{"id":97,"date":"2022-06-20T16:20:56","date_gmt":"2022-06-20T15:20:56","guid":{"rendered":"https:\/\/insdc.org\/?page_id=97"},"modified":"2022-07-21T14:54:02","modified_gmt":"2022-07-21T13:54:02","slug":"controlled-vocabulary-typematerial-qualifer","status":"publish","type":"page","link":"https:\/\/www.insdc.org\/submitting-standards\/controlled-vocabulary-typematerial-qualifer\/","title":{"rendered":"Controlled vocabulary for \/type_material qualifier"},"content":{"rendered":"<p>Type material is a taxonomic term that ties formal names to specimens that can be used for identification and description of a new taxonomic entity.<\/p>\n<p>Reference: <span>Nucleic Acids Res.<\/span> 2015 Jan;43(Database issue):D1086-98. doi: 10.1093\/nar\/gku1127.<\/p>\n<p>INSDC will automatically populate this qualifier from the NCBI taxonomy database to flag sequences of form type in the INSDC databases (ENA\/GenBank\/DDBJ).<\/p>\n<p>The controlled vocabulary used for various types can be found in the below table.<\/p>\n<p> <\/p>\n<table border=\"0\">\n<tbody>\n<tr>\n<td><strong>Type Name<\/strong><\/td>\n<td><strong>Synonym<\/strong><\/td>\n<td><strong>Nomenclatures*<\/strong><\/td>\n<td><strong>Comment<\/strong><\/td>\n<\/tr>\n<tr>\n<td>type material<\/td>\n<td> <\/td>\n<td>BZ<\/td>\n<td>basic type material \u2013 this is default type (except for Archaea and Bacteria)<\/td>\n<\/tr>\n<tr>\n<td>type strain<\/td>\n<td> <\/td>\n<td>P<\/td>\n<td>deposited in at least two different culture collections \u2013 default type for Archaea and Bacteria<\/td>\n<\/tr>\n<tr>\n<td>reference material<\/td>\n<td> <\/td>\n<td>BZ<\/td>\n<td>non-type material designated for reference purposes (except for Archaea and Bacteria)<\/td>\n<\/tr>\n<tr>\n<td>reference strain<\/td>\n<td> <\/td>\n<td>P<\/td>\n<td>non-type material designated for reference purposes (for Archaea and Bacteria)<\/td>\n<\/tr>\n<tr>\n<td>neotype strain<\/td>\n<td> <\/td>\n<td>P<\/td>\n<td>replacement culture for a type that has been lost<\/td>\n<\/tr>\n<tr>\n<td>holotype<\/td>\n<td> <\/td>\n<td>BZ<\/td>\n<td>single name-bearing type specimen<\/td>\n<\/tr>\n<tr>\n<td>isotype<\/td>\n<td> <\/td>\n<td>B<\/td>\n<td>duplicate specimen of the holotype<\/td>\n<\/tr>\n<tr>\n<td>paratype<\/td>\n<td> <\/td>\n<td>BZ<\/td>\n<td>other specimens designated in the original type series<\/td>\n<\/tr>\n<tr>\n<td>neotype<\/td>\n<td> <\/td>\n<td>BZ<\/td>\n<td>single name-bearing specimen designated when holotype is lost<\/td>\n<\/tr>\n<tr>\n<td>epitype<\/td>\n<td> <\/td>\n<td>B<\/td>\n<td>other specimen designated in subsequent type series<\/td>\n<\/tr>\n<tr>\n<td>syntype<\/td>\n<td> <\/td>\n<td>BZ<\/td>\n<td>one of a name-bearing series of type specimens<\/td>\n<\/tr>\n<tr>\n<td>isosyntype<\/td>\n<td> <\/td>\n<td>B<\/td>\n<td>duplicate specimen of a syntype<\/td>\n<\/tr>\n<tr>\n<td>lectotype<\/td>\n<td> <\/td>\n<td>BZ<\/td>\n<td>syntype subsequently designated as the single name-bearing type<\/td>\n<\/tr>\n<tr>\n<td>paralectotype<\/td>\n<td> <\/td>\n<td>Z<\/td>\n<td>syntype not subsequently designated as lectotypes<\/td>\n<\/tr>\n<tr>\n<td>hapantotype<\/td>\n<td> <\/td>\n<td>Z<\/td>\n<td>protist assemblage collectively designated as holotype<\/td>\n<\/tr>\n<tr>\n<td>allotype<\/td>\n<td> <\/td>\n<td>Z<\/td>\n<td>designated type specimen of opposite sex to the holotype<\/td>\n<\/tr>\n<tr>\n<td>isoparatype<\/td>\n<td> <\/td>\n<td>B<\/td>\n<td>duplicate specimen of a paratype<\/td>\n<\/tr>\n<tr>\n<td>isoneotype<\/td>\n<td> <\/td>\n<td>B<\/td>\n<td>duplicate specimen of a neotype<\/td>\n<\/tr>\n<tr>\n<td>isolectotype<\/td>\n<td> <\/td>\n<td>B<\/td>\n<td>duplicate specimen of a lectotype<\/td>\n<\/tr>\n<tr>\n<td>isoepitype<\/td>\n<td> <\/td>\n<td>B<\/td>\n<td>duplicate specimen of an epitype<\/td>\n<\/tr>\n<tr>\n<td>culture