GENCODE
GENCODE is a comprehensive and high-quality reference annotation of the human and mouse genomes, providing evidence-based gene annotations including protein-coding genes, long non-coding RNAs, small RNAs, pseudogenes, and other genomic features based on manual curation and computational analysis.
[]
[{"category": "Product", "description": "Comprehensive gene annotations for human genome in GTF format", "format": "gff", "id": "gencode.human.gtf", "name": "GENCODE Human Annotations GTF", "original_source": ["gencode"], "product_url": "https://www.gencodegenes.org/human/"}, {"category": "Product", "description": "Comprehensive gene annotations for mouse genome in GTF format", "format": "gff", "id": "gencode.mouse.gtf", "name": "GENCODE Mouse Annotations GTF", "original_source": ["gencode"], "product_url": "https://www.gencodegenes.org/mouse/"}, {"category": "Product", "description": "GENCODE Primary transcript set capturing minimal transcripts at protein coding genes", "format": "gff", "id": "gencode.primary", "name": "GENCODE Primary Transcripts", "original_source": ["gencode"], "product_url": "https://www.gencodegenes.org/pages/gencode_primary/"}, {"category": "GraphProduct", "description": "Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access.", "dump_format": "neo4j", "id": "ubkg.neo4j", "name": "UBKG Neo4j Docker Distribution", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}, {"category": "GraphProduct", "description": "Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access.", "format": "csv", "id": "ubkg.csv", "name": "UBKG Ontology CSV Files", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}]
{"activity_status": "active", "category": "DataSource", "creation_date": "2025-11-26T00:00:00Z", "description": "GENCODE is a comprehensive and high-quality reference annotation of the human and mouse genomes, providing evidence-based gene annotations including protein-coding genes, long non-coding RNAs, small RNAs, pseudogenes, and other genomic features based on manual curation and computational analysis.", "domains": ["genomics"], "homepage_url": "https://www.gencodegenes.org/", "id": "gencode", "last_modified_date": "2025-11-26T00:00:00Z", "layout": "resource_detail", "name": "GENCODE", "products": [{"category": "Product", "description": "Comprehensive gene annotations for human genome in GTF format", "format": "gff", "id": "gencode.human.gtf", "name": "GENCODE Human Annotations GTF", "original_source": ["gencode"], "product_url": "https://www.gencodegenes.org/human/"}, {"category": "Product", "description": "Comprehensive gene annotations for mouse genome in GTF format", "format": "gff", "id": "gencode.mouse.gtf", "name": "GENCODE Mouse Annotations GTF", "original_source": ["gencode"], "product_url": "https://www.gencodegenes.org/mouse/"}, {"category": "Product", "description": "GENCODE Primary transcript set capturing minimal transcripts at protein coding genes", "format": "gff", "id": "gencode.primary", "name": "GENCODE Primary Transcripts", "original_source": ["gencode"], "product_url": "https://www.gencodegenes.org/pages/gencode_primary/"}, {"category": "GraphProduct", "description": "Turnkey neo4j distributions that deploy fully-indexed, standalone UBKG instances as neo4j graph databases, running in a Docker container. Requires UMLS API key to access.", "dump_format": "neo4j", "id": "ubkg.neo4j", "name": "UBKG Neo4j Docker Distribution", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}, {"category": "GraphProduct", "description": "Ontology CSV files that can be imported into a neo4j instance to create a UBKG database. Requires UMLS API key to access.", "format": "csv", "id": "ubkg.csv", "name": "UBKG Ontology CSV Files", "original_source": ["hgnc", "loinc", "icd10", "snomedct", "uberon", "pato", "cl", "doid", "obi", "obib", "edam", "hsapdv", "sbo", "mi", "chebi", "mp", "ordo", "uniprot", "uo", "mondo", "efo", "pgo", "gencode", "reactome", "hra", "hubmap", "sennet", "stellar", "dct", "clinvar", "connectivitymap", "hp", "mp", "msigdb", "wikipathways", "clingen", "string", "4dn", "erccrbp", "erccreg", "faldo", "glycordf", "glycocoo", "gtex", "kidsfirst", "lincs", "motrpac", "mw", "npo", "sckan", "disgenet", "biomarker", "opentargets"], "product_url": "https://ubkg-downloads.xconsortia.org/", "secondary_source": ["ubkg"]}], "synonyms": ["GENCODE", "Encyclopedia of genes and gene variants"], "taxon": ["NCBITaxon:9606", "NCBITaxon:10090"]}