Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records | Zendy

Scott Federhen | Zendy; Karen Clark | Zendy; Tanya Barrett | Zendy; Helen Parkinson | Zendy; James Ostell | Zendy; Yuichi Kodama | Zendy; Jun Mashima | Zendy; Yasukazu Nakamura | Zendy; Guy Cochrane | Zendy; Ilene KarschMizrachi | Zendy

Open Access

Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records

Author(s) -

Scott Federhen,

Karen Clark,

Tanya Barrett,

Helen Parkinson,

James Ostell,

Yuichi Kodama,

Jun Mashima,

Yasukazu Nakamura,

Guy Cochrane,

Ilene KarschMizrachi

Publication year - 2014

Publication title -

standards in genomic sciences

Language(s) - English

Resource type - Journals

ISSN - 1944-3277

DOI - 10.4056/sigs.4851102

Subject(s) - biology , identifier , metadata , whole genome sequencing , strain (injury) , taxonomy (biology) , genome , organism , computational biology , genetics , gene , world wide web , ecology , computer science , anatomy , programming language

Microbial genome sequence submissions to the International Nucleotide Sequence Database Collaboration (INSDC) have been annotated with organism names that include the strain identifier. Each of these strain-level names has been assigned a unique 'taxid' in the NCBI Taxonomy Database. With the significant growth in genome sequencing, it is not possible to continue with the curation of strain-level taxids. In January 2014, NCBI will cease assigning strain-level taxids. Instead, submitters are encouraged provide strain information and rich metadata with their submission to the sequence database, BioProject and BioSample.

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