Reference Database Catalog
129 enabled reference-database plugins are registered in OmniBioAI. Source analysis found 125 with an upstream-client implementation and 2 template scaffolds (2 not classified).
About this data (generated 2026-09-26)
This page is generated from omnibioai-workbench at commit 57a37dea001f, generated 2026-09-26. See Reference Data for how this layer differs from local organism assets and the biomedical knowledge indexes. Everything below is a fact about source, not about any deployment: no plugin is asserted to be deployed or operationally verified, and no external database was contacted.
How to read this table
- Implementation is a source-structure classification.
IMPLEMENTED: A non-test, non-client module of the plugin invokes the upstream client and the service module does not match the scaffold template.TEMPLATE_SCAFFOLD: The service module matches the scaffold template (fixed OK health payload; search returns an empty result set) and no non-test, non-client module invokes the upstream client.UNKNOWN: Neither pattern could be established from source. IMPLEMENTED is a statement about source structure. It is not evidence that the upstream resource was reached, that credentials are configured, or that results are correct. - Tests (static) is a count of test functions found in the plugin's test source, and mocked means mocking constructs were found. Mocked tests do not exercise the upstream resource. 129 of 129 plugins have test files (17849 test functions in total).
- Live E2E reports whether a live end-to-end test file exists and whether an environment gate pattern was detected in it. 122 plugins have such a file; 113 show an environment gate pattern and 9 do not (
ensembl,gwas_catalog,pride,rcsb_pdb,reactome,sgd,ucsc,uniprot,wormbase), which needs interpretation and is not resolved here. A test file existing is not evidence that the upstream resource was reached; no live test was run. - Access signal shows only signals declared in plugin test source (0 controlled-access, 0 API-key). Signals are read only from flags declared in plugin test source. Their absence is NOT evidence that a resource is open or free to use, and none of this is a licensing determination. The access classification for every entry is REVIEW_REQUIRED.
- Groups are documentation display groups, not a plugin taxonomy: Display groups are a documentation-discovery convenience. The manifests carry no authoritative sub-category; nothing here is written back to a manifest.
- Declared actions: Every one of these manifests declares zero
actions. That does not mean the plugins have no behaviour: reference_db behaviour is reached through the executor, the manifest capability and input/output contracts, the plugin views and an action parameter handled inside the executor.
Versions
0.1.0: 11.0.0: 1231.1.0: 32.0.0: 2
Catalog by group
Genes, Variants & Clinical Genetics (38)
Gene and transcript references, variant and population catalogs, and clinical-genetics evidence resources.
| Plugin | Slug | Version | Implementation | Tests (static) | Live E2E | Access signal | Description |
|---|---|---|---|---|---|---|---|
| 1000 Genomes / IGSR | thousand_genomes | 1.0.0 | IMPLEMENTED | 95 static · mocked | file · env-gated | Read-only integration with IGSR (International Genome Sample Resource, www.internationalgenome.org), the live Elasticsearch-backed API that stewards… Also relevant to: Expression, Omics & Cohorts. | |
| CIViC | civic | 1.0.0 | IMPLEMENTED | 70 static · mocked | file · env-gated | Read-only integration with CIViC (Clinical Interpretation of Variants in Cancer, civicdb.org), the open, expert-moderated knowledgebase of clinical… | |
| ClinGen Integration | clingen | 1.0.0 | IMPLEMENTED | 140 static · mocked | file · env-gated | Read-only, structured access to the Clinical Genome Resource (ClinGen): gene-disease validity classifications, gene- and region-level dosage… | |
| Clinvitae Integration | clinvitae | 1.0.0 | TEMPLATE_SCAFFOLD | 17 static · mocked | file · env-gated | Read-only access to Clinvitae reference data for biomedical research, annotation, and workflow use. | |
| COSMIC Integration | cosmic | 1.0.0 | IMPLEMENTED | 200 static · mocked | file · env-gated | Read-only integration with COSMIC (Catalogue Of Somatic Mutations In Cancer, cancer.sanger.ac.uk), a licensed cancer-genomics resource curated by the… | |
| CPIC | cpic | 1.0.0 | IMPLEMENTED | 60 static · mocked | file · env-gated | Read-only integration with the Clinical Pharmacogenetics Implementation Consortium (CPIC) database via its public PostgREST API (api.cpicpgx.org/v1).… Also relevant to: Drugs, Chemistry & Metabolomics. | |
