CZ CELLxGENE
CZ CELLxGENE is a platform for finding, downloading, exploring, and analyzing single-cell datasets through a public data portal, integrated analysis interfaces, and the CELLxGENE Census programmatic access layer.
[{"category": "Organization", "contact_details": [{"contact_type": "email", "value": "cellxgene@chanzuckerberg.com"}, {"contact_type": "url", "value": "https://cellxgene.cziscience.com/"}], "label": "Chan Zuckerberg Initiative"}]
[{"category": "GraphicalInterface", "description": "Main CZ CELLxGENE Discover portal for browsing public single-cell collections, datasets, gene expression views, and analysis tools.", "format": "http", "id": "cellxgene.portal", "name": "CZ CELLxGENE Discover", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "cellxgene"}], "product_url": "https://cellxgene.cziscience.com/"}, {"category": "GraphicalInterface", "description": "Search and download interface for public curated collections and datasets available through CZ CELLxGENE Discover.", "format": "http", "id": "cellxgene.datasets", "name": "CZ CELLxGENE Datasets Browser", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "cellxgene"}], "product_url": "https://cellxgene.cziscience.com/datasets"}, {"category": "ProgrammingInterface", "description": "Documentation and entry point for the CELLxGENE Census API and data object used to query standardized single-cell expression data in R and Python.", "format": "http", "id": "cellxgene.census", "is_public": true, "name": "CZ CELLxGENE Census", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "cellxgene"}], "product_url": "https://chanzuckerberg.github.io/cellxgene-census/"}, {"category": "DocumentationProduct", "description": "Official documentation for CZ CELLxGENE Discover, Explorer, Gene Expression, and Annotate workflows.", "format": "http", "id": "cellxgene.docs", "name": "CZ CELLxGENE Documentation", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "cellxgene"}], "product_url": "https://cellxgene.cziscience.com/docs"}, {"category": "ProgrammingInterface", "connection_url": "cl-kg-neo4j-db.cellgeni.sanger.ac.uk:443", "description": "Publicly available Neo4j instance for CL-KG.", "id": "cl-kg.api.neo4j", "is_neo4j": true, "is_public": true, "name": "CL-KG Neo4j graph instance", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "cl-kg"}, {"relation_type": "prov:hadPrimarySource", "source": "cl"}, {"relation_type": "prov:hadPrimarySource", "source": "cellxgene"}], "product_url": "https://cellular-semantics.sanger.ac.uk/browser/"}, {"category": "ProgrammingInterface", "description": "REST API for searching identifiers and special keywords, mapping between data sources with a chain-query syntax, and retrieving entries across the integrated BioBTree databases.", "format": "http", "id": "biobtree.api", "is_public": true, "name": "BioBTree REST API", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "biobtree"}, {"relation_type": "prov:hadPrimarySource", "source": "alphafold"}, {"relation_type": "prov:hadPrimarySource", "source": "alphamissense"}, {"relation_type": "prov:hadPrimarySource", "source": "bao"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "bindingdb"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "brenda"}, {"relation_type": "prov:hadPrimarySource", "source": "cellphonedb"}, {"relation_type": "prov:hadPrimarySource", "source": "cellxgene"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "chembl"}, {"relation_type": "prov:hadPrimarySource", "source": "cl"}, {"relation_type": "prov:hadPrimarySource", "source": "clinicaltrialsgov"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "collectri"}, {"relation_type": "prov:hadPrimarySource", "source": "corum"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dbsnp"}, {"relation_type": "prov:hadPrimarySource", "source": "eco"}, {"relation_type": "prov:hadPrimarySource", "source": "efo"}, {"relation_type": "prov:hadPrimarySource", "source": "encode"}, {"relation_type": "prov:hadPrimarySource", "source": "ensembl"}, {"relation_type": "prov:hadPrimarySource", "source": "expressionatlas"}, {"relation_type": "prov:hadPrimarySource", "source": "fantom5"}, {"relation_type": "prov:hadPrimarySource", "source": "gencc"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "gwascatalog"}, {"relation_type": "prov:hadPrimarySource