Microformats Wiki - User contributions [en]

User:CyndyParr

2007-12-31T14:08:33Z

CyndyParr:

Cynthia (Cyndy) Sims Parr

==My background==

I am still not sure if I am a scientist or an engineer. My doctorate is in biology and my primary interests are in behavior, ecology, and evolution (other keywords: bioacoustics, birds, cooperative breeding). On the other hand, my research for the last eight years or so has almost exclusively been in human-computer interaction and semantic web technology. Always my interest in technology serves my favorite biological domains. Except for a short time when I acted as a systems administrator for a large multi-national financial company.

Currently I hold two research faculty positions where I lead small teams of programmers on a variety of biodiversity-related projects.

==My philosophy==

*Collaboration
*Bottom-up over top-down
*Darwinian
*Structured over unstructured
*Informal over formal
*Good enough over perfect
*Transparency

==More==

My [http://www.umiacs.umd.edu/~csparr webpage] should provide ample linkage.

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User:CyndyParr

2007-01-10T18:43:34Z

CyndyParr:

species-brainstorming

2007-01-10T18:20:16Z

CyndyParr: /* Response by Cyndy Parr */

=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)
***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)
***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)

*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'''.
***Fair enough [[User:CyndyParr|CyndyParr]] 10:20, 10 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. 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.
*****My concern still stands that there is no consistent mark-up usage that I can find.
****''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)
*[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.
***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!
***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".
***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)

==See also==
{{species}}

species-brainstorming

2007-01-05T18:33:45Z

CyndyParr:

=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"].

*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]]")

====Examples====

Extreme case (Pied Wagtail, a bird):

<pre><nowiki>

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

Motacilla
alba
yarrellii

Pied Wagtail
Linnaeus
1758

</nowiki></pre>

Simplified equivalent of the above:

<pre><nowiki>

Motacilla alba
yarrellii

</nowiki></pre>

Sub-species (animal, common name displayed):
<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>

=====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"

"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")

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.

==See also==
{{species}}

species

2006-10-24T20:33:48Z

CyndyParr: /* Contributors */

=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 [http://www.calacademy.org/research/informatics/sblum/pub/biodiv_informatics.html biodiversity informatics] - "the application of information technology to the domain of biodiversity".

Also, for interest, see Note 4, on [http://www.w3.org/MarkUp/future/papers/rothenburg-19980412.html 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 [http://ukmoths.org.uk/ UK Moths] first, if not found try [http://www.nhm.ac.uk/research-curation/projects/lepindex/index.html 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:

# marking-up a taxonomical name (or taxon-common name pair) in such a way that its components can be recognised by computers '''or'''
# 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]] 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==
*[http://en.wikipedia.org/wiki/Scientific_classification Wikipedia: Scientific classification]
**[http://en.wikipedia.org/wiki/Binomial_nomenclature Wikipedia: Binomial nomenclature]
**[http://en.wikipedia.org/wiki/Trinomial_nomenclature Wikipedia: Trinomial nomenclature]
**[http://en.wikipedia.org/wiki/Taxon Wikipedia: Taxon]
**[http://en.wikipedia.org/wiki/Cultivar Wikipedia: Cultivars]
**[http://en.wikipedia.org/wiki/Variety_%28biology%29 Wikipedia: Varieties]
**[http://en.wikipedia.org/wiki/Subvariety Wikipedia: Sub-varieties]
**[http://en.wikipedia.org/wiki/Form_%28botany%29 Wikipedia: forms]
*[http://www.iczn.org/ http://www.iczn.org/ International Commission on Zoological Nomenclature]
**[http://en.wikipedia.org/wiki/Binomial_nomenclature Wikipedia: International Commission on Zoological Nomenclature]
*[http://www.iczn.org/ International Code of Botanical Nomenclature]
*[http://www.rhs.org.uk/rhsplantfinder/plantnaming.asp RHS Plant Finder: The naming of plants]
*[http://www.ishs.org/sci/icracpco.htm International Code of Nomenclature for Cultivated Plants]
*[http://www.tdwg.org/index.html Taxonomic Databases Working Group]
*[http://www.hortax.org.uk/ Hortax] - The Names of Garden Plants
*[http://www.bgbm.fu-berlin.de/iapt/nomenclature/code/SaintLouis/0000St.Luistitle.htm www.bgbm.fu-berlin.de/iapt/nomenclature/code/SaintLouis/0000St.Luistitle.htm]
*[http://species.wikimedia.org/wiki/Main_Page WikiSpecies]
*[http://en.wiktionary.org/wiki/taxonomy Wiktionary: Taxonomy]
*[http://jbi.nhm.ku.edu/index.php/jbi/article/view/25 Biodiversity Informatics: Taxonomic names, metadata, and the Semantic Web]

==Contributors==
*[[User:AndyMabbett|Andy Mabbett]] (proponent)
*[[User:RogerHyam|Roger Hyam]] (interested party?)
*[[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:KierenPitts|Kieren Pitts]], [http://www.ilrt.bris.ac.uk/ ILRT - Institute for Learning and Research Technology] and the [http://www.amentsoc.org/ Amateur Entomologists' Society] (proponent)
*[[User:CyndyParr|Cyndy Parr]], [http://spire.umbc.edu Spire project] (interested party)

==See also==
Here's some work-in-progress:

*[[species-examples]]
*[[species-brainstorming]]

==Implementations (pending)==
*[http://www.spacefornature.co.uk/biorec/taxoncheck.htm 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.