TDWG Taxon Rank LSID Ontology
Roger Hyam
TDWG Biodiversity Information Standards
2006-11-15
2015-07-01
Ontology describing a controlled vocabulary for taxon ranks.
0.3
Enumerated ranks of a taxon (scientific organism name) in a taxonomic hierarchy. This list is intended to be interoperable between name providers for
bacteria, viruses, fungi, plants, and animals. It is not assumed that in each taxonomic group all ranks have to be used. The enumeration attempts to strike a balance between listing all
possible rank terms, and remaining comprehensible. For example, the "infra-" ranks specifically mentioned in BioCode have been included (although very rarely used), but the additional
intermediate zoological ranks (micro, nano, pico, etc.) are not included. Whether the selection of infraspecific ranks (some informal ranks, esp. from bacteriology, may be missing!) probably
needs some discussion. However, it is believed that this list may help to start developing data sets that can easily be integrated across the barriers of Language and taxonomic traditions.
Not included in the list are the botanical "notho-" ranks, which are used to designate hybrids (nothospecies, nothogenus). It is assumed they can be generated from separate information that
the taxon is a hybrid. ICBN 4.4 states: "The subordinate ranks of nothotaxa are the same as the subordinate ranks of non-hybrid taxa, except that nothogenus is the highest rank permitted".
The following publications have been consulted to determine the number of type terms that should be included and to prepare the semantic definitions: The Berlin Taxonomic Information Model,
MoReTax view (Berendsohn & al., http://www.bgbm.org/scripts/ASP/BGBMModel/Catalogues.asp?Cat=MT DiversityTaxonomy model version 0.7 (G. Hagedorn & T. Grafenhan 2002,
http://160.45.63.11/Workbench/Taxonomy/Model/InformationModels.html) ABCD version 1.44, types HigherTaxonRankType and RankAbbreviationType, by W. Berendsohn, reviewed by D. Hobern TaxCat2 -
Database of Botanical Taxonomic Categories by Jorg Ochsmann, IPK Gatersleben; http://mansfeld.ipk-gatersleben.de/TaxCat2/default.htm A several ranks have been added
to the original list to better accommodate names from ICNCP. (RDH). Many thanks for review and help go to Dr. Walter Gams.
Version 0.3 removed subclass declarations to classes outside of this ontology in accordance with Recommendation 2.9 of the VoMaG Report http://www.gbif.org/resource/80862
Taxon Rank Term
The class for construction controlled vocabularies of ranks. Equivalent to TCS TaxonomicRankEnum.
cand.
cand.
Candidatus' rank is proposed in bacteriology for putative taxa, which could not yet be studied sufficiently to warrant the creation of a name with a known rank. (Murray, R.G.E.
& Schleifer, K.H.: Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes. Int. J. Syst. Bacteriol., 1994, 44, 174-176).
tax. infrasp.
tax. infrasp.
infraspecific tax. of undefined rank -- Undefined ranks (using either no rank identifier in botany, or using greek letters or symbols like stars, crosses) occur in very old
publications. Most frequently these are to be interpreted as varieties, but occasionally they are forms or subspecies (see Stearn, W.T. 1957: Species plantarum (Facsimile); Introduction. 1.
London, p. 90-95, 160-161, 163). The interpretation of these cases requires taxonomic knowledge that may not be available at the time when data are parsed. Such lack of knowledge can be
expressed using this rank identifier.
f. sp.
f. sp.
The ICBN does not formally cover formae specialis (art. 4, note 3). However, because of the economic importance of pathogenic f. sp., and since it is common practice to handle
them as if the code would apply (i. e. priority usually observed, name quoted with author), they are included here.
subsubfm.
subsubfm.
subsubform
subfm.
subfm.
subform
fm.
fm.
Form, race, variety are not subject to regulation in zoology; see ICZN Article 1.3.4
subsubvar.
subsubvar.
sub-sub-variety
subvar.
subvar.
sub-variety
var.
var.
Form, race, variety are not subject to regulation in zoology; see ICZN Article 1.3.4 Examples: Pinus nigra var. caramanica (= "P. nigra subsp. nigra var.
caramanica"; Taxus baccata var. variegata
pathovar.
pathovar.
patho-variety
biovar.
biovar.
bio-variety
infrasp.
infrasp.
infraspecies
aggr.
aggr.
subspecific aggregate (= group, complex) -- A loosely defined group of subspecies. Zoology: "Aggregate - a group of subspecies within a species. An aggregate may be
denoted by a group name interpolated in parentheses."
subsp.
subsp.
subspecies -- Examples: Pinus nigra subsp. nigra Homo sapiens sapiens
sp.
sp.
species -- Examples: Taxus baccata, Homo sapiens
aggr.
aggr.