| dbNSFP Integration | dbnsfp | 1.0.0 | IMPLEMENTED | 221 static · mocked | file · env-gated | Variant functional-annotation integration for dbNSFP (Database for Nonsynonymous SNPs' Functional Predictions; official home www.dbnsfp.org… | |
| dbSNP | dbsnp | 1.0.0 | IMPLEMENTED | 309 static · mocked | file · env-gated | Search and retrieve public NCBI dbSNP variant data -- rsID identity, alleles (including multiallelic records), assembly-specific genomic placements… | |
| dbVar | dbvar | 1.0.0 | IMPLEMENTED | 35 static · mocked | file · env-gated | Read-only access to NCBI dbVar structural-variation studies and variants through documented NCBI E-utilities. | |
| DECIPHER | decipher | 1.0.0 | IMPLEMENTED | 15 static · mocked | file · env-gated | Privacy-preserving DECIPHER integration exposing verified official-interface metadata and connectivity only; clinical/genomic lookup capabilities are… | |
| DGV Integration | dgv | 1.0.0 | IMPLEMENTED | 235 static · mocked | none | Read-only access to DGV structural-variation releases through validated local snapshots. | |
| Ensembl Integration | ensembl | 1.0.0 | IMPLEMENTED | 264 static · mocked | file · gate not detected | Search and retrieve public Ensembl genome annotation, genes, transcripts, exons, genomic regions, sequences, variants, cross-references, comparative… Also relevant to: Model Organisms. | |
| Gene2Phenotype (EMBL-EBI) | gene2phenotype | 1.0.0 | IMPLEMENTED | 51 static · mocked | file · env-gated | Read-only integration with Gene2Phenotype (G2P, ebi.ac.uk/gene2phenotype), EMBL-EBI's expert-curated dataset of gene-disease associations organised… | |
| GeneCards Integration | gene_cards | 1.0.0 | UNKNOWN | 16 static · mocked | none | GeneCards (Weizmann Institute / LifeMap Sciences) status connector: LICENSE_REQUIRED, no data actions. The GeneCards API is documented only to… | |
| GeneReviews | genereviews | 1.0.0 | IMPLEMENTED | 66 static · mocked | file · env-gated | Read-only, metadata-only integration with GeneReviews (NCBI Bookshelf NBK1116, University of Washington), the collection of expert-authored… | |
| Genomics England PanelApp | panelapp | 1.0.0 | IMPLEMENTED | 60 static · mocked | file · env-gated | Read-only integration with Genomics England PanelApp (panelapp.genomicsengland.co.uk), the crowd-sourced, expert-reviewed repository of… | |
| gnomAD | gnomad | 1.0.0 | IMPLEMENTED | 380 static · mocked | file · env-gated | Read-only integration with gnomAD (the Genome Aggregation Database, v4.1), providing structured programmatic access to population-scale human genomic… | |
| GWAS Summary Stats Integration | gwas_summary_stats | 1.0.0 | TEMPLATE_SCAFFOLD | 17 static · mocked | file · env-gated | Read-only access to GWAS Summary Stats reference data for biomedical research, annotation, and workflow use. | |
| HGMD | hgmd | 1.0.0 | IMPLEMENTED | 286 static · mocked | file · env-gated | Read-only integration with the Human Gene Mutation Database (HGMD), a licensed/proprietary clinical-variant resource operated by QIAGEN Digital… | |
| HGNC | hgnc | 1.0.0 | IMPLEMENTED | 324 static · mocked | file · env-gated | Search and retrieve authoritative human gene nomenclature from the HUGO Gene Nomenclature Committee (HGNC) -- approved gene symbol/name, status… | |
| LOVD | lovd | 1.0.0 | IMPLEMENTED | 84 static · mocked | file · env-gated | Read-only integration with LOVD (Leiden Open Variation Database), Global Variome shared LOVD (databases.lovd.nl/shared, LOVD3), through its public… | |
| MARRVEL Integration | marrvel | 1.0.0 | IMPLEMENTED | 95 static · mocked | file · env-gated | Read-only, structured access to MARRVEL (Model organism Aggregated Resources for Rare Variant ExpLoration) -- verified public gene, variant, and… | |
| Mastermind Integration | mastermind | 1.0.0 | IMPLEMENTED | 81 static · mocked | file · env-gated | Licensed, read-only integration with Genomenon's Mastermind Genomic Search Engine API v2: entity normalisation (suggestions), article counts and… | |
| MaveDB | mavedb | 1.0.0 | IMPLEMENTED | 79 static · mocked | file · env-gated | Read-only integration with MaveDB, the public database of multiplexed assays of variant effect (deep mutational scans, saturation genome editing… | |
| MedGen | medgen | 1.0.0 | IMPLEMENTED | 47 static · mocked | file · env-gated | Read-only integration with NCBI MedGen, the portal of human medical-genetics concepts (diseases and phenotypes). Provides concept lookup by… | |
| NCBI ClinVar Integration | clinvar | 1.0.0 | IMPLEMENTED | 374 static · mocked | file · env-gated | Search and retrieve public NCBI ClinVar clinical variant interpretation data -- variant identity and genomic context, clinical significance… | |
