From 507e53af2ed029cbaf8cc7a7637a07d3d528dcb4 Mon Sep 17 00:00:00 2001 From: Manish Kumar Date: Fri, 25 Sep 2026 22:36:14 -0500 Subject: [PATCH] Mark 7 more implemented reference databases on the landing page MaveDB, CPIC, TCGA (via GDC), BindingDB, Pharos, Drugs@FDA and GeneReviews now have working connectors on workbench main (PRs #652-#658), so they lose the "scaffold" tag and get card text describing what each connector does. Counts move from 100 implemented / 30 scaffolded to 107 / 23 in the section header and the catalogs tile. Co-Authored-By: Claude Opus 5.5 --- index.html | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/index.html b/index.html index c01e6a1..716b54d 100644 --- a/index.html +++ b/index.html @@ -764,7 +764,7 @@

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 - CPIC scaffoldPharmacogenomic prescribing guidelines GeneCards scaffoldIntegrated human gene summaries - GeneReviews scaffoldExpert-authored disease reviews GWAS Summary Statistics scaffoldFull summary statistics for GWAS LOVD scaffoldLocus-specific variant databases Mastermind scaffoldVariant evidence from the literature - 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

20

Drugs 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 - BindingDB scaffoldMeasured protein–ligand binding affinities - Drugs@FDA scaffoldFDA-approved drug products and applications - 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 ↗