taxa

39989 rows


Description

This table lists all taxa in the database. Most taxa are biological taxa; however, some are biometric measures and some are physical parameters.

Columns

Column Type Size Nulls Auto Default Children Parents Comments
taxonid serial 10 nextval('ndb.seq_taxa_taxonid'::regclass)
datasettaxonnotes.taxonid fk_datasettaxonnotes_taxaC
ecolgroups.taxonid fk_ecolgroups_taxaC
externaltaxa.taxonid fk_externaltaxa_taxaC
formtaxa.affinityid fk_formtaxa_taxa1C
formtaxa.taxonid fk_formtaxa_taxaR
isostratdata.taxonid fk_isostratdata_taxaR
samples.taxonid fk_samples_taxaR
specimendates.taxonid sd_txidR
synonyms.invalidtaxonid fk_synonyms_invalidtaxaC
synonyms.validtaxonid fk_synonyms_validtaxaR
synonymy.reftaxonid fk_synonymy_taxa2R
synonymy.taxonid fk_synonymy_taxa1C
taxa.highertaxonid fk_highertaxonidR
taxaalthierarchy.highertaxonid fk_taxaalthierarchy_taxa1R
taxaalthierarchy.taxonid fk_taxaalthierarchy_taxaC
taxonpaths.taxonid taxonpaths_taxonid_fkeyR
variables.taxonid fk_variables_taxaC

An arbitrary Taxon identification number.

taxoncode varchar 64 null

A code for the Taxon. These codes are useful for other software or output for which the complete name is too long. Because of the very large number of taxa, codes can be duplicated for different Taxa Groups. In general, these various Taxa Groups are analyzed separately, and no duplication will occur within a dataset. However, if Taxa Groups are combined, unique codes can be generated by prefixing with the TaxaGroupID, For example:
*VPL:Cle Clethra
*MAM:Cle Clethrionomys
A set of conventions has been established for codes. In some cases conventions differ depending on whether the organism is covered by rules of botanical nomenclature (BN) or zoological nomenclature (ZN).
*Genus – Three-letter code, first letter capitalized, generally the first three unless already used.
**Ace Acer
**Cle Clethrionomys
*Subgenus – The genus code plus a two-letter subgenus code, first letter capitalized, separated by a period.
**Pin.Pi Pinus subg. Pinus
**Syn.Mi Synaptomys (Mictomys)
*Species – The genus code plus a two-letter, lower-case species code, separated by a period.
**Ace.sa Acer saccharum
**Ace.sc Acer saccharinum
**Cle.ga Clethrionomys gapperi
*Subspecies or variety – The species code a two-letter, lower-case subspecies code, separated by a period.
**Aln.vi.si Alnus viridis subsp. Sinuata
**Bis.bi.an Bison bison antiquus
*Family – Six-letter code, first letter capitalized, consisting of three letters followed by «eae» (BN) or «dae» (ZN).
**Roseae Rosaceae
**Bovdae Bovidae
*Subfamily or tribe – (BN) Family code plus two-letter subfamily code, first letter capitalized, separated by a priod. (ZN) Six-letter code, first letter capitalized, consisting of three letters followed by «nae».
**Asteae.As Asteraceae subf. Asteroideae
**Asteae.Cy Asteraceae tribe Cynarea
**Arvnae Arvicolinae
*Order – (BN) Six-letter code, first letter capitalized, consisting of three letters followed by «les». (ZN) Six-letter code, first letter capitalized, consisting of three letters, followed by the last three letters of the order name, unless the order name is ≤6 letters long, in which case the code = the order name. Zoological orders do not have a common ending.
**Ercles Ericales
**Artyla Artiodactyla
**Rodtia Rodentia
*Taxonomic levels higher than order – Six-letter code, first letter capitalized, consisting of three letters, followed by the last three letters of the order name, unless the order name is ≤6 letters long, in which case the code = the order name..
**Magida Magnoliopsida
**Magyta Magnoliophyta
**Mamlia Mammalia
*Types – The conventional taxon code followed by «-type».
**Aln.in-t Alnus incana-type
**Amb-t Ambrosia-type
*cf. – «cf. » is placed in the proper position.
**Odc.cf.he Odocoileus cf. O. hemionus
**cf.Odc.he cf. Odocoileus hemionus
**cf.Odc cf. Odocoileus
*aff. – «aff. » is abbreviated to «af. ».
**af.Can.di aff. Canis dirus
*? – «?» is placed in the proper position.
**?Pro.lo ?Procyon lotor
*Alternative names – A slash is placed between the conventional abbreviations for the alternative taxa.
**Ost/Cpn Ostrya/Carpinus
**Mstdae/Mepdae Mustelidae/Mephitidae
*Undifferentiated taxa – (BN) «.ud» is added to the code. (ZN) «.sp » is added to the code.
**Aln.ud Alnus undiff.
**Roseae.ud Rosaceae undiff.
**Mms.sp Mammuthus sp.
**Taydae.sp Tayassuidae sp
*Parenthetic modifiers – The conventional taxon code with an appropriate abbreviation for the modifier separated by periods. Multiple modifiers also separated by periods. *Abbreviations for pollen morphological modifiers follow Iversen and Troels-Smith (1950).
**Raneae.C3 Ranunculaceae (tricolpate)
**Raneae.Cperi Ranunculaceae (pericolpate)
**Pineae.ves.ud Pinaceae (vesiculate) undiff.
**Myteae.Csyn.psi Myrtaceae (syncolpate, psilate)
**Bet.>20µ Betula (>20 µm)
*Non-biological taxa – Use appropriate abbreviations.
**bulk.dens Bulk density
**LOI Loss-on-ignition
**Bet.pol.diam Betula mean pollen-grain diameter

