is a Data Source.
The Encyclopedia of DNA Elements (ENCODE) is an NHGRI-funded international consortium and data resource that catalogs functional elements in the human genome and related model systems using large-scale functional genomics assays, standardized processing pipelines, and openly accessible metadata.
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| encode.portal | ENCODE Portal | www.encodeproject.org | Graphical Interface | http | Main ENCODE portal for searching, bro... |
| encode.api | ENCODE REST API | rest-api | Programming Interface | json | REST API for retrieving ENCODE metada... |
| encode.experiment-matrix | ENCODE Experiment Matrix | ?type=Experiment | Graphical Interface | http | Experiment matrix interface for brows... |
| encode.annotations | ENCODE Encyclopedia Annotations | ?type=Annotation&encyclopedia_version=current&annotation_type=candidate+Cis-Regulatory+Elements&annotation_type=chromatin+state&annotation_type=representative+DNase+hypersensitivity+sites&status=released | Graphical Interface | http | Encyclopedia annotations view for rel... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| chea-kg.graph | ChEA-KG Database | ❔ | Graph | neo4j | had primary source | Neo4j knowledge graph integrating tra... |
| chea-kg.libraries | ChEA-KG Library Downloads | index.html#content4-13 | Product | http | had primary source | Download catalog for ChEA3 transcript... |
| chea.libraries | ChEA Library Downloads | index.html#content4-13 | Product | http | had primary source | Download catalog for ChEA3 transcript... |
| lncrnalyzr.graph | lncRNAlyzr Knowledge Graph | lncRNAlyzr | Graph | neo4j | had primary source | Neo4j knowledge graph containing lncR... |
| harmonizome.downloads | Harmonizome Downloads | download | Product | mixed | was derived from | Harmonizome 3.0 processed dataset dow... |
| harmonizome.kg-neo4j | Harmonizome Knowledge Graph Neo4j Database | harmonizome-kg.maayanlab.cloud | Graph | neo4j | was derived from | Neo4j knowledge graph serialization o... |
| biobtree.api | BioBTree REST API | api | Programming Interface | http | had primary source | REST API for searching identifiers an... |
| genecards.web.interface | GeneCards Web Interface | www.genecards.org | Graphical Interface | http | had primary source | Web-based interface for searching and... |
| biobtree.graph.human-subgraph | BioBTree Knowledge Graph - Human Subgraph (KGX) | 20816742 | Graph | kgx | had primary source | Human-scoped, Neo4j-ready subgraph of... |
| genomickb.graph | GenomicKB Graph Dump | genomickb-a-knowledgebase-for-the-human-genome | Graph | http | had primary source | GenomicKB 1.0 Neo4j Database Dump (Re... |
The Encyclopedia of DNA Elements (ENCODE) is an ongoing international consortium funded by NHGRI to identify and organize functional elements in the genome, including regulatory elements, protein-binding sites, chromatin features, and RNA-level signals. The ENCODE portal serves as the main public access point for consortium experiments, processed files, metadata, standards, and integrative annotations.
Current ENCODE portal documentation emphasizes standardized assays, shared experimental guidelines, uniform analysis pipelines, and explicit quality metrics across major assay classes such as ChIP-seq, ATAC-seq, DNase-seq, RNA-seq, eCLIP, methylation assays, chromatin conformation assays, and single-cell methods. The public REST API exposes released ENCODE objects in JSON and supports structured programmatic search over experiments, biosamples, files, publications, and annotations.
Created: May 21, 2026 | Last modified: September 23, 2026