species-brainstorming-fr

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m (Proposition Epouvantail)
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m (Reverted edits by CnabaStroc (Talk) to last version by ChristopheDucamp)
 
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:<pre><nowiki><span class="species">Anas platyrhynchos</span></nowiki></pre>
:<pre><nowiki><span class="species">Anas platyrhynchos</span></nowiki></pre>
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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.)  
+
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.)
-
It would also allow for more specific searching (do I mean "crow" or do I mean "Corvus corone"?).
+
Ceci permettrait aussi une recherche plus spécifique (ai-je voulu dire "corneille" ou suis-je en train de vouloir dire "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.
+
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===
===Proposition Epouvantail===
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**family (alt: "familia")
**family (alt: "familia")
**subfamily (alt: "subfamilia")
**subfamily (alt: "subfamilia")
-
**rank (alt: "taxorank", "taxon-rank", et al) - "unranked". Voir  [http://names.ubio.org/browser/classifications.php?conceptID=2463046] ; pourrait aussi être utilisé là où il y a dispute sur un rang, ou l'auteur n'a simplement pas de capacité oui de volonté de déclarer le rang plus explicitement.
+
**rank (alt: "taxorank", "taxon-rank", et al) - "unranked". Voir  [http://names.ubio.org/browser/classifications.php?conceptID=2463046] ; 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")
**binominal ("binominal name" alt: "binomial")
***genus
***genus
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</nowiki></pre>
</nowiki></pre>
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and :
+
et :
<pre><nowiki>
<pre><nowiki>
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Espèces re-classifiées (animal) :
Espèces re-classifiées (animal) :
<pre><nowiki>
<pre><nowiki>
-
     The species was classified as
+
     L'espèce a été reclassifiée sous
     <span class="species">
     <span class="species">
         <abbr class="binominal" title="Bartramia longicauda">Tringa longicauda</abbr>
         <abbr class="binominal" title="Bartramia longicauda">Tringa longicauda</abbr>
-
         by Johann Bechstein in 1812.
+
         par Johann Bechstein en 1812.
     </span>
     </span>
</nowiki></pre>
</nowiki></pre>
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Le travail est actuellement en cours, sur [http://www.nhm.ac.uk/hosted_sites/tdwg/ TDWG] pour développer un [http://wiki.gbif.org/guidwiki/wikka.php?wakka=HomePage système de GUID - identifiant- vraiment global] fondé sur les [http://wiki.gbif.org/guidwiki/wikka.php?wakka=LSID LSID]s. [http://xml.coverpages.org/lsid.html Plus sur les LSIDs].
Le travail est actuellement en cours, sur [http://www.nhm.ac.uk/hosted_sites/tdwg/ TDWG] pour développer un [http://wiki.gbif.org/guidwiki/wikka.php?wakka=HomePage système de GUID - identifiant- vraiment global] fondé sur les [http://wiki.gbif.org/guidwiki/wikka.php?wakka=LSID LSID]s. [http://xml.coverpages.org/lsid.html Plus sur les LSIDs].
-
Dans l'exemple suivant un NBN GUID est fourni. Cette GUID serait utilisable sur le [http://www.searchnbn.net/speciesInfo/taxonomy.jsp?searchTerm=lutra%20lutra&spKey=NBNSYS0000005133 Portail NBN], [http://nbn.nhm.ac.uk/nhm/bin/nbntaxa.dll/taxon_details?taxon_key=NBNSYS0000005133 The NHM Species Dictionary], dans 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).
+
Dans l'exemple suivant un NBN GUID est fourni. Cette GUID serait utilisable sur le [http://www.searchnbn.net/speciesInfo/taxonomy.jsp?searchTerm=lutra%20lutra&spKey=NBNSYS0000005133 Portail NBN], [http://nbn.nhm.ac.uk/nhm/bin/nbntaxa.dll/taxon_details?taxon_key=NBNSYS0000005133 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).
<pre><nowiki>
<pre><nowiki>
     <span class="sci nbn-NBNSYS0000005133">
     <span class="sci nbn-NBNSYS0000005133">
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</nowiki>
</nowiki>
</pre>
</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:
+
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 :  
<pre><nowiki>
<pre><nowiki>
     <span class="species">
     <span class="species">
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</nowiki>
</nowiki>
</pre>
</pre>
-
As a further alternative, the [[abbr-design-pattern]] could potentially be used, although this is semantically questionable:
+
Comme alternative allant plus loin, le [[abbr-design-pattern-fr|abbr-design-pattern]] pourrait être potentiellement être utilisé, même si ceci peut être potentiellement questionnable :  
<pre><nowiki>
<pre><nowiki>
     <span class="species">
     <span class="species">
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</nowiki>
</nowiki>
</pre>
</pre>
-
