biocOnIce 2026-11

biocOnIce is public biological annotation (genes, transcripts, exons, identifier mappings, ontologies, interactions, publications and more) as flat Parquet, one file per table. The code is at https://github.com/seandavi/bioc-on-ice.

This is the monthly archive release 2026-11. It is a copy of the weekly release 2026-11-01, which passed bioconice gate (see gate.json). Cite and pin it by the 2026-11 revision. Tags are never deleted. For the newest release, queried in place, use https://data.bioconice.cancerdatasci.org/latest/ instead.

Download, then query

Download the release, then query the local files. Do not query hf:// paths in place: anonymous requests are rate-limited, and one query makes many requests, so repeated queries fail with HTTP 429.

hf download seandavis/bioconice --repo-type dataset --revision 2026-11 --local-dir bioconice-2026-11

One table only:

hf download seandavis/bioconice --repo-type dataset --revision 2026-11 --local-dir bioconice-2026-11 \
  --include annotation/gene.parquet

DuckDB: views.sql creates one view per table over paths relative to the download directory, so run it from there:

cd bioconice-2026-11
duckdb bioconice.duckdb < views.sql
duckdb bioconice.duckdb -c "SELECT count(*) FROM annotation.gene"

restore.sql materialises every table into the database instead and checks the row counts against manifest.json: duckdb bioconice-local.duckdb < restore.sql, from the same directory.

Python (polars):

import polars as pl

genes = pl.scan_parquet("bioconice-2026-11/annotation/gene.parquet").head(10).collect()

R (arrow):

genes <- arrow::read_parquet("bioconice-2026-11/annotation/gene.parquet")

Provenance

Release	2026-11-01
Published at	2026-11-01T16:16:42+00:00
Code (git SHA)	127de1e0578cbffe0db891ed258a03601c6a8dfc
Gate reference	https://data.bioconice.cancerdatasci.org/v2026-10-31
Gate passed at	2026-11-01T16:22:33+00:00

Sources and their upstream versions:

Source	Version
bedbase_bed	2026-09-01
bedbase_bedset	2026-09-01
bedbase_bedset_membership	2026-09-01
biogrid	5.0.261
bugsigdb	v1.3.1
cellosaurus	56.0
cellxgene	2026-09-18
cellxgene_census	2025-11-08
complexportal	2026-01-09
encode_experiment	2026-09-18
encode_file	2026-09-18
ensembl	116
eqtlcatalogue	7
gwas_catalog	2026-09-15
hgnc	2026-09-18
icite	2026-08
intact	2026-01-09
mane	1.5
ncbi_gene	2026-08-07
ncbi_gene	2026-09-12
ncbi_gene2accession	2026-08-07
ncbi_gene2accession	2026-09-18
ncbi_gene2go	2026-08-07
ncbi_gene2go	2026-09-12
ncbi_gene2pubmed	2026-08-07
ncbi_gene2pubmed	2026-09-12
ncbi_gene_group	2026-09-18
ncbi_gene_orthologs	2026-09-18
obo_cl	http://purl.obolibrary.org/obo/cl/releases/2026-06-08/cl.json
obo_doid	http://purl.obolibrary.org/obo/doid/releases/2026-08-31/doid.owl
obo_efo	http://www.ebi.ac.uk/efo/releases/v3.94.0/efo.owl
obo_go	http://purl.obolibrary.org/obo/go/releases/2026-07-26/go.owl
obo_hsapdv	http://purl.obolibrary.org/obo/life-stages/releases/2025-01-23/components/hsapdv.owl
obo_mmusdv	http://purl.obolibrary.org/obo/life-stages/releases/2025-01-23/components/mmusdv.owl
obo_mondo	http://purl.obolibrary.org/obo/mondo/releases/2026-09-01/mondo.owl
obo_uberon	http://purl.obolibrary.org/obo/uberon/releases/2026-06-19/uberon.json
pubtator3_chemical	2026-09-19
pubtator3_disease	2026-09-19
pubtator3_gene	2026-09-19
pubtator3_mutation	2026-09-19
pubtator3_species	2026-09-19
rnacentral	27
wikipathways	20260910

The full record is manifest.json: per table its row count, sha256, columns and their documentation, and every provenance.release row.

