compression technology (or switch it on, even), it's much harder to change an established microformat standard. - [[User:CharlesRoper| 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
***'''Conceded''', and "taxoclass" applied to the above. "classis" would be an alternative. [[User:AndyMabbett|AndyMabbett]] 09:15, 22 Oct 2006 (PDT)

* 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?:
:<pre><nowiki>Podiceps</nowiki></pre>
** 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? - [[User:AndyMabbett|AndyMabbett]]
**** This kind of aggregates are often used by birdwatchers (in Finland). How about separating the names with a slash (or some other sign)?: - [[User:MikkoBiomi|MikkoBiomi]]
:<pre><nowiki>Phylloscopus trochilus/Phylloscopus collybita</nowiki></pre>
:<pre><nowiki>Anser/Branta</nowiki></pre>

* Should we allow divisions of "binominal" with no parent "species", such as:
:<pre><nowiki>Larus glaucoides kumlieni</nowiki></pre>

* 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?

* Is "bin" (short for binominal) the most appropriate term for a taxon name? When subspecies, var, subvar, etc. are nested, then surely it becomes [http://en.wikipedia.org/wiki/Trinomial_nomenclature 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 [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)

====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 [http://www.westmidlandbirdclub.com/ladywalk/latest.htm West Midland Bird Club's Latest news from Ladywalk] and [http://www.birdforum.net/showthread.php?t=48505 In and around South Staffordshire 2006 (blog)] for simple examples.

==Bill Hull==
[http://www.mangoverde.com/ 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===

[http://www.tdwg.org/index.html 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 [http://tdwg2006.tdwg.org/ 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 ([[User:RogerHyam|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

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

* "Hopefully I'll have more time for things like this in the New Year, but expect it all be done and dusted by then!!" - Malcolm Storey, [http://www.bioimages.org.uk/ BioImages]

===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 [http://www.bgbm.org/iapt/nomenclature/code/SaintLouis/0007Ch1Art003.htm], [http://www.bgbm.org/iapt/nomenclature/code/SaintLouis/0008Ch1Art004.htm]

AIUI ICBN only goes down to species.

ICZN isn't so easy: [http://www.nhm.ac.uk/hosted_sites/iczn/]

: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)

Myxomycetes are the exception - they're in kingdom protozoa which falls under ICZN but they fall under the ICBN name space. (Hence "Trichia").

===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.

===Typography===
what about ''Adalia 2-punctata'', and ''Adalia bipunctata'' (not to mention those with hyphens [or apostrophes] which may get left out. And what about accented characters)?

:''Adalia 2-punctata'' is an abbreviation of ''Adalia bipunctata'', so:

:<pre><nowiki><abbr class="binominal" title="Adalia bipunctata">Adalia 2-punctata</abbr></nowiki></pre>
[[User:AndyMabbett|AndyMabbett]] 09:55, 21 Oct 2006 (PDT)

===Gaps===
The hierarchy is not always fully populated. Not every species belongs to a class. Maybe this was where fungi are different. In Paul Kirk's databases (which are the official ones used to drive the checklists and NBN) he has fixed fields for the higher level taxa which means that only certain ranks can be used. The blanks he fills in (mostly!!) with "insertae sedis" (think it's Latin for "unknown seat"). In my database I use a self-join which gives much more flexibility. Anyway there are lots of "insertae sedis" in Paul's database!

===Homonyms===
''Apion carduorum'' sensu Morris 1990 is ''Apion gibbirostre'' (Gyllenhal, 1813). ''Apion carduorum'' Kirby, 1808 is a different species.

:You'd mark the former up as something like
:<pre><nowiki><abbr class="binominal" title="Apion gibbirostre">''Apion carduorum'' sensu Morris 1990</abbr></nowiki></pre>

:[[User:AndyMabbett|AndyMabbett]] 12:21, 5 Oct 2006 (PDT)

===Citations for authorites===
If people are citing the authority in full they would include the literature reference, not just the date e.g.
:''Cuphophyllus niveus'' (Scop.) Bon, ''Doc. Mycol.'' 14(56): 11 (1985)[1984]

==Hyppo==
===Nomenclatural challenge===
You asked for comments. One challenge I see is the difference in Nomenclature for Animalia and Plantae (coming from the old 2 kingdom system). For Plantae the International Code of Botanical Nomenclature[http://www.bgbm.org/iapt/nomenclature/code/SaintLouis/0000St.Luistitle.htm] is used and for Animalia the code from [http://www.iczn.org/ http://www.iczn.org/]. Animalia code is not officially accepted but ICZN tries to be authoritive starting from 2008.

