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biosimulators / edamontology

EDAM is an ontology of bioscientific data analysis and data management.
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DOI representing all stable versions, resolving to the latest: 10.5281/zenodo.822690

DOI of the latest stable EDAM version 1.25: 10.5281/zenodo.3899895

Current status of the 'main' development file: Build status

Latest documentation: Documentation Status

Twitter: @edamontology (follow).

What is EDAM?

EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within computational biology, bioinformatics, and bioimage informatics. EDAM includes types of data and data identifiers, data formats, operations, and topics related to data analysis in life sciences. 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 figure).

EDAM is particularly suitable for semantic annotations and categorisation of diverse resources related to bioscientific data analysis: e.g. tools, workflows, or training materials. EDAM is also useful in data management, for recording provenance metadata of processed bioscientific data.

Viewing and download

EDAM can be browsed online at the NCBO BioPortal, at OLS, <!---->and in the EDAM Browser.

The all-newest unstable version can be browsed and commented at the NCBO BioPortal and WebProtégé (free registration required).

The latest stable version is always downloable from http://edamontology.org/EDAM.owl | tsv | csv. For older versions, see http://edamontology.org/page#Download or /releases.

EDAM relations figure

Documentation

Comprehensive documentation and guidelines are available via readthedocs (maintained here).

A quick overview is at the http://edamontology.org home page.

Citing EDAM

If you refer to EDAM or its part in a scholarly publication, please cite:

Ison, J., Kalaš, M., Jonassen, I., Bolser, D., Uludag, M., McWilliam, H., Malone, J., Lopez, R., Pettifer, S. and Rice, P. (2013). EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics, 29(10): 1325-1332. 10.1093/bioinformatics/btt113 PMID: 23479348 Open access

EDAM releases are citable with DOIs too, for cases when that is needed. 10.5281/zenodo.822690 represents all releases and resolves to the DOI of the last stable release.

Research notice

Please note that this repository is participating in a study into sustainability of open source projects. Data will be gathered about this repository for approximately the next 12 months, starting from June 2021.

Data collected will include number of contributors, number of PRs, time taken to close/merge these PRs, and issues closed.

For more information, please visit our informational page or download our participant information sheet.