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Genome Data

Metadata record for a Genome

Data Type: genome

Primary Key: genome_id

Attributes

_version_ ( number)
additional_metadata ( array of case insensitive strings)
altitude ( case insensitive string)
antimicrobial_resistance ( array of case insensitive strings)
antimicrobial_resistance_evidence ( case insensitive string)
assembly_accession ( string)
assembly_method ( case insensitive string)
authors ( case insensitive string)
bioproject_accession ( string)
biosample_accession ( string)
biovar ( case insensitive string)
body_sample_site ( case insensitive string)
body_sample_subsite ( case insensitive string)
cds ( integer)
cds_ratio ( number)
cell_shape ( case insensitive string)
checkm_completeness ( number)
checkm_contamination ( number)
chromosomes ( integer)
clade ( string)
class ( case insensitive string)
coarse_consistency ( number)
collection_date ( string)
collection_year ( integer)
comments ( array of case insensitive strings)
common_name ( string)
completion_date ( date)
contig_l50 ( integer)
contig_n50 ( integer)
contigs ( integer)
core_families ( integer)
core_family_ratio ( number)
culture_collection ( case insensitive string)
date_inserted ( date)
date_modified ( date)
depth ( case insensitive string)
disease ( array of case insensitive strings)
family ( case insensitive string)
fine_consistency ( number)
gc_content ( number)
genbank_accessions ( case insensitive string)
genome_id * ( string)
genome_length ( integer)
genome_name ( case insensitive string)
genome_quality ( string)
genome_quality_flags ( array of strings)
genome_status ( case insensitive string)
genus ( case insensitive string)
geographic_group ( case insensitive string)
geographic_location ( case insensitive string)
gram_stain ( case insensitive string)
h1_clade_global ( array of strings)
h1_clade_us ( array of strings)
h3_clade ( array of strings)
h5_clade ( array of strings)
h_type ( integer)
habitat ( case insensitive string)
host_age ( case insensitive string)
host_common_name ( case insensitive string)
host_gender ( case insensitive string)
host_group ( case insensitive string)
host_health ( case insensitive string)
host_name ( case insensitive string)
host_scientific_name ( case insensitive string)
hypothetical_cds ( integer)
hypothetical_cds_ratio ( number)
isolation_comments ( case insensitive string)
isolation_country ( case insensitive string)
isolation_site ( case insensitive string)
isolation_source ( case insensitive string)
kingdom ( case insensitive string)
lab_host ( case insensitive string)
latitude ( case insensitive string)
lineage ( string)
longitude ( case insensitive string)
mat_peptide ( integer)
missing_core_family_ids ( array of strings)
mlst ( case insensitive string)
motility ( case insensitive string)
n_type ( integer)
ncbi_project_id ( string)
nearest_genomes ( array of strings)
optimal_temperature ( case insensitive string)
order ( case insensitive string)
organism_name ( case insensitive string)
other_clinical ( array of case insensitive strings)
other_environmental ( array of case insensitive strings)
other_names ( array of case insensitive strings)
other_typing ( array of case insensitive strings)
outgroup_genomes ( array of strings)
owner ( string)
oxygen_requirement ( case insensitive string)
p2_genome_id ( integer)
partial_cds ( integer)
partial_cds_ratio ( number)
passage ( case insensitive string)
pathovar ( case insensitive string)
patric_cds ( integer)
ph1n1_like ( string)
phenotype ( array of case insensitive strings)
phylum ( case insensitive string)
plasmids ( integer)
plfam_cds ( integer)
plfam_cds_ratio ( number)
public ( boolean)
publication ( string)
reference_genome ( string)
refseq_accessions ( case insensitive string)
refseq_cds ( integer)
refseq_project_id ( string)
rrna ( integer)
salinity ( case insensitive string)
season ( string)
segment ( string)
segments ( integer)
sequencing_centers ( case insensitive string)
sequencing_depth ( case insensitive string)
sequencing_platform ( case insensitive string)
sequencing_status ( case insensitive string)
serovar ( case insensitive string)
species ( case insensitive string)
sporulation ( case insensitive string)
sra_accession ( string)
state_province ( case insensitive string)
strain ( case insensitive string)
subclade ( string)
subtype ( string)
superkingdom ( case insensitive string)
taxon_id ( integer)
taxon_lineage_ids ( array of strings)
taxon_lineage_names ( array of strings)
temperature_range ( case insensitive string)
trna ( integer)
type_strain ( case insensitive string)
user_read ( array of strings)
user_write ( array of strings)

API

GET :genome_id

Retrieve a genome data object by genome_id

EXAMPLE

https://www.bv-brc.org/api/genome/1313.5458

Try It!

QUERY :query

Query for genome data objects with an RQL Query

Return Formats

Requests may include an HTTP ACCEPT header from this list to transform the data into the requested type.

application/json - Returns results as an array of JSON objects
application/solr+json - Results results in SOLR JSON response format
text/csv - Returns results in Comma Separated values (CSV) format. Columns are separated by ','. Multi-value columns are separated by ';'. Rows are separated by new line
text/tsv - Returns results in Tab Separated values (TSV) format. Columns are separated by a tab. Multi-value columns are separated by ';'. Rows are separated by new line
application/vnd.openxmlformats - Returns objects as an MS Excel document

EXAMPLES

Query for genome data objects with a genome_id equal to 1313.5458. Return results as a JSON Array.
```
https://www.bv-brc.org/api/genome/?eq(genome_id,1313.5458)
```
Try It!
Query for sequences with taxon_id == 1313, limit to 5 sequences. Return TSV data.
```
https://www.bv-brc.org/api/genome/?eq(taxon_id,1313)&limit(5)&http_accept=text/tsv
```
Try It!