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The ITS2 Database
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The NCBI BioCollections Database.

Shobha Sharma1, Stacy Ciufo1, Elena Starchenko1

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA.

Database : the Journal of Biological Databases and Curation
|April 25, 2018
PubMed
Summary
This summary is machine-generated.

GenBank submissions increasingly use sequences from vouchered specimens. The National Center for Biotechnology Information BioCollections Database now links these sequences to their originating natural history collections for better data traceability.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Museum Studies
  • Biodiversity Informatics

Background:

  • GenBank submissions contain an increasing number of sequences derived from scientifically vouchered specimens.
  • These specimens are housed in diverse natural history collections, including living collections, herbaria, museums, and culture collections.
  • Accurate specimen identification and clear association with their originating institutions are crucial for the validity and reproducibility of genomic studies.

Purpose of the Study:

  • To establish a centralized database for linking sequence data to their source institutions.
  • To improve the traceability and accessibility of sequence records derived from natural history collections.
  • To facilitate cross-referencing between sequence data and institutional collection holdings.

Main Methods:

  • Development and implementation of the National Center for Biotechnology Information (NCBI) BioCollections Database.
  • Establishing a system to associate GenBank sequence submissions with their corresponding specimen vouchers and home institutions.
  • Enabling cross-linking functionalities for quick identification of records from specific collections.

Main Results:

  • The NCBI BioCollections Database successfully links specimen vouchers and associated sequence records to their home institutions.
  • This facilitates the identification of all records originating from each collection through cross-linking.
  • Provides a centralized resource for managing and accessing biodiversity-related sequence data.

Conclusions:

  • The NCBI BioCollections Database enhances the integrity and utility of sequence data derived from natural history collections.
  • It provides a critical infrastructure for biodiversity research, enabling better data provenance and discovery.
  • This initiative supports the integration of molecular data with traditional taxonomic and collection-based research.