Vendor Examples — Cyto External Data Integration Tests

Related blog post: https://thavlik.dev/blog/2026-02-23/cyto-vendor-examples

This crate contains integration tests and usage examples for all external data vendors that Cyto interacts with. The goal is maximum reproducibility and guaranteed correctness across the entire Cyto ecosystem: WSI, genomics, proteomics, ontologies, structures, and cancer datasets.

Every vendor test demonstrates:

• Expected API behavior
• Known stable identifiers (e.g., BRCA2, ENST00000380152)
• HTTP patterns (REST, FTP, GraphQL, binary formats)
• Decompression, parsing, and edge-case handling
• Resilience to vendor quirks (timeouts, alternate formats, slow endpoints)

This repo acts as both:

1. A reference implementation for Cyto vendor fetches
2. A test suite that validates correctness against live upstream APIs
3. A coverage roadmap, showing which vendors have been integrated and which remain

---

CLI Dump Command

The binary now exposes a Clap CLI for dumping example payloads into a local output tree.

cargo run -- dump
cargo run -- dump genes
cargo run -- dump genes --count 2
cargo run -- dump proteins --vendor ncbi,uniprot
cargo run -- dump images -o /tmp/cyto-dump
OUT_DIR=/tmp/cyto-dump cargo run -- dump variants

Key behavior:

• dump with no entity subcommand runs all supported entity types.
• dump <entity> only runs that entity type.
• --out / -o / OUT_DIR controls the root output directory. The default is dump/.
• The target output is always cleared before writing:
  • cargo run -- dump removes the full output root first.
  • cargo run -- dump genes removes only dump/genes (or the equivalent path under --out).
• --count N writes N unique examples per vendor for the selected entity type.
• --vendor vendor1,vendor2 filters the selected entity type(s) to the listed vendors.

Output layout:

dump/<entity>/<vendor>_<entity>_0.<ext>
dump/<entity>/<vendor>_<entity>_1.<ext>
dump/<entity>/<vendor>_<entity>_2.<ext>

Notes:

• JSON responses are written as pretty-printed .json files.
• Native text formats keep their upstream file types, for example .fasta, .gtf, .obo, .chain, .cif, and image outputs such as .dcm or the GTEx tile image extension.
• Each discrete example is written to its own file. Multi-record formats like FASTA, GTF, OBO, and UCSC chain files are split so one dumped example maps to one output file.
• The CLI samples unique examples without replacement. If you ask for more unique records than a vendor/entity source can provide, the command fails instead of repeating the same example.
• Run cargo run -- dump --help and cargo run -- dump <entity> --help to inspect the full command surface.

---

Why This Exists

The world of scientific data is sprawling and inconsistent. Cyto aims to make it feel like Docker Hub for biology — predictable, clean, typed, and uniform.

But underneath, each vendor has:

• Different error semantics
• Different throttling behavior
• Different naming conventions
• Different file formats
• Strong or weak uptime guarantees

This repository encodes all that nuance in executable tests.

---

Vendor Support Matrix

Tier Definitions

• Tier 0 — Canonical / Source of Truth Government or foundational institutions; must be rock-solid.

• Tier 1 — High-Authority / Regulated Extremely important and high quality; not canonical but close.

• Tier 2 — Secondary Databases Strong integrators, cross-linkers, utilities; occasional gaps.

• Tier 3 — Niche / Research-Grade Useful but not essential or with uptime/licensing issues.

Tested? Column

• ✔️ = Implemented test suite exists
• ❌ = Planned, but not implemented yet (roadmap)
• ➖ = Not applicable (non-API bulk download or incompatible licensing)

---

📊 Comprehensive Vendor Table

Below is the full vendor matrix with Tier and Tested? status.

Note that ontology data will exist in a separate layer above "pullable" artifacts. These data are attached to pullable artifacts on-demand as annotations, preserving clean API responses for the 99% of users that don't require ontology. Ontology vendors are nonetheless listed here for completedness.