taxonname varchar 80 null

Name of the taxon. Most TaxonNames are biological taxa; however, some are biometric measures and some are physical parameters. In addition, some biological taxa may have parenthetic non-Latin modifers, e.g. «Betula (>20 µm)» for Betula pollen grains >20 µm in diameter. In general, the names used in Neotoma are those used by the original investigator. In particular, identifications are not changed, although Dataset notes can be added to the database regarding particular identifications. However, some corrections and synonymizations are made. These include:
*Misspellings are corrected.
*Nomenclatural, homotypic, or objective synonyms may be applied. Because these synonyms unambiguously refer to the same taxon, no change in identification is implied. For example, the old family name for the grasses «Gramineae» is changed to «Poaceae».
*Taxonomic, heterotypic, or subjective synonyms may be applied if the change does not effectively assign the specimen to a different taxon. Although two names may have been based on different type specimens, if further research has shown that these are in fact the same taxon, the name is changed to the accepted name. These synonymizations should not cause confusion. However, uncritical synonymization, although taxonomically correct, can result in loss of information, and should be avoided. For example, although a number of recent studies have shown that the Taxodiaceae should be merged with the Cupressaceae, simply synonymizing Taxodiaceae with Cupressaceae may expand the universe of taxa beyond that implied by the original investigator. For example, a palynologist in the southeastern United States may have used «Taxodiaceae» to imply «Taxodium», which is the only genus of the family that has occurred in the region since the Pliocene, but used the the family name because, palynologically, Taxodiuim cannot be differentiated from other Taxodiaceae. However, well preserved Taxodium pollen grains can be differentiated from the other Cupressaceous genera in the region, Juniperus and Chamaecyperus. Thus, the appropriate synonymization for «Taxodiaceae» in this region would be «Taxodium» or «Taxodium-type», which would retain the original taxonomic precision. On the other hand, the old «TCT» shorthand for «Taxodiaceae/Cupressaceae/Taxaceae» now becomes «Cupressaceae/Taxaceae» with no loss of information.
*For alternative taxonomic designations, the order may be changed. For example, «Ostrya/Carpinus» would be substituted for «Carpinus/Ostrya».

author varchar 128 null

Author(s) of the name. Neither the pollen database nor FAUNMAP stored author names, so these do not currently exist in Neotoma for plant and mammal names. These databases follow standard taxonomic references (e.g. Flora of North America, Flora Europaea, Wilson and Reeder’s Mammal Species of the World), which, of course, do cite the original authors. However, for beetles, the standard practice is to cite original author names; therefore, this field was added to Neotoma.

valid bool 1 null
highertaxonid int4 10 null
taxa.taxonid fk_highertaxonidR

The TaxonID of the next higher taxonomic rank, for example, the HigherTaxonID for «Bison» is the TaxonID for «Bovidae». For «cf.’s» and «-types», the next higher rank may be much higher owing to the uncertainty of the identification; the HigherTaxonID for «cf. Bison bison» is the TaxonId for «Mammalia». The HigherTaxonID implements the taxonomic hierarchy in Neotoma.

extinct bool 1 null

True if the taxon is extinct, False if extant.

taxagroupid varchar 3 null
taxagrouptypes.taxagroupid fk_taxagroupidR

The TaxaGroupID facilitates rapid extraction of taxa groups that are typically grouped together for analysis. Some of these groups contain taxa in different classes or phyla. For example, vascular plants include the Spermatophyta and Pteridophyta; the herps include Reptilia and Amphibia; the testate amoebae include taxa from different phyla. Field links to the TaxaGroupTypes table.

publicationid int4 10 null
publications.publicationid fk_publicationidR

Publication identification number. Field links to the Publications table.

validatorid int4 10 null
contacts.contactid fk_validatoridR
validatedate date 13 null
notes text 2147483647 null

Free form notes or comments about the Taxon.

recdatecreated timestamp 22 timezone('UTC'::text, now())
recdatemodified timestamp 22 null

Indexes

Constraint Name Type Sort Column(s)
taxa_pkey Primary key Asc taxonid
ix_taxagroupid_taxa Performance Asc taxagroupid
ix_taxonname_taxa Performance Asc taxonname
taxonames_idx Performance Asc taxonname
taxonname_btree Performance Asc taxonname

Relationships