| NCBI Integration | ncbi | 1.0.0 | IMPLEMENTED | 243 static · mocked | file · env-gated | Secure, read-only gateway to NCBI's public Entrez E-utilities for Gene, Protein, Nucleotide/Nuccore, and Taxonomy -- controlled search (esearch)… Also relevant to: Expression, Omics & Cohorts; Proteins, Structure & Interactions. | |
| NHGRI-EBI GWAS Catalog Integration | gwas_catalog | 1.0.0 | IMPLEMENTED | 324 static · mocked | file · gate not detected | Search and retrieve public NHGRI-EBI GWAS Catalog evidence -- studies, publications, EFO/ontology traits, reported associations (risk alleles… | |
| OMIM | omim | 1.0.0 | IMPLEMENTED | 146 static · mocked | none | Read-only integration with OMIM (Online Mendelian Inheritance in Man, api.omim.org), the authoritative catalog of human genes and Mendelian genetic… | |
| OncoKB Integration | oncokb | 1.0.0 | IMPLEMENTED | 117 static · mocked | file · env-gated | Licensed, read-only integration with OncoKB's web API (Memorial Sloan Kettering precision oncology knowledge base): oncogenic effect, levels of… | |
| PharmGKB | pharmgkb | 1.0.0 | IMPLEMENTED | 274 static · mocked | file · env-gated | Read-only integration with PharmGKB (the Pharmacogenomics Knowledgebase), accessed through its current official API host, ClinPGx… Also relevant to: Drugs, Chemistry & Metabolomics. | |
| PharmVar Integration | pharmvar | 1.0.0 | IMPLEMENTED | 121 static · mocked | file · env-gated | Read-only, structured access to the official PharmVar (Pharmacogene Variation Consortium, https://www.pharmvar.org) API: pharmacogene lookup… Also relevant to: Drugs, Chemistry & Metabolomics. | |
| PheGenI Integration | phegeni | 1.0.0 | IMPLEMENTED | 184 static · mocked | none | Read-only, structured access to NCBI PheGenI (Phenotype-Genotype Integrator): phenotype, gene, and variant search and phenotype–genotype association… | |
| SNPedia Integration | snpedia | 1.0.0 | IMPLEMENTED | 267 static · mocked | file · env-gated | Read-only integration with SNPedia (www.snpedia.com), a community-editable wiki of dbSNP variant/genotype information, via SNPedia's official… | |
| TOPMed | topmed | 2.0.0 | IMPLEMENTED | 89 static · mocked | file · env-gated | Read-only NHLBI TOPMed (Trans-Omics for Precision Medicine) aggregate allele counts on GRCh38, read from NCBI dbSNP's Variation Services API where… Also relevant to: Expression, Omics & Cohorts. | |
| UCSC Genome Browser | ucsc | 1.0.0 | IMPLEMENTED | 218 static · mocked | file · gate not detected | Search and retrieve public UCSC Genome Browser genome databases, chromosome/sequence information, tracks, and region/feature data for use in… Also relevant to: Expression, Omics & Cohorts. | |
| VarCards Integration | varcards | 1.1.0 | IMPLEMENTED | 26 static · mocked | file · env-gated | VarCards / VarCards2 (integrated genetic and clinical variant-interpretation databases) status connector. Status only: reports whether the VarCards2… | |
| VarSome Integration | varsome | 1.0.0 | IMPLEMENTED | 96 static · mocked | file · env-gated | Licensed, read-only integration with the VarSome API (Saphetor): aggregated variant annotation from 100+ databases with automated germline ACMG and… |
Expression, Omics & Cohorts (19)
Expression atlases, sequence and functional-genomics archives, cancer and cell-line resources, and controlled-access cohorts.
| Plugin | Slug | Version | Implementation | Tests (static) | Live E2E | Access signal | Description |
|---|---|---|---|---|---|---|---|
| All of Us (public aggregate data) | all_of_us | 1.0.0 | IMPLEMENTED | 70 static · mocked | file · env-gated | Read-only connector to the NIH All of Us Research Program's PUBLIC aggregate tier, via the anonymous public Data Browser API… Also relevant to: Genes, Variants & Clinical Genetics. | |
| ArrayExpress | arrayexpress | 1.0.0 | IMPLEMENTED | 266 static · mocked | file · env-gated | Search and retrieve public EMBL-EBI ArrayExpress functional-genomics experiments -- organism, experiment/study type, experimental factors, sample… | |
| cBioPortal | cbioportal | 1.0.0 | IMPLEMENTED | 69 static · mocked | file · env-gated | Read-only integration with the public cBioPortal for Cancer Genomics (www.cbioportal.org) REST API: search cancer genomics studies, study detail… | |
| CCLE | ccle | 1.0.0 | IMPLEMENTED | 100 static · mocked | file · env-gated | Read-only CCLE (Cancer Cell Line Encyclopedia) cell-line omics from the Broad's DepMap Public releases: model metadata (ACH id, cell line and CCLE… | |