Vendor	Domain	API / Access	Tier	Tested?	Notes
NCBI (Entrez, SRA, GenBank, RefSeq)	Genomics, sequences, assemblies, taxonomy	REST (E-utils)	0	✔️	Canonical US source
ENA	Nucleotide archive, raw reads	FTP + REST	0	✔️	Mirrors much SRA content
GENCODE (GTF, FASTA)	Gene models, transcripts, proteins	FTP	0	✔️	Authoritative gene annotation
UCSC Genome Browser	Tracks, chain files, GC content	HTTP	0	✔️	Canonical track repository
UniProt	Protein sequences + metadata	REST	0	✔️	Canonical protein namespace
RCSB PDB	Protein structures (3D)	GraphQL + REST	0	✔️	Canonical structure repo
GO (Gene Ontology)	Biological process ontology	OBO	0	✔️	Canonical ontology
HPO	Clinical phenotype ontology	OBO	0	✔️	Canonical clinical phenotype ontology
MeSH	Medical subject headings	REST	0	✔️	Canonical clinical vocabulary
ClinVar	Variant pathogenicity	REST	0	✔️	Canonical clinical variant database
dbSNP	SNP IDs	REST	0	✔️	Canonical SNP identifier namespace
dbVar	Structural variants	REST	0	✔️	Canonical structural variant repository
ENSEMBL	Annotation, variation, cross-links	REST	1	✔️	High-value but API uptime varies
gnomAD	Population allele frequencies	REST	1	✔️	Essential variant frequency resource
GDC (TCGA)	Cancer genomics, WSI metadata	REST	1	✔️	Main TCGA access point
CPTAC	Proteogenomics + WSI	HTTPS / portal	1	✔️	Open-access cohorts only; includes WSI metadata
GTEx Histology	Tissue histology images	Cloud bucket	1–2	✔️	FOV-based histology; not WSI-native
AlphaFold DB	Predicted protein structures	REST	1	❌	Planned
InterPro	Protein families & integration	REST	1–2	❌	Annotates protein domains across multiple databases
Pfam	Protein motifs & domains	FTP / REST	1	❌	Protein family models
Reactome	Biological pathways	REST	1	❌	Open-access pathway knowledgebase
Expression Atlas (EBI)	Bulk & differential expression	REST	1	❌	Microarray & RNA-seq expression across conditions
Single Cell Expression Atlas (SCEA)	Single-cell expression data	REST + N/a	1–2	❌	API for metadata only; matrices are bulk
Human Cell Atlas (HCA)	Single-cell atlases	REST (Azul/Matrix)	1	❌	JSON metadata + matrix endpoints
CellxGene / CZ Biohub	scRNA-seq datasets & annotations	REST	1–2	❌	Metadata API + dataset downloads
PanglaoDB	scRNA-seq cell-type markers	REST	1–2	❌	Useful for cell-type assignment
PRIDE (EBI)	Proteomics datasets	REST + FTP	1	❌	Canonical proteomics submissions
MetaboLights (EBI)	Metabolomics datasets	REST	1–2	❌	SDRF-based metadata
MGnify (EBI Metagenomics)	Metagenomics, microbiomes	REST	1	❌	Canonical pipeline outputs for microbiome data
BV-BRC (PATRIC / BRC)	Bacteria & viruses, AMR, virulence	REST	1	❌	Major pathogen informatics resource
NCBI Virus	Viral genomes & metadata	REST	1	❌	Public viral sequences; structured metadata
CIViC	Clinical variant interpretations	REST	1	❌	Curated oncology variant evidence
ZINC15	Small-molecule ligand library	REST	1	❌	Searchable compound metadata
MMDB (NCBI)	3D structures	REST	1	❌	Complementary to PDB
SABIO-RK	Enzyme reaction kinetics	REST	1–2	❌	Structured biochemical kinetics
LIPID MAPS	Lipids & pathways	REST	1–2	❌	Lipid classifications & reactions
BioGRID	Protein interactions & genetics	REST	1	❌	Canonical PPI/interaction dataset
STRING DB	Protein interaction networks	REST	1	❌	Network-based biological associations
IntAct (EBI)	Molecular interaction evidence	REST	1–2	❌	Curated interaction repository
ComplexPortal	Protein complexes	REST	1–2	❌	Structured protein complex definitions
ChEBI	Chemical ontology & structures	REST	1	❌	Chemical entity ontology
TCIA	Radiology collections	REST	2	❌	Canonical radiology repository
Imaging Data Commons (IDC)	Cancer radiology collections	DICOMweb + BigQuery	2	❌	Cloud-hosted DICOM; complements TCIA
Open-i (NLM)	Biomedical figures incl. radiology	REST search	2–3	❌	Image search engine
ClinicalTrials.gov	Trials, drugs, conditions	REST	1–2	❌	Canonical clinical trials registry
DrugCentral	Drug labels, indications, MoA	REST	1	❌	Open pharmacology resource
ChEMBL	Bioactive molecules, assays	REST	1	❌	Major chemical biology resource
PubChem	Small molecules, assays, structures	REST + FTP	0–1	❌	Canonical chemical database
BioSamples (EBI)	Sample metadata	REST	1	❌	Underpins many EBI datasets
BioStudies / BioProjects	Study metadata	REST	1–2	❌	Study-level organization
OncoKB	Precision oncology knowledgebase	REST (restricted)	1–2	➖	API key required
LOINC	Lab/clinical measurement codes	Restricted	2	➖	Controlled terminology
ICD-10 / ICD-O	Diagnostic and oncologic codes	Restricted	2–3	➖	WHO licensing
COSMIC	Somatic mutation catalog	Restricted	1–2	➖	Commercial license