from reference<\/td>\n<td> <\/td>\n<td>BZ<\/td>\n<td>living eukaryotic culture derived from reference material<\/td>\n<\/tr>\n<tr>\n<td>culture from type material<\/td>\n<td>ex-type<\/td>\n<td>BZ<\/td>\n<td>living eukaryotic culture derived from type material<\/td>\n<\/tr>\n<tr>\n<td>culture from paratype<\/td>\n<td>ex-paratype<\/td>\n<td>BZ<\/td>\n<td>living eukaryotic culture derived from paratype<\/td>\n<\/tr>\n<tr>\n<td>culture from neotype<\/td>\n<td>ex-neotype<\/td>\n<td>BZ<\/td>\n<td>living eukaryotic culture derived from neotype<\/td>\n<\/tr>\n<tr>\n<td>culture from lectotype<\/td>\n<td>ex-lectotype<\/td>\n<td>BZ<\/td>\n<td>living eukaryotic culture derived from lectotype<\/td>\n<\/tr>\n<tr>\n<td>culture from hapantotype<\/td>\n<td> <\/td>\n<td>Z<\/td>\n<td>living eukaryotic culture derived from hapantotype<\/td>\n<\/tr>\n<tr>\n<td>culture from isosyntype<\/td>\n<td>ex-isosyntype<\/td>\n<td>B<\/td>\n<td>living eukaryotic culture derived from isosyntype<\/td>\n<\/tr>\n<tr>\n<td>culture from isotype<\/td>\n<td>ex-isotype<\/td>\n<td>B<\/td>\n<td>living eukaryotic culture derived from isotype<\/td>\n<\/tr>\n<tr>\n<td>culture from isoparatype<\/td>\n<td>ex-isoparatype<\/td>\n<td>B<\/td>\n<td>living eukaryotic culture derived from isoparatype<\/td>\n<\/tr>\n<tr>\n<td>culture from isoneotype<\/td>\n<td>ex-isoneotype<\/td>\n<td>B<\/td>\n<td>living eukaryotic culture derived from isoneotype<\/td>\n<\/tr>\n<tr>\n<td>culture from isolectotype<\/td>\n<td>ex-isolectotype<\/td>\n<td>B<\/td>\n<td>living eukaryotic culture derived from isolectotype<\/td>\n<\/tr>\n<tr>\n<td>culture from holotype<\/td>\n<td>ex-holotype<\/td>\n<td>BZ<\/td>\n<td>living eukaryotic culture derived from holotype<\/td>\n<\/tr>\n<tr>\n<td>culture from epitype<\/td>\n<td>ex-epitype<\/td>\n<td>B<\/td>\n<td>living eukaryotic culture derived from epitype<\/td>\n<\/tr>\n<tr>\n<td>culture from syntype<\/td>\n<td>ex-syntype<\/td>\n<td>BZ<\/td>\n<td>living eukaryotic culture derived from syntype<\/td>\n<\/tr>\n<tr>\n<td>culture from isoepitype<\/td>\n<td>ex-isoepitype<\/td>\n<td>B<\/td>\n<td>living eukaryotic culture derived from isoepitype<\/td>\n<\/tr>\n<tr>\n<td>pathotype strain<\/td>\n<td> <\/td>\n<td>P<\/td>\n<td>strain designated as the type for the associated pathovar<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p> <\/p>\n<p>*NOTE: Nomenclature letter coding is explained in the following table: <\/p>\n<p>B International Code of Nomenclature for algae, fungi, and plants <\/p>\n<p>P International Code of Nomenclature of Prokaryotes <\/p>\n<p>V International Committee on Taxonomy of Viruses <\/p>\n<p>Z The International Code of Zoological Nomenclature <\/p>\n","protected":false},"excerpt":{"rendered":"<p>Type material is a taxonomic term that ties formal names to specimens that can be used for identification and description of a new taxonomic entity. Reference: Nucleic Acids Res. 2015 Jan;43(Database issue):D1086-98. doi: 10.1093\/nar\/gku1127. INSDC will automatically populate this qualifier from…<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":233,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"acf":[],"_links":{"self":[{"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages\/97"}],"collection":[{"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/comments?post=97"}],"version-history":[{"count":2,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages\/97\/revisions"}],"predecessor-version":[{"id":99,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages\/97\/revisions\/99"}],"up":[{"embeddable":true,"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/pages\/233"}],"wp:attachment":[{"href":"https:\/\/www.insdc.org\/wp-json\/wp\/v2\/media?parent=97"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}