", "source": "hgnc"}, {"relation_type": "prov:hadPrimarySource", "source": "hmdb"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "intact"}, {"relation_type": "prov:hadPrimarySource", "source": "interpro"}, {"relation_type": "prov:hadPrimarySource", "source": "jaspar"}, {"relation_type": "prov:hadPrimarySource", "source": "lipidmaps"}, {"relation_type": "prov:hadPrimarySource", "source": "mesh"}, {"relation_type": "prov:hadPrimarySource", "source": "mirdb"}, {"relation_type": "prov:hadPrimarySource", "source": "mondo"}, {"relation_type": "prov:hadPrimarySource", "source": "msigdb"}, {"relation_type": "prov:hadPrimarySource", "source": "ncbigene"}, {"relation_type": "prov:hadPrimarySource", "source": "ncbitaxon"}, {"relation_type": "prov:hadPrimarySource", "source": "orphanet"}, {"relation_type": "prov:hadPrimarySource", "source": "pdb"}, {"relation_type": "prov:hadPrimarySource", "source": "pharmgkb"}, {"relation_type": "prov:hadPrimarySource", "source": "pubchem"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "refseq"}, {"relation_type": "prov:hadPrimarySource", "source": "rhea"}, {"relation_type": "prov:hadPrimarySource", "source": "rnacentral"}, {"relation_type": "prov:hadPrimarySource", "source": "signor"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "surechembl"}, {"relation_type": "prov:hadPrimarySource", "source": "swisslipid"}, {"relation_type": "prov:hadPrimarySource", "source": "uberon"}, {"relation_type": "prov:hadPrimarySource", "source": "uniprot"}], "product_url": "https://sugi.bio/biobtree/api/"}, {"category": "GraphProduct", "compatibility": [{"standard": "biolink", "version": "4.2.1"}], "compression": "gzip", "description": "Human-scoped, Neo4j-ready subgraph of the BioBTree knowledge graph, exported as a biolink-typed KGX graph (~40M nodes / ~132M edges, ~8.3 GB compressed across separate node and edge files). A practical projection of the full graph for human-centric biomedical use. Published on Zenodo.", "edge_count": 132075627, "format": "kgx", "id": "biobtree.graph.human-subgraph", "license": {"id": "https://creativecommons.org/licenses/by-nc-sa/4.0/", "label": "CC-BY-NC-SA-4.0"}, "name": "BioBTree Knowledge Graph - Human Subgraph (KGX)", "node_categories": ["biolink:BiologicalProcess", "biolink:Cell", "biolink:CellLine", "biolink:CellularComponent", "biolink:CodingSequence", "biolink:Disease", "biolink:DiseaseOrPhenotypicFeature", "biolink:Drug", "biolink:Exon", "biolink:Gene", "biolink:GrossAnatomicalStructure", "biolink:MacromolecularComplex", "biolink:MolecularActivity", "biolink:NoncodingRNAProduct", "biolink:NucleicAcidSequenceMotif", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:ProteinDomain", "biolink:ProteinFamily", "biolink:Publication", "biolink:RegulatoryRegion", "biolink:SequenceVariant", "biolink:SmallMolecule", "biolink:Transcript"], "node_count": 40160474, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "biobtree"}, {"relation_type": "prov:hadPrimarySource", "source": "alphafold"}, {"relation_type": "prov:hadPrimarySource", "source": "alphamissense"}, {"relation_type": "prov:hadPrimarySource", "source": "bao"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "bindingdb"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "brenda"}, {"relation_type": "prov:hadPrimarySource", "source": "cellphonedb"}, {"relation_type": "prov:hadPrimarySource", "source": "cellxgene"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "chembl"}, {"relation_type": "prov:hadPrimarySource", "source": "cl"}, {"relation_type": "prov:hadPrimarySource", "source": "clinicaltrialsgov"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "collectri"}, {"relation_type": "prov:hadPrimarySource", "source": "corum"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dbsnp"}, {"relation_type": "prov:hadPrimarySource", "source": "eco"}, {"relation_type": "prov:hadPrimarySource", "source": "efo"}, {"relation_type": "prov:hadPrimarySource", "source": "encode"}, {"relation_type": "prov:hadPrimarySource", "source": "ensembl"}, {"relation_type": "prov:hadPrimarySource", "source": "expressionatlas"}, {"relation_type": "prov:hadPrimarySource", "source": "fantom5"}, {"relation_type": "prov:hadPrimarySource", "source": "gencc"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "gwascatalog"}, {"relation_type": "prov:hadPrimarySource", "source": "hgnc"}, {"relation_type": "prov:hadPrimarySource", "source": "hmdb"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "intact"}, {"relation_type": "prov:hadPrimarySource", "source": "interpro"}, {"relation_type": "prov:hadPrimarySource", "source": "jaspar"}, {"relation_type": "prov:hadPrimarySource", "source": "lipidmaps"}, {"relation_type": "prov:hadPrimarySource", "source": "mesh"}, {"relation_type": "prov:hadPrimarySource", "source": "mirdb"}, {"relation_type": "prov:hadPrimarySource", "source": "mondo"}, {"relation_type": "prov:hadPrimarySource", "source": "msigdb"}, {"relation_type": "prov:hadPrimarySource", "source": "ncbigene"}, {"relation_type": "prov:hadPrimarySource", "source": "ncbitaxon"}, {"relation_type": "prov:hadPrimarySource", "source": "orphanet"}, {"relation_type": "prov:hadPrimarySource", "source": "pdb"}, {"relation_type": "prov:hadPrimarySource", "source": "pharmgkb"}, {"relation_type": "prov:hadPrimarySource", "source": "pubchem"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "refseq"}, {"relation_type": "prov:hadPrimarySource", "source": "rhea"}, {"relation_type": "prov:hadPrimarySource", "source": "rnacentral"}, {"relation_type": "prov:hadPrimarySource", "source": "signor"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "surechembl"}, {"relation_type": "prov:hadPrimarySource", "source": "swisslipid"}, {"relation_type": "prov:hadPrimarySource", "source": "uberon"}, {"relation_type": "prov:hadPrimarySource", "source": "uniprot"}], "predicates": ["biolink:actively_involved_in", "biolink:affects", "biolink:associated_with", "biolink:close_match", "biolink:derives_from", "biolink:directly_physically_interacts_with", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:gene_product_of", "biolink:has_adverse_event", "biolink:has_gene_product", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:in_clinical_trials_for", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:member_of", "biolink:mentions", "biolink:orthologous_to", "biolink:paralogous_to", "biolink:participates_in", "biolink:physically_interacts_with", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:transcribed_from", "biolink:translates_to", "biolink:treats_or_applied_or_studied_to_treat"], "product_url": "https://zenodo.org/records/20816742"}, {"category": "GraphProduct", "description": "The NLM-CKN knowledge graph of cellular phenotypes. It is built from triple assertions (subject-predicate-object) that link single-cell genomics experimental data (from the CELLxGENE Census) and computationally derived NS-Forest marker genes to the Cell Ontology and other reference ontologies, augmented with literature-derived assertions from text mining/NLP. The graph is produced by the NLM-CKN ETL pipeline as an ArangoDB archive and served via the web application at https://nlm-ckn.org.", "format": "http", "id": "nlm-ckn.graph", "name": "nlm-ckn-graph", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "nlm-ckn"}, {"relation_type": "prov:hadPrimarySource", "source": "cellxgene"}, {"relation_type": "prov:hadPrimarySource", "source": "pubmed"}], "product_url": "https://nlm-ckn.org", "secondary_source": [{"relation_type": "prov:wasInfluencedBy", "source": "cl"}, {"relation_type": "prov:wasInfluencedBy", "source": "uberon"}, {"relation_type": "prov:wasInfluencedBy", "source": "pato"}, {"relation_type": "prov:wasInfluencedBy", "source": "mondo"}, {"relation_type": "prov:wasInfluencedBy", "source": "hsapdv"}]}]
{"activity_status": "active", "category": "DataSource", "contacts": [{"category": "Organization", "contact_details": [{"contact_type": "email", "value": "cellxgene@chanzuckerberg.com"}, {"contact_type": "url", "value": "https://cellxgene.cziscience.com/"}], "label": "Chan Zuckerberg Initiative"}], "creation_date": "2026-05-28T00:00:00Z", "description": "CZ CELLxGENE is a platform for finding, downloading, exploring, and analyzing single-cell datasets through a public data portal, integrated analysis interfaces, and the CELLxGENE Census programmatic access layer.", "domains": ["biomedical", "genomics"], "homepage_url": "https://cellxgene.cziscience.com/", "id": "cellxgene", "last_modified_date": "2026-06-18T00:00:00Z", "layout": "resource_detail", "license": {"id": "https://creativecommons.org/licenses/by/4.0/", "label": "CC-BY-4.0", "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png"}, "name": "CZ CELLxGENE", "products": [{"category": "GraphicalInterface", "description": "Main CZ CELLxGENE Discover portal for browsing public single-cell collections, datasets, gene expression views, and analysis tools.", "format": "http", "id": "cellxgene.portal", "name": "CZ CELLxGENE Discover", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "cellxgene"}], "product_url": "https://cellxgene.cziscience.com/"}, {"category": "GraphicalInterface", "description": "Search and download interface for public curated collections and datasets available through CZ CELLxGENE Discover.", "format": "http", "id": "cellxgene.datasets", "name": "CZ CELLxGENE Datasets Browser", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "cellxgene"}], "product_url": "https://cellxgene.cziscience.com/datasets"}, {"category": "ProgrammingInterface", "description": "Documentation and entry point for the CELLxGENE Census API and data object used to query standardized single-cell expression data in R and Python.", "format": "http", "id": "cellxgene.census", "is_public": true, "name": "CZ CELLxGENE Census", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "cellxgene"}], "product_url": "https://chanzuckerberg.github.io/cellxgene-census/"}, {"category": "DocumentationProduct", "description": "Official documentation for CZ CELLxGENE Discover, Explorer, Gene Expression, and Annotate workflows.", "format": "http", "id": "cellxgene.docs", "name": "CZ CELLxGENE Documentation", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "cellxgene"}], "product_url": "https://cellxgene.cziscience.com/docs"}, {"category": "ProgrammingInterface", "connection_url": "cl-kg-neo4j-db.cellgeni.sanger.ac.uk:443", "description": "Publicly available Neo4j instance for CL-KG.", "id": "cl-kg.api.neo4j", "is_neo4j": true, "is_public": true, "name": "CL-KG Neo4j graph instance", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "cl-kg"}, {"relation_type": "prov:hadPrimarySource", "source": "cl"}, {"relation_type": "prov:hadPrimarySource", "source": "cellxgene"}], "product_url": "https://cellular-semantics.sanger.ac.uk/browser/"}, {"category": "ProgrammingInterface", "description": "REST API for searching identifiers and special keywords, mapping between data sources with a chain-query syntax, and retrieving entries across the integrated BioBTree databases.", "format": "http", "id": "biobtree.api", "is_public": true, "name": "BioBTree REST API", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "biobtree"}, {"relation_type": "prov:hadPrimarySource", "source": "alphafold"}, {"relation_type": "prov:hadPrimarySource", "source": "alphamissense"}, {"relation_type": "prov:hadPrimarySource", "source": "bao"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "bindingdb"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "brenda"}, {"relation_type": "prov:hadPrimarySource", "source": "cellphonedb"}, {"relation_type": "prov:hadPrimarySource", "source": "cellxgene"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "chembl"}, {"relation_type": "prov:hadPrimarySource", "source": "cl"}, {"relation_type": "prov:hadPrimarySource", "source": "clinicaltrialsgov"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "collectri"}, {"relation_type": "prov:hadPrimarySource", "source": "corum"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dbsnp"}, {"relation_type": "prov:hadPrimarySource", "source": "eco"}, {"relation_type": "prov:hadPrimarySource", "source": "efo"}, {"relation_type": "prov:hadPrimarySource", "source": "encode"}, {"relation_type": "prov:hadPrimarySource", "source": "ensembl"}, {"relation_type": "prov:hadPrimarySource", "source": "expressionatlas"}, {"relation_type": "prov:hadPrimarySource", "source": "fantom5"}, {"relation_type": "prov:hadPrimarySource", "source": "gencc"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "gwascatalog"}, {"relation_type": "prov:hadPrimarySource", "source": "hgnc"}, {"relation_type": "prov:hadPrimarySource", "source": "hmdb"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "intact"}, {"relation_type": "prov:hadPrimarySource", "source": "interpro"}, {"relation_type": "prov:hadPrimarySource", "source": "jaspar"}, {"relation_type": "prov:hadPrimarySource", "source": "lipidmaps"}, {"relation_type": "prov:hadPrimarySource", "source": "mesh"}, {"relation_type": "prov:hadPrimarySource", "source": "mirdb"}, {"relation_type": "prov:hadPrimarySource", "source": "mondo"}, {"relation_type": "prov:hadPrimarySource", "source": "msigdb"}, {"relation_type": "prov:hadPrimarySource", "source": "ncbigene"}, {"relation_type": "prov:hadPrimarySource", "source": "ncbitaxon"}, {"relation_type": "prov:hadPrimarySource", "source": "orphanet"}, {"relation_type": "prov:hadPrimarySource", "source": "pdb"}, {"relation_type": "prov:hadPrimarySource", "source": "pharmgkb"}, {"relation_type": "prov:hadPrimarySource", "source": "pubchem"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "refseq"}, {"relation_type": "prov:hadPrimarySource", "source": "rhea"}, {"relation_type": "prov:hadPrimarySource", "source": "rnacentral"}, {"relation_type": "prov:hadPrimarySource", "source": "signor"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "surechembl"}, {"relation_type": "prov:hadPrimarySource", "source": "swisslipid"}, {"relation_type": "prov:hadPrimarySource", "source": "uberon"}, {"relation_type": "prov:hadPrimarySource", "source": "uniprot"}], "product_url": "https://sugi.bio/biobtree/api/"}, {"category": "GraphProduct", "compatibility": [{"standard": "biolink", "version": "4.2.1"}], "compression": "gzip", "description": "Human-scoped, Neo4j-ready subgraph of the BioBTree knowledge graph, exported as a biolink-typed KGX graph (~40M nodes / ~132M edges, ~8.3 GB compressed across separate node and edge files). A practical projection of the full graph for human-centric biomedical use. Published on Zenodo.", "edge_count": 132075627, "format": "kgx", "id": "biobtree.graph.human-subgraph", "license": {"id": "https://creativecommons.org/licenses/by-nc-sa/4.0/", "label": "CC-BY-NC-SA-4.0"}, "name": "BioBTree Knowledge Graph - Human Subgraph (KGX)", "node_categories": ["biolink:BiologicalProcess", "biolink:Cell", "biolink:CellLine", "biolink:CellularComponent", "biolink:CodingSequence", "biolink:Disease", "biolink:DiseaseOrPhenotypicFeature", "biolink:Drug", "biolink:Exon", "biolink:Gene", "biolink:GrossAnatomicalStructure", "biolink:MacromolecularComplex", "biolink:MolecularActivity", "biolink:NoncodingRNAProduct", "biolink:NucleicAcidSequenceMotif", "biolink:OrganismTaxon", "biolink:Pathway", "biolink:PhenotypicFeature", "biolink:Protein", "biolink:ProteinDomain", "biolink:ProteinFamily", "biolink:Publication", "biolink:RegulatoryRegion", "biolink:SequenceVariant", "biolink:SmallMolecule", "biolink:Transcript"], "node_count": 40160474, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "biobtree"}, {"relation_type": "prov:hadPrimarySource", "source": "alphafold"}, {"relation_type": "prov:hadPrimarySource", "source": "alphamissense"}, {"relation_type": "prov:hadPrimarySource", "source": "bao"}, {"relation_type": "prov:hadPrimarySource", "source": "bgee"}, {"relation_type": "prov:hadPrimarySource", "source": "bindingdb"}, {"relation_type": "prov:hadPrimarySource", "source": "biogrid"}, {"relation_type": "prov:hadPrimarySource", "source": "brenda"}, {"relation_type": "prov:hadPrimarySource", "source": "cellphonedb"}, {"relation_type": "prov:hadPrimarySource", "source": "cellxgene"}, {"relation_type": "prov:hadPrimarySource", "source": "chebi"}, {"relation_type": "prov:hadPrimarySource", "source": "chembl"}, {"relation_type": "prov:hadPrimarySource", "source": "cl"}, {"relation_type": "prov:hadPrimarySource", "source": "clinicaltrialsgov"}, {"relation_type": "prov:hadPrimarySource", "source": "clinvar"}, {"relation_type": "prov:hadPrimarySource", "source": "collectri"}, {"relation_type": "prov:hadPrimarySource", "source": "corum"}, {"relation_type": "prov:hadPrimarySource", "source": "ctd"}, {"relation_type": "prov:hadPrimarySource", "source": "dbsnp"}, {"relation_type": "prov:hadPrimarySource", "source": "eco"}, {"relation_type": "prov:hadPrimarySource", "source": "efo"}, {"relation_type": "prov:hadPrimarySource", "source": "encode"}, {"relation_type": "prov:hadPrimarySource", "source": "ensembl"}, {"relation_type": "prov:hadPrimarySource", "source": "expressionatlas"}, {"relation_type": "prov:hadPrimarySource", "source": "fantom5"}, {"relation_type": "prov:hadPrimarySource", "source": "gencc"}, {"relation_type": "prov:hadPrimarySource", "source": "go"}