Yet another alternative, using a [http://www.ubio.org/index.php?pagename=home uBio] LSID as the GUID:
+
Encore une autre alternative, en utilisant un LSID [http://www.ubio.org/index.php?pagename=home uBio] comme le GUID :
<pre><nowiki>
<pre><nowiki>
     <span class="species urn:lsid:ubio.org:namebank:8341384">
     <span class="species urn:lsid:ubio.org:namebank:8341384">
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</nowiki>
</nowiki>
</pre>
</pre>
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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.
+
uBio a une [http://www.ubio.org/index.php?pagename=soap_tools interface de services web SOAP] librement disponible qui rend l'extraction de données pour l'intelligence taxonomique relativement facile.
====Questions====
====Questions====
-
* Is "sci" the best attribute name for the top-level?  
+
* Est-ce que "sci" est le meilleur attribut pour niveau-le-plus haut ?
-
** No - Scott Reynen
+
** Non - Scott Reynen
-
*** What do you think would be better? - Andy Mabbett
+
*** Qu'est-ce qui serait le mieux selon vous ? - Andy Mabbett
-
**** Assuming "sci" is short for "scientific name", I propose "scientific-name".
+
**** En supposant que "sci" est le diminutif pour "scientific name", je propose "scientific-name".
-
***** It is. That's 12 extra characters! - Andy Mabbett
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***** Ce l'est. Cela fait 12 caractères en plus ! - 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
+
** '''Taxon''' est une bien meilleure solution [http://en.wiktionary.org/wiki/taxon]. C'est court, cela a du sens et cohérent avec les autres noms de classes. - 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
+
*** 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
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**** The OED defines ''taxon'' as "A taxonomic group". See also the URL cited, [http://en.wiktionary.org/wiki/taxon]. - Andy Mabbett
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**** L'OED définit ''taxon'' comme "A taxonomic group". Voir aussi l'URL citée, [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
+
***** 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 [http://tdwg.napier.ac.uk/index.php?pagename=VotingDraftIntroduction TCS] - Charles Roper
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** or '''Biota''' - Andy Mabbett
+
** ou '''Biota''' - Andy Mabbett
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*'''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)
+
*'''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. [[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)
+
* Est-ce que "bin", var", "cult", etc., devraient être écrits en entier (Je pense que non, pour éviter les tailles de fichiers bedonnantes)
-
** Yes - Scott Reynen
+
** Oui - Scott Reynen
-
***'''Conceded''', and applied to the above. What about "subsp", etc? [[User:AndyMabbett|AndyMabbett]] 09:15, 22 Oct 2006 (PDT)
+
***'''Accordé''', et appliqué au-dessus. Que penser de "subsp", etc ? [[User:AndyMabbett|AndyMabbett]] 09:15, 22 Oct 2006 (PDT)
-
* Should other attribute names be abbreviated for brevity?  
+
* Y'a-t-il d'autres noms d'attributs qui pourraient être abrégés pour la concision ?
-
** 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
+
** Non la concision n'est pas un des [[naming-principles-fr|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
*** 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
*** 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

Current revision

Contents

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.]

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

<span class="bin"><span class="genus">Podiceps</span></span>
<span class="bin">Phylloscopus trochilus/Phylloscopus collybita</span>
<span class="bin"><span class="genus">Anser</span>/<span class="genus">Branta</span></span>
<span class="binominal">Larus glaucoides <span class="sub">kumlieni</span></span>


A ajouter

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:

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).

Malcolm Storey

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

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.

--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"

"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.

Réponse d'Andy Mabbett

Thank you very much for your detailed contribution. I have a few responses:

  <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)

(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)

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:

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

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)

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-brainstorming-fr was last modified: Wednesday, December 17th, 2008

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