species-brainstorming-fr

Species (Espèces) - Brainstorming

Note : Le nom original du microformat, "species", va probablement changer, probablement vers "biota" ou "taxon". Le précédent a été maintenu ici, pour éviter de faire trop de changements répétitifs et peut-être des éditions redondantes.

mis à jour! La nouvelle version beta d'Operator détecte Species. Une page test est disponible. Les travaux sur les deux continuent !

Andy Mabbett

Proposition

Il devrait y avoir, je crois, un microformat "species" pour le balisage des noms de plantes et d'animaux, pour inclure leurs noms scientifiques. Imaginez :

<abbr class="species" title="Anas platyrhynchos">Mallard</abbr>

ou

<span class="species">Anas platyrhynchos</span>

Le microformat permettrait aux agents utilisateurs d'être configurés pour exécuter des recherches sur les bases de données en ligne d'espèces, selons les préférences utilisateur. La spécification de la classe taxonomique aiderait les agents utilisateurs à savoir quelles seraient les bases de données pertinentes (par ex, utiliser la base de données A pour les plantes, mais la base B pour les mammifères et la base C pour les insectes.)

Ceci permettrait aussi une recherche plus spécifique (ai-je voulu dire "corneille" ou suis-je en train de vouloir dire "Corvus corone" ?)

La spécification encouragerait, mais ne mandaterai pas, la capitalisation correcte de noms scientifiques, par conséquent "Anas platyrhynchos'" pas "anas platyrhynchos" ni (si ce n'est historiquement) "Anas Platyrhynchos". Un rappel que de tels noms devraient être stylés en italiques sera aussi inclus.

Proposition Epouvantail

Je suis en train de tendre vers ce modèle, imbriqué selon les composants du microformat, pas de manière taxonomique :

[Note : dans une taxonomie, les niveaux tels que "subphylum", "class" ou "order" sont connus comme un "rank"].

[Note : Ceci est conçu de façon que toutes ces classes (X)HTML soient optionnellement' disponibles pour les auteurs, mais elles n'ont besoin d'utiliser que celles qui s'appliquent à leurs besoins particuliers. Comparez, par exemple, avec toutes les classes et tous les types disponibles dans la hCard.]

• species (nom scientifique ; aka nom botanique) (mieux : taxon; ou biota)
  • domain (alternativement : "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". Voir [1] ; pourrait aussi être utilisé là où il y a dispute sur un rang, ou l'auteur n'a simplement pas de capacité ou de volonté de déclarer plus explicitement le rang.
  • 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 (ou phase) (cad "Gyrfalcons, par exemple a une phase grise et une phase blanche" [2]; "L'oie des neiges (C. c. caerulescens), apparaît communément dans deux variantes de plumage. Les oiseaux en phase-blanche sauf ceux avec des ailes noires, mais certaines oies en phase bleu on un plumage gris-bleu remplaçant la plupart du blanc sauf sur la taile le cou et le bout des ailes." [3])
  • trade ("trade name")
  • breed (e.g. Bull Terrier)
  • sense (botanical - voir exemples)
  • authority
    • year (...of authority)
  • cname ("common name" - ceci devrait être "common" ou "vernacular"?)
  • guid
  • vgroup ("vernacular group" (alt: "vernacular-group") - il existe probablement un meilleur terme pour ça. Souvent un genre ou une famille n'encapsule pas un groupe particulier d'espèces d'une façon pratique ou utile. Par exemple, il est difficile de séparer les espèces de champignons et les espèces de lichen parce qu'elles sont taxonomiquement imbriquées. De ce fait, dans les bases de données taxonomiques, un groupe vernaculaire de "champignons" et "lichen" est souvent appliqué aux espèces qui tombent dans l'un ou l'autre de ces groupes. Un groupe vernaculaire pourrait être considéré similaire à un nom commun, mais pour des groupes d'espèces. Voir le portail NBN pour un exemple de groupes vernaculaires en utilisation ; ces noms de groupes sont aussi utilisés dans le logiciel Recorder d'enregistrement biologique.
  • ? gender (utile pour les espèces exhibant dimorphisme sexuel - "trouve moi une image d'un pilet mâle" ; "Je veux acheter un houx femelle - une valeur binaire , mâle ou femelle ; ou incluant neutre, hermaphrodite, unspecified et/ ou mixé?)- voir #Développement Futur
  • ? age bracket (adult/ juvenile/ seed/ egg/ nymph/ nestling/ pup/ cub/ instar1/ instar2 etc. - besoin d'être plus travaillé) - voir #Développement Futur
  • ? count (un nombre, ou représentation de quelque autre valeur - none, unspecified, "present", etc) - voir #Développement Futur
  • [nom à suggérer ("type", "role"?)] un indicateur de type, par ex. pour les abeilles, "queen" ou "worker" [Q : Y'a-t-il un nom approprié dans la communauté scientifique pour les distinctions ?]

