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

https://doi.org/10.1093/nar/gkr1163
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/s0076-6879(96)66012-1openalex-snapshot
[10] Entrez: Molecular biology database and retrieval system
inferredcites →https://doi.org/10.1038/nbt.1823openalex-snapshot
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
inferredcites →https://doi.org/10.1038/ng1007-1181openalex-snapshot
The NCBI dbGaP database of genotypes and phenotypes
inferredcites →https://doi.org/10.1038/ng1010-813openalex-snapshot
Public data archives for genomic structural variation
inferredcites →https://doi.org/10.1056/nejmoa1106920openalex-snapshot
Origins of the E. coli Strain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany
inferredcites →https://doi.org/10.1093/nar/29.1.308openalex-snapshot
dbSNP: the NCBI database of genetic variation
inferredcites →https://doi.org/10.1093/nar/gkh073openalex-snapshot
Database resources of the National Center for Biotechnology Information: update
inferredcites →https://doi.org/10.1093/nar/gkm846openalex-snapshot
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions
inferredcites →https://doi.org/10.1093/nar/gkm884openalex-snapshot
The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata
inferredcites →https://doi.org/10.1093/nar/gkp1078openalex-snapshot
Archiving next generation sequencing data
inferredcites →https://doi.org/10.1093/nar/gkp919openalex-snapshot
MicrobesOnline: an integrated portal for comparative and functional genomics
inferredcites →https://doi.org/10.1093/nar/gkq1079openalex-snapshot
GenBank
inferredcites →https://doi.org/10.1093/nar/gkq1146openalex-snapshot
NCBI Epigenomics: a new public resource for exploring epigenomic data sets
inferredcites →https://doi.org/10.1093/nar/gkq1150openalex-snapshot
The International Nucleotide Sequence Database Collaboration
inferredcites →https://doi.org/10.1093/nar/gkq1172openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferredcites →https://doi.org/10.1093/nar/gkq1184openalex-snapshot
NCBI GEO: archive for functional genomics data sets--10 years on
inferredcites →https://doi.org/10.1093/nar/gkr1006openalex-snapshot
The International Nucleotide Sequence Database Collaboration
inferredcites →https://doi.org/10.1093/nar/gkr1100openalex-snapshot
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
inferredcites →https://doi.org/10.1093/nar/gkr1163openalex-snapshot
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata
inferredcites →https://doi.org/10.1093/nar/gkr937openalex-snapshot
The BioSample Database (BioSD) at the European Bioinformatics Institute
inferredcites →https://doi.org/10.1186/1471-2105-5-130openalex-snapshot
GDR (G enome D atabase for R osaceae): integrated web resources for Rosaceae genomics and genetics research

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Modeling community standards for metadata as templates makes data FAIR
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Improving data archiving practices in ancient genomics
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Opening doors to physical sample tracking and attribution in Earth and environmental sciences
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Characterization of TRPA channels in the starfish Patiria pectinifera: involvement of thermally activated TRPA1 in thermotaxis in marine planktonic larvae
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Identification of novel mazEF/pemIK family toxin-antitoxin loci and their distribution in the Staphylococcus genus
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Factors associated with plasmid antibiotic resistance gene carriage revealed using large-scale multivariable analysis
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Amynthas corticis genome reveals molecular mechanisms behind global distribution
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A genomic view of the bacterial family Endozoicomonadaceae in marine symbioses
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Gypsy moth genome provides insights into flight capability and virus–host interactions
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Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications
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MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework
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PATRIC as a unique resource for studying antimicrobial resistance
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Practical selection of representative sets of RNA-seq samples using a hierarchical approach
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CistromeMeta: a large language model powered tool for automated ChIP-seq metadata extraction
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EcoGene-RefSeq: EcoGene tools applied to the RefSeq prokaryotic genomes
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mimicMe: a web server for prediction and analysis of host-like proteins in microbial pathogens
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MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive
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CorkOakDB—The Cork Oak Genome Database Portal
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Increasing metadata coverage of SRA BioSample entries using deep learning–based named entity recognition
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Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank
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Standardized naming of microbiome samples in Genomes OnLine Database
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GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture
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The text2term tool to map free-text descriptions of biomedical terms to ontologies
