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

Scott Federhen,Yuichi Kodama,Yasukazu Nakamura,Tanya Barrett,Jun Mashima,Helen Parkinson,James Ostell,Karen Clark,Ilene Karsch-Mizrachi,Guy Cochrane

doi:10.4056/sigs.4851102

Abstract

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.

Highlights

The NCBI taxonomy database provides the organism nomenclature and classification that is used in sequence entries by the International Nucleotide Sequence Database Collaboration (INSDC [1]; comprising GenBank, ENA and the DDBJ) [2]
The NCBI Taxonomy Group is responsible for curating names for taxa that are regulated by the relevant codes of nomenclature [3,4,5], for providing informal names for specimens that are not identified with Linnaean species binomials, and for maintaining the ‘taxid’ namespace
It has been almost twenty years since the first bacterial genomes started to appear in the sequence databases, beginning with Haemophilus influenzae in 1995, followed within a year by Escherichia coli

Summary

Introduction

The NCBI taxonomy database provides the organism nomenclature and classification that is used in sequence entries by the International Nucleotide Sequence Database Collaboration (INSDC [1]; comprising GenBank, ENA and the DDBJ) [2]. For the convenience of those at INSDC institutes and their users, the taxonomy group started assigning strain-level taxids for prokaryotes with complete genome sequences, e.g.: “Haemophilus influenzae Rd” [7] and “Escherichia coli K12” [8]. Our recognition that the curation of strain-level taxids will not remain possible under such growth, and that alternative data resources relating to biological samples are maturing at the INSDC partner institutes, has led us to a review of our practices in

Results

Conclusion