EDAM: Ontology of bioscientific data analysis and data management

EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within scientific data analysis and data management (both within and beyond life sciences and imaging). EDAM includes topics, operations, types of data and data identifiers, and data formats. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use (see figures below).

EDAM is particularly suitable for semantic annotations and categorisation of diverse scientific resources: e.g. tools, workflows, learning materials, or standards. EDAM is also useful in data management itself, for recording provenance metadata of processed scientific data.

EDAM is a community project and its development can be followed and contributed to at GitHub.

Viewing

EDAM can be graphically browsed online at:

NCBO ontology browser (BioPortal) (all-newest "unstable" version)
EBI Ontology Look-up Service (OLS) (latest stable version)
EDAM Browser (new: all versions!)
WebProtégé (free registration required)

Downloads

https://edamontology.org/EDAM.owl (The all-newest, possibly "unstable" released version)

https://edamontology.org/EDAM_1.25.owl (The latest stable version is at the moment 1.25)

https://edamontology.org/EDAM_stable.owl (Always the latest stable version, in OWL format)

https://edamontology.org/EDAM.tsv (The latest version available in TSV format)

https://edamontology.org/EDAM_1.25.tsv (Stable version 1.25, as tab-separated values (TSV))

https://edamontology.org/EDAM.csv (The latest version available in CSV format)

https://edamontology.org/EDAM_1.25.csv (Stable version 1.25, as comma-separated values (CSV))

https://edamontology.org/EDAM.obo (The last version available in OBO format is an ancient EDAM version 1.2. Because the conversion from OWL to OBO hasn't yet fully been automated for EDAM, we do not provide newer versions in the OBO format yet.)

https://github.com/edamontology/edamontology/releases (All stable releases of EDAM)

https://raw.githubusercontent.com/edamontology/edamontology/main/EDAM_dev.owl (Unreleased development version)

Documentation

Comprehensive documentation and guidelines are available on ReadTheDocs (maintained here).

Contacts

Twitter: @edamontology (follow).

All development, and the preferred request and discussion channel is GitHub: https://github.com/edamontology/edamontology

Community chat is on Gitter: https://gitter.im/edamontology/edamontology

Scope

EDAM includes 4 main sections of concepts (sub-ontologies):

Topic - “A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.”
Operation - “A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs).”
Data - “Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.”
Format - “A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.”

Noteworthy sub-section:

Data -> Identifier - “A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things).”

EDAM concepts

EDAM concepts. Boxes indicate sections (sub-ontologies) of EDAM, with example concepts.

Architecture

EDAM includes 4 types of content:

Concepts - All concepts have a name (the term or label) and definition. Further, a concept may have simple relations to other EDAM concepts, as well other intrinsic properties, e.g. an identifier may have a regular expression defining its syntax.
Hierarchy - Every concept (excluding the top level) is related to one or more other concepts within the same section of EDAM by a specialisation/generalisation relation (subsumption, is a), forming a directed acyclic graph (DAG). Hence EDAM consists of 4 primary hierarchies (connected DAGs), for the 4 main sections: Topic, Operation, Data, and Format.
Relations - In addition to the hierarchy, concepts in EDAM can be related with each other by additional types of relations (see illustration below). These supplement the definitions of concepts and strengthen internal consistency of EDAM. They can be used also outside of EDAM, for example in annotated data.
Properties - In addition to standardised attributes such a primary term and a definition, some concepts in EDAM contain additional information, e.g. a link to the documentation of a Format, or a regular expression for an Identifier. EDAM includes the definitions of these properties (attributes) which can also be used outside of EDAM.

EDAM relations

EDAM architecture is simple. Boxes indicate top-level concepts (sections, sub-ontologies), and lines indicate types of relations.

Publications

An up-to-date description of EDAM is available in the following extended abstract and poster.

If you use, or refer to EDAM or its part, please cite:

Melissa Black, Lucie Lamothe, Hager Eldakroury, Mads Kierkegaard, Ankita Priya, Anne Machinda, Uttam Singh Khanduja, Drashti Patoliya, Rashika Rathi, Tawah Peggy Che Nico, Gloria Umutesi, Claudia Blankenburg, Anita Op, Precious Chieke, Omodolapo Babatunde, Steve Laurie, Steffen Neumann, Veit Schwämmle, Ivan Kuzmin, Chris Hunter, Jonathan Karr, Jon Ison, Alban Gaignard, Bryan Brancotte, Hervé Ménager, Matúš Kalaš (2022). EDAM: the bioscientific data analysis ontology (update 2021) [version 1; not peer reviewed]. F1000Research, 11(ISCB Comm J): 1. Poster. Open access