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bedrock.bio

genbank.assembly_summary

import bedrock_bio as bb

rel = bb.load_table('genbank.assembly_summary')

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
sources assembly_accession bioproject_accession biosample_accession wgs_master_accession is_historical version_status refseq_exclusion_reason assembly_not_live_date is_reference ... assembly_replicon_count assembly_scaffold_count assembly_contig_count annotation_provider annotation_name annotation_date total_gene_count protein_coding_gene_count non_coding_gene_count pubmed_ids
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCA_000001215.4 PRJNA13812 SAMN02803731 None False latest None NaT True ... 7 1869 2441 FlyBase FlyBase Release 6.54 2023-12-13 17872 13962 3543 [10731132, 12537568, 12537572, 12537573, 12537...
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCA_000001405.14 PRJNA31257 NaN None True replaced None 2013-12-21 False ... 24 249 350 Genome Reference Consortium Annotation submitted by Genome Reference Conso... 2013-06-28 37 13 24 [7219534, 10508508, 10591208, 10830953, 112370...
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCA_000001405.29 PRJNA31257 NaN None False latest None NaT True ... 24 473 999 Genome Reference Consortium Annotation submitted by Genome Reference Conso... 2017-11-21 37 13 24 [7219534, 10508508, 10830953, 11237011, 117800...
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCA_000001635.2 PRJNA20689 NaN None True replaced None 2012-08-21 False ... 21 162 605 Genome Reference Consortium Annotation submitted by Genome Reference Conso... 2012-01-09 <NA> <NA> <NA> [12954771, 19468303, 21750661]
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCA_000001635.9 PRJNA20689 NaN None False latest None NaT True ... 21 101 305 Genome Reference Consortium Annotation submitted by Genome Reference Conso... 2003-09-05 13 13 0 [12954771, 19468303, 21750661]

Description

Section titled “Description”

Selected current and historical GenBank genome assemblies, one row per versioned GCA assembly.

Partitions

Section titled “Partitions”

Not partitioned.

Schema

Section titled “Schema”
Column Type Description
sources STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[] Source provenance for the row.
assembly_accession TEXT Versioned GenBank assembly accession (GCA accession).
bioproject_accession TEXT NCBI BioProject accession associated with the assembly, if supplied.
biosample_accession TEXT NCBI BioSample accession associated with the assembly, if supplied.
wgs_master_accession TEXT GenBank Nucleotide accession and version for the Whole Genome Shotgun project master record, if applicable.
is_historical BOOLEAN Whether this row originated from NCBI’s historical, rather than current, GenBank assembly summary.
version_status TEXT NCBI status of the assembly version, such as latest, replaced, suppressed, or withdrawn.
refseq_exclusion_reason TEXT NCBI reason the assembly is excluded from RefSeq, if supplied.
assembly_not_live_date DATE Date NCBI marked the assembly as no longer live, if applicable.
is_reference BOOLEAN Whether NCBI designates the assembly as a reference genome.
organism_taxon_id TEXT Opaque string NCBI taxonomy ID assigned to the organism represented by this assembly; maps to registry.taxa.taxon_id.
species_taxon_id TEXT Opaque string NCBI taxonomy ID assigned to the assembly’s species.
organism_name TEXT Scientific organism name reported by NCBI.
infraspecific_names STRUCT(type TEXT, name TEXT)[] Infraspecific names reported by NCBI, parsed into type and name pairs.
isolate TEXT Isolate name reported by NCBI, if supplied.
assembly_level TEXT Assembly completeness classification reported by NCBI.
release_type TEXT Release classification reported by NCBI.
genome_representation TEXT Extent of genome representation reported by NCBI.
sequence_release_date DATE Date the assembly sequence was released in an INSDC database.
assembly_name TEXT Readable NCBI assembly label; it is not globally unique.
assembly_submitter TEXT Organization or individual that submitted the assembly.
refseq_assembly_accession TEXT Paired RefSeq assembly accession (GCF accession), if NCBI provides one.
is_identical_to_refseq BOOLEAN Whether NCBI reports the paired RefSeq assembly as identical; null when no comparison is available.
assembly_url TEXT NCBI directory URL for the GenBank assembly package and its files.
relation_to_type_material TEXT Relationship of the organism to type material reported by NCBI, if supplied.
assembly_type TEXT Ploidy or assembly type reported by NCBI, if supplied.
organism_group TEXT NCBI organism group, if supplied.
assembly_size BIGINT Total assembly length in base pairs, if supplied.
assembly_size_ungapped BIGINT Total ungapped assembly length in base pairs, if supplied.
assembly_gc_fraction FLOAT Assembly GC content as a fraction from zero through one, if supplied.
assembly_replicon_count INT Number of replicons in the assembly, if supplied.
assembly_scaffold_count INT Number of scaffolds in the assembly, if supplied.
assembly_contig_count INT Number of contigs in the assembly, if supplied.
annotation_provider TEXT Organization that supplied the current annotation, if supplied.
annotation_name TEXT NCBI annotation release name or version, if supplied.
annotation_date DATE Date of the current annotation release, if supplied.
total_gene_count INT Total annotated gene count, if supplied.
protein_coding_gene_count INT Protein-coding annotated gene count, if supplied.
non_coding_gene_count INT Non-coding annotated gene count, if supplied.
pubmed_ids TEXT[] PubMed identifiers associated with the assembly.