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

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.

SUBMITTER: Federhen S

PROVIDER: S-EPMC4149001 | biostudies-other | 2014 Jun

REPOSITORIES: biostudies-other

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

Federhen Scott S Clark Karen K Barrett Tanya T Parkinson Helen H Ostell James J Kodama Yuichi Y Mashima Jun J Nakamura Yasukazu Y Cochrane Guy G Karsch-Mizrachi Ilene I

Standards in genomic sciences 20140129 3

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 enco ...[more]

PMID: 25197497

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