BioProject XML Schema
This is a XML Schema specification of BioProject data. A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project.
Description
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This is a XML Schema specification of BioProject data. A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project.
metasource: Fairsharing.orgversion: FAIRsharing.org: BioProject XML Schema; BioProject XML Schema; DOI: https://doi.org/10.25504/FAIRsharing.rk682s; Last edited: Feb. 7, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Webpage:
https://www.ncbi.nlm.nih.gov/data_specs/schema/other/bioproject/Webpage
More detailed information about this field from each metasource.
https://www.ncbi.nlm.nih.gov/data_specs/schema/other/bioproject/
metasource: Fairsharing.orgversion: FAIRsharing.org: BioProject XML Schema; BioProject XML Schema; DOI: https://doi.org/10.25504/FAIRsharing.rk682s; Last edited: Feb. 7, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Licence:
Name: NCBI Data Policies and DisclaimerLicence name
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NCBI Data Policies and Disclaimer
metasource: Fairsharing.orgversion: FAIRsharing.org: BioProject XML Schema; BioProject XML Schema; DOI: https://doi.org/10.25504/FAIRsharing.rk682s; Last edited: Feb. 7, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Licence URL
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http://www.ncbi.nlm.nih.gov/home/about/policies.shtml
metasource: Fairsharing.orgversion: FAIRsharing.org: BioProject XML Schema; BioProject XML Schema; DOI: https://doi.org/10.25504/FAIRsharing.rk682s; Last edited: Feb. 7, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications:
Publications
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BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata
PMID: 22139929
metasource: Fairsharing.org
version: FAIRsharing.org: BioProject XML Schema; BioProject XML Schema; DOI: https://doi.org/10.25504/FAIRsharing.rk682s; Last edited: Feb. 7, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications
More detailed information about this field from each metasource.
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata
PMID: 22139929
metasource: Fairsharing.org
version: FAIRsharing.org: BioProject XML Schema; BioProject XML Schema; DOI: https://doi.org/10.25504/FAIRsharing.rk682s; Last edited: Feb. 7, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata
PubMed citations: 149.
149 articles citing: BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata
High Performance Integration Pipeline for Viral and Epitope Sequences. PMID:35822815
A database of animal metagenomes. PMID:35710683
Identification of Promoter Region Markers Associated With Altered Expression of Resistance-Nodulation-Division Antibiotic Efflux Pumps in Acinetobacter baumannii. PMID:35663863
Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. PMID:35585929
Genomic Sequencing of Bacillus cereus Sensu Lato Strains Isolated from Meat and Poultry Products in South Africa Enables Inter- and Intranational Surveillance and Source Tracking. PMID:35475639
Robust Mutation Profiling of SARS-CoV-2 Variants from Multiple Raw Illumina Sequencing Data with Cloud Workflow. PMID:35456492
FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research. PMID:35418585
NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories. PMID:35283794
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank. PMID:35230423
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package. PMID:35169842
Public human microbiome data are dominated by highly developed countries. PMID:35167588
Quantitative Analysis and Visualization of the Interaction Between Intestinal Microbiota and Type 1 Diabetes in Children Based on Multi-Databases. PMID:34976889
RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse. PMID:34876495
GenBank. PMID:34850943
PLSDB: advancing a comprehensive database of bacterial plasmids. PMID:34850116
BioSamples database: FAIRer samples metadata to accelerate research data management. PMID:34747489
Orchestrating an Optimized Next-Generation Sequencing-Based Cloud Workflow for Robust Viral Identification during Pandemics. PMID:34681121
The roles of antimicrobial resistance, phage diversity, isolation source and selection in shaping the genomic architecture of Bacillus anthracis. PMID:34402777
Hidden Viral Sequences in Public Sequencing Data and Warning for Future Emerging Diseases. PMID:34399612
Current Approaches for Advancement in Understanding the Molecular Mechanisms of Mycotoxin Biosynthesis. PMID:34360643
Practical selection of representative sets of RNA-seq samples using a hierarchical approach. PMID:34252927
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. PMID:34168315
Designing Multi-Antigen Vaccines Against Acinetobacter baumannii Using Systemic Approaches. PMID:33936107
Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition. PMID:33914028
Phylogenetic Distribution of Polysaccharide-Degrading Enzymes in Marine Bacteria. PMID:33815349
AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata. PMID:33691615
Antibiotic Resistance in Shiga Toxigenic Escherichia coli Isolates from Surface Waters and Sediments in a Mixed Use Urban Agricultural Landscape. PMID:33652953
A community resource for paired genomic and metabolomic data mining. PMID:33589842
Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential. PMID:33541265
metaXplor: an interactive viral and microbial metagenomic data manager. PMID:33527143
Amynthas corticis genome reveals molecular mechanisms behind global distribution. PMID:33514865
An empirical meta-analysis of the life sciences linked open data on the web. PMID:33479214
CorkOakDB-The Cork Oak Genome Database Portal. PMID:33382885
HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes. PMID:33221926
GenBank. PMID:33196830
Combinatorial expression of GPCR isoforms affects signalling and drug responses. PMID:33149304
Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens. PMID:33103064
G-Quadruplexes in the Archaea Domain. PMID:32967357
Comparative genomic analysis of eutherian fibroblast growth factor genes. PMID:32758140
Planet Microbe: a platform for marine microbiology to discover and analyze interconnected 'omics and environmental data. PMID:32735679
Responsible, practical genomic data sharing that accelerates research. PMID:32694666
KGHC: a knowledge graph for hepatocellular carcinoma. PMID:32646496
Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB). PMID:32463383
ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses. PMID:32449934
Promoting best practice in nucleotide sequence data sharing. PMID:32433467
EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities. PMID:32392342
The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments. PMID:32219223
*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments. PMID:32170312
A systems approach to infectious disease. PMID:32060427
Tripal EUtils: a Tripal module to increase exchange and reuse of genome assembly metadata. PMID:31960040
Multi-species annotation of transcriptome and chromatin structure in domesticated animals. PMID:31884969
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes. PMID:31728526
GenBank. PMID:31665464
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. PMID:31665441
Phage integration alters the respiratory strategy of its host. PMID:31650957
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. PMID:31626589
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. PMID:31614509
Quantifying the impact of public omics data. PMID:31383865
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. PMID:31244651
Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases. PMID:31210270
Cyberbiosecurity Challenges of Pathogen Genome Databases. PMID:31157218
An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines. PMID:30894373
New insights from uncultivated genomes of the global human gut microbiome. PMID:30867587
The variable quality of metadata about biological samples used in biomedical experiments. PMID:30778255
Gypsy moth genome provides insights into flight capability and virus-host interactions. PMID:30642971
PDX Finder: A portal for patient-derived tumor xenograft model discovery. PMID:30535239
Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research. PMID:30412219
BioSamples database: an updated sample metadata hub. PMID:30407529
GenBank. PMID:30365038
Tripal Developer Toolkit. PMID:30295719
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories. PMID:30166985
BioPS: System for screening and assessment of biofuel-production potential of cyanobacteria. PMID:30096176
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. PMID:30012108
More than fishing for a cure: The promises and pitfalls of high throughput cancer cell line screens. PMID:29953899
Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. PMID:29854196
The NCBI BioCollections Database. PMID:29688360
A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it. PMID:29479297
A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells. PMID:29320760
Principles and methods of in-silico prioritization of non-coding regulatory variants. PMID:29288389
New extension software modules to enhance searching and display of transcriptome data in Tripal databases. PMID:29220446
GenBank. PMID:29140468
Identification of novel mazEF/pemIK family toxin-antitoxin loci and their distribution in the Staphylococcus genus. PMID:29044211
PATRIC as a unique resource for studying antimicrobial resistance. PMID:28968762
Authentication of M14 melanoma cell line proves misidentification of MDA-MB-435 breast cancer cell line. PMID:28940260
Rapid, High-Throughput Identification of Anthrax-Causing and Emetic Bacillus cereus Group Genome Assemblies via BTyper, a Computational Tool for Virulence-Based Classification of Bacillus cereus Group Isolates by Using Nucleotide Sequencing Data. PMID:28625989
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. PMID:28535296
In silico gene expression profiling in Cannabis sativa. PMID:28529696
Characterization of TRPA channels in the starfish Patiria pectinifera: involvement of thermally activated TRPA1 in thermotaxis in marine planktonic larvae. PMID:28526851
Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive. PMID:28449062
Plant specimen contextual data consensus. PMID:28369359
Orchestrating differential data access for translational research: a pilot implementation. PMID:28330491
Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids. PMID:28286183
Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive. PMID:28038678
Virus Variation Resource - improved response to emergent viral outbreaks. PMID:27899678
GenBank. PMID:27899564
Pathogen metadata platform: software for accessing and analyzing pathogen strain information. PMID:27634291
Toward Accurate and Quantitative Comparative Metagenomics. PMID:27565341
DNA barcoding and taxonomy: dark taxa and dark texts. PMID:27481786
Antimicrobial Resistance Prediction in PATRIC and RAST. PMID:27297683
Energy efficiency trade-offs drive nucleotide usage in transcribed regions. PMID:27098217
Complete genome of Pseudomonas chlororaphis strain UFB2, a soil bacterium with antibacterial activity against bacterial canker pathogen of tomato. PMID:26634018
Database resources of the National Center for Biotechnology Information. PMID:26615191
GenBank. PMID:26590407
Assembly: a resource for assembled genomes at NCBI. PMID:26578580
