BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata

By Tanya Barrett, Karen Clark, R. Gevorgyan, Vyatcheslav Gorelenkov, E. Gribov, Ilene Karsch-Mizrachi, Michael Kimelman, Kim D. Pruitt, S. Resenchuk, Tatiana A. Tatusova and 2 more. Nucleic Acids Res., 2011

326 citations recorded by the source corpus.

As the volume and complexity of data sets archived at NCBI grow rapidly, so does the need to gather and organize the associated metadata. Although metadata has been collected for some archival databases, previously, there was no centralized approach at NCBI for collecting this information and using it across databases. The BioProject database was recently established to facilitate organization and classification of project data submitted to NCBI, EBI and DDBJ databases. It captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. Concomitantly, the BioSample database is being developed to capture descriptive information about the biological samples investigated in projects. BioProject and BioSample records link to corresponding data stored in archival repositories. Submissions are supported by a web-based Submission Portal that guides users through a series of forms for input of rich metadata describing their projects and samples. Together, these databases offer improved ways for users to query, locate, integrate and interpret the masses of data held in NCBI's archival repositories. The BioProject and BioSample databases are available at http://www.ncbi.nlm.nih.gov/bioproject and http://www.ncbi.nlm.nih.gov/biosample, respectively.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/6700612ce9dba090ab754dd6517b16d02a23638f

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Citations in the corpus

Gene: a gene-centered information resource at NCBI (2014, unknown): “Coverage tracks corresponding to reads from individual BioSamples (8) can be loaded from the Expression tab on the Configure Page and provide a visual indication of differential expression in tissues and developmental stages.”
Assembly: a resource for assembled genomes at NCBI (2015, methodology): “Historically identifiers from the NCBI Taxonomy and BioProject databases (3,4) could serve as proxies for assembly identifiers because it was rare to have more than one genome assembly for the same organism.”
Database resources of the National Center for Biotechnology Information (2014, unknown): “The BioSample database provides annotation for biological samples used in a variety of studies submitted to NCBI, including genomic sequencing, microarrays, genome wide association studies (GWAS) and epigenomics (16).”
GenBank (2012, background): “gov/bioproject), developed at NCBI and subsequently adopted across the INSDC, allows submitters to register large-scale sequencing projects under a unique project identifier, enabling reliable linkage between sequencing projects and the data they produce (10).”
Virus Variation Resource – improved response to emergent viral outbreaks (2016, background): “The individual columns within the table can be selected to display specific sets of metadata and hyperlinked GenBank and BioSample accessions (29).”
The International Nucleotide Sequence Database Collaboration (2011, background): “The new BioProject database (3), which has superseded Genome Project, enables submitters to describe initiatives that include data from transcriptome, metagenome, targeted locus and multi-isolate studies that initiate from a single organization, consortium or funding initiative.”
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database (2019, background): “The antibiotic molecule branch is another area of active curation: while 80% (278 out of 342) of ARO antibiotic terms are harmonized with the NCBI BioSample database (28), CARD curation rules require each antibiotic in the ARO to be cross-referenced to a PubChem ID (PCID), which some molecules lack.”
Database resources of the National Center for Biotechnology Information (2011, background): “gov/ biosample/) is a new resource that provides annotation for biological samples used in a variety of studies submitted to NCBI, including genomic sequencing, microarrays, GWAS and epigenomics (2).”
Ribosomal Database Project: data and tools for high throughput rRNA analysis (2013, background): “This allows researchers to jump directly to RDP sequence records from the corresponding records in the NCBI’s Nucleotide and BioProject databases (11).”
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples (2018, methodology): “The NCBI BioSample Database; Barrett et al. 2012).”
NCBI GEO: archive for functional genomics data sets—update (2012, methodology): “All GEO series are now brokered to NCBI’s BioProject database (12).”
PATRIC, the bacterial bioinformatics database and analysis resource (2013, methodology): “PATRIC automatically gathers genome metadata from a variety of sources, including the original GenBank records, BioProject and BioSample (9) by parsing more than 60 different metadata ﬁelds, and retrieving information from free-text genome descriptions and organizing it into a structured format.”