DrugBank	Drugs, interactions, mechanisms	REST (restricted)	2–3	➖	Paid API; cannot redistribute
BioCyc / MetaCyc	Pathways & metabolism	Restricted	2–3	➖	Paid licensing; limited API
BRENDA	Enzyme kinetics	Restricted	2–3	➖	Licensing required
GISAID	Viral sequences (SARS-CoV-2, influenza)	Restricted	2–3	➖	No public API; controlled-access
IMG/M (JGI)	Microbial genomes & metagenomes	Restricted	2–3	➖	Login required
NHANES	Health & nutrition surveys	N/a	3	➖	Bulk tables only; no API
CDC Wonder	Epidemiology statistics	REST	2	❌	Global & US health stats
Our World in Data (OWID)	Global health metrics	REST	2	❌	Epidemiology & mortality data
WHO GHO API	World health statistics	REST	2	❌	Official WHO global health API
UNData API	Population & health statistics	REST	3	❌	Broad global datasets
Camelyon16/17	Breast cancer WSI	N/a	2	➖	Bulk-only WSI dataset
NIH ChestX-ray14	Chest radiographs	N/a	2	➖	Bulk dataset; no API
CheXpert	Chest radiographs + labels	N/a	2	➖	Bulk-only; no API
MIMIC-CXR	Chest radiographs + reports	N/a	2	➖	Bulk PhysioNet; no public API
PadChest	Chest radiographs + NLP labels	N/a	2	➖	Bulk-only dataset
DeepLesion	CT lesion dataset	N/a	2	➖	Bulk-only; no API
MIDRC / RICORD	COVID-19 radiology	N/a	2	➖	Bulk-only from TCIA
BIMCV COVID-19+	Chest X-ray/CT	N/a	3	➖	Bulk-only
EMPIAR	Raw EM volumes	REST-like + N/a	1	❌	Image metadata API; volumes bulk-only
EMDB	EM density maps	REST	2	❌	Structured metadata
Image Data Resource (IDR)	Microscopy & EM	REST (OMERO)	1–2	❌	Metadata API; images bulk
BioImage Archive (EBI)	Microscopy datasets	REST metadata	1–2	❌	General microscopy repository
Kasthuri EM / MICrONS	Connectomics EM	N/a	2	➖	Bulk large-scale volumes
MitoEM	Mitochondrial EM segmentation	N/a	2	➖	Benchmark dataset; no API
SNEMI3D	Connectomics EM	N/a	2	➖	Classic EM segmentation benchmark
CREMI	Connectomics EM	N/a	2	➖	Bulk segmentation benchmark
EPFL CVLab EM	2D EM segmentation	N/a	3	➖	Small EM dataset
Allen Cell Explorer	Live-cell imaging	N/a	2–3	➖	High-quality imaging; no API
CEM500K	Connectomics EM	N/a	3	➖	Bulk-only large dataset
CARD (AMR)	Antibiotic resistance genes	N/a	2–3	➖	Bulk-only AMR gene database
VFDB	Bacterial virulence factors	N/a	2–3	➖	Bulk-only; no API
SILVA	rRNA reference sequences	N/a	2	➖	Widely used microbiome taxonomy
Greengenes2	Microbial taxonomy	N/a	2–3	➖	Updated Greengenes; no API
RDP Classifier	16S reference classifier	N/a	3	➖	Training datasets only
TargetScan	miRNA target predictions	N/a	2	➖	Bulk-only; no REST API
miRBase	microRNA sequences & annotations	FTP / REST (limited)	1–2	❌	Limited API endpoints
HMDB (Human Metabolome DB)	Metabolomics	N/a + limited API	2	➖	Partial API; primary access bulk
MassIVE (UCSD)	Proteomics & metabolomics	N/a + partial API	2	➖	Some JSON endpoints
PeptideAtlas	Peptide evidence	N/a	2	➖	Bulk datasets
Cell Ontology (CL)	Cell-type ontology	OBO	0–1	❌	Core cell ontology
Uberon	Anatomy ontology	OBO	0–1	❌	Multi-species anatomy
Sequence Ontology (SO)	Sequence feature ontology	OBO	0–1	❌	Used heavily in genome annotation
Disease Ontology (DO)	Disease classification	OBO	0–1	❌	Open disease ontology
HGMD (Human Gene Mutation Database)	Clinical variants	Restricted	2–3	➖	Commercial clinical mutation database; no public API
VarSome	Variant annotation & ACMG classification	Restricted (REST)	2	➖	Paid API; integrated knowledge graph
DECIPHER	Clinical structural variation	REST	1–2	❌	Patient phenotypes + CNVs; partial API
LOVD	Community gene/variant databases	REST	1–2	❌	Variant submissions for specific genes
MGI (Mouse Genome Informatics)	Model organism — mouse	REST	1	❌	Mouse genetics, alleles, phenotypes
RGD (Rat Genome Database)	Model organism — rat	REST	1	❌	Rat genomics, disease models, pathways
FlyBase	Model organism — Drosophila	REST	1	❌	Fly gene models, alleles, interactions
WormBase / WBPS	Model organism — C. elegans	REST	1	❌	Genes, phenotypes, pathways
ZFIN	Model organism — zebrafish	REST	1	❌	Developmental phenotypes, expression
SGD (Yeast Genome Database)	Model organism — yeast	REST	1	❌	Saccharomyces cerevisiae reference DB
Xenbase	Model organism — Xenopus	REST	1–2	❌	Frog developmental biology
Phytozome / Araport / TAIR	Plant genomics	Restricted	3	➖	Arabidopsis & plant resources; licensing required
Gramene	Plant comparative genomics	REST	2	❌	Phylogenomic and annotation resource
Plant Reactome	Plant pathways	REST	2	❌	Plant pathway knowledgebase
OMA (Orthologous Matrix)	Orthology	REST	1–2	❌	High-quality ortholog predictions
OrthoDB	Ortholog clusters	REST	1–2	❌	Hierarchical orthology database