The two different nomenclatural systems differ in a few areas, and they affect markup.

*Subgenus (Plantae): ''Dendroceros'' subg. ''Apoceros''
*Subgenus (Animalia): ''Sula (Morus)''

*Subspecies (Plantae): ''Begonia grandis'' ssp. ''evansiana''
*Subspecies (Animalia): ''Gorilla beringei graueri''
:--[[User:Hyppo|Hyppo]] 14:23, 9 Oct 2006 (PDT)

:I would mark those up as:

:<pre><nowiki>Dendroceros subg. Apoceros</nowiki></pre>

:<pre><nowiki>Sula Morus</nowiki></pre>

:<pre><nowiki>Begonia grandis ssp. evansiana''</nowiki></pre>

:<pre><nowiki>Gorilla beringei graueri</nowiki></pre>

:With wrapping class="biota" and possibly kingdom, attributes.

:[[User:AndyMabbett|AndyMabbett]] 11:37, 10 Oct 2006 (PDT)

==Cyndy Parr==

The ideas expressed here are promising. Below are my comments on all the preceding -- as I have time I'll organize, elaborate, and try to move parts into the right discussion threads above.

In the [http://spire.umbc.edu Spire project] we have been developing ontologies in OWL for taxonomic names and hierarchies. Ideally, we'd like to have a microformat where people can tag a scientific name and an application can then check an ontology of their choice for more information (richer semantics).

We would discourage full expression of the Linnaean hierarchy except for those who are maintaining such classifications (such as uBio). The rest of the hierarchy can be retrieved ontologically as necessary.

Better to tie the scientific name (taxon name) to the authority or ontology from which it came. I.e. for those who are able to provide information on taxonomic concepts, support for TCS (Taxonomic Concept Schema) fields would be important.

I prefer "taxon" or "taxon-name" or TaxonName over biota (which is plural, and too close to biotic which has a far larger scope than taxa). Would prefer "binomial" to "binominal"
*I also favour "taxon" over "biota" simply because it the more commonly used term. I also prefer "binomial". I did a quick straw poll of various experts and all favoured binomial. Neither is technically incorrect, but binomial is more commonly used. Indeed, a Google search for binomial returns 6,580,000 results while binominal returns 342,000 and a "did you mean: binomial" prompt. --[[User:CharlesRoper|Charles Roper]] 04:12, 9 Jan 2007 (PST)
**This [http://www.googlebattle.com/index.php?domain=%22binomial+name%22+-equation&domain2=%22binominal+name%22+-equation&submit=Go%21 binomial vs. binominal Google battle] seems even more conclusive. [[User:AndyMabbett|Andy Mabbett]] 06:17, 9 Jan 2007 (PST)
"class" is difficult not only because of the confusion with the programming concept of classes, but because it is a taxonomic rank. However, most of us have figured out the difference by now so this is not critical.

"cname" should be "comname" or "common-name" or "vernacular" to make it more obvious what the information is. A sub-component would be the language for which that common name is used ( something like an HTML attribute lang="en")
*I also favour "common-name" or "vernacular" --[[User:CharlesRoper|Charles Roper]] 04:12, 9 Jan 2007 (PST)

There are known conflicts between names across kingdoms (as current codes of nomenclature allow these). Thus specification of kingdom may be encouraged. Disambiguation could be handled by applications outside the microformats (this could be difficult), or they could be dealt with in the core microformat: e.g. plant-taxon or fungal-taxon or animal-taxon.

A sightings microformat is a good idea and I would be interested in being involved in that. We've been toying with this in OWL and also using structured blogging over at http://fieldmarking.reger.com

Your terms such as gender (better: sex), age bracket (better: life stage), count, type (better: depending on the meaning, caste or morph) all belong in a specimen or sighting microformat and used in combination with the taxon microformat, not be part of it.

