is a Knowledge Graph.
The Data Distillery Knowledge Graph (DDKG) integrates summarized ("distilled") data from multiple NIH Common Fund Data Coordinating Centers (DCCs) within a knowledge graph, as part of the Common Fund Data Ecosystem (CFDE). Its schema is based on the Unified Biomedical Knowledge Graph (UBKG), which builds on the UMLS and adds over 180 ontologies and standards. The DDKG is accessible through a web interface, a programmatic API, and downloadable per-DCC subgraphs.
John Erol Evangelista
Github: jeevangelista
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| cfde-ddkg.portal | DDKG Web Interface | dd-kg-ui.cfde.cloud | Graphical Interface | http | Interactive web interface for browsin... |
| cfde-ddkg.downloads | DDKG Downloads Manifest | downloads.json (5.1 KB) | Product | json | JSON manifest listing downloadable DD... |
| cfde-ddkg.hubmap | DDKG HuBMAP Subgraph | HuBMAP.zip (68.9 KB) | Graph | csv | Data Distillery HuBMAP subgraph (buil... |
| cfde-ddkg.idg | DDKG IDG Subgraph | IDG.zip (27.9 MB) | Graph | csv | Data Distillery IDG subgraph (build o... |
| cfde-ddkg.glygen | DDKG GlyGen Subgraph | GlyGen.zip (41.8 MB) | Graph | csv | Data Distillery GlyGen subgraph (buil... |
| cfde-ddkg.gtex | DDKG GTEx Subgraph | GTEx.zip (391.1 MB) | Graph | csv | Data Distillery GTEx subgraph (build ... |
| cfde-ddkg.sparc | DDKG SPARC Subgraph | SPARC.zip (193.6 KB) | Graph | csv | Data Distillery SPARC subgraph (build... |
| cfde-ddkg.hgnchpo | DDKG HGNC-HPO Subgraph | HGNCHPO.zip (14.5 MB) | Graph | csv | Data Distillery HGNC-HPO subgraph (bu... |
| cfde-ddkg.clinvar | DDKG ClinVar Subgraph | CLINVAR.zip (2.4 MB) | Graph | csv | Data Distillery ClinVar subgraph (bui... |
| cfde-ddkg.motrpac | DDKG MoTrPAC Subgraph | MoTrPAC.zip (1.2 MB) | Graph | csv | Data Distillery MoTrPAC subgraph (bui... |
| cfde-ddkg.hgncuniprot | DDKG HGNC-UniProt Subgraph | HGNCUNIPROT.zip (915.1 KB) | Graph | csv | Data Distillery HGNC-UniProt subgraph... |
| cfde-ddkg.kf | DDKG Kids First Subgraph | KF.zip (3.2 MB) | Graph | csv | Data Distillery Kids First subgraph (... |
| cfde-ddkg.lincs | DDKG LINCS Subgraph | LINCS.zip (11.6 MB) | Graph | csv | Data Distillery LINCS subgraph (build... |
| cfde-ddkg.hgnc-enzyme | DDKG HGNC Enzyme Genes Subgraph | hgnc_enzyme.zip (82.5 KB) | Graph | csv | Data Distillery HGNC Enzyme Genes sub... |
| cfde-ddkg.archs4 | DDKG ARCHS4 Subgraph | ARCHS4.zip (10.8 MB) | Graph | csv | Data Distillery ARCHS4 subgraph (buil... |
| cfde-ddkg.mw | DDKG Metabolomics Workbench Subgraph | MW.zip (2.1 MB) | Graph | csv | Data Distillery Metabolomics Workbenc... |
| cfde-ddkg.msigdb | DDKG MSigDB Subgraph | MSIGDB.zip (32.5 MB) | Graph | csv | Data Distillery MSigDB subgraph (buil... |
| cfde-ddkg.ercc | DDKG ERCC Subgraph | ERCC.zip (386.5 MB) | Graph | csv | Data Distillery ERCC subgraph (build ... |
| cfde-ddkg.4dn | DDKG 4DN Subgraph | 4DN.zip (49.2 MB) | Graph | csv | Data Distillery 4DN subgraph (build o... |
| cfde-ddkg.api | DDKG API | api-doc | Programming Interface | http | REST API for searching DDKG nodes, re... |
| cfde-ddkg.dictionary | DDKG Data Dictionary | DataDistilleryDataDictionary0228.html (186.8 KB) | Documentation | http | Data dictionary describing the DDKG n... |
The Common Fund Data Ecosystem (CFDE) aims to facilitate better integration, and reuse of Common Fund data to accelerate discoveries in biomedical research. The Data Distillery project aims to integrate summarized (“distilled”) Common Fund data within a knowledge graph. The purpose of the Data Distillery Knowledge Graph (DDKG) is to link multiple sources of expertly curated data, thus providing data integration across multiple Common Fund data coordinating centers (DCCs). The summarized data are provided by participating DCCs and funded as part of the Common Fund Data Ecosystem (CFDE) project. The DDKG schema is based on the Unified Biomedical Knowledge Graph (UBKG) which originates from the Unified Medical Language System (UMLS). The UBKG supports the DDKG with over 180 different ontologies and standards supporting the Common Fund data that either are native to UMLS or were explicitly added to support biomolecular data. The DDKG can be used to create simple to complex queries, and use the results for a range of different applications related to the use of Common Fund data.
The September 2024 build is distributed as one zipped set of CSV node and edge files per contributing DCC dataset, listed in the downloads manifest. The DDKG is described in a 2025 bioRxiv preprint (doi:10.1101/2025.08.11.666099).
Created: March 09, 2025 | Last modified: October 09, 2026