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bedrock.bio

ncbi_taxonomy.citations

import bedrock_bio as bb

rel = bb.load_table('ncbi_taxonomy.citations')

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
sources citation_id citation_key medline_id pubmed_id url text taxon_ids
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax... 100 Mellado E et al. (1995) None 7547290 None Mellado, E., Moore, E.R., Nieto, J.J., and Ven... [42055, 42566]
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax... 1000 Citrobacter intermedius None NaN None Bergey's Manual of Systematic Bacteriology (19... [66695]
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax... 10000 Prevot AR (1938c) None NaN None Prevot, A.R. \"Etudes de systematique bacterie... [816, 817, 818, 823, 1730, 1736, 1737, 28117, ...
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax... 10001 Holdeman LV et al. (1977) None NaN None Holdeman, L.V., Cato, E.P., Moore, W.E.C.: Ana... [905, 28114, 39489, 83339, 84025]
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/pub/tax... 10002 Dai SK et al. (unpublished_2002) None NaN None Dai, S.K., Lin, H.P., and Liu, J.K. [No title]... [185668]

Description

Section titled “Description”

Literature citations associated with NCBI Taxonomy nodes, one row per citation.

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.
citation_id TEXT NCBI Taxonomy citation ID.
citation_key TEXT NCBI citation key, if supplied.
medline_id TEXT MEDLINE identifier, if assigned; null when NCBI supplies zero.
pubmed_id TEXT PubMed identifier, if assigned; null when NCBI supplies zero.
url TEXT Citation URL, if supplied.
text TEXT Citation text. NCBI’s escaped newlines, tabs, quotes, and backslashes remain encoded.
taxon_ids TEXT[] Taxonomy IDs associated with the citation, split from NCBI’s space-delimited field.