Tables

81 files, 94.2 GB in total.

Table	File	Rows	Size (GB)
provenance.release	provenance/release.parquet	44	0.00
raw.ncbi__gene2ensembl	raw/ncbi__gene2ensembl.parquet	19,922,787	0.29
raw.ncbi__gene_info	raw/ncbi__gene_info.parquet	72,175,792	1.18
raw.ncbi__gene_history	raw/ncbi__gene_history.parquet	27,395,424	0.10
raw.bugsigdb__full_dump	raw/bugsigdb__full_dump.parquet	7,425	0.00
raw.ensembl__gtf	raw/ensembl__gtf.parquet	334,547,700	3.12
reference.genome	reference/genome.parquet	276	0.00
annotation.gene	annotation/gene.parquet	7,419,569	0.04
annotation.ncbi__gene	annotation/ncbi__gene.parquet	72,153,077	1.05
annotation.transcript	annotation/transcript.parquet	14,092,671	0.09
annotation.exon	annotation/exon.parquet	143,333,679	2.05
annotation.identifier_mapping	annotation/identifier_mapping.parquet	464,335,857	4.79
raw.ncbi__gene2pubmed	raw/ncbi__gene2pubmed.parquet	82,882,628	0.17
annotation.ncbi__gene_pubmed	annotation/ncbi__gene_pubmed.parquet	82,882,628	0.43
raw.ncbi__gene2accession	raw/ncbi__gene2accession.parquet	288,151,046	3.57
raw.ncbi__gene2go	raw/ncbi__gene2go.parquet	124,738,605	0.59
annotation.ncbi__gene_go	annotation/ncbi__gene_go.parquet	124,738,605	1.10
raw.icite__metadata	raw/icite__metadata.parquet	41,035,229	12.07
annotation.icite__publication	annotation/icite__publication.parquet	41,035,229	3.51
annotation.icite__metrics	annotation/icite__metrics.parquet	41,035,229	0.57
raw.cellxgene__dataset	raw/cellxgene__dataset.parquet	2,228	0.00
resource.cellxgene__dataset	resource/cellxgene__dataset.parquet	2,228	0.00
raw.obo__cl	raw/obo__cl.parquet	70,707	0.00
raw.obo__uberon	raw/obo__uberon.parquet	102,486	0.00
raw.obo__mondo	raw/obo__mondo.parquet	178,267	0.01
raw.obo__efo	raw/obo__efo.parquet	269,697	0.01
raw.obo__hsapdv	raw/obo__hsapdv.parquet	1,004	0.00
raw.obo__mmusdv	raw/obo__mmusdv.parquet	606	0.00
raw.obo__go	raw/obo__go.parquet	123,546	0.00
raw.obo__doid	raw/obo__doid.parquet	41,594	0.00
ontology.term	ontology/term.parquet	273,258	0.02
ontology.relationship	ontology/relationship.parquet	514,649	0.00
raw.bedbase__bed	raw/bedbase__bed.parquet	663,721	0.04
raw.bedbase__bedset	raw/bedbase__bedset.parquet	22,188	0.01
raw.bedbase__bedset_membership	raw/bedbase__bedset_membership.parquet	578,552	0.01
resource.bedbase__bedfile	resource/bedbase__bedfile.parquet	663,721	0.04
resource.bedbase__bedset	resource/bedbase__bedset.parquet	22,188	0.00
annotation.icite__citation	annotation/icite__citation.parquet	928,458,585	8.14
raw.pubtator3__gene	raw/pubtator3__gene.parquet	74,519,899	0.69
raw.pubtator3__disease	raw/pubtator3__disease.parquet	168,305,967	1.80
raw.pubtator3__chemical	raw/pubtator3__chemical.parquet	146,957,635	1.58
raw.pubtator3__species	raw/pubtator3__species.parquet	48,958,091	0.46
raw.pubtator3__mutation	raw/pubtator3__mutation.parquet	8,135,311	0.13
annotation.pubtator3__mention	annotation/pubtator3__mention.parquet	478,216,071	2.87
resource.resource_relationship	resource/resource_relationship.parquet	3,734,643	0.06
raw.encode__experiment	raw/encode__experiment.parquet	28,642	0.00
raw.encode__file	raw/encode__file.parquet	1,659,000	0.26