où sont optionnelles et il est possible d'inférer en partant du plus simple :

<abbr class="binominal" title="Anas platyrhynchos">Mallard</abbr>

ou

<span class="binominal">Anas platyrhynchos</span>

que le genre est Anas et l'espèce est platyrhynchos (et par conséquent, ce que "binominal" est à "sci"; comme "adr" l'est vers "hCard")

Une espèce (Citrine Wagtail, un oiseau):

    <span class="species">
	<span class="binominal">Motacilla citreola</span>
    </span>

Sous-espèce (animal) :

    <span class="species">
        <span class="binominal">Larus glaucoides</span>
        <span class="subsp">kumlieni</span>
    </span>

Varieté (plante) :

  <span class="species">
    <span class="binominal">Pisum sativum</span>
    var. <span class="variety">macrocarpon</span> 
  </span> 

Espèce (animal, nom commun affiché) :

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

Espèce (animal, nom scientifique affiché) :

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

Chamignon, kingdom inclus :

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

Même nom pour différentes générations :

    <p class="species">
        An unidentified
         <abbr class="taxoclass" title="Aves"> 
         <abbr class="genus" title="Oenanthe">
         <span class="common">
            Wheatear
         </span>
         </abbr>
         </abbr>
    </p>

et :

    <p class="species">
        An unidentified
         <abbr class="taxoclass" title="Magnoliopsida"> 
         <abbr class="genus" title="Oenanthe">
         <span class="common">
            Water Dropwort
         </span>
         </abbr>
         </abbr>
        sp.
    </p>

Espèce (animal avec authority et year):

    <span class="species"> 
        <span class="binominal">Pica pica</span> 
        <span class="authority">Linnaeus</span>, 
        (<span class="year">1758</span>) 
    </span>

Espèces re-classifiées (animal) :

    L'espèce a été reclassifiée sous
    <span class="species">
        <abbr class="binominal" title="Bartramia longicauda">Tringa longicauda</abbr>
        par Johann Bechstein en 1812.
    </span>

Un exemple plus extrême, là où il y a un besoin de décrire une hiérarchie taxonomique complète :

  <span class="species">
    <span class="domain">Eukarya</span>
    <span class="kingdom">Animalia</span>
    <span class="subkingdom">Eumetazoa</span>
    <span class="superphylum">Deuterostomia</span>
    <span class="phylum">Chordata</span>
    <span class="subphylum">Vertebrata</span>
    <span class="taxoclass">Aves</span>
    <span class="subclass">Neognathae</span>
    <span class="order">Passeriformes</span>
    <span class="suborder">Passeri</span>
    <span class="parvordo">Passerida</span>
    <span class="superfamily">Passeroidea</span>
    <span class="family">Motacillidae</span>
    <span class="binominal">
	<span class="genus">Motacilla</span>
	<span class="specific">alba</span>
	<span class="subspecies">yarrellii</span>
    </span>
    <span class="cname">Pied Wagtail</span>
    <span class="authority">Linnaeus</span>
    <span class="year">1758</span>
  </span>

Exprimer une espèce avec une GUID

Le travail est actuellement en cours, sur TDWG pour développer un système de GUID - identifiant- vraiment global fondé sur les LSIDs. Plus sur les LSIDs.

