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Type material in the NCBI Taxonomy Database.

Federhen S - Nucleic Acids Res. (2014)

Bottom Line: Type material is the taxonomic device that ties formal names to the physical specimens that serve as exemplars for the species.For the prokaryotes these are strains submitted to the culture collections; for the eukaryotes they are specimens submitted to museums or herbaria.This has important implications for many NCBI resources, some of which are outlined below.

View Article: PubMed Central - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA federhen@ncbi.nlm.nih.gov.

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Sequence from type in Cercopithecus lomamiensis. Clockwise from top: (1) taxonomy entry for Cercopithecus lomamiensis. (2) GenBank flatfile format for accession JN106060. (3) Holotype specimen page at the Yale Peabody Museum, Mammal Collection.
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Figure 3: Sequence from type in Cercopithecus lomamiensis. Clockwise from top: (1) taxonomy entry for Cercopithecus lomamiensis. (2) GenBank flatfile format for accession JN106060. (3) Holotype specimen page at the Yale Peabody Museum, Mammal Collection.

Mentions: Figure 3 (taken from the January 2014 NCBI News announcement of sequence-from-type) shows one of the entries associated with the description of Cercopithecus lomamiensis, a new species of primate described in 2012 (31). As is often the case, this was first submitted to GenBank with an unpublished manuscript name, and was originally indexed with the informal name ‘Cercopithecus sp. ASB-2012’, now listed as an ‘equivalent name’. Type material (taken from the paper) is listed explicitly in the entry—YPM MAM 14080 (circled) is the holotype specimen; the rest are paratypes (this information is not surfaced in the taxonomy browser, but it is recorded in the database). The GenBank flatfile entry is annotated with the structured specimen voucher ‘YPM:MAM:14080’—this is a Darwin Core triplet identifier, and indicates that the institution and collection codes can be found in our BioCollection database, where they are registered as the Yale Peabody Museum, Mammal Collection. This is one of the collections that are associated with a URL formula, so the voucher is hotlinked to the corresponding specimen page at the museum web site, shown in the lower left. This is not the flashiest example of a specimen page—some include photos, some keep track of sequence derived from their specimens and link back to GenBank—but this is the first animal sequence entry from a holotype specimen which links to both the full-text description of the species (in PubMed Central and at PLoS ONE) and to the specimen page at the museum. This is common in the prokaryotes, where the full text of the taxonomic literature is generally accessible from PubMed and the culture collections are online, but is rare for the higher eukaryotes, where the taxonomic literature is often not in PubMed at all (though Zootaxa has just started to send abstracts, and ZooKeys sends full-text to PubMed Central), and most natural history collections are just starting to digitize their collections (the NSF is actively funding this effort). We will continue to capture as much sequence from type as possible in the higher eukaryotes, concentrating on sequence submissions from papers that describe new species, but the real type bonanza for GenBank is in the microbes, which will be the focus of the remainder of this paper.


Type material in the NCBI Taxonomy Database.

Federhen S - Nucleic Acids Res. (2014)

Sequence from type in Cercopithecus lomamiensis. Clockwise from top: (1) taxonomy entry for Cercopithecus lomamiensis. (2) GenBank flatfile format for accession JN106060. (3) Holotype specimen page at the Yale Peabody Museum, Mammal Collection.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4383940&req=5

Figure 3: Sequence from type in Cercopithecus lomamiensis. Clockwise from top: (1) taxonomy entry for Cercopithecus lomamiensis. (2) GenBank flatfile format for accession JN106060. (3) Holotype specimen page at the Yale Peabody Museum, Mammal Collection.
Mentions: Figure 3 (taken from the January 2014 NCBI News announcement of sequence-from-type) shows one of the entries associated with the description of Cercopithecus lomamiensis, a new species of primate described in 2012 (31). As is often the case, this was first submitted to GenBank with an unpublished manuscript name, and was originally indexed with the informal name ‘Cercopithecus sp. ASB-2012’, now listed as an ‘equivalent name’. Type material (taken from the paper) is listed explicitly in the entry—YPM MAM 14080 (circled) is the holotype specimen; the rest are paratypes (this information is not surfaced in the taxonomy browser, but it is recorded in the database). The GenBank flatfile entry is annotated with the structured specimen voucher ‘YPM:MAM:14080’—this is a Darwin Core triplet identifier, and indicates that the institution and collection codes can be found in our BioCollection database, where they are registered as the Yale Peabody Museum, Mammal Collection. This is one of the collections that are associated with a URL formula, so the voucher is hotlinked to the corresponding specimen page at the museum web site, shown in the lower left. This is not the flashiest example of a specimen page—some include photos, some keep track of sequence derived from their specimens and link back to GenBank—but this is the first animal sequence entry from a holotype specimen which links to both the full-text description of the species (in PubMed Central and at PLoS ONE) and to the specimen page at the museum. This is common in the prokaryotes, where the full text of the taxonomic literature is generally accessible from PubMed and the culture collections are online, but is rare for the higher eukaryotes, where the taxonomic literature is often not in PubMed at all (though Zootaxa has just started to send abstracts, and ZooKeys sends full-text to PubMed Central), and most natural history collections are just starting to digitize their collections (the NSF is actively funding this effort). We will continue to capture as much sequence from type as possible in the higher eukaryotes, concentrating on sequence submissions from papers that describe new species, but the real type bonanza for GenBank is in the microbes, which will be the focus of the remainder of this paper.

Bottom Line: Type material is the taxonomic device that ties formal names to the physical specimens that serve as exemplars for the species.For the prokaryotes these are strains submitted to the culture collections; for the eukaryotes they are specimens submitted to museums or herbaria.This has important implications for many NCBI resources, some of which are outlined below.

View Article: PubMed Central - PubMed

Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA federhen@ncbi.nlm.nih.gov.

Show MeSH