Ensembl Compara	Orthology / phylogeny	REST	1	❌	Part of Ensembl, but separate API endpoints
GWAS Catalog	Genome-wide association studies	REST	1	❌	Curated trait–variant associations
eQTL Catalogue	eQTL & QTL studies	REST	1	❌	Uniform reprocessing of QTL datasets
UK Biobank	Genomics & clinical cohort	Restricted	3	➖	Controlled-access dataset
BioBank Japan	Clinical biobank	Restricted	3	➖	Large Japanese cohort; controlled access
IUPHAR Guide to Pharmacology	Drug targets, ligands, GPCRs	REST	1–2	❌	Pharmacology reference curated by IUPHAR
ChemSpider	Chemical structures	REST (key required)	2	➖	API requires registration; broad chemical metadata
PHASTER	Prophage & phage element annotation	REST	1–2	❌	Bacteriophage detection in microbial genomes
EnteroBase	Enteric pathogen genomics	REST	1–2	❌	Salmonella, E. coli, Campylobacter, more
IMG/VR (Virus/Phage)	Viral & phage genomes	Restricted	2–3	➖	Part of JGI IMG ecosystem; login needed
CRyPTIC TB AMR Database	Tuberculosis resistance profiles	N/a	3	➖	Bulk-only; no API
MetaPhlAn database	Microbiome taxonomic markers	N/a	3	➖	Bulk reference database only
Kraken2 / Bracken DBs	Microbiome classification indices	N/a	3	➖	Bulk-only k-mer taxonomic databases
GTDB (Genome Taxonomy Database)	Microbial taxonomy	N/a	2–3	➖	Widely used in metagenomics; bulk-only
Earth Microbiome Project	Microbiome survey	N/a	3	➖	Bulk metadata + sequence archives
BMRB (Biological Magnetic Resonance DB)	NMR spectroscopy	REST	2	❌	Protein & metabolite NMR data
OpenFold training data	Protein structure ML datasets	N/a	3	➖	Bulk ML training sets
OpenStructure datasets	Structural biology ML sets	N/a	3	➖	Bulk ML training assets
EuropePMC	Literature metadata	REST	1–2	❌	Large open biomedical literature store
Semantic Scholar API	Scholarly metadata & citations	REST	2	❌	Good for NLP & citation graph extraction
CORD-19	COVID-19 research corpus	N/a	3	➖	Bulk paper corpus
NCBI BioSample	Biological sample metadata	REST	1	❌	Parallel to EBI BioSamples
iGEM Registry of Standard Parts	Synthetic biology parts	REST (MediaWiki API)	2	❌	DNA parts, promoters, plasmids
JBEI ICE Repository	SynBio plasmids & parts	REST	2	❌	Open-source ICE platform
SynBioHub	Synthetic biology parts	REST	2	❌	SBOL-formatted biological components
dbNSFP	Variant scoring annotations	N/a	2	➖	Bulk functional prediction database
CADD	Variant deleteriousness scores	N/a	2–3	➖	Bulk prediction files only
PolyPhen / SIFT	Protein-level variant effect prediction	N/a	3	➖	Web servers only; no API
REVEL / M-CAP / MutPred	Variant effect prediction	N/a	3	➖	Bulk downloads only
GTEx Expression (portal)	Expression quantifications	REST	1	❌	Distinct from histology; expression matrices via API
Earth Human Microbiome Project	Human microbiome	N/a	3	➖	Bulk-only metadata
FHIR Terminology Service (HL7)	Clinical vocab expansions	REST	1–2	❌	Provides ValueSet expansion & concept lookup
Allen Brain Atlas	CNS gene expression & cell types	REST	1–2	❌	Spatial transcriptomics + expression; ISH, RNA-seq, cell types
EyePACS Diabetic Retinopathy	Retinal imaging	N/a	2	➖	Bulk ophthalmology dataset; no API
APTOS / Kaggle DR	Retinal imaging	N/a	2	➖	Bulk-only DR classification dataset
MESSIDOR	Retinal imaging	N/a	2	➖	Classic DR imaging benchmark; no API
ISIC Archive	Dermatology / skin cancer	REST	1–2	❌	Public skin lesion image archive
HAM10000	Dermatology / skin cancer	N/a	2	➖	Bulk lesion classification dataset
PH2 Dataset	Dermatology (dermoscopy)	N/a	3	➖	Small bulk-only dermoscopy dataset
ENCODE Portal	Epigenomics, regulatory genomics	REST	1	❌	ATAC-seq, ChIP-seq, DNase-seq, TF binding; ChIP-seq, ATAC-seq, RNA-seq metadata & files; ChIP-seq, ATAC-seq, DNase-seq
Roadmap Epigenomics	Epigenomics	N/a	2	➖	Bulk-only consortium data; Bulk metadata; no unified API; Bulk-only epigenome maps
ReMap Regulatory Atlas	Transcription factor binding	REST	1–2	❌	Integrated TF-binding meta-analysis; TFBS & epigenomic peak catalogs; Harmonized TF binding peak collections
Cistrome Data Browser	ChIP-seq / ATAC-seq regulatory data	REST	1–2	❌	TF and histone mark binding
GTRD (TF Binding Database)	Transcription factor binding sites	N/a	2–3	➖	Aggregated TF-binding predictions
JASPAR	TF binding motifs	REST	1–2	❌	Canonical open TF motif database; Open transcription factor motif database; Curated transcription factor motif models
10x Genomics Visium Public Datasets	Spatial transcriptomics	N/a	2	➖	Bulk dataset downloads; no public REST API; Visium datasets; bulk-only
SpatialDB	Spatial transcriptomics index	REST	2	❌	Aggregates spatial-omics datasets; Aggregated spatial transcriptomics datasets
