is a Knowledge Graph.
The NLM Cell Knowledge Network, a knowledge graph that contains knowledge about cellular phenotypes (cell types and cell states) that has been gathered through single cell technologies and related experiments. NLM-CKN is populated using validated computational analysis pipelines and natural language processing of scientific literature and integrated with other public sources of relevant knowledge about genes, anatomical structures, diseases, and drugs.
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| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| nlm-ckn.graph | nlm-ckn-graph | nlm-ckn.org | Graph | http | The NLM-CKN knowledge graph of cellul... |
| nlm-ckn.ui | nlm-ckn-ui | nlm-ckn-ui | Graphical Interface | http | The NLM-CKN web application, a Django... |
| nlm-ckn.schema | nlm-ckn-schema | ckn-schema.yaml (73.4 KB) | Data Model | yaml | LinkML data model (schema) for cell p... |
| nlm-ckn.etl | nlm-ckn-etl | nlm-ckn-etl | Process | python | The NLM-CKN ETL pipeline, which produ... |
| nlm-ckn.harvester | cellxgene-harvester | cellxgene-harvester | Process | python | The cellxgene-harvester package, whic... |
| nlm-ckn.scsilhouette | scsilhouette | scsilhouette | Process | python | The scsilhouette Python package, part... |
| nlm-ckn.nsforest-qc | sc-nsforest-qc-nf | sc-nsforest-qc-nf | Process | mixed | The sc-nsforest-qc-nf Nextflow workfl... |
A knowledge graph that contains knowledge about cellular phenotypes (cell types and cell states) that has been gathered through single cell technologies and related experiments. NLM-CKN is populated using validated computational analysis pipelines and natural language processing of scientific literature and integrated with other public sources of relevant knowledge about genes, anatomical structures, diseases, and drugs.
The NLM-CKN infrastructure spans several coordinated repositories: the cellxgene-harvester selects and filters single-cell datasets from the CELLxGENE Census; the sc-nsforest-qc-nf Nextflow workflow (using scsilhouette and NSForest) generates marker genes and quality metrics; the NLM-CKN ETL pipeline builds the ArangoDB knowledge graph from those results and source ontologies (following the NLM-CKN schema); and the NLM-CKN UI serves it at nlm-ckn.org.
Created: April 17, 2025 | Last modified: September 23, 2026