EDAM Ontology
EDAM is an ontology of bioscientific data analysis and data management, covering topics, operations, data, identifiers, and formats. It supports semantic annotation of tools, workflows, training, and provenance metadata across life sciences.
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{"activity_status": "active", "category": "Ontology", "contacts": [{"category": "Individual", "contact_details": [{"contact_type": "github", "value": "joncison"}], "label": "Jon Ison"}, {"category": "Individual", "contact_details": [{"contact_type": "github", "value": "matuskalas"}], "label": "Mat\u00fa\u0161 Kala\u0161"}, {"category": "Individual", "contact_details": [{"contact_type": "github", "value": "hmenager"}], "label": "Herv\u00e9 M\u00e9nager"}], "creation_date": "2025-06-04T00:00:00Z", "description": "EDAM is an ontology of bioscientific data analysis and data management, covering topics, operations, data, identifiers, and formats. It supports semantic annotation of tools, workflows, training, and provenance metadata across life sciences.", "domains": ["information technology", "biological systems"], "homepage_url": "https://edamontology.org/", "id": "edam", "last_modified_date": "2025-10-15T00:00:00Z", "layout": "resource_detail", "license": {"id": "https://creativecommons.org/licenses/by-sa/4.0/", "label": "CC-BY-SA-4.0", "logo": "https://mirrors.creativecommons.org/presskit/buttons/80x15/png/by-sa.png"}, "name": "EDAM Ontology", "products": [{"category": "OntologyProduct", "description": "EDAM OWL release", "format": "owl", "id": "edam.owl", "name": "EDAM OWL", "original_source": ["edam", "dc", "skos"], "product_file_size": 3373041, "product_url": "http://edamontology.org/EDAM.owl", "secondary_source": ["edam"]}, {"category": "OntologyProduct", "description": "EDAM TSV export", "format": "tsv", "id": "edam.tsv", "name": "EDAM TSV", "original_source": ["edam", "dc", "skos"], "product_file_size": 1977072, "product_url": "https://edamontology.org/EDAM.tsv", "secondary_source": ["edam"]}, {"category": "OntologyProduct", "description": "EDAM CSV export", "format": "csv", "id": "edam.csv", "name": "EDAM CSV", "original_source": ["edam", "dc", "skos"], "product_file_size": 1977072, "product_url": "https://edamontology.org/EDAM.csv", "secondary_source": ["edam"]}, {"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"]}], "publications": [{"authors": ["Ison J", "Kala\u0161 M", "Jonassen I", "Bolser D", "Uludag M", "et al."], "doi": "10.1093/bioinformatics/btt113", "id": "doi:10.1093/bioinformatics/btt113", "journal": "Bioinformatics", "preferred": true, "title": "EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats", "year": "2013"}], "repository": "https://github.com/edamontology/edamontology"}