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Scientific work,
connected across your stack
Reference knowledge,
one query away
Reference-database plugins give scientists and AI agents read-only access to the genomic, clinical, protein, chemical and ontology resources that analyses depend on, from variant interpretation to target discovery.
-
130 reference databases across 9 categories · 100 implemented · 30 scaffolded
+
130 reference databases across 9 categories · 107 implemented · 23 scaffolded
Browse the full catalog in the docs ↗
@@ -787,6 +787,7 @@
Reference knowledge,
one query away
ClinGenGene–disease validity and dosage sensitivity
ClinVarClinical significance of human variants
COSMICCancer Gene Census via licensed downloads
+
CPICPharmacogenomic guidelines and dosing recommendations
dbNSFPFunctional predictions for missense variants
dbSNPrsIDs, alleles and genomic placements
dbVarNCBI structural-variation studies and variants
@@ -794,12 +795,14 @@
Reference knowledge,
one query away
DGVStructural variants from validated local snapshots
EnsemblGenes, transcripts, sequences, variants and homology
Gene2PhenotypeCurated gene–disease panels from EMBL-EBI
+
GeneReviewsExpert disease reviews by gene and OMIM
Genomics England PanelAppExpert-reviewed diagnostic gene panels
gnomADPopulation allele frequencies and gene constraint
GWAS CatalogStudies, traits and reported associations
HGMDLicensed clinical variants via a local or gateway provider
HGNCApproved human gene symbols and names
MARRVELRare-variant evidence across model organisms
+
MaveDBMultiplexed assays of variant effect scores
MedGenMedical-genetics concepts, genes and features
NCBI EntrezGene, protein, nucleotide and taxonomy search
OMIMMendelian genes, disorders and inheritance
@@ -809,13 +812,10 @@
Reference knowledge,
one query away
SNPediaCommunity variant and genotype annotations
UCSC Genome BrowserGenome databases, tracks and region data
Clinvitae scaffoldAggregated clinical variant reports
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CPIC scaffoldPharmacogenomic prescribing guidelines
GeneCards scaffoldIntegrated human gene summaries
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GeneReviews scaffoldExpert-authored disease reviews
GWAS Summary Statistics scaffoldFull summary statistics for GWAS
LOVD scaffoldLocus-specific variant databases
Mastermind scaffoldVariant evidence from the literature
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MaveDB scaffoldMultiplexed assays of variant effect
NCBI Gene scaffoldGene records and annotation
OncoKB scaffoldPrecision-oncology variant knowledge
RefSeq scaffoldNCBI reference sequences
@@ -839,12 +839,12 @@
Reference knowledge,
one query away
NCBI GEOExpression series, datasets, platforms and samples
NCBI SRASequence Read Archive studies, runs and samples
PanglaoDBSingle-cell cell-type marker genes
+
TCGAOpen-access TCGA cases, files and mutations via GDC
All of Us scaffoldControlled-access research cohort
CCLE scaffoldCancer cell-line omics profiles
dbGaP scaffoldControlled-access genotype–phenotype studies
DepMap scaffoldCancer dependency and CRISPR screens
EGA scaffoldControlled-access genome–phenome archive
-
TCGA scaffoldThe Cancer Genome Atlas cohorts
UK Biobank scaffoldControlled-access population cohort
@@ -874,24 +874,24 @@ Reference knowledge,
one query away
Drugs, Chemistry & Metabolomics
20Drugs and targets, chemical compounds, enzymes, lipids, metabolomics and toxicogenomics.
+
BindingDBMeasured protein–ligand binding affinities
BRENDAEnzyme kinetics, reactions and inhibitors
ChEBICurated small molecules, structures and roles
CTDChemical–gene–disease relationships, indexed locally
DGIdbDrug–gene interactions and druggable genes
DrugBankLicensed drug, product and interaction lookup
DrugCentralApproved drugs, targets and indications
+
Drugs@FDAFDA drug applications, products and submissions
Guide to PHARMACOLOGYDrug targets and their ligands
HMDBAvailability status only; access is gated
LIPID MAPSLipid structures and classification
MassBankMass-spectrometry reference spectra
MetaboLightsMetabolomics studies, assays and protocols
OpenFDAAdverse events, labels, recalls and NDC
+
PharosDrug targets by development level, ligands and diseases
PubChemCompounds, substances and bioassays
RxNormNormalized drug names, NDCs and drug classes
SwissLipidsCurated lipid structures and metabolism
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BindingDB scaffoldMeasured protein–ligand binding affinities
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Drugs@FDA scaffoldFDA-approved drug products and applications
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Pharos scaffoldIlluminating the Druggable Genome targets
SIDER scaffoldMarketed drug side effects
T3DB scaffoldToxins and their targets
@@ -954,7 +954,7 @@
Reference knowledge,
one query away
NVIDIA BioNeMoOpen biomolecular models and recipes
- Entries tagged scaffold are registered but not yet connected to their upstream resource; the other 100 call it in source. A few connectors report availability status only, where the upstream offers no usable API. Licensed resources (for example COSMIC, DrugBank, HGMD) need your own licence and credentials. Counts are from the docs catalog generated 2026-09-19, updated for connectors implemented since; no entry is asserted as deployed or operationally verified.
+ Entries tagged scaffold are registered but not yet connected to their upstream resource; the other 107 call it in source. A few connectors report availability status only, where the upstream offers no usable API. Licensed resources (for example COSMIC, DrugBank, HGMD) need your own licence and credentials. Counts are from the docs catalog generated 2026-09-19, updated for connectors implemented since; no entry is asserted as deployed or operationally verified.
@@ -972,7 +972,7 @@ What's in the platform
1000+Workflows869 in the docs catalog, across 102 domainsEngine mix in docs catalog: Nextflow 861 · WDL 5 · Snakemake 2 · CWL 1
501Workbench pluginsAcross 22 categories, including 66 integrations
12,276TES tool definitions8 execution backends · 9,061 auto-imported and not yet verified
- 130Reference database plugins100 implemented · 30 scaffolded
+ 130Reference database plugins107 implemented · 23 scaffolded
219API routesFound in source across 8 services · 109 documented publicly
Plugin, tool, reference database and API counts are read from the documentation's generated catalogs (19 Sep 2026). They describe what is registered or configured in source, not that every entry has been tested or deployed. How to read these figures ↗