A loosely defined group of species. Zoology: "Aggregate - a group of species, other than a subgenus, within a genus. An aggregate may be denoted by a group name
interpolated in parentheses." -- The Berlin/MoreTax model notes: "[these] aren't taxonomic ranks but cirumscriptions because on the one hand they are necessary for the
concatenation of the fullname and on the other hand they are necessary for distinguishing the aggregate or species group from the microspecies." Compare subspecific aggregate for a
group of subspecies within a species!
tax. infragen.
tax. infragen.
infrageneric tax. of undefined rank -- A name that appear between a genus name and a species epitheton and is not clearly marked as series or section, or other may be assigned
to this rank until the true rank can be assigned by a taxonomic expert.
subser.
subser.
subseries
ser.
ser.
series
subsect.
subsect.
subsection
sect.
sect.
section
infragen.
infragen.
infragenus
subgen.
subgen.
subgenus
gen.
gen.
genus -- Examples: Magnolia Homo
infratrib.
infratrib.
infratribe
subtrib.
subtrib.
subtribe
trib.
trib.
tribe
supertrib.
supertrib.
supertribe
infrafam.
infrafam.
infrafamily
subfam.
subfam.
subfamily -- Examples: Magnolioideae
fam.
fam.
family -- Examples: Magnoliaceae Hominidae
superfam.
superfam.
superfamily -- Examples: Magnoliacea
infraord.
infraord.
infraorder
subord.
subord.
suborder -- Examples: Magnolineae Catarrhini
ord.
ord.
order -- Examples: Magnoliales Primates
superord.
superord.
superorder -- Examples: Magnolianae
infracl.
infracl.
infraclass
subcl.
subcl.
subclass -- Examples: Magnoliidae Eutheria
cl.
cl.
class -- Examples: Magnoliopsida Mammalia
supercl.
supercl.
superclass
infraphyl.
infraphyl.
infraphylum (= infradivision)
infradiv.
infradiv.
infraphylum (= infradivision)
subphyl.
subphyl.
subphylum (= subdivision) -- Examples: Magnoliophytina Vertebrata
subdiv.
subdiv.
subphylum (= subdivision) -- Examples: Magnoliophytina Vertebrata
phyl.
phyl.
phylum (= division) -- Examples: Magnoliophyta Chordata
div.
div.
phylum (= division) -- Examples: Magnoliophyta Chordata
superphyl.
superphyl.
superphylum (= superdivision)
superdiv.
superdiv.
superphylum (= superdivision)
infrareg.
infrareg.
infrakingdom
subreg.
subreg.
subkingdom
reg.
reg.
kingdom -- Examples: Plantae Animalia
superreg.
superreg.
super kingdom -- Examples: Eucaryota
dom.
dom.
domain (= empire) -- Examples: Archaea (= Archaeobacteria), Bacteria (= Eubacteria), Eukarya (= Eukaryota)
domain (= empire) -- Examples: Archaea (= Archaeobacteria), Bacteria (= Eubacteria), Eukarya (= Eukaryota)
tax. supragen.
tax. supragen.
suprageneric tax. of undefined rank -- This value indicates that the rank of a name is unknown. Compare "incertae sedis" which is commonly used as a
replacement for a taxon to group all taxa whose position in the classification or phylogenetic tree is uncertain.
cult.
cult.
cultivar -- The epithet is usually output in single quotes and may contain multiple words, see ICBN §28. Examples: Taxus baccata 'Variegata', Juniperus
×pfitzeriana 'Wilhelm Pfitzer'; Magnolia 'Elizabeth' (= a hybrid, no species epithet).
convar.
convar.
Used in cultivated plants (ICNCP), but deprecated, see 'Some notes on problems of taxonomy and nomenclature of cultivated plants' by J. Ochsmann,
http://www.genres.de/IGRREIHE/IGRREIHE/DDD/22-08.pdf
grex
grex
a rank equivalent to cultivar group used principly for artificial hybrid swams in Orchidaceae.
cultivar. group
cultivar. group
cultivar-group
graft-chimaera
graft-chimaera
graft-chimaera
Denomination Class
Denomination Class
Denomination classes are constructs under ICNCP for defining the scope within which a cultivar or Group epithet must be unique.