TDWG Taxon Rank LSID Ontology Roger Hyam TDWG Biodiversity Information Standards 2006-11-15 $Date: 2007-11-19 11:47:59 +0100 (Mon, 19 Nov 2007) $ Ontology describing a controlled vocabulary for taxon ranks. 0.2 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. 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.