Dans l'exemple suivant un NBN GUID est fourni. Cette GUID serait utilisable sur le Portail NBN, The NHM Species Dictionary, dans Recorder 2002 and Recorder 6, et dans la boîte à outils d'enregistremen ayant suivi OpenRecorder. Parce qu'il y a différents GUIDs pour différentes bases de données, le type de GUID peut être indiqué avec un code suivi d'un tiret suivi par le GUID (par ex. nbn-NBNSYS0000005133).

    <span class="sci nbn-NBNSYS0000005133">
        <span class="binominal">Lutra lutra</span>
    </span>

Alternativement, le GUID pourrait être exprimé comme un élément dans son propre droit, avec le type GUID étant exprimé sous un nom de classe secondaire :

    <span class="species">
        <span class="binominal">Lutra lutra</span>
        <span class="uid nbn">NBNSYS0000005133</span>
    </span>

Comme alternative allant plus loin, le abbr-design-pattern pourrait être potentiellement être utilisé, même si ceci peut être potentiellement questionnable :

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

Encore une autre alternative, en utilisant un LSID uBio comme le GUID :

    <span class="species urn:lsid:ubio.org:namebank:8341384">
      <span class="cname">Green Sandpiper</span>
      <span class="binominal">Tringa ochropus</span>
    </span>

uBio a une interface de services web SOAP librement disponible qui rend l'extraction de données pour l'intelligence taxonomique relativement facile.

Questions

• Est-ce que "sci" est le meilleur attribut pour niveau-le-plus haut ?
  • Non - Scott Reynen
    • Qu'est-ce qui serait le mieux selon vous ? - Andy Mabbett
      • En supposant que "sci" est le diminutif pour "scientific name", je propose "scientific-name".
        • Ce l'est. Cela fait 12 caractères en plus ! - Andy Mabbett
  • Taxon est une bien meilleure solution [4]. C'est court, cela a du sens et cohérent avec les autres noms de classes. - Andy Mabbett
    • Je pense que "taxonname" ou "taxon-name" serait une meilleure valeur pour l'attribut de classe. C'est plus descriptif des données dont vous essayez de définir le format. Taxon fait plus référence au groupage de classification auquel je pensais. L'attribut class est utilisé fréquemment pour l'applciation de stylisme CSS par conséquent la classe au niveau le plus haut a au moins besoin d'être complètement distincte de ce que j'ai pensé pour éviter les conflits avec d'autres valeurs d'attributs de classes dans la page et les fichiers CSS. - Tony Prichard
      • L'OED définit taxon comme "A taxonomic group". Voir aussi l'URL citée, [5]. - Andy Mabbett
        • Je suis d'accord sur le fait que taxon serait le nom le plus approprié. Ce pourrait être considéré comme un raccourci de TaxonConcept (ou TaxonName), qui est le terme utilisé par le TCS - Charles Roper
  • ou Biota - Andy Mabbett
• Species est utilisé au-dessus, pour la recherche d'avoir un nom à utiliser, mais "biota" ou "taxon" seront probablement utilisés dans la version finale. AndyMabbett 09:15, 22 Oct 2006 (PDT)

• Est-ce que "bin", var", "cult", etc., devraient être écrits en entier (Je pense que non, pour éviter les tailles de fichiers bedonnantes)
  • Oui - Scott Reynen
    • Accordé, et appliqué au-dessus. Que penser de "subsp", etc ? AndyMabbett 09:15, 22 Oct 2006 (PDT)

• Y'a-t-il d'autres noms d'attributs qui pourraient être abrégés pour la concision ?
  • Non la concision n'est pas un des principes de nommage. "bin", "var" et "cult" laissent tous un sens ambigu, ce qui pose problème. Nous devrions "Utiliser des noms de classes fondés sur des noms extraits du schéma original", c'est à dire des mots complets ou des phrases où ils ne sont pas spécialement longs. - 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
        • 341 species, 58Kb. 'Nuff said? AndyMabbett 11:53, 26 Sep 2006 (PDT)
          • Your bird list page can be 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. - 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. 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?:

<span class="bin"><span class="genus">Podiceps</span></span>

• • There are also species aggregates and groups to be considered Grey/Dark Dagger sp., where it is one of two species but where the genus Acronicta cannot be used as there are more than the two species in the genus - Tony Prichard
    • Any suggestions? Or other examples? - AndyMabbett
      • This kind of aggregates are often used by birdwatchers (in Finland). How about separating the names with a slash (or some other sign)?: - MikkoBiomi

