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pathogenicity_label
|
Labeling according to pathogenicity - either non-pathogenic to humans (NHP) or pathogenic to humans (HP).
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genome_id
|
Genome ID from Bacterial and Viral Bioinformatics Resource Center (BV-BRC) database.
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genome_name
|
Genome name.
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strain
|
Strain name according to National Center for Biotechnology Information (NCBI) taxonomy.
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species
|
Species name according to NCBI taxonomy.
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genus
|
Genus name according to NCBI taxonomy.
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family
|
Family name according to NCBI taxonomy.
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order
|
Order name according to NCBI taxonomy.
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class
|
Class name according to NCBI taxonomy.
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phylum
|
Phylum name according to NCBI taxonomy.
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biosample_accession
|
Biosample accession number ID from NCBI.
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taxon_id
|
Taxon ID from NCBI taxonomy.
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serovar
|
Taxonomy below subspecies; a variant which is usually based on its antigenic properties. Same as serotype (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).
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biovar
|
Variant distinguished by its unique biochemical or physiological traits (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).
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pathovar
|
Taxonomy below subspecies; a variety usually based on its pathogenic properties. Sometimes used as equivalent to subspecies. (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/)
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mlst
|
Genotypic identifier based on housekeeping gene sequences.
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other_typing
|
Strain typing or characterization methods beyond the standard approaches such as MLST (Multilocus Sequence Typing). Each "genotype" followed by a number (e.g., genotype:1 or genotype:1903) denotes a unique genetic profile or pattern that has been identified in the microbial species under investigation.
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culture_collection
|
Reference to a deposited microbial strain in a repository, identified by a unique accession number.
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type_strain
|
Indication if it is a type strain (‘yes’ or ‘’). A type strain is a nomenclatural standard for a particular bacterial species, serving as a reference point for its definition and identification.
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completion_date
|
Date of project completion.
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publication
|
Associated scientific publication identifier.
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bioproject_accession
|
Unique identifier to corresponding project in NCBI.
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assembly_accession
|
Unique identifier to corresponding genome assembly in NCBI. Refers to a specific version of a genome assembly submitted to a database like NCBI's GenBank.
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genbank_accessions
|
Unique identifier(s) of GenBank assembly/assemblies in NCBI.
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refseq_accessions
|
Unique identifiers assigned to sequences within the Reference Sequence (RefSeq) database. RefSeq sequences are curated by NCBI staff and collaborators.
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sequencing_centers
|
Sequencing center (e.g. University ‘x’, Hospital ‘y’).
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sequencing_platform
|
Sequencing platform (e.g. Illumina, PacBio).
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sequencing_depth
|
Average number of times each nucleotide in a genome is sequenced.
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assembly_method
|
Methodology used to assemble the genomic sequences.
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chromosomes
|
Number of associated chromosomes.
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plasmids
|
Number of associated plasmids.
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contigs
|
Number of associated contigs.
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genome_length
|
Genome length measured in base pairs (bp).
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gc_content
|
Measure of the proportion of guanine (G) and cytosine (C) nucleotides in the DNA sequence, expressed as a percentage of the total nucleotide composition.
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patric_cds
|
Number of protein-coding sequences (CDS) annotated or sourced from PATRIC (previous version of BV-BRC).
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refseq_cds
|
Number of protein-coding sequences (CDS) annotated or sourced from RefSeq database.
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isolation_source
|
Corresponding origin of isolation. This attribute provides information about the ecological niche or source of the bacterial strain.
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isolation_comments
|
Additional notes or comments regarding the isolation of a specific bacterial strain.
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collection_date
|
Date on which a specific bacterial strain was collected or isolated from its source.
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isolation_country
|
Country associated with the biological sample isolation.
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geographic_location
|
Geographical descriptors associated with the biological sample isolation.
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other_environmental
|
Supplementary attribute to describe specific environmental conditions or contexts associated with the biological sample.
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host_gender
|
Host gender.
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host_age
|
Host age.
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host_health
|
Host health status or condition.
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body_sample_site
|
Specific anatomical site or location from which the biological sample was collected.
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other_clinical
|
Additional clinical information or metadata associated with the biological sample.