| Cellosaurus (SIB) | cellosaurus | 1.0.0 | IMPLEMENTED | 43 static · mocked | file · env-gated | Read-only integration with Cellosaurus (cellosaurus.org, SIB Swiss Institute of Bioinformatics), the reference knowledge resource on cell lines… Also relevant to: Ontologies & Phenotype. | |
| dbGaP | dbgap | 1.0.0 | IMPLEMENTED | 87 static · mocked | file · env-gated | Read-only connector to the public metadata layer of dbGaP (NCBI Database of Genotypes and Phenotypes): study search and study descriptions via the… | |
| DepMap Gene Dependency | depmap | 1.0.0 | IMPLEMENTED | 92 static · mocked | file · env-gated | Read-only CRISPR gene-dependency integration with DepMap (Broad Institute Cancer Dependency Map). Serves Chronos gene effect (negative = more… | |
| EBI BioSamples | biosamples | 1.0.0 | IMPLEMENTED | 64 static · mocked | file · env-gated | Read-only integration with EBI BioSamples (www.ebi.ac.uk/biosamples), EMBL-EBI's unified cross-repository sample registry. Distinct from this… | |
| EBI Expression Atlas | expression_atlas | 1.0.0 | IMPLEMENTED | 72 static · mocked | file · env-gated | Read-only integration with EBI's Expression Atlas (www.ebi.ac.uk/gxa) -- cross-species (animals/plants/fungi/protists), cross-experiment baseline and… | |
| EGA | ega | 1.0.0 | IMPLEMENTED | 89 static · mocked | file · env-gated | Read-only connector to the public metadata layer of EGA, the European Genome-phenome Archive (EMBL-EBI and CRG), through its anonymous public… | |
| ENA | ena | 1.0.0 | IMPLEMENTED | 333 static · mocked | file · env-gated | Search and retrieve public sequencing metadata from the EMBL-EBI European Nucleotide Archive (ENA) -- studies/projects, samples, experiments, runs… | |
| GTEx | gtex | 1.0.0 | IMPLEMENTED | 216 static · mocked | file · env-gated | Read-only integration with the GTEx (Genotype-Tissue Expression) Consortium's official public GTEx Portal API v2 (gtexportal.org/api/v2), publicly… | |
| ICGC Integration | icgc | 1.0.0 | IMPLEMENTED | 77 static · mocked | file · env-gated | The original ICGC DCC Data Portal (dcc.icgc.org) officially closed in June 2024. This connector reads ICGC's own still-live, keyless, S3-compatible… | |
| LINCS (L1000 / Connectivity Map) | lincs | 1.0.0 | IMPLEMENTED | 71 static · mocked | file · env-gated | Live, keyless read-only integration with iLINCS (www.ilincs.org, University of Cincinnati BD2K-LINCS DCIC), the LINCS Data Portal's REST API for… | |
| NCBI GEO Integration | geo | 1.0.0 | IMPLEMENTED | 37 static · mocked | file · env-gated | Structured, live access to NCBI's Gene Expression Omnibus (GEO) -- gene expression/functional genomics series (GSE), curated datasets (GDS)… | |
| NCBI SRA Integration | sra | 1.0.0 | IMPLEMENTED | 284 static · mocked | file · env-gated | Search and retrieve public NCBI Sequence Read Archive metadata -- studies, experiments, samples, runs, BioProject/BioSample cross-references, and… | |
| PanglaoDB | panglaodb | 1.0.0 | IMPLEMENTED | 286 static · mocked | file · env-gated | Read-only integration with PanglaoDB (panglaodb.se), a single-cell RNA-seq resource providing a community-curated compendium of cell-type marker… | |
| TCGA (GDC) | tcga | 1.0.0 | IMPLEMENTED | 72 static · mocked | file · env-gated | Read-only connector to The Cancer Genome Atlas (TCGA) open-access data through the live NCI Genomic Data Commons (GDC) API (api.gdc.cancer.gov): the… | |
| UK Biobank Showcase Field Catalogue | uk_biobank | 2.0.0 | IMPLEMENTED | 86 static · mocked | file · env-gated | Read-only lookup of the UK Biobank Data Showcase's PUBLIC metadata: the data-field catalogue (title, units, value type, instancing/arraying, category… Also relevant to: Genes, Variants & Clinical Genetics. |
Ontologies & Phenotype (11)
Ontologies and vocabularies, and phenotype, disease and gene-disease association resources.
| Plugin | Slug | Version | Implementation | Tests (static) | Live E2E | Access signal | Description |
|---|---|---|---|---|---|---|---|
| BioPortal Integration | bioportal | 1.0.0 | IMPLEMENTED | 245 static · mocked | file · env-gated | Read-only integration with the NCBO BioPortal REST API (data.bioontology.org) -- the world's largest open repository of biomedical ontologies (SNOMED… | |
| Cell Ontology | cell_ontology | 1.0.0 | IMPLEMENTED | 61 static · mocked | file · env-gated | Live, read-only access to the Cell Ontology (CL) -- an OBO Foundry ontology of cell types -- served through EBI's Ontology Lookup Service (OLS4).… | |
| DISEASES (Jensen Lab) | diseases_db | 1.0.0 | IMPLEMENTED | 48 static · mocked | file · env-gated | Read-only integration with DISEASES (diseases.jensenlab.org), the Jensen Lab's weekly-updated resource of human gene-disease associations. Every… | |