<span class="bin">Phylloscopus trochilus/Phylloscopus collybita</span>

<span class="bin"><span class="genus">Anser</span>/<span class="genus">Branta</span></span>

• Should we allow divisions of "binominal" with no parent "species", such as:

<span class="binominal">Larus glaucoides <span class="sub">kumlieni</span></span>

• Is the "fungus" example OK, given that Amanita muscaria is not an abbreviation of "funghi"?
  • I do not like the use of the abbr tag at all in the examples given. The abbr tag is for abbreviations with the suggestion that the title is used for the full name. The implication in the Mallard example is that Mallard is an abbreviation for the scientific name, it is not it is a different type of name - Tony Prichard

• Do the "authority" and "date" pair need a joint wrapper?

• Is "bin" (short for binominal) the most appropriate term for a taxon name? When subspecies, var, subvar, etc. are nested, then surely it becomes trinomial? Would simply name or TaxonName not be more flexible? - Charles Roper

A ajouter

• Animal hybrids
• GUID (Globally Unique Identifier). When referencing to a taxon name, there is also often the need to provide a GUID which relates to a taxonomic concept database (such as the NHM Species Dictionary). By providing a GUID, ambiguity is removed. - Charles Roper
  • Thank you. AndyMabbett 11:55, 26 Sep 2006 (PDT)

Développement futur

Instead of including gender, age-bracket and count, we could allow for a furture microformat, called, perhpas, "sighting", which might have the components:

• sighting
  • species (a "species" microformat)
    • set (one or more)
      • count
      • age-bracket
      • gender
  • location (hCard or geo)
  • date-time

See West Midland Bird Club's Latest news from Ladywalk and In and around South Staffordshire 2006 (blog) for simple examples.

Bill Hull

My website has 17000+ photos of 4700+ bird species. There are also a handful of butterflies (organized very poorly as I am unaware of any published butterfly world taxonomies) and shortly will have a number of dragon/damselflies. The site is made up of static pages but is built from a database so it is easy for me to add it new HTML tags to the pages. If you are interested in some prototyping at some point I can probably build stuff into the pages. - Bill Hull

Roger Hyam

Groupe de Travail sur Bases de Données Taxonomiques

TDWG is the organisation for standardisation in exchange of biodiversity data. The organisation is currently undergoing a degree of re-organisation and is developing an architecture to integrate the different standards it produces with each other and with those in use in the semantic web and geospatial communities. Part of this architecture will be a central ontology for things like scientific biological names.

Because of its role in bridging technologies the application that manages the ontology will need to be able to express the same basic semantics in multiple formats (e.g. RDFS, OWL, Geography Mark Up, OBO etc). It seems logical that this application should also generate basic microformat definitions for each of the classes it contains. If we have an ontology defining 'Taxon Name' and 'specific epithet' for example the same notion should be mapped to as many technologies as possible.

TDWG is also supporting a system for Globally Unique Identifiers based on Life Science Identifiers for biodiveristy objects such as taxon names, specimens, herbaria etc which it would be cool to integrate into any microformat.

There is a meeting in St Louis, USA, October 2006 where the way forward for the ontology will be discussed. Decisions made at the meeting will govern what is possible. It is difficult to take this further without concensus from that meeting.

If it is after October 2006 and you are interested in learning more please contact me (Roger Hyam).

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

Malcolm Storey

(extrait des emails adressés à Andy Mabbett, avec l'aimable autorisation de l'auteur)

• "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, 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 [6], [7]

AIUI ICBN only goes down to species.

ICZN isn't so easy: [8]

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:

<abbr class="binominal" title="Adalia bipunctata">Adalia 2-punctata</abbr>

AndyMabbett 09:55, 21 Oct 2006 (PDT)

Fossés

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!