STOmics (BGI)	Spatial omics	N/a	2–3	➖	Bulk downloads; no public API
Slide-seq / Slide-seqV2	Spatial transcriptomics	N/a	2	➖	Bulk bead-based spatial RNA-seq; Bulk GEO-based datasets
STARmap	Spatial transcriptomics	N/a	3	➖	High-resolution spatial RNA imaging
MERFISH Public Datasets	Spatial transcriptomics	N/a	2	➖	Bulk-only spatial imaging data; Bulk-only spatial datasets
TriTrypDB	Parasitology genomics (Trypanosomes)	REST	1–2	❌	Part of EuPathDB
PlasmoDB	Malaria parasite genomics	REST	1–2	❌	Major Plasmodium resource
VectorBase	Vector insect genomics (mosquitoes)	REST	1–2	❌	Mosquito, tick, sandfly genomics
FungiDB	Fungal pathogens	REST	1–2	❌	Fungal parasite genomics
EuPathDB (umbrella)	Parasitology databases	REST	1–2	❌	Aggregates PlasmoDB, TriTrypDB, ToxoDB, more
Metabolomics Workbench	Metabolomics	REST	1–2	❌	NIH metabolomics repository
MassBank (Japan)	Mass spectra (metabolomics)	REST	2	❌	High-quality MS spectra reference
MoNA (MassBank of North America)	Mass spectra	REST	2	❌	North American MS spectra archive
ToxCast	Toxicology screens (HTS)	REST	1–2	❌	EPA high-throughput toxicity assays
Tox21	Toxicology screens	N/a	2	➖	Bulk HTS toxicology dataset; Joint NIH–EPA toxicity screening
EPA CompTox Dashboard	Chemical toxicity & exposure	REST	1–2	❌	Unified EPA toxicology/chemical metadata
CTD (Comparative Toxicogenomics DB)	Gene–chemical–disease interactions	REST	1–2	❌	Toxico-genomic relationships
AIRR Data Commons	Immune repertoire sequences (TCR/BCR)	REST	1–2	❌	Standardized immune repertoire metadata; Adaptive immune receptor repertoires
VDJdb	T-cell receptor sequences	REST	1–2	❌	Curated TCR specificity database
ImmPort	Immunology studies	REST	1–2	❌	NIH immunology data portal; Immune profiling & flow/mass cytometry data
IEDB	Immune epitope database	REST	1–2	❌	Antibody & T-cell epitope repository
MIMIC-IV (clinical EHR)	Clinical EHR, ICU data	Restricted	2–3	➖	PhysioNet credential required; no open API
eICU Collaborative Research DB	ICU clinical data	Restricted	2–3	➖	Clinical EHR-like dataset
OMOP Example Data Sets	Clinical EHR example datasets	N/a	3	➖	Demo EHR tables; no API
NeuroMorpho.org	Neuronal morphology reconstructions	REST	1–2	❌	Canonical neuron structure repository; Digital neuron reconstructions
OpenNeuro	Neuroimaging (MRI/MEG/EEG) datasets	REST + N/a	2	❌	Metadata API; imaging bulk; BIDS datasets; bulk-only
Human Connectome Project (HCP)	Human brain MRI & connectomics	Restricted	3	➖	Access-controlled large neuroimaging dataset; Controlled-access MRI & phenotype data
GlyGen	Glycans, glycoproteins, glycan interactions	REST	1–2	❌	Glycomics metadata & structures
CAZy	Carbohydrate-active enzymes	N/a	2–3	➖	No API; curated carbohydrate enzyme families
Exposome Explorer	Human chemical exposures	N/a	3	➖	Epidemiological exposome database
EPA Envirofacts	Environmental chemical & pollutant data	REST	2–3	❌	Environmental exposure APIs; Chemical/toxicological environmental exposure
PubMed API (E-Utilities)	Literature metadata	REST	0–1	❌	Explicit listing for literature search
OBO Foundry Registry	Ontology metadata	N/a	3	➖	Registry of OBO ontologies; no API
IHME / GBD (Global Burden of Disease)	Epidemiology & mortality	REST	2–3	❌	Global disease burden datasets
UN WHO Mortality Tables	Mortality statistics	N/a	3	➖	Bulk-download-only
Cellosaurus	Cell-line ontology & metadata	REST	1–2	❌	Canonical cell-line registry; IDs widely used in research
DepMap	Cancer cell-line genetics (CRISPR, RNAi)	REST + bulk	1–2	❌	Gene essentiality, copy-number, expression; CCLE-aligned
CCLE (Cancer Cell Line Encyclopedia)	Cancer cell-line molecular profiles	N/a + partial API	2	➖	Expression/CNV/mutation data; bulk downloads primarily
PomBase	Model organism — fission yeast	REST	1–2	❌	Schizosaccharomyces pombe gene models, alleles, interactions
Rhea	Curated biochemical reactions	REST	1–2	❌	High-quality enzyme reaction knowledgebase linked to UniProt
ECOD	Protein domain classification	N/a	2–3	➖	Hierarchical structural domain database; bulk-only
FooDB	Food constituent metabolomics	REST	2	❌	Food-related chemical compounds linked to nutrition & metabolomics
USDA FoodData Central	Nutrition & biochemical food composition	REST	2	❌	Authoritative nutrient profiles; useful for diet–metabolomics studies
ClinGen Dosage Map	Gene dosage sensitivity	REST	1–2	❌	Haploinsufficiency & triplosensitivity curation
IMGT	Immunogenetics (TCR/BCR)	REST	1–2	❌	Canonical antibody & receptor sequence DB
dbGaP	Controlled-access human genomics	Restricted	3	➖	Massive human cohort datasets; no public API
