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bedrock.bio

refseq.sequence_annotations

import bedrock_bio as bb

rel = bb.load_table('refseq.sequence_annotations')
rel = rel.filter("assembly_accession = 'GCF_000001215.4'")

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
sources assembly_accession sequence_accession start end is_forward_strand sequence_annotation_id annotation_type annotation_method db_xrefs annotation_name associated_gene_symbol allele_name is_pseudogene function experiments is_partial is_start_partial is_end_partial note
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_024511.2 14917 19524 True id-NC_024511.2:14917..19524 sequence_feature RefSeq [{'db': 'FLYBASE', 'id': 'FBgn0013687'}] None None None False None [] False False False A+T region%3B control region

Description

Section titled “Description”

RefSeq sequence annotations, one row per interval. annotation_type classifies each annotation, and an annotation ID can label multiple intervals.

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001215.4'
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
    • 'GCF_000001635.20'
    • 'GCF_000001635.27'
    • 'GCF_000001735.3'
    • 'GCF_000001735.4'
    • 'GCF_000002035.6'
    • 'GCF_000002525.2'
    • 'GCF_000002655.1'
    • 'GCF_000002765.6'
    • 'GCF_000002855.4'
    • 'GCF_000002945.1'
    • 'GCF_000002945.2'
    • 'GCF_000002985.6'
    • 'GCF_000003195.3'
    • 'GCF_000003625.3'
    • 'GCF_000005845.2'
    • 'GCF_000006565.2'
    • 'GCF_000006665.1'
    • 'GCF_000006745.1'
    • 'GCF_000006845.1'
    • 'GCF_000006885.1'
    • 'GCF_000006925.2'
    • 'GCF_000007545.1'
    • 'GCF_000007565.2'
    • 'GCF_000007785.1'
    • 'GCF_000008765.1'
    • 'GCF_000008805.1'
    • 'GCF_000009045.1'
    • 'GCF_000009085.1'
    • 'GCF_000009205.2'
    • 'GCF_000013465.1'
    • 'GCF_000015005.1'
    • 'GCF_000016305.1'
    • 'GCF_000025565.1'
    • 'GCF_000027305.1'
    • 'GCF_000146045.2'
    • 'GCF_000167675.1'
    • 'GCF_000174395.2'
    • 'GCF_000195955.2'
    • 'GCF_000195995.1'
    • 'GCF_000196035.1'
    • 'GCF_000196095.1'
    • 'GCF_000226075.1'
    • 'GCF_000237925.1'
    • 'GCF_000285655.3'
    • 'GCF_000409795.2'
    • 'GCF_000767705.1'
    • 'GCF_001077675.1'
    • 'GCF_001433935.1'
    • 'GCF_001457595.1'
    • 'GCF_001593425.2'
    • 'GCF_002863925.1'
    • 'GCF_009914755.1'
    • 'GCF_016772045.2'
    • 'GCF_017654675.1'
    • 'GCF_020379485.1'
    • 'GCF_047675955.1'
    • 'GCF_049354715.1'
    • 'GCF_902167145.1'

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 Partition column. Versioned RefSeq assembly accession (GCF accession).
sequence_accession TEXT Versioned RefSeq nucleotide sequence accession on which the annotation is located; joins refseq.assembly_sequences.sequence_accession.
start INT 1-based inclusive start coordinate of the annotated interval.
end INT 1-based inclusive end coordinate of the annotated interval.
is_forward_strand BOOLEAN Whether the annotated interval is on the forward strand; null when the GFF strand is unspecified.
sequence_annotation_id TEXT Local GFF3 ID of the annotation; not a stable RefSeq identifier and can recur across intervals.
annotation_type TEXT Source GFF3 sequence annotation feature type.
annotation_method TEXT NCBI GFF column-2 annotation method or source, if supplied.
db_xrefs STRUCT(db TEXT, id TEXT)[] Database cross-references from GFF Dbxref; each item has a database and identifier, which may contain colons.
annotation_name TEXT Annotation name from GFF standard_name, if supplied.
associated_gene_symbol TEXT Gene symbol from GFF gene, if supplied; this is not a local GFF gene ID join.
allele_name TEXT Allele name from GFF allele, if supplied.
is_pseudogene BOOLEAN Whether GFF pseudo=true marks the annotation as pseudogenic.
function TEXT Free text functional description from GFF function, if supplied.
experiments TEXT[] Percent-decoded experimental evidence entries from the comma-separated GFF experiment attribute.
is_partial BOOLEAN Whether NCBI marks the annotation as partial with GFF partial=true.
is_start_partial BOOLEAN Whether NCBI marks the column-4 start boundary as partial with GFF start_range.
is_end_partial BOOLEAN Whether NCBI marks the column-5 end boundary as partial with GFF end_range.
note TEXT Free text GFF Note annotation, if supplied.