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GeniePool 2.0: advancing variant analysis through CHM13-T2T, AlphaMissense, gnomAD V4 integration, and variant co-occurrence queries
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Ontology application and use at the ENCODE DCC
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An Ebola virus-centered knowledge base
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New extension software modules to enhance searching and display of transcriptome data in Tripal databases
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Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research
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The NCBI BioCollections Database
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AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture
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Tripal Developer Toolkit
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Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases
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Tripal EUtils: a Tripal module to increase exchange and reuse of genome assembly metadata
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Genome-wide evolutionary characterization and expression analysis of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED gene family in Brachypodium distachyon
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*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments
inferred← citeshttps://doi.org/10.1093/gigascience/giab001openalex-snapshot
metaXplor: an interactive viral and microbial metagenomic data manager
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Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package
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Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database
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Toward total recall: Enhancing data FAIRness through AI-driven metadata standardization
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Plant specimen contextual data consensus
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Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive
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Ecological constraints and evolutionary trade-offs shape nitrogen fixation across habitats
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Mapping Geological Events and Nitrogen Fixation Evolution Onto the Timetree of the Evolution of Nitrogen-Fixation Genes
inferred← citeshttps://doi.org/10.1093/nar/gkaa1023openalex-snapshot
GenBank
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HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes
inferred← citeshttps://doi.org/10.1093/nar/gkaa372openalex-snapshot
EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities
inferred← citeshttps://doi.org/10.1093/nar/gkaa412openalex-snapshot
ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses
inferred← citeshttps://doi.org/10.1093/nar/gkaa637openalex-snapshot
Planet Microbe: a platform for marine microbiology to discover and analyze interconnected ‘omics and environmental data
inferred← citeshttps://doi.org/10.1093/nar/gkab1046openalex-snapshot
BioSamples database: FAIRer samples metadata to accelerate research data management
inferred← citeshttps://doi.org/10.1093/nar/gkab1111openalex-snapshot
PLSDB: advancing a comprehensive database of bacterial plasmids
inferred← citeshttps://doi.org/10.1093/nar/gkab1135openalex-snapshot
GenBank
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PDCM Finder: an open global research platform for patient-derived cancer models
inferred← citeshttps://doi.org/10.1093/nar/gkac863openalex-snapshot
CottonMD: a multi-omics database for cotton biological study
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DNA Damage Atlas: an atlas of DNA damage and repair
inferred← citeshttps://doi.org/10.1093/nar/gkad847openalex-snapshot
MiST 4.0: a new release of the microbial signal transduction database, now with a metagenomic component
inferred← citeshttps://doi.org/10.1093/nar/gkad875openalex-snapshot
gcPathogen: a comprehensive genomic resource of human pathogens for public health
inferred← citeshttps://doi.org/10.1093/nar/gkad965openalex-snapshot
NCBI GEO: archive for gene expression and epigenomics data sets: 23-year update
inferred← citeshttps://doi.org/10.1093/nar/gkae1114openalex-snapshot
GenBank 2025 update
inferred← citeshttps://doi.org/10.1093/nar/gkae858openalex-snapshot
PerturBase: a comprehensive database for single-cell perturbation data analysis and visualization
inferred← citeshttps://doi.org/10.1093/nar/gkae913openalex-snapshot
scLTdb: a comprehensive single-cell lineage tracing database
inferred← citeshttps://doi.org/10.1093/nar/gkae928openalex-snapshot
Dog10K: an integrated Dog10K database summarizing canine multi-omics
inferred← citeshttps://doi.org/10.1093/nar/gkaf1118openalex-snapshot
Metalog: curated and harmonised contextual data for global metagenomics samples
inferred← citeshttps://doi.org/10.1093/nar/gkaf1190openalex-snapshot
GMrepo v3: a curated human gut microbiome database with expanded disease coverage and enhanced cross-dataset biomarker analysis
inferred← citeshttps://doi.org/10.1093/nar/gkaf1194openalex-snapshot
ResMicroDb: a comprehensive database and analysis platform for the human respiratory microbiome
inferred← citeshttps://doi.org/10.1093/nar/gkr1006openalex-snapshot
The International Nucleotide Sequence Database Collaboration
inferred← citeshttps://doi.org/10.1093/nar/gkr1184openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferred← citeshttps://doi.org/10.1093/nar/gkr1196openalex-snapshot
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection
inferred← citeshttps://doi.org/10.1093/nar/gks1084openalex-snapshot
The International Nucleotide Sequence Database Collaboration
inferred← citeshttps://doi.org/10.1093/nar/gks1112openalex-snapshot
The EBI enzyme portal
