From 124a1d48817f9eae3575b68e84068c11dd8dc0f3 Mon Sep 17 00:00:00 2001 From: Manish Kumar Date: Sat, 26 Sep 2026 14:39:09 -0500 Subject: [PATCH] Update reference-database status to the current Workbench registry The reference-database section still showed 130 plugins with 23 template scaffolds (107 implemented). Reconciled against the Workbench plugin registry on main (2026-09-26), using the docs catalog generator's source classification: - 129 reference databases: NCBI Gene, RefSeq and Orphadata were removed from Workbench as duplicates of the NCBI and Orphanet connectors; Rhea and Pathway Commons were added (Pathways group). - 126 implemented: the scaffold tag is removed from the 20 connectors built since (OncoKB, VarSome, Mastermind, LOVD, TOPMed, All of Us, CCLE, dbGaP, DepMap, EGA, UK Biobank, SIDER, T3DB, VarCards, dbMTS, BioCyc, MSigDB...). T3DB, VarCards and dbMTS are marked "availability status only"; SIDER's card states its actual scope (drug-name search over operator-supplied release files). - 1 licence-required: GeneCards (no public API documentation; terms prohibit scraping and AI use). - 2 scaffolds remain: Clinvitae and GWAS Summary Statistics. Filter, group, summary and catalog-tile counts updated; cards sorted alphabetically with dimmed entries last. Docs-catalog anchor links are unchanged (they target the currently published docs). Co-Authored-By: Claude Opus 5.5 --- index.html | 61 +++++++++++++++++++++++++++--------------------------- 1 file changed, 30 insertions(+), 31 deletions(-) diff --git a/index.html b/index.html index 716b54d..549755a 100644 --- a/index.html +++ b/index.html @@ -764,23 +764,23 @@

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 · 107 implemented · 23 scaffolded + 129 reference databases across 9 categories · 126 implemented · 1 licence-required · 2 scaffolded Browse the full catalog in the docs ↗
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Genes, Variants & Clinical Genetics

40

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

+

Genes, Variants & Clinical Genetics

38

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 @@ -801,36 +801,39 @@

Reference knowledge,
one query away

GWAS CatalogStudies, traits and reported associations HGMDLicensed clinical variants via a local or gateway provider HGNCApproved human gene symbols and names + LOVDLocus-specific variant databases MARRVELRare-variant evidence across model organisms + MastermindVariant evidence from the literature MaveDBMultiplexed assays of variant effect scores MedGenMedical-genetics concepts, genes and features NCBI EntrezGene, protein, nucleotide and taxonomy search OMIMMendelian genes, disorders and inheritance + OncoKBPrecision-oncology variant knowledge PharmGKBPharmacogenomic annotations via ClinPGx PharmVarPharmacogene star alleles and haplotypes PheGenIPhenotype–genotype associations from NCBI SNPediaCommunity variant and genotype annotations + TOPMedDeep-sequencing variant frequencies UCSC Genome BrowserGenome databases, tracks and region data + VarCardsAvailability status only; no data access + VarSomeVariant classification and annotation Clinvitae scaffoldAggregated clinical variant reports - GeneCards scaffoldIntegrated human gene summaries + GeneCards licence requiredCommercial licence required; not connected GWAS Summary Statistics scaffoldFull summary statistics for GWAS - LOVD scaffoldLocus-specific variant databases - Mastermind scaffoldVariant evidence from the literature - NCBI Gene scaffoldGene records and annotation - OncoKB scaffoldPrecision-oncology variant knowledge - RefSeq scaffoldNCBI reference sequences - TOPMed scaffoldDeep-sequencing variant frequencies - VarCards scaffoldIntegrated coding-variant annotation - VarSome scaffoldVariant classification and annotation

Expression, Omics & Cohorts

19

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

+ All of UsControlled-access research cohort ArrayExpressFunctional-genomics experiments from EMBL-EBI cBioPortalCancer genomics studies and mutations + CCLECancer cell-line omics profiles CellosaurusCell-line identity, origin and hierarchy + dbGaPControlled-access genotype–phenotype studies + DepMapCancer dependency and CRISPR screens EBI BioSamplesCross-repository sample registry + EGAControlled-access genome–phenome archive ENASequencing studies, samples, runs and analyses Expression AtlasBaseline and differential expression across species GTExTissue expression and eQTLs from the GTEx Portal @@ -840,12 +843,7 @@

Reference knowledge,
one query away

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 - UK Biobank scaffoldControlled-access population cohort + UK BiobankControlled-access population cohort
@@ -891,13 +889,13 @@

Reference knowledge,
one query away

PharosDrug targets by development level, ligands and diseases PubChemCompounds, substances and bioassays RxNormNormalized drug names, NDCs and drug classes + SIDERSIDER 4.1 drug-name search over operator-supplied release files SwissLipidsCurated lipid structures and metabolism - SIDER scaffoldMarketed drug side effects - T3DB scaffoldToxins and their targets + T3DBAvailability status only; no data access
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Ontologies, Disease & Phenotype

12

Biomedical ontologies, phenotype vocabularies and gene–disease association resources.

+

Ontologies, Disease & Phenotype

11

Biomedical ontologies, phenotype vocabularies and gene–disease association resources.

BioPortalSearch across hundreds of biomedical ontologies Cell OntologyCell-type terms via EBI OLS @@ -910,7 +908,6 @@

Reference knowledge,
one query away

MondoDisease terms mapped to OMIM, Orphanet, DOID and ICD Open TargetsTarget–disease evidence and prioritisation OrphanetRare diseases, genes and epidemiology - Orphadata scaffoldOrphanet rare-disease data products
@@ -928,23 +925,25 @@

Reference knowledge,
one query away

Non-coding RNA & Regulation

6

Regulatory elements, transcription-factor binding profiles and non-coding RNA.

+ dbMTSAvailability status only; no data access ENCODEExperiments, biosamples and regulatory files JASPARTranscription-factor binding profiles miRBaseMature and precursor miRNA sequences RfamNon-coding RNA families and clans TargetScanmiRNA target-site predictions, indexed locally - dbMTS scaffoldVariants in miRNA target sites
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Pathways

6

Curated pathway and metabolic-network knowledgebases.

+

Pathways

8

Curated pathway and metabolic-network knowledgebases.

+ BioCycPathway/genome databases KEGGPathways, orthology, enzymes and compounds MetaCycMetabolic pathways, reactions and compounds + MSigDBAnnotated gene-set collections + Pathway CommonsIntegrated pathway and interaction data (BioPAX) ReactomePathways, reactions and gene mapping + RheaCurated biochemical reactions (SIB) WikiPathwaysCommunity pathways with genes and metabolites - BioCyc scaffoldPathway/genome databases - MSigDB scaffoldAnnotated gene-set collections
@@ -954,7 +953,7 @@

Reference knowledge,
one query away

NVIDIA BioNeMoOpen biomolecular models and recipes
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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.

+

Entries tagged scaffold are registered but not yet connected to their upstream resource; licence required marks a resource whose terms or undocumented API rule out integration until a licence is arranged. The other 126 are implemented in source; a few of them report availability status only, where the upstream offers no usable access. Licensed resources (for example COSMIC, DrugBank, OncoKB, VarSome, Mastermind, BioCyc) need your own licence and credentials. Counts reflect the Workbench plugin registry on 2026-09-26; no entry is asserted as deployed or operationally verified.

@@ -972,7 +971,7 @@

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 plugins107 implemented · 23 scaffolded + 129Reference database plugins126 implemented · 1 licence-required · 2 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 ↗