Catalog

Every source is served the same way: snapshot-pinned, count-reconciled, and provable with verify(). 10 sources ship in the first wave; the rest are coming soon — 64 in all, the same primary databases as everyone else, but trustworthy.

Ensembl

Genomics & sequence

Vertebrate genome annotation: genes, transcripts, regulation, comparative genomics, variation.First wave

gnomAD

Genomics & sequence

Population allele frequencies aggregated from >800k exomes and genomes.First waveODbL · isolated

NCBI E-utilities

Genomics & sequence

Entrez programmatic access to GenBank, Gene, PubMed and dozens of NCBI databases.First waveindex/proxy

dbSNP

Genomics & sequence

NCBI catalog of short genetic variation (SNPs and small indels) with rsIDs.Coming soon

ENA

Genomics & sequence

European Nucleotide Archive: raw reads, assemblies and sequence records at EMBL-EBI.Coming soon

GENCODE

Genomics & sequence

Comprehensive gene annotation for the human and mouse reference genomes.Coming soon

GEO

Genomics & sequence

Gene Expression Omnibus: functional genomics series, samples and platforms at NCBI.Coming soonindex/proxy

GWAS Catalog

Genomics & sequence

EBI/NHGRI curated catalog of published genome-wide association study results.Coming soon

RefSeq

Genomics & sequence

NCBI curated, non-redundant reference sequences for genomes, transcripts and proteins.Coming soon

SRA

Genomics & sequence

Sequence Read Archive: raw high-throughput sequencing reads (mirrored free on AWS/GCP).Coming soonindex/proxy

UCSC Genome Browser

Genomics & sequence

Reference genome assemblies and annotation tracks with a public download/API surface.Coming soon

AlphaFold DB

Structure

DeepMind/EMBL-EBI predicted protein structures across whole proteomes.First waveCC-BY

PDB

Structure

Worldwide Protein Data Bank: experimentally determined 3D macromolecular structures.First waveCC0

CATH

Structure

Hierarchical classification of protein-domain structures (Class, Architecture, Topology, Homology).Coming soon

EMDB

Structure

Electron Microscopy Data Bank: 3D cryo-EM maps, tomograms and subtomogram averages.Coming soon

PDBe

Structure

Protein Data Bank in Europe: wwPDB archive with enriched annotations and APIs.Coming soon

UniProt

Proteins & families

Universal protein sequence and functional annotation knowledgebase (Swiss-Prot/TrEMBL).First waveCC-BY

InterPro

Proteins & families

Integrated protein families, domains and functional sites from member signature databases.Coming soon

Pfam

Proteins & families

Protein families represented by curated multiple alignments and HMMs (within InterPro).Coming soon

PROSITE

Proteins & families

Protein domains, families and functional sites described as patterns and profiles.Coming soon

ChEMBL

Chemistry & drugs

Curated bioactive molecules with drug-like properties and bioactivity measurements.First waveCC-BY-SA · isolated

PubChem

Chemistry & drugs

NCBI open chemistry database of compounds, substances and bioassays.First wave

BindingDB

Chemistry & drugs

Measured binding affinities between proteins and small-molecule ligands.Coming soonCC-BY

ChEBI

Chemistry & drugs

Chemical Entities of Biological Interest: ontology of small molecular entities.Coming soonCC-BY

DrugBank

Chemistry & drugs

Drug and drug-target knowledgebase; only CC0 vocabulary/structures subsets redistributable.Coming soonCC-BY-NC · redirect

Guide to PHARMACOLOGY

Chemistry & drugs

IUPHAR/BPS expert-curated drug targets and their ligands with pharmacology.Coming soonCC-BY-SA

ClinVar

Clinical & variants

NCBI archive of human variant-phenotype relationships and clinical interpretations.First wave

CIViC

Clinical & variants

Crowd-curated clinical interpretation of variants in cancer.Coming soonCC0

ClinicalTrials.gov

Clinical & variants

NLM registry and results database of clinical studies worldwide.Coming soon

COSMIC

Clinical & variants

Catalogue Of Somatic Mutations In Cancer; proprietary/academic-only, not rehosted.Coming soonredirect

dbGaP

Clinical & variants

NCBI database of genotypes and phenotypes; controlled-access via DAR only.Coming soongated

DisGeNET

Clinical & variants

Integrated gene-disease and variant-disease association collection.Coming soon

OMIM

Clinical & variants

Online Mendelian Inheritance in Man: catalog of human genes and genetic disorders.Coming soon