===Response by Andy Mabbett===
Thank you very much for your detailed contribution. I have a few responses:

*We would discourage full expression of the Linnaean hierarchy except for those who are maintaining such classifications (such as uBio).
** Why? Also, I'm not aware of any microformat which is restricted to a subset of users, nor how this would be done. How would you suggest that someone mark up this: "Not all of the Passeriformes sing"?
*** I would prefer express this something like so:
<pre><nowiki>

Passeriformes

</nowiki></pre>
Or, to simplify further:
<pre><nowiki>
Passeriformes
</nowiki></pre>
Or, at the simplest level:
<pre><nowiki>
Passeriformes
</nowiki></pre>
Simply marking up the word as a taxon would lighten the load of any parser, making its job much simpler. --[[User:CharlesRoper|Charles Roper]] 10:50, 8 Jan 2007 (PST)
***Your first example requires the author of that page to find LSID, even assuming that they know such a thing exists. How is that "paving the cowpaths"? Your latter example removes semantic detail which is included in the straw-man proposal. It is akin to removing all the children of "adr" in hCard. I think your parser-load issue is a red herring. [[User:AndyMabbett|Andy Mabbett]] 11:07, 8 Jan 2007 (PST)
**** I would argue that finding and using an LSID would not be a difficult task for any author who is using a microformat. I don't see how it is any more difficult - in fact I see it as being easier - than manually marking up ranks. Why is parser-load a red herring? --[[User:CharlesRoper|Charles Roper]] 12:26, 8 Jan 2007 (PST)
***Nice example (having done my doctoral work on a Passerine that may or may not be singing...). Absolutely I'd recommending marking up "Passeriformes" but no need to go on to specify "Aves." I'm still grokking microformats so I don't think we've got a conflict. [[User:CyndyParr|CyndyParr]] 10:20, 10 Jan 2007 (PST)
****''Aves'' is available for use, but not required, so indeed, we don't have conflict ;-) [[User:AndyMabbett|Andy Mabbett]] 10:42, 10 Jan 2007 (PST)
*The rest of the hierarchy can be retrieved ontologically as necessary.
**That's a use-case once the uF is published, certainly. the proposal doesn't require that the hierarchy be marked-up, it merely allows for it, in cases where it is '''already published'''.
***I've yet to see any consistent examples of a hierarchy being marked-up using class names resembling those found in the proposal. A microformat is supposed take (and perhaps tweak, or clean up) mark-up practises that are '''already in use''', not invent new ones. In other words, microformats should pave the cowpaths. While allowing for the marking-up of the hierarchy is fair enough (I understand the reasons for wanting that option), I believe the vast majority of authors do not need that facility, or (from my own experience) do not have time or energy to make use of anything more complex than simply marking-up a piece of text as a taxonomic name. In its current state, I don't believe the current species microformat proposal fulfils any of the "philosophy of microformats" points raised in [http://ifindkarma.typepad.com/relax/2004/12/microformats.html this article]. I believe the added complexity acts as a disincentive potential users and is also clearly confusing. With taxonomic intelligence (hierarchies, synonymy, etc) being available from elsewhere (e.g. uBio), why have it embedded in the microformat? What examples of this kind of usage are there and what leads you to believe authors '''will''' use it, if it's available? [[rel-license]] is an example of a microformat that is simple and holds intelligence elsewhere. I believe simplicity is the key to a successful species microformat. --[[User:CharlesRoper|Charles Roper]] 10:50, 8 Jan 2007 (PST)
****''I've yet to see any consistent examples of a hierarchy being marked-up using class names resembling those found in the proposal.'' Perhaps not but, unlike other uFs, in taxonomy there exist clearly defined standards for the names of the components of taxonomic names. This is akin to the pre-existing class names from vCard, as used in hCard.
*****Not so: vCard is widely used standard already and thus it was a natural progression to develop hCard. There is no software based vCard equivalent of the taxonomic hierarchy in common use that I am aware of.
****''A microformat is supposed take (and perhaps tweak, or clean up) mark-up practises that are '''already in use''''' Taxonomic classes ''''are '''' already in use.