From e2e13f56250e8a578d2feee29afe16dc9d1a7273 Mon Sep 17 00:00:00 2001 From: Manish Kumar Date: Fri, 25 Sep 2026 17:26:59 -0500 Subject: [PATCH] Mark 10 newly implemented reference databases on the landing page CIViC, ChEBI, DGIdb, Mondo, Disease Ontology, RxNorm, cBioPortal, WikiPathways, PANTHER and MedGen now have working connectors on workbench main (PRs #641-#651), so they lose the "scaffold" tag and get card text describing what each connector does. Counts move from 90 implemented / 40 scaffolded to 100 / 30 in the section header and the catalogs tile. Co-Authored-By: Claude Opus 5.5 --- index.html | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/index.html b/index.html index 7f4050d..2b76f87 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 · 90 implemented · 40 scaffolded + 130 reference databases across 9 categories · 100 implemented · 30 scaffolded Browse the full catalog in the docs ↗
@@ -783,6 +783,7 @@

Reference knowledge,
one query away

Genes, Variants & Clinical Genetics

40

Gene nomenclature and annotation, population and structural variation, and clinical-genetics evidence.

1000 Genomes / IGSRPopulation samples, data collections and files + CIViCCancer variant evidence items and assertions ClinGenGene–disease validity and dosage sensitivity ClinVarClinical significance of human variants COSMICCancer Gene Census via licensed downloads @@ -799,6 +800,7 @@

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one query away

HGMDLicensed clinical variants via a local or gateway provider HGNCApproved human gene symbols and names MARRVELRare-variant evidence across model organisms + MedGenMedical-genetics concepts, genes and features NCBI EntrezGene, protein, nucleotide and taxonomy search OMIMMendelian genes, disorders and inheritance PharmGKBPharmacogenomic annotations via ClinPGx @@ -806,7 +808,6 @@

Reference knowledge,
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PheGenIPhenotype–genotype associations from NCBI SNPediaCommunity variant and genotype annotations UCSC Genome BrowserGenome databases, tracks and region data - CIViC scaffoldClinical interpretation of cancer variants Clinvitae scaffoldAggregated clinical variant reports CPIC scaffoldPharmacogenomic prescribing guidelines GeneCards scaffoldIntegrated human gene summaries @@ -815,7 +816,6 @@

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LOVD scaffoldLocus-specific variant databases Mastermind scaffoldVariant evidence from the literature MaveDB scaffoldMultiplexed assays of variant effect - MedGen scaffoldNCBI medical genetics concepts NCBI Gene scaffoldGene records and annotation OncoKB scaffoldPrecision-oncology variant knowledge RefSeq scaffoldNCBI reference sequences @@ -828,6 +828,7 @@

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Expression, Omics & Cohorts

19

Sequencing archives, expression atlases, samples, cell lines and cancer cohorts.

ArrayExpressFunctional-genomics experiments from EMBL-EBI + cBioPortalCancer genomics studies and mutations CellosaurusCell-line identity, origin and hierarchy EBI BioSamplesCross-repository sample registry ENASequencing studies, samples, runs and analyses @@ -839,7 +840,6 @@

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NCBI SRASequence Read Archive studies, runs and samples PanglaoDBSingle-cell cell-type marker genes All of Us scaffoldControlled-access research cohort - cBioPortal scaffoldCancer genomics studies and alterations CCLE scaffoldCancer cell-line omics profiles dbGaP scaffoldControlled-access genotype–phenotype studies DepMap scaffoldCancer dependency and CRISPR screens @@ -859,6 +859,7 @@

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IntActMolecular interactions and Complex Portal InterProProtein families, domains and signatures OrthoDBHierarchical orthologous gene groups + PANTHERGene families, orthologs and enrichment PDB-REDORe-refined crystallographic structures PDBeStructure entries, molecules and residues PDBsumAvailability status only; service offline @@ -868,14 +869,15 @@

Reference knowledge,
one query away

RCSB PDBStructures, entities, assemblies and ligands STRINGProtein–protein interaction networks UniProtProtein sequences, function and annotation - PANTHER scaffoldGene families, function and pathways

Drugs, Chemistry & Metabolomics

20

Drugs and targets, chemical compounds, enzymes, lipids, metabolomics and toxicogenomics.

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 Guide to PHARMACOLOGYDrug targets and their ligands @@ -885,13 +887,11 @@

Reference knowledge,
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MetaboLightsMetabolomics studies, assays and protocols OpenFDAAdverse events, labels, recalls and NDC PubChemCompounds, substances and bioassays + RxNormNormalized drug names, NDCs and drug classes SwissLipidsCurated lipid structures and metabolism BindingDB scaffoldMeasured protein–ligand binding affinities - ChEBI scaffoldChemical entities of biological interest - DGIdb scaffoldDrug–gene interactions and druggability Drugs@FDA scaffoldFDA-approved drug products and applications Pharos scaffoldIlluminating the Druggable Genome targets - RxNorm scaffoldNormalized clinical drug names SIDER scaffoldMarketed drug side effects T3DB scaffoldToxins and their targets
@@ -901,15 +901,15 @@

Reference knowledge,
one query away

BioPortalSearch across hundreds of biomedical ontologies Cell OntologyCell-type terms via EBI OLS + Disease OntologyHuman disease terms and cross-references DISEASESScored gene–disease associations DisGeNETGene–disease and variant–disease associations Gene OntologyGO terms, hierarchy and annotations Human Phenotype OntologyPhenotype terms and disease annotations Monarch InitiativeCross-species biomedical knowledge graph + MondoDisease terms mapped to OMIM, Orphanet, DOID and ICD Open TargetsTarget–disease evidence and prioritisation OrphanetRare diseases, genes and epidemiology - Disease Ontology scaffoldHuman disease terms and hierarchy - Mondo scaffoldUnified disease ontology Orphadata scaffoldOrphanet rare-disease data products
@@ -942,9 +942,9 @@

Reference knowledge,
one query away

KEGGPathways, orthology, enzymes and compounds MetaCycMetabolic pathways, reactions and compounds ReactomePathways, reactions and gene mapping + WikiPathwaysCommunity pathways with genes and metabolites BioCyc scaffoldPathway/genome databases MSigDB scaffoldAnnotated gene-set collections - WikiPathways scaffoldCommunity-curated pathways
@@ -954,7 +954,7 @@

Reference knowledge,
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NVIDIA BioNeMoOpen biomolecular models and recipes
-

Entries tagged scaffold are registered but not yet connected to their upstream resource; the other 90 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; no entry is asserted as deployed or operationally verified.

+

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.

@@ -972,7 +972,7 @@

What's in the platform

869WorkflowsIn 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 plugins90 implemented · 40 scaffolded + 130Reference database plugins100 implemented · 30 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 ↗