OpenFDA

Clinical & variants

FDA open APIs for drug, device and food adverse-event and label data.Coming soonCC0

Orphanet

Clinical & variants

Reference resource on rare diseases, orphan drugs and associated genes.Coming soonCC-BY

TCGA

Clinical & variants

The Cancer Genome Atlas; open tier indexable, controlled tier gated pass-through.Coming soongated

NCBI Virus

Pathogen surveillance

Curated viral sequences and metadata derived over GenBank/RefSeq.First waveindex/proxy

BV-BRC

Pathogen surveillance

Bacterial and Viral Bioinformatics Resource Center: pathogen genomes and analysis.Coming soon

Nextstrain

Pathogen surveillance

Real-time phylogenetic tracking of pathogen evolution and outbreaks.Coming soon

Gene Ontology

Pathways & ontologies

Standardized vocabulary of gene molecular functions, processes and components.Coming soonCC-BY

Human Phenotype Ontology

Pathways & ontologies

Standardized vocabulary of human phenotypic abnormalities for genomic medicine.Coming soonCC-BY

JASPAR

Pathways & ontologies

Open database of transcription-factor binding profiles (position matrices).Coming soonCC-BY

KEGG

Pathways & ontologies

Pathway, disease and drug knowledgebase; redistribution restricted, redirect only.Coming soonredirect

Monarch Initiative

Pathways & ontologies

Cross-species integration of genes, phenotypes and diseases.Coming soonCC-BY

MSigDB

Pathways & ontologies

Molecular Signatures Database of annotated gene sets; only clean subsets rehostable.Coming soonCC-BY-SA · isolated

Open Targets

Pathways & ontologies

Integrated target-disease evidence and tractability for drug discovery.Coming soon

Reactome

Pathways & ontologies

Curated, peer-reviewed human biological pathways and reactions.Coming soonCC0

WikiPathways

Pathways & ontologies

Community-curated biological pathway models, openly editable.Coming soonCC0

CELLxGENE

Expression & single-cell

CZI single-cell expression corpus with standardized annotations and an API.Coming soon

DepMap

Expression & single-cell

Cancer Dependency Map: CRISPR/RNAi gene-essentiality across cell lines.Coming soon

ENCODE

Expression & single-cell

Encyclopedia of DNA Elements: functional genomics across cell types and assays.Coming soon

Expression Atlas

Expression & single-cell

EBI baseline and differential gene/protein expression across conditions.Coming soonCC-BY

GTEx

Expression & single-cell

Tissue-specific gene expression and eQTLs across human tissues.Coming soon

MetaboLights

Proteomics & metabolomics

EBI repository for metabolomics studies and reference metabolite data.Coming soonCC0

PRIDE

Proteomics & metabolomics

EBI proteomics identifications database of mass-spectrometry experiments.Coming soonCC-BY

BioGRID

Interactions

Curated genetic and protein interactions across organisms.Coming soonMIT

IntAct

Interactions

EBI molecular-interaction database of experimentally verified interactions.Coming soonCC-BY

STRING

Interactions

Known and predicted protein-protein functional association networks.Coming soonCC-BY

arXiv

Literature

Open-access preprint archive across physics, math, CS and quantitative biology.Stage 6

Europe PMC

Literature

Life-sciences literature: full text, abstracts and linked data at EBI.Coming soon

FlyBase

Model organisms

Reference database of Drosophila genes, genomes and genetics.Coming soonCC-BY

MGI

Model organisms

Mouse Genome Informatics: mouse genes, alleles, phenotypes and strains.Coming soonCC-BY

SGD

Model organisms

Saccharomyces Genome Database: budding yeast genes and functional annotation.Coming soonCC-BY

WormBase

Model organisms

Biology and genome of C. elegans and related nematodes.Coming soonCC0

No sources match this filter.

The First wave sources are in active build; Coming soon sources arrive through the same engine factory. This is the intended catalog surface, not a live count.

Try one

$ pinakes catalog $ pinakes get --source-id uniprot --ids P0DTC2 1 record · served_from snapshot@v7 · manifest written $ pinakes verify --manifest @manifest.json reproduced 1/1 · hash match · reproducible: true

Roadmap: KEGG is index/proxy-only under its restrictive license, so it is deferred. Controlled-access sources — TCGA, dbGaP — arrive in Stage 5. The remaining primary databases follow through the engine factory: same engine, any corpus.