EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications).

Prefix

edam

Keywords

analysis bioinformatics data acquisition data transformation life science obo ontology subject agnostic

Links

Homepage Repository OBO OWL

Contact

Matúš Kalaš   0000-0002-1509-4981   matuskalas

Pattern for Local Unique Identifiers

Local identifiers in EDAM Ontology should match this regular expression:
^(data|topic|operation|format)\_\d{4}$

Example Local Unique Identifier

data_1664   Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from EDAM Ontology should match this regular expression:
^edam:(data|topic|operation|format)\_\d{4}$

Example CURIE

edam:data_1664

Publications

• 2013 EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
• 2021 EDAM: the bioscientific data analysis ontology (update 2021)
• 2020 edamontology/edamontology: EDAM 1.25

A summary of the relations in the Bioregistry schema can be found here.

Has Parts (bfo:0000051 )

edam.data edam.format edam.operation edam.topic

The metaregistry provides mappings between the Bioregistry and other registries. There are 10 mappings to external registries for this resource with 2 unique external prefixes.

When using this resource in RDF, the following URI format should be used:

http://edamontology.org/$1

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier data_1664 is used to demonstrate the providers available for EDAM Ontology. A guide for curating additional providers can be found here.

Additional providers curated in the Bioregistry are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.