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

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 signif...

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Detalles Bibliográficos
Autores principales: Federhen, Scott, Clark, Karen, Barrett, Tanya, Parkinson, Helen, Ostell, James, Kodama, Yuichi, Mashima, Jun, Nakamura, Yasukazu, Cochrane, Guy, Karsch-Mizrachi, Ilene
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Michigan State University 2014
Materias:
Editorial/Commentary
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4149001/
https://www.ncbi.nlm.nih.gov/pubmed/25197497
http://dx.doi.org/10.4056/sigs.4851102
Descripción
Sumario: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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