| DisGeNET | disgenet | 1.0.0 | IMPLEMENTED | 148 static · mocked | none | Read-only integration with DisGeNET (api.disgenet.com), a comprehensive discovery platform of gene-disease, variant-disease, and disease-disease… Also relevant to: Genes, Variants & Clinical Genetics. | |
| Gene Ontology | gene_ontology | 1.0.0 | IMPLEMENTED | 23 static · mocked | file · env-gated | Official Gene Ontology term, hierarchy, evidence-code, and cross-species gene/function annotation access using the GO API and go-basic JSON release. | |
| Human Disease Ontology | disease_ontology | 1.0.0 | IMPLEMENTED | 45 static · mocked | file · env-gated | Read-only integration with the Human Disease Ontology (DOID, disease-ontology.org), a standardized ontology of human disease. Provides term lookup… | |
| Human Phenotype Ontology | hpo | 1.0.0 | IMPLEMENTED | 33 static · mocked | file · env-gated | First-class, release-pinned access to official Human Phenotype Ontology terms, hierarchy, annotations, releases, cross-references, and downloadable… | |
| Monarch Initiative | monarch | 1.0.0 | IMPLEMENTED | 74 static · mocked | file · env-gated | Read-only integration with the Monarch Initiative's v3 API (api-v3.monarchinitiative.org) -- a cross-species, cross-category biomedical knowledge… | |
| Mondo Disease Ontology | mondo | 1.0.0 | IMPLEMENTED | 46 static · mocked | file · env-gated | Read-only integration with Mondo (the Monarch Disease Ontology), which harmonizes disease definitions across OMIM, Orphanet, DOID, NCIt, MeSH, ICD… | |
| Open Targets | opentargets | 1.0.0 | IMPLEMENTED | 273 static · mocked | file · env-gated | Read-only integration with the Open Targets Platform (platform.opentargets.org) -- a systematic, EBI/GSK/Wellcome-backed resource for target… Also relevant to: Drugs, Chemistry & Metabolomics; Genes, Variants & Clinical Genetics. | |
| Orphanet | orphanet | 1.0.0 | IMPLEMENTED | 221 static · mocked | file · env-gated | Read-only integration with Orphanet's official Orphadata resources -- the free, keyless, CC BY 4.0 live JSON REST API (api.orphadata.com) plus, for… Also relevant to: Genes, Variants & Clinical Genetics. |
Proteins, Structure & Interactions (18)
Protein sequence, family, domain and structure resources, molecular and cell-cell interaction resources, and proteomics repositories.
| Plugin | Slug | Version | Implementation | Tests (static) | Live E2E | Access signal | Description |
|---|---|---|---|---|---|---|---|
| BioGRID | biogrid | 1.0.0 | IMPLEMENTED | 210 static · mocked | file · env-gated | Read-only integration with the BioGRID REST Service (webservice.thebiogrid.org), the Biological General Repository for Interaction Datasets -- a… | |
| CellChat | cellchat | 1.0.0 | IMPLEMENTED | 276 static · mocked | file · env-gated | Local, indexed cell-cell communication and ligand-receptor interaction knowledge layer backed by CellChatDB -- the manually curated ligand-receptor… Also relevant to: Expression, Omics & Cohorts. | |
| DIP | dip | 1.0.0 | IMPLEMENTED | 201 static · mocked | file · env-gated | Status/compatibility integration for DIP (Database of Interacting Proteins, David Eisenberg lab, UCLA DOE-MBI), a curated database of experimentally… | |
| eggNOG Integration | eggnog | 1.0.0 | IMPLEMENTED | 88 static · mocked | file · env-gated | Read-only integration with eggNOG (eggnogdb.org, eggNOG 7), EMBL's orthology and functional-annotation database -- protein records, ortholog lookups… | |
| Human Protein Atlas Integration | hpa | 1.0.0 | IMPLEMENTED | 113 static · mocked | file · env-gated | Read-only, structured access to the official Human Protein Atlas individual-gene-entry and customized search/download interfaces: gene/protein… Also relevant to: Expression, Omics & Cohorts. | |
| IntAct | intact | 1.0.0 | IMPLEMENTED | 246 static · mocked | file · env-gated | Read-only integration with EMBL-EBI's IntAct Molecular Interaction Database (www.ebi.ac.uk/intact) and the Complex Portal it curates into -- a… | |
| InterPro Integration | interpro | 1.0.0 | IMPLEMENTED | 326 static · mocked | file · env-gated | Search and retrieve public InterPro protein family, domain, functional-site, and signature classification data -- entry metadata, hierarchy… | |
| OrthoDB Integration | orthodb | 1.0.0 | IMPLEMENTED | 76 static · mocked | file · env-gated | Read-only, live integration with OrthoDB's public REST API (data.orthodb.org) -- a hierarchical catalog of orthologous protein-coding gene groups… | |
| PANTHER | panther | 1.0.0 | IMPLEMENTED | 67 static · mocked | file · env-gated | Read-only integration with PANTHER (Protein ANalysis THrough Evolutionary Relationships, USC) through the public PANTHER web services: gene family… Also relevant to: Pathways. | |