[[User:AndyMabbett|Andy Mabbett]]
*****My concern still stands that there is no consistent mark-up usage that I can find.
***Fair enough [[User:CyndyParr|CyndyParr]] 10:20, 10 Jan 2007 (PST)
****''I believe the vast majority of authors [...] do not have time or energy to make use of anything more complex than simply marking-up a piece of text as a taxonomic name''' and - as has been pointed out previously, they will be able to do the latter, and nobody will force them to do the former. Why should they not, though, be able to do the latter should they wish?
*****As I say, I find the concept of allowing the full suite of ranks to be fair - I understand your desire to have them in there. I just feel that the complexity they add to the specification will put off authors and confuse them. I also maintain that very few authors will make use of this extra complexity. Should we have some sort of poll to try and determine how many people would be able to make use of the full proposal? I'm not totally against having all of the ranks in the Species microformat, I've just yet to be convinced they are necessary or conducive to adoption of the standard. --[[User:CharlesRoper|Charles Roper]] 12:26, 8 Jan 2007 (PST)
****''What examples of this kind of usage are there'' Those on [[species-examples]], e.g. Wikipedia.
*****I've yet to find any consistent mark-up usage.--[[User:CharlesRoper|Charles Roper]] 12:26, 8 Jan 2007 (PST)
****''[[rel-license]] is an example of a microformat that is simple and holds intelligence elsewhere'''' It holds no intelligence elsewhere, which was not already on the pre-microformatting page.[[User:AndyMabbett|Andy Mabbett]] 11:07, 8 Jan 2007 (PST)
*****The license on the end of the rel-license link is the intelligence. To look at it from a different angle, why not embed the license information within class attributes? Why not have a full license microformat, just in case some author needs it? Rel-license as it stands serves the needs of most authors most of the time, which is a fundamental philosophy of microformats.
*Better to tie the scientific name (taxon name) to the authority or ontology from which it came.
**That would require the publisher to add extra data, which they might not wish to publish, nor, indeed, have to hand. Microformats are about recognising what data is '''already''' published and then enabling people to add semantics which identify the type of data on their pages.
***I'm just suggesting support for such authority or ontology for those of us who think it important [[User:CyndyParr|CyndyParr]] 10:20, 10 Jan 2007 (PST)
****Again, the option to do so is in the current proposal. [[User:AndyMabbett|Andy Mabbett]] 10:42, 10 Jan 2007 (PST)
*[common names] A sub-component would be the language for which that common name is used (something like an HTML attribute lang="en")
**Indeed, but that's already available, and (on properly constructed pages) should already be on the parent container. [[User:AndyMabbett|Andy Mabbett]]
***Fair enough [[User:CyndyParr|CyndyParr]] 10:20, 10 Jan 2007 (PST)
*conflicts between names across kingdoms (as current codes of nomenclature allow these). Thus specification of kingdom may be encouraged.
**already in the proposal! [[User:AndyMabbett|Andy Mabbett]]
***but perhaps the proposal could be more explicit about the importance of kingdom given its important role in disambiguating species names (using a name of any other rank is less desirable given instability and required application overhead). I realize that I'm going beyond the microformat itself to "best practices" but please forgive me; I've been wrangling with taxonomic databases for a long time. [[User:CyndyParr|CyndyParr]] 10:20, 10 Jan 2007 (PST)
*Disambiguation could be handled by applications outside the microformats
**Not sure what you mean here, since all parsing is done "outside microformats". [[User:AndyMabbett|Andy Mabbett]]
***Thanks for the clarification [[User:CyndyParr|CyndyParr]] 10:20, 10 Jan 2007 (PST)
***Another reason to make use of nameservers, rather than embedding the information within the microformat. --[[User:CharlesRoper|Charles Roper]] 10:50, 8 Jan 2007 (PST)
**** And how is enforcing the use of nameservers "paving the cowpaths"? [[User:AndyMabbett|Andy Mabbett]] 11:07, 8 Jan 2007 (PST)
*****The use of nameservers isn't enforced; it's optional (if disambiguation or further taxonomic intelligence is required). --[[User:CharlesRoper|Charles Roper]] 12:26, 8 Jan 2007 (PST)
******Agreed [[User:CyndyParr|CyndyParr]] 10:20, 10 Jan 2007 (PST)

(I'm either in agreement with your other points, or ambivalent.)