Homonymes

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

<abbr class="binominal" title="Apion gibbirostre">''Apion carduorum'' sensu Morris 1990</abbr>

AndyMabbett 12:21, 5 Oct 2006 (PDT)

Citations pour les autorités

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]

Perhaps we should allow for the inclusion of an hCitation? Andy Mabbett 15:08, 28 Feb 2007 (PST)

Hyppo

Défi de nomenclature

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[9] is used and for Animalia the code from 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

--Hyppo 14:23, 9 Oct 2006 (PDT)

I would mark those up as:

<span class=genus">Dendroceros</span> subg. <span class="subgenus">Apoceros</span>

<span class=genus">Sula</span> <span class="subgenus">Morus</span>

<span class="binominal">Begonia grandis</span> ssp. <span class="subspecies">evansiana''</span>

<span class="binominal">Gorilla beringei</span> <span class="subspecies">graueri</span>

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

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 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. --Charles Roper 04:12, 9 Jan 2007 (PST)
  • This binomial vs. binominal Google battle seems even more conclusive. 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" --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.

Réponse d'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:

  <span class="taxon lsidres:urn:lsid:ubio.org:namebank:21833">
    <i class="sci-name">Passeriformes</i>
  </span>

Or, to simplify further:

  <i class="taxon sci-name lsidres:urn:lsid:ubio.org:namebank:21833">Passeriformes</i>

Or, at the simplest level:

  <i class="taxon">Passeriformes</i>

Simply marking up the word as a taxon would lighten the load of any parser, making its job much simpler. --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. 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? --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. CyndyParr 10:20, 10 Jan 2007 (PST)
      • Aves is available for use, but not required, so indeed, we don't have conflict ;-) 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 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. --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.Andy Mabbett
        • My concern still stands that there is no consistent mark-up usage that I can find.
    • Fair enough 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. --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.--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.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 CyndyParr 10:20, 10 Jan 2007 (PST)
      • Again, the option to do so is in the current proposal. 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. Andy Mabbett
    • Fair enough 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! 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. 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". Andy Mabbett
    • Thanks for the clarification CyndyParr 10:20, 10 Jan 2007 (PST)
    • Another reason to make use of nameservers, rather than embedding the information within the microformat. --Charles Roper 10:50, 8 Jan 2007 (PST)
      • And how is enforcing the use of nameservers "paving the cowpaths"? 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). --Charles Roper 12:26, 8 Jan 2007 (PST)
          • Agreed 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 list?

Andy Mabbett 11:06, 5 Jan 2007 (PST)

• I am now! 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.. 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 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. 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 (sensu stricto)" is used to mean "in the sense of the original author".

Use cases: So how do we:

1. 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
2. tag species allowing for new nomenclature to arise which may obsolete what we're using
3. 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.
4. tag species in [others'] documents that are tagged automatically and where the specific nomenclature being used is unknown or ambiguous
5. address issues where competing nomenclatures exist side-by-side, or transition periods
6. tag species that have some clues as to which nomenclature is being used, e.g. the date of publication, and the author.
7. tag a taxon which is now considered paraphyletic
8. 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.

<span species="Pongo pygmaeus" old-synonym="Pongo pygmaeus pygmaeus">Bornean Orangutan</span>

• 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? Pengo 19:49, 28 Jan 2007 (PST)

Response to Pengo by Andy Mabbett

Thank you for your expert contribution. Of your proposed solutions, the common (or vernacular) name, UID and author/ year are already in the current proposal. It may be sensible to have a "synonym" property (as used on http://en.wikipedia.org/wiki/Doronomyrmex_pocahontas), but I don't think "old-synonym" is particularly well named. Perhaps, if it's needed at all, "formerly" would be better? It is worth remembering, though, that the microformat is meant for labelling what people already publish and, for instance, http://en.wikipedia.org/wiki/Bornean_Orangutan refers to Pongo pygmaeus, not any previous name. Andy Mabbett 02:20, 30 Jan 2007 (PST)