| PDB-REDO | pdb_redo | 1.0.0 | IMPLEMENTED | 233 static · mocked | file · env-gated | Read-only integration with PDB-REDO, the automated re-refinement and validation databank for crystallographic Protein Data Bank entries. Retrieves… | |
| PDBe Integration | pdbe | 1.0.0 | IMPLEMENTED | 437 static · mocked | file · env-gated | Search and retrieve public PDBe (Protein Data Bank in Europe / EMBL-EBI) structural-biology data -- entry metadata, experimental methods… | |
| PDBsum | pdbsum | 1.0.0 | IMPLEMENTED | 187 static · mocked | file · env-gated | Status/compatibility integration for PDBsum (Laskowski/Thornton, EMBL-EBI), the structural-summary database for PDB entries. PDBsum never published a… | |
| Pfam Integration | pfam | 1.0.0 | IMPLEMENTED | 31 static · mocked | file · env-gated | Read-only Pfam 38.2 family, clan, membership, and UniProt domain-annotation access through the official EMBL-EBI InterPro REST API. | |
| PRIDE Archive Integration | pride | 1.0.0 | IMPLEMENTED | 227 static · mocked | file · gate not detected | Search and retrieve public PRIDE Archive proteomics datasets and ProteomeXchange metadata -- projects, publications, experimental/instrument… Also relevant to: Expression, Omics & Cohorts. | |
| ProteomeXchange Integration | proteomexchange | 1.0.0 | IMPLEMENTED | 50 static · mocked | file · env-gated | Read-only integration with ProteomeXchange's ProteomeCentral PROXI (ProteomeXchange Interface) JSON API -- cross-repository proteomics dataset… Also relevant to: Expression, Omics & Cohorts. | |
| RCSB PDB Integration | rcsb_pdb | 1.0.0 | IMPLEMENTED | 267 static · mocked | file · gate not detected | Search and retrieve public RCSB Protein Data Bank structural data -- structures, polymer/non-polymer entities, chains, biological assemblies… | |
| STRING Database Integration | string_db | 1.0.0 | IMPLEMENTED | 298 static · mocked | file · env-gated | Read-only integration with the STRING database (string-db.org), providing secure, structured programmatic access to protein identifier… | |
| UniProt Integration | uniprot | 1.0.0 | IMPLEMENTED | 323 static · mocked | file · gate not detected | Search and retrieve public UniProt protein knowledgebase data -- protein identity, sequences, isoforms, functional annotations (function, catalytic… |
Pathways (8)
Metabolic and signalling pathway databases and gene-set collections.
| Plugin | Slug | Version | Implementation | Tests (static) | Live E2E | Access signal | Description |
|---|---|---|---|---|---|---|---|
| BioCyc Integration | biocyc | 1.0.0 | IMPLEMENTED | 90 static · mocked | file · env-gated | Licensed, read-only integration with the BioCyc web services (SRI International): organism database list and KB versions, pathway/genome objects in… | |
| KEGG Integration | kegg | 1.0.0 | IMPLEMENTED | 348 static · mocked | file · env-gated | Search and retrieve public KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway/molecular knowledge -- pathways, genes, KEGG Orthology (KO)… | |
| MetaCyc | metacyc | 0.1.0 | IMPLEMENTED | 167 static · mocked | file · env-gated | Read-only integration with the official MetaCyc metabolic pathway database and the BioCyc Web Services platform that serves it: bounded search… | |
| MSigDB Integration | msigdb | 1.0.0 | IMPLEMENTED | 70 static · mocked | file · env-gated | Read-only integration with the Molecular Signatures Database (Broad Institute / UC San Diego) through its official versioned release files and gene… Also relevant to: Ontologies & Phenotype. | |
| Pathway Commons Integration | pathway_commons | 1.0.0 | IMPLEMENTED | 10 static · mocked | none | Read-only access to Pathway Commons' integrated BioPAX model and official graph API for cross-database pathway search, retrieval, traversal… | |
| Reactome Integration | reactome | 1.0.0 | IMPLEMENTED | 319 static · mocked | file · gate not detected | Search and retrieve public Reactome pathway knowledgebase data -- pathways, pathway hierarchy, reactions/events, gene/protein-to-pathway mapping… | |
| Rhea Biochemical Reaction Integration | rhea | 1.0.0 | IMPLEMENTED | 12 static · mocked | none | Read-only access to the official Rhea biochemical reaction knowledgebase REST interface for curated reaction equations, ChEBI participants, EC… | |
| WikiPathways | wikipathways | 1.0.0 | IMPLEMENTED | 65 static · mocked | file · env-gated | Read-only integration with WikiPathways, the open, community-curated biological pathway database, through its official bulk JSON API… |
Drugs, Chemistry & Metabolomics (20)
Drug, compound, target-binding and regulatory resources, and metabolite, lipid and mass-spectrometry references.