Genome Nexus	Variant annotation aggregator	REST	1–2	❌	Harmonizes ClinVar, COSMIC, OncoKB, gnomAD
SnpEff DB	Variant annotation reference	N/a	2	➖	Used by SnpEff pipelines; downloaded reference sets
VEP Cache	Variant Effect Predictor reference	N/a	2	➖	Offline Ensembl VEP annotation caches
gnomAD-SV	Structural variants	REST	1–2	❌	Separate SV endpoints from SNVs
PAMDB	Pseudomonas metabolomics	N/a	2–3	➖	Bulk downloads; bacteria-specific metabolome
MiGA	Microbial genome classification	REST	1–2	❌	Taxonomic & phylogenomic classification
ENVO (Environment Ontology)	Environmental metadata ontology	OBO	0–1	❌	Used in microbiome & metagenomics metadata
Veterinary Pathogen DBs (APHA / VeNom)	Animal pathogens & clinical terms	N/a / restricted	3	➖	Used in veterinary microbiology & epidemiology
PubChem BioAssay (AID)	HTS bioassays	REST + FTP	1	❌	Massive assay database; essential for chemogenomics
ToxCast / Tox21	Toxicology HTS assays	REST + bulk	1–2	❌	EPA’s high-throughput toxicity screens
Open Targets Platform	Drug–gene–disease graph	REST	1	❌	High-quality integrated biomedical knowledge graph
FAERS	FDA adverse event reports	REST	1–2	❌	OpenFDA pharmacovigilance API
SIDER	Drug side effects	N/a	2	➖	Side-effect profiles; bulk structured data
DrugSideEffectsDB	Drug adverse effect resource	N/a	2–3	➖	Alternative side-effect knowledgebase
BrainMap / BrainInfo	Neuroanatomy ontology	REST	1–2	❌	Classic neuroanatomy structured ontology
Allen Brain Observatory	Ephys & imaging	REST	1–2	❌	Calcium imaging, electrophysiology datasets
Neurosynth	fMRI meta-analysis	REST	1–2	❌	Automated cognitive-neuroscience associations
NITRC	Neuroimaging tools & data	N/a	2–3	➖	Repository of MRI/EEG datasets
ABCD Study	Child brain development (MRI, psych)	Restricted	3	➖	Controlled-access high-value cohort
OpenFDA	Drugs, devices, adverse events	REST	1–2	❌	FDA regulatory + safety data
CMS Medicare Data	Utilization & reimbursement	N/a	3	➖	Bulk statistical files
HCUP / NIS	Hospital discharge statistics	Restricted	3	➖	Controlled access; widely used in health services research
ICD-11	Diagnostic classification (modern)	N/a	3	➖	WHO coding system; limited API
OMIM	Mendelian diseases	Restricted	2–3	➖	Commercial license; no open API
Bgee Expression Atlas	Cross-species expression	REST	1–2	❌	Anatomically-mapped expression data; Distinct from Expression Atlas (EBI); Cross-species expression atlas
GUDMAP / RBK	Developmental expression (GU tract)	N/a	2	➖	Bulk downloads only; Bulk-only developmental atlas
Addgene Sequence API	Plasmid sequence retrieval	REST	2	❌	Programmatic access to deposited plasmid sequences
Synthego CRISPR Guides	gRNA design & activity	REST	1–2	❌	CRISPR guide activity predictions
Broad GPP Perturbation Data	CRISPR & RNAi datasets	N/a	2	➖	Bulk DepMap-related perturbation screens; Bulk-only gene perturbation screens
Perturb-seq / CROP-seq (GEO-linked)	Single-cell perturbation datasets	N/a	2	➖	Bulk-only; no API
PDBe-KB	Structural annotations around PDB	REST	1–2	❌	Functional/biophysical annotations; Function & biophysical annotation layer over PDB
ProteomeXchange	Proteomics metadata aggregator	REST	1–2	❌	Umbrella for PRIDE, MassIVE, PeptideAtlas
BioModels	Systems biology models (SBML)	REST	1–2	❌	Curated mathematical models; SBML models & curation
JWS Online	Kinetic models	REST	1–2	❌	SBML model execution & metadata; SBML model server
SwissPalm	Protein palmitoylation	N/a	2–3	➖	Bulk-only; PTM database; Bulk PTM dataset
IHME GBD	Global Burden of Disease	N/a	3	➖	Bulk-only global health metrics; No unified public API
VAERS	Vaccine adverse events	REST	1–2	❌	CDC/FDA open vaccine safety reporting; CDC/FDA vaccine safety data
EuroStat Health API	EU health & epidemiology	REST	2–3	❌	European health statistics; Harmonized EU datasets
Monarch Initiative	Gene–disease–phenotype graph	REST	1–2	❌	Cross-species knowledge graph; Cross-species integrative biomedical KG
BioPortal (NCBO)	Biomedical ontology repository	REST	1–2	❌	Hundreds of ontologies; essential for NLP; Programmatic access to hundreds of ontologies
Wikidata Biomedical	Crowd-sourced structured biomedical graph	REST/SPARQL	1–2	❌	Huge linked-data knowledge graph; Community-curated structured biomedical data
OpenBEL	Biological expression language graphs	REST	1–2	❌	Cause–effect biological network models
MIMIC-III/IV Clinical Notes	Clinical text corpus	Restricted	3	➖	Requires credentialing; deidentified ICU notes
i2b2 NLP Challenges	Clinical NLP corpora	N/a	3	➖	Gold-standard datasets for medication, diagnosis, de-ID tasks
n2c2 NLP Datasets	Clinical text annotation	Restricted	3	➖	Successor to i2b2; requires data use agreement