resource.encode__experiment	resource/encode__experiment.parquet	28,642	0.00
resource.encode__file	resource/encode__file.parquet	1,659,000	0.22
raw.hgnc__complete_set	raw/hgnc__complete_set.parquet	45,083	0.00
annotation.hgnc__gene	annotation/hgnc__gene.parquet	45,083	0.00
raw.ncbi__gene_orthologs	raw/ncbi__gene_orthologs.parquet	18,877,923	0.09
raw.ncbi__gene_group	raw/ncbi__gene_group.parquet	51,196	0.00
annotation.ortholog	annotation/ortholog.parquet	37,755,846	0.27
raw.ncbi__mane_summary	raw/ncbi__mane_summary.parquet	19,437	0.00
annotation.mane__transcript	annotation/mane__transcript.parquet	19,437	0.00
raw.cellosaurus__release	raw/cellosaurus__release.parquet	3,188,709	0.01
annotation.cellosaurus__cell_line	annotation/cellosaurus__cell_line.parquet	168,970	0.00
annotation.cellosaurus__xref	annotation/cellosaurus__xref.parquet	473,381	0.00
annotation.cellosaurus__disease	annotation/cellosaurus__disease.parquet	124,953	0.00
raw.wikipathways__gmt	raw/wikipathways__gmt.parquet	1,957	0.00
annotation.wikipathways__pathway	annotation/wikipathways__pathway.parquet	1,957	0.00
annotation.wikipathways__gene_pathway	annotation/wikipathways__gene_pathway.parquet	76,046	0.00
raw.eqtlcatalogue__dataset	raw/eqtlcatalogue__dataset.parquet	758	0.00
raw.eqtlcatalogue__tabix_ftp_paths	raw/eqtlcatalogue__tabix_ftp_paths.parquet	758	0.00
resource.eqtlcatalogue__dataset	resource/eqtlcatalogue__dataset.parquet	758	0.00
raw.gwas_catalog__associations	raw/gwas_catalog__associations.parquet	1,192,604	0.05
raw.gwas_catalog__studies	raw/gwas_catalog__studies.parquet	230,057	0.01
clinical.gwas_catalog__study	clinical/gwas_catalog__study.parquet	230,057	0.01
clinical.gwas_catalog__association	clinical/gwas_catalog__association.parquet	1,192,472	0.09
raw.rnacentral__id_mapping	raw/rnacentral__id_mapping.parquet	264,333,345	2.63
annotation.rnacentral__rna	annotation/rnacentral__rna.parquet	2,753,423	0.01
raw.biogrid__interactions	raw/biogrid__interactions.parquet	2,936,093	0.10
raw.intact__mitab	raw/intact__mitab.parquet	1,788,408	0.39
annotation.interaction	annotation/interaction.parquet	4,722,393	0.03
raw.complexportal__complex	raw/complexportal__complex.parquet	20,579	0.00
annotation.complexportal__complex	annotation/complexportal__complex.parquet	20,579	0.00
annotation.complexportal__participant	annotation/complexportal__participant.parquet	101,561	0.00
annotation.signature_taxon	annotation/signature_taxon.parquet	59,486	0.00
raw.metadata	raw/metadata.parquet	40,737,811	2.22
annotation.pubmed__article	annotation/pubmed__article.parquet	41,336,046	37.14

License

The terms are mixed. Each table keeps the terms of its upstream source; the sources and versions are listed above and in manifest.json (provenance). Where a source requires a notice to travel with its data, the table comment carries it (views.sql).

Citation

DOIs are not minted. Cite the tag:

@misc{bioconice_2026_11,
  title  = {biocOnIce, release 2026-11},
  author = {Davis, Sean},
  year   = {2026},
  url    = {https://huggingface.co/datasets/seandavis/bioconice/tree/2026-11}
}