| Plugin | Slug | Version | Implementation | Tests (static) | Live E2E | Access signal | Description |
|---|---|---|---|---|---|---|---|
| BindingDB | bindingdb | 1.0.0 | IMPLEMENTED | 80 static · mocked | file · env-gated | Read-only integration with BindingDB (The Binding Database) through its public REST web services: measured binding affinities (Ki, IC50, Kd, EC50 in… | |
| BRENDA Enzyme Database | brenda | 1.0.0 | IMPLEMENTED | 285 static · mocked | file · env-gated | Authenticated, release-pinned access to the official BRENDA enzyme information system via its SOAP web service: enzyme lookup by EC number, EC… | |
| ChEBI | chebi | 1.0.0 | IMPLEMENTED | 62 static · mocked | file · env-gated | Read-only integration with ChEBI (Chemical Entities of Biological Interest, EMBL-EBI) through the public ChEBI 2.0 REST API: compound records (names… | |
| CTD Integration | ctd | 1.0.0 | IMPLEMENTED | 88 static · mocked | file · env-gated | Locally-indexed access to CTD (Comparative Toxicogenomics Database, ctdbase.org) chemical, disease, and curated chemical/gene-disease relationship… Also relevant to: Genes, Variants & Clinical Genetics. | |
| DGIdb | dgidb | 1.0.0 | IMPLEMENTED | 49 static · mocked | file · env-gated | Read-only integration with DGIdb (Drug-Gene Interaction Database, dgidb.org), which aggregates drug-gene interaction claims and druggable-gene… | |
| DrugBank Integration | drugbank | 1.0.0 | IMPLEMENTED | 136 static · mocked | file · env-gated | Licensed, read-only integration with DrugBank's Clinical API (api.drugbank.com) -- drug name/synonym/brand-name search, product lookup by NDC/DPD/EMA… | |
| DrugCentral Integration | drugcentral | 1.0.0 | IMPLEMENTED | 244 static · mocked | file · env-gated | Read-only integration with DrugCentral's public DRS REST API (uxn2ycvimg.us-east-2.awsapprunner.com, linked from drugcentral.org/download)… | |
| Drugs@FDA | drugsatfda | 1.0.0 | IMPLEMENTED | 87 static · mocked | file · env-gated | Read-only integration with Drugs@FDA through the openFDA endpoint api.fda.gov/drug/drugsfda.json: FDA-approved drug applications (NDA, ANDA, BLA)… | |
| HMDB | hmdb | 1.0.0 | IMPLEMENTED | 125 static · mocked | file · env-gated | Status/compatibility integration for HMDB (Human Metabolome Database, Wishart Research Group, University of Alberta). Two independent access barriers… | |
| IUPHAR/BPS Guide to PHARMACOLOGY | guidetopharmacology | 1.0.0 | IMPLEMENTED | 54 static · mocked | file · env-gated | Read-only integration with the IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, www.guidetopharmacology.org), the expert-curated database of drug targets… | |
| LIPID MAPS Integration | lipidmaps | 1.0.0 | IMPLEMENTED | 112 static · mocked | file · env-gated | Read-only integration with LIPID MAPS (lipidmaps.org)'s public REST API -- lipid compound lookup/search by LIPID MAPS ID, InChIKey, molecular… | |
| MassBank | massbank | 1.0.0 | IMPLEMENTED | 85 static · mocked | file · env-gated | Read-only integration with MassBank Europe's live REST API (massbank.eu/MassBank-api) for mass-spectrometry reference spectra: record retrieval by… | |
| MetaboLights | metabolights | 1.0.0 | IMPLEMENTED | 280 static · mocked | file · env-gated | Search and retrieve public metabolomics study metadata from EMBL-EBI MetaboLights -- studies, ISA-Tab sample/assay sheets, protocols, publications… | |
| OpenFDA Integration | openfda | 1.0.0 | IMPLEMENTED | 31 static · mocked | file · env-gated | Read-only, structured access to seven verified FDA OpenFDA datasets: drug adverse events, labels, enforcement recalls, NDC products, device adverse… | |
| Pharos | pharos | 1.0.0 | IMPLEMENTED | 88 static · mocked | file · env-gated | Read-only integration with NCATS Pharos, the web interface to TCRD (Target Central Resource Database) from the NIH Illuminating the Druggable Genome… | |
| PubChem | pubchem | 1.0.0 | IMPLEMENTED | 279 static · mocked | file · env-gated | Read-only integration with the NCBI PubChem public chemical database (pubchem.ncbi.nlm.nih.gov), queried through PubChem's official public PUG-REST… | |
| RxNorm | rxnorm | 1.0.0 | IMPLEMENTED | 78 static · mocked | file · env-gated | Read-only integration with RxNorm, the U.S. National Library of Medicine's normalized naming system for clinical drugs, through the public NLM RxNav… | |
| SIDER 4.1 Bulk Reference | sider | 1.0.0 | UNKNOWN | 19 static · mocked | file · env-gated | Local drug-name search over the official SIDER 4.1 bulk release (EMBL Side Effect Resource, released 2015-10-21). Searches the operator-supplied… | |
| SwissLipids Integration | swisslipids | 1.0.0 | IMPLEMENTED | 71 static · mocked | file · env-gated | Read-only access to SwissLipids (swisslipids.org), the SIB Swiss Institute of Bioinformatics' expert-curated knowledgebase of lipid structures… | |
| T3DB Integration | t3db | 1.1.0 | IMPLEMENTED | 26 static · mocked | file · env-gated | T3DB (Toxin and Toxin-Target Database; Wishart Research Group, University of Alberta) status connector. Status only: reports whether t3db.ca is… |
Non-coding RNA & Regulation (6)
Non-coding RNA families, miRNA targets, transcription-factor motifs and functional-genomics regulatory data.