MedMentions	Biomedical entity annotations	N/a	2	➖	PubMed abstracts annotated with UMLS concepts
BC5CDR	Chemical–disease interaction corpus	N/a	2	➖	Widely used for biomedical NER & relation extraction
CRAFT Corpus	Full-text biomedical annotations	N/a	2–3	➖	Ontology-grounded annotations
BioASQ	QA over biomedical ontologies	N/a	2–3	➖	Benchmark for semantic QA
SemEval BioNLP Tracks	Biomedical event extraction	N/a	3	➖	Gold-standard text-mining annotations
PMC Open Access Subset	Full-text articles	N/a	2–3	➖	Bulk download; no structured REST
seqFISH Public Datasets	High-plex spatial transcriptomics	N/a	2	➖	Bulk-only access
HuBMAP	Human tissue atlas (spatial)	REST	1–2	❌	Spatial transcriptomics & CCF ontology
CRISPRbrain	CRISPR screens in neurons	REST	1–2	❌	Functional genomic screens
BioGRID ORCS	Genome-wide CRISPR screen results	REST	1–2	❌	CRISPR knockout/activation datasets
GenomeCRISPR	CRISPR knockout phenotypes	N/a	2	➖	Historical CRISPR screens; bulk-only
Project Score (Sanger)	CRISPR knockout screens	N/a	2	➖	Essentiality screens complement DepMap
Achilles Project	Historical RNAi/CRISPR essentiality	N/a	3	➖	Legacy DepMap precursor
EPA CompTox / DSSTox	Chemical toxicity & identifiers	REST	1–2	❌	Environmental chemical safety database
ADMETlab	Drug ADMET predictions	N/a	2–3	➖	Bulk prediction datasets
TCRD (IDG)	Understudied drug targets	REST	1–2	❌	Illuminating the Druggable Genome project
ENCODE cCRE Registry	Candidate regulatory elements	REST	1	❌	Consolidated enhancer/promoter catalogs
Cistrome DB	TF ChIP-seq peaks	REST	1–2	❌	Curated transcription factor & histone mark peaks
GTRD	Transcription factor binding	N/a	2–3	➖	Aggregated ChIP-seq peak meta-collection
EpiMap	Epigenomic atlas	N/a	2–3	➖	Large enhancer & methylation maps, bulk-only
SCREEN (ENCODE)	Enhancer atlas	N/a	2	➖	Bulk-only structured enhancer data
MyVariant.info	Variant annotation aggregator	REST	1	❌	Unified variant-level annotations
MyGene.info	Gene annotation aggregator	REST	1	❌	High-speed gene metadata API
VariantValidator	HGVS validation	REST	1–2	❌	Validates & normalizes HGVS expressions
RefSeqGene / LRG	Stable gene loci	N/a	2	➖	Long-term stable genomic reference loci
gnomAD Constraint Metrics	Gene constraint/LoF intolerance	REST	1–2	❌	Distinct from allele frequency endpoints
PhosphoSitePlus	PTMs (phospho, acetyl, etc.)	Restricted	2–3	➖	Gold-standard PTM database
dbPTM	PTM annotations	N/a	2–3	➖	Bulk PTM dataset
iPTMnet	PTM interaction networks	REST	1–2	❌	Integrates PTMs and regulatory interactions
DisProt	Intrinsically disordered proteins	REST	1–2	❌	Curated disorder annotations
TMHMM / Phobius	Membrane topology predictions	N/a	2–3	➖	Predictor datasets; bulk-only
REACH (EU Chemical Safety)	Chemical safety	Restricted	3	➖	No public API
ECHA eChemPortal	Chemical safety data	N/a	3	➖	Bulk chemical hazard data
NIH ToxRefDB	Toxicology studies	N/a	2–3	➖	Historical animal toxicology data
Ensembl Metazoa	Multispecies annotation	REST	1	❌	Non-vertebrate Ensembl
Ensembl Plants	Plant genomes	REST	1	❌	Part of Ensembl ecosystem
Ensembl Fungi	Fungal genomics	REST	1	❌	Non-animal Ensembl
Ensembl Bacteria	Bacterial genomics	REST	1	❌	Microbial genomes metadata
JGI MycoCosm	Fungal genomics	Restricted	2–3	➖	Requires login; no open API
Virus Pathogen Resource (ViPR)	Viral genomics & metadata	REST	1–2	❌	Coronavirus, filovirus, flavivirus datasets
Influenza Research Database (IRD)	Flu genomics	REST	1–2	❌	Major influenza sequence & metadata resource
CAMI Benchmarks	Metagenomics benchmarking	N/a	3	➖	Benchmark datasets for microbiome pipelines
AMRFinderPlus DB	AMR gene reference	N/a	2–3	➖	Bulk AMR reference used clinically
Exposome-Explorer	Exposure biomarkers	N/a	2–3	➖	Environmental & dietary exposure markers
EPA AQS	Air quality system	REST	2	❌	Environmental exposure data
DailyMed SPL	Drug labeling XML	REST	1–2	❌	Structured FDA drug labeling
UNII (GSRS)	Ingredient identifier system	REST	1–2	❌	Global substance registration system
Synthego Guide Design API	CRISPR gRNA design	REST	1–2	❌	Computational CRISPR guide predictions
Perturb-seq / CROP-seq	Single-cell CRISPR perturbation datasets	N/a	2–3	➖	Bulk GEO/SRA datasets
SNOMED CT	Clinical terminology	Restricted	2–3	➖	Core clinical concepts; license via SNOMED International
RxNorm	Normalized drug terminology	REST (via UMLS)	1–2	➖	US drug vocabulary; integrated with SNOMED/LOINC; UMLS license required
UMLS Metathesaurus	Terminology hub (200+ vocabularies)	REST / bulk files	2–3	➖	Maps ICD, SNOMED, LOINC, RxNorm, etc.; strict licensing & sign-up