ENCODE data at the ENCODE portal. PMID:26527727
A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome. PMID:26473382
A Novel Quality Measure and Correction Procedure for the Annotation of Microbial Translation Initiation Sites. PMID:26204119
An Ebola virus-centered knowledge base. PMID:26055098
Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses. PMID:25905099
Ontology application and use at the ENCODE DCC. PMID:25776021
Update on RefSeq microbial genomes resources. PMID:25510495
The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data. PMID:25477381
GenBank. PMID:25414350
Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation. PMID:25411636
Database resources of the National Center for Biotechnology Information. PMID:25398906
Gene: a gene-centered information resource at NCBI. PMID:25355515
SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes. PMID:25309735
Advancing the microbiome research community. PMID:25303518
CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities. PMID:25270877
Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records. PMID:25197497
Genome-wide screening of pathogenicity islands in Mycobacterium tuberculosis based on the genomic barcode visualization. PMID:25108673
Standardized metadata for human pathogen/vector genomic sequences. PMID:24936976
Evaluation of a pooled strategy for high-throughput sequencing of cosmid clones from metagenomic libraries. PMID:24911009
Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. PMID:24456465
Ribosomal Database Project: data and tools for high throughput rRNA analysis. PMID:24288368
Updates to BioSamples database at European Bioinformatics Institute. PMID:24265224
Database resources of the National Center for Biotechnology Information. PMID:24259429
PATRIC, the bacterial bioinformatics database and analysis resource. PMID:24225323
GenBank. PMID:24217914
Relative amino acid composition signatures of organisms and environments. PMID:24204807
DDBJ progress report: a new submission system for leading to a correct annotation. PMID:24194602
Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive. PMID:24167589
MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. PMID:24152717
EcoGene-RefSeq: EcoGene tools applied to the RefSeq prokaryotic genomes. PMID:23736533
Reuse of public genome-wide gene expression data. PMID:23269463
GenBank. PMID:23193287
NCBI Epigenomics: what's new for 2013. PMID:23193265
Database resources of the National Center for Biotechnology Information. PMID:23193264
Clone DB: an integrated NCBI resource for clone-associated data. PMID:23193260
NCBI GEO: archive for functional genomics data sets--update. PMID:23193258
The International Nucleotide Sequence Database Collaboration. PMID:23180798
DDBJ new system and service refactoring. PMID:23180790
The EBI enzyme portal. PMID:23175605
SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models. PMID:23110173
Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens. PMID:23035931
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:22144685
Database resources of the National Center for Biotechnology Information. PMID:22140104
The International Nucleotide Sequence Database Collaboration. PMID:22080546
Tags:
Tags
More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.org
version: FAIRsharing.org: BioProject XML Schema; BioProject XML Schema; DOI: https://doi.org/10.25504/FAIRsharing.rk682s; Last edited: Feb. 7, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
data storage
metasource: Fairsharing.org
version: FAIRsharing.org: BioProject XML Schema; BioProject XML Schema; DOI: https://doi.org/10.25504/FAIRsharing.rk682s; Last edited: Feb. 7, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
experimental measurement
metasource: Fairsharing.org
version: FAIRsharing.org: BioProject XML Schema; BioProject XML Schema; DOI: https://doi.org/10.25504/FAIRsharing.rk682s; Last edited: Feb. 7, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
genomic assembly
metasource: Fairsharing.org
version: FAIRsharing.org: BioProject XML Schema; BioProject XML Schema; DOI: https://doi.org/10.25504/FAIRsharing.rk682s; Last edited: Feb. 7, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: BioProject XML Schema; BioProject XML Schema; DOI: https://doi.org/10.25504/FAIRsharing.rk682s; Last edited: Feb. 7, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Tags
More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: BioProject XML Schema; BioProject XML Schema; DOI: https://doi.org/10.25504/FAIRsharing.rk682s; Last edited: Feb. 7, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
data storage
metasource: Fairsharing.orgversion: FAIRsharing.org: BioProject XML Schema; BioProject XML Schema; DOI: https://doi.org/10.25504/FAIRsharing.rk682s; Last edited: Feb. 7, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
experimental measurement
metasource: Fairsharing.orgversion: FAIRsharing.org: BioProject XML Schema; BioProject XML Schema; DOI: https://doi.org/10.25504/FAIRsharing.rk682s; Last edited: Feb. 7, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
genomic assembly
metasource: Fairsharing.orgversion: FAIRsharing.org: BioProject XML Schema; BioProject XML Schema; DOI: https://doi.org/10.25504/FAIRsharing.rk682s; Last edited: Feb. 7, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
sequencing
metasource: Fairsharing.orgversion: FAIRsharing.org: BioProject XML Schema; BioProject XML Schema; DOI: https://doi.org/10.25504/FAIRsharing.rk682s; Last edited: Feb. 7, 2021, 9:09 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
data storage experimental measurement genomic assembly sequencing
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