Thank you again - do stick around. Are you on the [[mailing-lists#microformats-discuss|mailing list]]?

[[User:AndyMabbett|Andy Mabbett]] 11:06, 5 Jan 2007 (PST)

*I am now! [[User:CyndyParr|CyndyParr]] 10:20, 10 Jan 2007 (PST)

==Pengo==

Unfortunately scientific names seem to change as often as common names. I have some examples and use cases this microformat needs to address, around the problems of ambiguity:

Ambiguity 1. Ambiguous scientific names.. ''[http://en.wikipedia.org/wiki/Sousa_chinensis Sousa chinensis]'' may either refer to '''Chinese White Dolphin''' (also known as ''Sousa chinensis chinensis'') or Humpback dolphin, also known as '''''Sousa''''' (genus) which includes up to five species or subspecies of dolphin including the Chinese White Dolphin. I don't care whether the Chinese White Dolphin is a species or subspecies, but the microformat needs to allow the user to be specific about which system is being addressed.

Ambiguity 2. Another example is the [http://en.wikipedia.org/wiki/Orangutan Orangutan]... or Orangutans. Organutans were once believed to be a single species, but are now considered two separate species. The problem is that the new scientific name for just the Bornean species (''Pongo pygmaeus'') is the same as the old scientific name which encompassed both species (''Pongo pygmaeus''). Meanwhile the new scientific name for the Sumatran Orangutan (''Pongo abelii'') is always unambiguous.

Ambiguity 3. ''[http://en.wikipedia.org/wiki/Doronomyrmex_pocahontas Doronomyrmex pocahontas]'' is an ant species that probably doesn't belong in the genus ''Doronomyrmex'', but rather ''Leptothorax''. But, until a full taxonomic study of the known species of ''Doronomyrmex'' and ''Leptothorax'' is carried out, it will stay there. Meanwhile the the term "''Leptothorax'' ([http://en.wiktionary.org/wiki/sensu_stricto sensu stricto])" is used to mean "in the sense of the original author".

Use cases:
So how do we:
# tag species in new documents, where we are using the most current nomenclature in the tags, to indicate that we don't mean the old nomenclature
# tag species allowing for new nomenclature to arise which may obsolete what we're using
# tag species in old documents, where we have updated the nomenclature in the tag, but the taxt may be referring to the old nomenclature, and we want to indicate that the updated nomenclature is being used.
# tag species in [others'] documents that are tagged automatically and where the specific nomenclature being used is unknown or ambiguous
# address issues where competing nomenclatures exist side-by-side, or transition periods
# tag species that have some clues as to which nomenclature is being used, e.g. the date of publication, and the author.
# tag a taxon which is now considered paraphyletic
# decide what's out of the scope of this microformat

Brainstorm solutions:
* Allow an "old-synonym" field, which strictly lists the previous name of the species (and never a newer name). So, e.g.
<pre><nowiki>Bornean Orangutan</nowiki></pre>
* Allow the English common name to be included, when it clears ambiguity. E.g. the "Chinese White Dolphin" has always been called that, regardless of whether it was considered a species or subspecies.
* Allow a taxonomy-year field for what year the taxonomy used in the tag comes from.
* Use a UID as described by others above.
* Have an ad-hoc "disambiguation" field which could include anything to disambiguate, such as years, synonyms, "sensu stricto", common names, authors (i.e. "in the sense of this author") etc. What goes in it for a particular taxon will develop from usage.
* Have a taxonomy-uncertain="true" field to indicate it has been (for example) automatically tagged and may not be accurate, so that other suggestions can be given by 3rd party software.

Basically I don't synonyms are necessary unless they are to show that the species was previously called something else, which may help to give a more exact meaning.

Comments? Are there already existing solutions to this problem in the real world?
[[User:PeNGo|Pengo]] 19:49, 28 Jan 2007 (PST)

==See also==
{{species}}

species-examples

2007-01-29T02:26:13Z

PeNGo: /* Wikipedia */ more detailed