, {"relation_type": "prov:hadPrimarySource", "source": "gwascatalog"}, {"relation_type": "prov:hadPrimarySource", "source": "hgnc"}, {"relation_type": "prov:hadPrimarySource", "source": "hmdb"}, {"relation_type": "prov:hadPrimarySource", "source": "hp"}, {"relation_type": "prov:hadPrimarySource", "source": "intact"}, {"relation_type": "prov:hadPrimarySource", "source": "interpro"}, {"relation_type": "prov:hadPrimarySource", "source": "jaspar"}, {"relation_type": "prov:hadPrimarySource", "source": "lipidmaps"}, {"relation_type": "prov:hadPrimarySource", "source": "mesh"}, {"relation_type": "prov:hadPrimarySource", "source": "mirdb"}, {"relation_type": "prov:hadPrimarySource", "source": "mondo"}, {"relation_type": "prov:hadPrimarySource", "source": "msigdb"}, {"relation_type": "prov:hadPrimarySource", "source": "ncbigene"}, {"relation_type": "prov:hadPrimarySource", "source": "ncbitaxon"}, {"relation_type": "prov:hadPrimarySource", "source": "orphanet"}, {"relation_type": "prov:hadPrimarySource", "source": "pdb"}, {"relation_type": "prov:hadPrimarySource", "source": "pharmgkb"}, {"relation_type": "prov:hadPrimarySource", "source": "pubchem"}, {"relation_type": "prov:hadPrimarySource", "source": "reactome"}, {"relation_type": "prov:hadPrimarySource", "source": "refseq"}, {"relation_type": "prov:hadPrimarySource", "source": "rhea"}, {"relation_type": "prov:hadPrimarySource", "source": "rnacentral"}, {"relation_type": "prov:hadPrimarySource", "source": "signor"}, {"relation_type": "prov:hadPrimarySource", "source": "string"}, {"relation_type": "prov:hadPrimarySource", "source": "surechembl"}, {"relation_type": "prov:hadPrimarySource", "source": "swisslipid"}, {"relation_type": "prov:hadPrimarySource", "source": "uberon"}, {"relation_type": "prov:hadPrimarySource", "source": "uniprot"}], "predicates": ["biolink:actively_involved_in", "biolink:affects", "biolink:associated_with", "biolink:close_match", "biolink:derives_from", "biolink:directly_physically_interacts_with", "biolink:enables", "biolink:expressed_in", "biolink:gene_associated_with_condition", "biolink:gene_product_of", "biolink:has_adverse_event", "biolink:has_gene_product", "biolink:has_part", "biolink:has_participant", "biolink:has_phenotype", "biolink:in_clinical_trials_for", "biolink:in_taxon", "biolink:interacts_with", "biolink:is_sequence_variant_of", "biolink:located_in", "biolink:member_of", "biolink:mentions", "biolink:orthologous_to", "biolink:paralogous_to", "biolink:participates_in", "biolink:physically_interacts_with", "biolink:related_to", "biolink:same_as", "biolink:subclass_of", "biolink:transcribed_from", "biolink:translates_to", "biolink:treats_or_applied_or_studied_to_treat"], "product_url": "https://zenodo.org/records/20816742"}, {"category": "GraphProduct", "description": "The NLM-CKN knowledge graph of cellular phenotypes. It is built from triple assertions (subject-predicate-object) that link single-cell genomics experimental data (from the CELLxGENE Census) and computationally derived NS-Forest marker genes to the Cell Ontology and other reference ontologies, augmented with literature-derived assertions from text mining/NLP. The graph is produced by the NLM-CKN ETL pipeline as an ArangoDB archive and served via the web application at https://nlm-ckn.org.", "format": "http", "id": "nlm-ckn.graph", "name": "nlm-ckn-graph", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "nlm-ckn"}, {"relation_type": "prov:hadPrimarySource", "source": "cellxgene"}, {"relation_type": "prov:hadPrimarySource", "source": "pubmed"}], "product_url": "https://nlm-ckn.org", "secondary_source": [{"relation_type": "prov:wasInfluencedBy", "source": "cl"}, {"relation_type": "prov:wasInfluencedBy", "source": "uberon"}, {"relation_type": "prov:wasInfluencedBy", "source": "pato"}, {"relation_type": "prov:wasInfluencedBy", "source": "mondo"}, {"relation_type": "prov:wasInfluencedBy", "source": "hsapdv"}]}], "publications": [{"authors": ["Shibla Abdulla", "Brian Aevermann", "CZI Cell Science Program"], "doi": "10.1093/nar/gkae1142", "id": "https://doi.org/10.1093/nar/gkae1142", "journal": "Nucleic Acids Research", "preferred": true, "title": "CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data", "year": "2025"}], "repository": "https://github.com/chanzuckerberg/single-cell-data-portal"}