inferred← citeshttps://doi.org/10.1093/nar/gks1152openalex-snapshot
DDBJ new system and service refactoring
inferred← citeshttps://doi.org/10.1093/nar/gks1164openalex-snapshot
Clone DB: an integrated NCBI resource for clone-associated data
inferred← citeshttps://doi.org/10.1093/nar/gks1171openalex-snapshot
NCBI Epigenomics: What’s new for 2013
inferred← citeshttps://doi.org/10.1093/nar/gks1189openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferred← citeshttps://doi.org/10.1093/nar/gks1193openalex-snapshot
NCBI GEO: archive for functional genomics data sets—update
inferred← citeshttps://doi.org/10.1093/nar/gks1195openalex-snapshot
GenBank
inferred← citeshttps://doi.org/10.1093/nar/gkt1030openalex-snapshot
GenBank
inferred← citeshttps://doi.org/10.1093/nar/gkt1066openalex-snapshot
DDBJ progress report: a new submission system for leading to a correct annotation
inferred← citeshttps://doi.org/10.1093/nar/gkt1081openalex-snapshot
Updates to BioSamples database at European Bioinformatics Institute
inferred← citeshttps://doi.org/10.1093/nar/gkt1099openalex-snapshot
PATRIC, the bacterial bioinformatics database and analysis resource
inferred← citeshttps://doi.org/10.1093/nar/gkt1146openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferred← citeshttps://doi.org/10.1093/nar/gkt1244openalex-snapshot
Ribosomal Database Project: data and tools for high throughput rRNA analysis
inferred← citeshttps://doi.org/10.1093/nar/gku1055openalex-snapshot
Gene: a gene-centered information resource at NCBI
inferred← citeshttps://doi.org/10.1093/nar/gku1062openalex-snapshot
Update on RefSeq microbial genomes resources
inferred← citeshttps://doi.org/10.1093/nar/gku1120openalex-snapshot
The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data
inferred← citeshttps://doi.org/10.1093/nar/gku1130openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferred← citeshttps://doi.org/10.1093/nar/gku1216openalex-snapshot
GenBank
inferred← citeshttps://doi.org/10.1093/nar/gku895openalex-snapshot
CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities
inferred← citeshttps://doi.org/10.1093/nar/gkv1160openalex-snapshot
ENCODE data at the ENCODE portal
inferred← citeshttps://doi.org/10.1093/nar/gkv1226openalex-snapshot
Assembly: a resource for assembled genomes at NCBI
inferred← citeshttps://doi.org/10.1093/nar/gkv1276openalex-snapshot
GenBank
inferred← citeshttps://doi.org/10.1093/nar/gkv1290openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferred← citeshttps://doi.org/10.1093/nar/gkw1065openalex-snapshot
Virus Variation Resource – improved response to emergent viral outbreaks
inferred← citeshttps://doi.org/10.1093/nar/gkw1070openalex-snapshot
GenBank
inferred← citeshttps://doi.org/10.1093/nar/gkx1094openalex-snapshot
GenBank
inferred← citeshttps://doi.org/10.1093/nar/gky1061openalex-snapshot
BioSamples database: an updated sample metadata hub
inferred← citeshttps://doi.org/10.1093/nar/gky984openalex-snapshot
PDX Finder: A portal for patient-derived tumor xenograft model discovery
inferred← citeshttps://doi.org/10.1093/nar/gky989openalex-snapshot
GenBank
inferred← citeshttps://doi.org/10.1093/nar/gkz935openalex-snapshot
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
inferred← citeshttps://doi.org/10.1093/nar/gkz956openalex-snapshot
GenBank
inferred← citeshttps://doi.org/10.1093/nar/gkz994openalex-snapshot
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes
inferred← citeshttps://doi.org/10.1093/ve/veae040openalex-snapshot
A parasite odyssey: An RNA virus concealed in Toxoplasma gondii
inferred← citeshttps://doi.org/10.1098/rstb.2015.0334openalex-snapshot
DNA barcoding and taxonomy: dark taxa and dark texts
inferred← citeshttps://doi.org/10.1099/mgen.0.000309openalex-snapshot
Pangenome of Acinetobacter baumannii uncovers two groups of genomes, one of them with genes involved in CRISPR/Cas defence systems associated with the absence of plasmids and exclusive genes for biofilm formation
inferred← citeshttps://doi.org/10.1099/mgen.0.000616openalex-snapshot
The roles of antimicrobial resistance, phage diversity, isolation source and selection in shaping the genomic architecture of Bacillus anthracis
inferred← citeshttps://doi.org/10.1099/mgen.0.001050openalex-snapshot
A multidrug-resistant Salmonella enterica Typhimurium DT104 complex lineage circulating among humans and cattle in the USA lost the ability to produce pertussis-like toxin ArtAB
inferred← citeshttps://doi.org/10.1099/mgen.0.001145openalex-snapshot
Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications
inferred← citeshttps://doi.org/10.1099/mgen.0.001633openalex-snapshot
Genomic surveillance of Salmonella enterica serotype Minnesota strains from poultry products imported into South Africa
inferred← citeshttps://doi.org/10.1101/2019.12.13.874909openalex-snapshot
Survey of Public Assay Data: Opportunities and Challenges to Understanding Antimicrobial Resistance
inferred← citeshttps://doi.org/10.1101/2022.01.13.476279openalex-snapshot
hAMRoaster: a tool for comparing performance of AMR gene detection software
inferred← citeshttps://doi.org/10.1101/2022.01.18.476746openalex-snapshot
Genomic surveillance of Bacillus cereus sensu lato strains isolated from meat and poultry products in South Africa enables inter- and intra-national surveillance and source tracking
inferred← citeshttps://doi.org/10.1101/2022.04.06.487395openalex-snapshot
A multidrug-resistant Salmonella enterica Typhimurium DT104 complex lineage circulating among humans and cattle in the United States lost the ability to produce pertussis-like toxin ArtAB
inferred← citeshttps://doi.org/10.1101/2022.09.16.508226openalex-snapshot
Re-exploiting multiple RNA-seq data to identify transcript variations in Podospora anserina
inferred← citeshttps://doi.org/10.1101/2023.12.05.570195openalex-snapshot
Predicting Phenotypic Traits Using a Massive RNA-seq Dataset
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