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antimicrobial_resistance
|
This field shows genomes that have been specifically tested against certain antibiotics and the resulting phenotype from that test. Note that a genome can have multiple antibiotic phenotypes, such as being resistant to one drug and susceptible to another. Values in this field include ‘Resistant’,’Susceptible’ or ‘Intermediate’ (https://www.bv-brc.org/docs/quick_references/organisms_taxon/antimicrobial_resistance.html).
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antimicrobial_resistance_evidence
|
Indicates the information source behind the AMR designation. Allowable values include "Computational Prediction”, "Computational Method" , and "AMR Panel” (https://www.bv-brc.org/docs/quick_references/organisms_taxon/antimicrobial_resistance.html)
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gram_stain_bvbrc
|
Gram staining information (“positive” or “negative”) sourced from BV-BRC.
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cell_shape
|
Cell shape information (e.g. Bacilli, Cocci).
|
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motility
|
Motility information (“yes”: motile, “no”: non-motile).
|
|
temperature_range
|
Indication on phenotype associated with range of temperature at which the organism is known to thrive, survive, or exhibit optimal growth (e.g. ‘Mesophilic’).
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optimal_temperature
|
Optimal temperature at which the organism is known to exhibit optimal growth.
|
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oxygen_requirement
|
Specific oxygen conditions a microorganism requires to survive; Values include ‘Aerobic’, ‘Anaerobic’, ‘Facultative’, or ‘Microaerophilic’.
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habitat
|
Natural or artificial habitat in which the bacteria resides or was found.
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disease
|
Host disease.
|
|
comments
|
Supplementary information in form of comments providing further contextual details.
|
|
additional_metadata
|
Supplementary metadata providing further contextual details.
|
|
env_broad_scale
|
Broad-scale environmental context (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).
|
|
env_local_scale
|
Local-scale environmental context (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).
|
|
env_medium
|
Environmental medium/material. keywords describing the material displaced by the entity during sampling (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).
|
|
isol_growth_condt
|
Description or url indication of isolation and growth condition specifications (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).
|
|
project_name
|
A concise name that describes the overall project (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).
|
|
pathogenicity_details
|
Additional bacterial strain information on pathogenicity (e.g;. ‘commensal’, or ‘diphtheria-like symptoms’).
|
|
host_disease
|
Name of relevant disease, e.g. Salmonella gastroenteritis (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).
|
|
host_health_state
|
Information regarding health state of the individual sampled at the time of sampling (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).
|
|
host_disease_outcome
|
Final outcome of disease, e.g., death, chronic disease, recovery.
|
|
host_description
|
Additional host information not included in other defined vocabulary fields (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).
|
|
host_disease_stage
|
Stage of disease at the time of sampling (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).
|
|
pathotype
|
Bacterial specific pathotype (e.g. Eschericia coli - STEC, UPEC) - https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/.
|
|
subsource_note
|
Subsource note. Further details about the origin, isolation method, or other relevant information regarding the sample used.
|
|
note
|
Additional note. This can include details about the source of the sequence, experimental conditions, characteristics of the organism, or any other relevant information.
|
|
description
|
Further details on isolation source or organism.
|
|
biotic_relationship
|
Observed biotic relationship (['', 'free living', 'parasite', 'commensal', ‘symbiont’]) - https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/
|
|
biome
|
Major environment type(s) where sample was collected (https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/).
|
|
host_status
|
Information on host health status.
|
|
risk_group
|
Risk group classification - based on their potential hazard to human health and the environment (species-level, ranges from 1 to 3; 3 representing the highest hazard).
|
|
Note on infection mode
|
Further details on infection mode.
|
|
checkm_compl_final
|
Genome completeness (%) according to CheckM tool v1.1.6.
|
|
checkm_contam_final
|
Genome contamination (%) according to CheckM tool v1.1.6.
|
|
disease_category
|
Disease category (e.g. “Respiratory diseases”).
|
|
disease_subcategory
|
Subcategory of the main disease category (e.g. “Pneumonia”). When the specific infectious disease name is not available, an associated keyword is given instead (e.g. “Pertussis”).
|
|
isolation_source_category
|
Isolation source category (e.g. “Respiratory tract”).
|
|
disease_comb
|
Combination of the disease category and disease subcategory (e.g. Respiratory Diseases - Pneumonia).
|