• Then most effective way to disambiguate is to use a UID. I feel other solutions would over-complicate the specification. I think we need to put some effort into populating the examples regrouped page with specific examples of publishing styles, e.g., plain binomials, plain common names, scientific names with common names, scientific names with synonyms, binomial with subspecies, etc. Charles Roper 05:25, 2 Feb 2007 (PST)
  • There are very few exmples of UIDs being published in-the-wild. Andy Mabbett 06:00, 2 Feb 2007 (PST)
    • I found a good source of synonym usage; see the Coleopterist's Checklist of Beetles of the British Isles: http://www.coleopterist.org.uk/checklist.htm. Look for the indented specific epithet names, e.g. in the family HALIPLIDAE, pallens Fowler, 1887 and halberti Bullock, 1928 are examples of synonyms, with the favoured specific epithet being confinis Stephens, 1828. On a more general note, checklists such as this are ripe for microformatting and are an excellent example of common markup practice. The species microformat could be used to great effect with content such as this, creating minable dictionaries of species names which are, in turn, essential tools in for use in biodiversity informatics. Charles Roper 14:43, 24 Feb 2007 (PST)
    • Re. UIDs: yes, we have an interesting chicken & egg situation here. Without a reliable way to publish a UID (other than making them human readable text, which is undesirable) how are we supposed to be able to make use of them? A microformat would be a good means with which to deploy UIDs, but it is frowned upon to implement a pattern that isn't already being practised. Judging by the messages here, on the discussion list and elsewhere, there is clearly a desire for linking taxon names with UIDs, particularly LSIDs, which look set to become the standard UID for taxonomic naming. Charles Roper 10:41, 2 Feb 2007 (PST)
      • Well, the proposal allows for the inclusion of UIDs (as with all the suggested attributes, some work on the exact format might need to be done), should people to chose to publish them; whether or not they do is not something for uFs to push for. Andy Mabbett 13:13, 2 Feb 2007 (PST)

Charles Roper

Synonymes

I found an interesting example of synonym usage in the Tiger Beetles of Connecticut checklist. In the particular example cited, the synonyms refer to, or are associated with, the species name - Cicindela duodecimguttata Dejean 1825. Synonyms are often mentioned alongside or near preferred scientific names; how should we tie them together, especially when, as in this case, the name and the synonym are not positioned close to one another, but are still clearly associated? As a segue to this question, how should multiple synonymous common names be represented? How about common names in different languages? For example, the Otter has many different common names.

I take it you refer to the text which may be paraphrased (by omitting some prose) as:

Cicindela duodecimguttata is known from 23 localities. Cicindela duodecimguttata, once classified as a subspecies of C. repanda, shares many traits with C. repanda. Where C. duodecimguttata occurs, the more common C. repanda is usually found.

Synonomies: Cicindela proteus Kirby 1837:9. Cicindela bucolica Casey 1913:28. Cicindela hudsonica Casey 1916:29. Cicindela edmontonensis Carr 1920:21

The problem would seem to be that C. repanda is referred to both as a species in its own right, and as a past synonym of C. duodecimguttata. If the whole thing is wrapped in one div class="biota", allowing the other listed synonyms to be included, then how is C. repanda to be marked up as a species in its own right?

I would mark up the first occurrence of each, then use the include-pattern to "attach" the other listed synonyms with the former (I've only included one synonym in the following, for clarity):

<span class="biota">

 <span class="binominal">Cicindela duodecimguttata</span>
 <object class="include" data="#C-proteus"></object>

</span>

is known from 23 localities. Cicindela duodecimguttata, once classified as a subspecies of

<span class="biota">

 <span class="binominal">C. repanda</span>

</span>

, shares many traits with C. repanda. Where C. duodecimguttata occurs, the more common C. repanda is usually found.

Synonomies: <span class="synonym" id="C-proteus">

 <span class="binominal">Cicindela proteus</span> [or maybe "synonym-binominal" ?]
 <span class="authority">Kirby</span>
 <span class="year">1837</span>:9.</span>

Cicindela bucolica Casey 1913:28. Cicindela hudsonica Casey 1916:29. Cicindela edmontonensis Carr 1920:21

I might then use the its entry on the "shares many traits" line to mark up C. repanda as an synonym, and include it in the same way.

Multiple and foreign-language common names would be catered for by allowing the common name attribute to be "0 or many" (the first such occurrence having precedence), and using a lang attribte where appropraite.

Andy Mabbett 14:42, 28 Feb 2007 (PST)

Voir aussi

• species
• exemples
  • exemples regroupés
• quantitative evidence
  • Initial quantitative examples
  • further quantitative examples
• brainstorming (comprend la proposition épouvantail ou le draft standard)