ATC	Drug classification (WHO ATC)	Restricted	2–3	➖	WHO Anatomical Therapeutic Chemical classification; licensing required
MedDRA	Adverse event terminology	Restricted	3	➖	Regulatory AE coding (trials, pharmacovigilance); paid license
CPT / HCPCS	Procedure / billing codes	Restricted	3	➖	US procedure & service codes (CPT via AMA, HCPCS via CMS)
GEO (Gene Expression Omnibus)	Functional genomics (microarray / RNA-seq)	REST (NCBI Entrez E-Utils)	1	❌	Canonical NCBI expression archive; raw and curated series/platforms
ArrayExpress (BioStudies)	Functional genomics archive	REST + FTP	1	❌	Legacy EBI archive; many datasets feed Expression Atlas
DDBJ	Nucleotide sequences (INSDC)	REST + FTP	0–1	❌	INSDC partner to ENA/NCBI; mostly mirrored content
cBioPortal	Cancer genomics meta-portal	REST	1	❌	Aggregates TCGA, MSK, GENIE, etc.; strong API and client libraries
ICGC ARGO / 25K	International cancer cohorts	REST (ARGO) + restricted	2–3	➖	Successor to classic ICGC; controlled-access for rich genomic/clinical data
KEGG	Pathways, drugs, disease, compounds	REST (KEGG API, licensed)	1–2	➖	Major pathway + systems biology DB; commercial use requires license
PharmGKB	Pharmacogenomics knowledgebase	REST	1–2	❌	Curated gene–drug–phenotype relations; PGx guidelines and pathways
OmicsDI (Omics Discovery Index)	Cross-repository omics index	REST	2	❌	Indexes GEO, PRIDE, ArrayExpress, MetaboLights, etc. for dataset discovery
FAIRsharing	Standards & database registry	REST / GraphQL (evolving)	3	❌	Meta-registry of databases/standards; good for auto-discovery and metadata
WikiPathways	Community biological pathways	REST + SPARQL	1–2	❌	CC0 pathways; complements Reactome/KEGG; useful for lightweight pathway access
Pathology WSI Benchmarks (Kaggle/Grand Challenge)	Histopathology ML benchmarks	N/a	2–3	➖	PANDA, NCT-CRC-HE, BACH, PCam, etc.
EGA (European Genome-phenome Archive)	Controlled-access human genomics + phenotypes	Restricted	3	➖	EU/EBI counterpart to dbGaP; controlled-access human omics and clinical metadata
MSigDB (Molecular Signatures DB)	Gene sets & pathways (GSEA)	Restricted (downloads/API-like)	2–3	➖	De facto standard for gene signatures; licensing constraints for redistribution
LINCS / Connectivity Map (CMap / CLUE)	Perturbation signatures (L1000, drugs, CRISPR)	REST + bulk	1–2	❌	Large-scale perturbation-expression signatures; useful for mechanism & repurposing
GDSC (Genomics of Drug Sensitivity in Cancer)	Cancer cell line drug response	N/a (bulk + portal)	2	➖	Dose–response data for many drugs across cell lines; complements DepMap/CCLE
Orphanet / ORDO	Rare diseases & orphan drugs	REST / bulk	1–2	❌	Rare disease registry + Orphanet Rare Disease Ontology; complements OMIM / HPO
ClinGen (Gene–Disease Validity / Actionability)	Clinical curation (beyond dosage)	REST	1–2	❌	Curated gene–disease validity, actionability, pharmacogenomics; you already list Dosage Map separately
MaveDB	Multiplexed assays of variant effect (MAVE)	REST + bulk	1–2	❌	Functional scores for many variants (deep mutational scans); great for variant interpretation
UniMod	Mass-spec modification definitions	N/a (downloads)	2	➖	Standardized PTM mass deltas (used by search engines); complements PTM/Proteomics DBs
Alliance of Genome Resources	Aggregated model-organism knowledge	REST	2	❌	Integrates MGI, SGD, ZFIN, FlyBase, WormBase, etc. under one umbrella API
Pathway Commons	Integrated pathway networks	REST	2	❌	Aggregates Reactome, PID, BioCyc subsets, WikiPathways, etc. into a unified graph

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Test Organization

All vendor examples live in src/ as *_test.rs files.

Organized by domain:

gdc_test.rs
gencode_test.rs
ucsc_test.rs
rcsb_test.rs
ncbi_tests.rs
ensembl_tests.rs
ena_test.rs
uniprot_test.rs
obo_test.rs
gnomad_test.rs
…

Each file:

• Demonstrates API usage
• Performs strict validation
• Provides copy-pasteable patterns for Cyto vendor modules
• Implements fallback strategies, headers, and better error reporting

All tests run with:

cargo test -- --nocapture

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Roadmap

Future expansions will:

• Expand coverage into radiology APIs

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Contributing

All additions must:

• Include a stable upstream identifier
• Include both a success case and at least one failure mode
• Be resilient to partial outages
• Avoid large downloads (use HEAD/range requests when possible)

Pull requests welcome.

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License

Apache 2.0 + MIT dual-license