| Plugin | Slug | Version | Implementation | Tests (static) | Live E2E | Access signal | Description |
|---|---|---|---|---|---|---|---|
| dbMTS Integration | dbmts | 1.1.0 | IMPLEMENTED | 26 static · mocked | file · env-gated | dbMTS (Liu Lab, University of South Florida; human microRNA target-site SNV predictions) status connector. Status only: reports whether the official… Also relevant to: Genes, Variants & Clinical Genetics. | |
| ENCODE Integration | encode | 1.0.0 | IMPLEMENTED | 114 static · mocked | file · env-gated | Read-only, structured access to the official ENCODE Project REST API (www.encodeproject.org) -- experiment search and accession lookup, biosample… Also relevant to: Expression, Omics & Cohorts. | |
| jaspar | jaspar | 1.0.0 | IMPLEMENTED | 18 static · mocked | file · env-gated | Read-only access to official JASPAR transcription-factor binding profiles, matrices, versions, species, taxa, collections and releases. | |
| miRBase | mirbase | 1.0.0 | IMPLEMENTED | 29 static · mocked | file · env-gated | Read-only, dataset-backed access to verified miRBase release 23 mature and precursor sequences and per-organism GFF3 genomic annotations. No REST API… | |
| Rfam Integration | rfam | 1.0.0 | IMPLEMENTED | 44 static · mocked | file · env-gated | Read-only Rfam non-coding RNA family, clan, keyword search, per-family genomic sequence-hit, and reference-genome summary access through the official… | |
| TargetScan Integration | targetscan | 1.0.0 | IMPLEMENTED | 75 static · mocked | file · env-gated | Read-only, locally-indexed access to TargetScan's miRNA target-site predictions (vert_80 / Release 8.0) -- TargetScan publishes no REST/JSON API (its… |
Model Organisms (7)
Species-specific model-organism genome and phenotype databases.
| Plugin | Slug | Version | Implementation | Tests (static) | Live E2E | Access signal | Description |
|---|---|---|---|---|---|---|---|
| FlyBase | flybase | 1.0.0 | IMPLEMENTED | 84 static · mocked | file · env-gated | Read-only, live integration with the official FlyBase REST API (api.flybase.org/api/v1.0), the Drosophila genome database curated by FlyBase.org. No… | |
| Mouse Genome Informatics (MGI) Integration | mgi | 1.0.0 | IMPLEMENTED | 71 static · mocked | file · env-gated | Read-only integration with MGI (informatics.jax.org), The Jackson Laboratory's international database resource for the laboratory mouse. MGI's own… | |
| Rat Genome Database (RGD) | rgd | 1.0.0 | IMPLEMENTED | 73 static · mocked | file · env-gated | Live, read-only integration with the official RGD (rgd.mcw.edu) REST webservice at rest.rgd.mcw.edu/rgdws -- gene lookup by RGD ID, symbol, or alias… | |
| SGD | sgd | 1.0.0 | IMPLEMENTED | 151 static · mocked | file · gate not detected | Read-only integration with SGD (Saccharomyces Genome Database, yeastgenome.org)'s live JSON backend -- locus/gene records, GO annotations, phenotype… | |
| TAIR Integration | tair | 1.0.0 | IMPLEMENTED | 55 static · mocked | file · env-gated | TAIR (arabidopsis.org) has operated under a Phoenix Bioinformatics subscription-funding model since 2013 and publishes no public REST/JSON API… | |
| WormBase Integration | wormbase | 1.0.0 | IMPLEMENTED | 123 static · mocked | file · gate not detected | Read-only, live integration with WormBase's REST field API (rest.wormbase.org), serving the WS298 final release (2025-11-27) of the C. elegans genome… | |
| ZFIN Integration | zfin | 1.0.0 | IMPLEMENTED | 79 static · mocked | file · env-gated | Locally-indexed, read-only integration with ZFIN (zfin.org), the official zebrafish model organism database. ZFIN publishes no REST/JSON API -- only… |
Other / Cross-domain (2)
Registered under the reference_db category but not a natural fit for any single scientific group above. See the note beside each entry.
| Plugin | Slug | Version | Implementation | Tests (static) | Live E2E | Access signal | Description |
|---|---|---|---|---|---|---|---|
| BioNeMo | bionemo | 1.0.0 | IMPLEMENTED | 301 static · mocked | file · env-gated | Discover NVIDIA BioNeMo's open-source models, recipes, and artifacts -- model/recipe metadata, per-repository license classification (BioNeMo is not… Registered under the reference_db category, but its manifest describes discovery of NVIDIA BioNeMo models, recipes and artifacts through the public GitHub API rather than access to a reference-data resource. It is counted with the other reference_db plugins because the registry is authoritative for category membership. | |
| ClinicalTrials.gov | clinicaltrials_gov | 1.0.0 | IMPLEMENTED | 233 static · mocked | file · env-gated | Read-only integration with the National Library of Medicine's official public ClinicalTrials.gov API v2 (clinicaltrials.gov/api/v2), publicly… |
Template scaffolds
2 plugins match the scaffold pattern. They are registered and enabled, but their service code returns a fixed OK health status and an empty search result without calling the upstream resource. This describes source structure only, not a judgment of the plugin: each is a placeholder whose upstream implementation has not been filled in.
Clinvitae Integration · GWAS Summary Stats Integration
Registry and manifest reconciliation
The registry and the manifests were compared field by field (slug, name, category, enabled, description, version, author, actions). Results: 129 MATCH.
Related pages
- Reference Data — the three reference-data layers and how they differ.
- Organism Reference Assets — a separate, independent inventory.
- Workbench Plugin Catalog — all 501 plugins across every category.
reference-db-catalog.json— the full machine-readable catalog.