Data Sources & Download¶

Auto-Downloadable Sources (18)¶

bioingest download-all --all --max-size 2gb

Source	ID	Format
UniProt	`uniprot`	TSV, FASTA, XML
Open Targets	`opentargets`	Parquet
Reactome	`reactome`	TSV
ChEMBL	`chembl`	SQLite, TSV
DISEASES 2.0	`diseases`	TSV
MarkerDB	`markerdb`	TSV
TTD	`ttd`	TSV, XLS
Complex Portal	`complex_portal`	TSV
HPA / Olink	`hpa_olink`	TSV
MeSH	`mesh`	XML
ICD-10-CM	`icd`	ZIP
PDB-KB / SIFTS	`pdb_complexes`	IDX, TSV.GZ
UK Biobank (Pan-UKB)	`ukb_disease_assoc`	TSV.BGZ
SomaLogic SomaScan	`somalogic`	TSV, SQLite
Gene Ontology	`gene_ontology`	OBO
Disease Ontology	`disease_ontology`	OBO
MONDO	`mondo`	OBO
EFO	`efo`	OBO

Commands¶

bioingest download                    # list all sources
bioingest download uniprot            # download default datasets
bioingest download uniprot --list     # show available datasets
bioingest download uniprot --all      # download everything
bioingest download-all --max-size 500mb  # all sources, skip large files

Features¶

Resumable — interrupted downloads resume from where they left off
Checksums — SHA-256 recorded in manifest.json per source
Selective — download specific datasets with --datasets X Y
Size limits — skip large files with --max-size