is a Knowledge Graph.
It is part of the OKN collection.
BiomarkerKB is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that organizes and integrates biomarker data from different public sources, providing researchers with comprehensive, integrated access to biomarker information. This resource also covers the BiomarkerKB Knowledge Graph (BKG), the graph representation of BiomarkerKB data (formerly registered separately as `biomarkerkg`), which is available as an interactive explorer, downloadable node and edge datasets, and OKN/FRINK SPARQL and Triple Pattern Fragments endpoints.
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Email: avi.maayan@mssm.edu
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| biomarker.portal | BiomarkerKB Web Portal | biomarkerkb.org | GraphicalInterface | http | Public web portal for BiomarkerKB pro... |
| biomarker.downloads | BiomarkerKB Data Downloads | data.biomarkerkb.org | Product | json | Downloadable BiomarkerKB datasets, in... |
| biomarker.api | BiomarkerKB API | api.biomarkerkb.org | ProgrammingInterface | http | Backend REST API that powers the Biom... |
| biomarker.kg | BiomarkerKB Knowledge Graph | Knowledge-Graph | GraphProduct | neo4j | Neo4j knowledge graph built from cura... |
| biomarker.obci | Ontology for Biomarkers of Clinical Interest (OBCI) | OBCI | OntologyProduct | owl | The Ontology for Biomarkers of Clinic... |
| biomarker.datamodel | BiomarkerKB Data Model | biomarker-partnership | DataModelProduct | json | The community-developed BiomarkerKB d... |
| biomarker.bkg.explorer | BKG Explorer | bkg.dev.maayanlab.cloud | GraphicalInterface | http | Web interface to explore and query th... |
| biomarker.bkg.nodes.anatomy | BKG Anatomy Nodes | Anatomy.nodes.zip (332 B) | GraphProduct | csv | Nodes from Uber-Anatomy Ontology |
| biomarker.bkg.nodes.biomarker | BKG Biomarker Nodes | Biomarker.nodes.zip (1.2 MB) | GraphProduct | csv | Nodes from GlyGen Biomarker Database |
| biomarker.bkg.nodes.compound | BKG Compound Nodes | Compound.nodes.zip (871 B) | GraphProduct | csv | Nodes from PubChem Database |
| biomarker.bkg.nodes.condition | BKG Condition Nodes | Condition.nodes.zip (5.4 KB) | GraphProduct | csv | Nodes from Human Disease Ontology |
| biomarker.bkg.nodes.role | BKG Role Nodes | Role.nodes.zip (276 B) | GraphProduct | csv | Nodes from OBCI |
| biomarker.bkg.nodes.variant | BKG Variant Nodes | Variant.nodes.zip (764.6 KB) | GraphProduct | csv | Nodes from dbSNP |
| biomarker.bkg.edges.anatomy | BKG Anatomy Edges | Anatomy.edges.zip (1.2 KB) | GraphProduct | csv | Biomarker to Anatomy relationships (d... |
| biomarker.bkg.edges.compound | BKG Compound Edges | Compound.edges.zip (1.3 KB) | GraphProduct | csv | Biomarker to Compound relationships (... |
| biomarker.bkg.edges.condition | BKG Condition Edges | Condition.edges.zip (1.1 MB) | GraphProduct | csv | Biomarker to Condition relationships ... |
| biomarker.bkg.edges.role | BKG Role Edges | Role.edges.zip (347.0 KB) | GraphProduct | csv | Biomarker to Role relationships (has_... |
| biomarker.bkg.edges.variant | BKG Variant Edges | Variant.edges.zip (1.0 MB) | GraphProduct | csv | Biomarker to Variant relationships (i... |
| biomarker.sparql | BiomarkerKB KG SPARQL | sparql | ProgrammingInterface | ❔ | SPARQL endpoint for BiomarkerKB KG |
| biomarker.tpf | BiomarkerKB KG TPF | biomarkerkg | ProgrammingInterface | ❔ | Triple Pattern Fragments endpoint for... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| ubkg.neo4j | UBKG Neo4j Docker Distribution | ubkg-downloads.xconsortia.org | GraphProduct | neo4j | had primary source | Turnkey neo4j distributions that depl... |
| ubkg.csv | UBKG Ontology CSV Files | ubkg-downloads.xconsortia.org | GraphProduct | csv | had primary source | Ontology CSV files that can be import... |
BiomarkerKB is a Common Fund Data Ecosystem (CFDE) sponsored project to develop a knowledgebase that organizes and integrates biomarker data from different public sources. It provides researchers with a unified platform for biomarker information access and analysis.
BiomarkerKB serves as a centralized resource for biomarker research, facilitating the discovery, validation, and application of biomarkers across various domains including:
The knowledgebase is designed to connect heterogeneous biomedical data sources into a unified structure, allowing researchers to explore complex relationships between biomarkers and various biological and clinical entities. The initial release integrates more than 200,000 biomarker-condition associations spanning genes, proteins, metabolites, and glycans.
BiomarkerKB integrates biomarker data harmonized from multiple authoritative resources, including OpenTargets, ClinVar, GWAS Catalog, MarkerDB, and OncoMX, as well as CFDE Data Coordinating Centers such as LINCS, Metabolomics Workbench, GlyGen, and EDRN. Curated biomarker data are ingested into a Neo4j knowledge graph and integrated with the CFDE Unified Biomedical Knowledge Graph (UBKG).
The project is developed by the clinical-biomarkers (Biomarker Partnership) team as part of the NIH Common Fund Data Ecosystem initiative, with a focus on making biomarker data FAIR (Findable, Accessible, Interoperable, and Reusable).
Created: May 29, 2025 | Last modified: July 15, 2026