edamontology / edamontology.org

Static EDAM website

DOI representing all stable versions, resolving to the latest:

DOI of the latest stable EDAM version 1.25:

Current status of the 'main' development file:

Latest documentation:

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.

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:

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 EDAM: the bioscientific data analysis ontology (update 2021) [version 1; not peer reviewed].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

EDAM releases are citable with DOIs too, for cases when that is needed. 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.

License

edamontology.org's Issues

The HTML doesn't render

Big thanks @inkuzmin for reporting!

@hmenager @veitveit @inkuzmin If you'll have a bit of time, could you please inspect the page source in your browser, and see if you can find the issue? I'll look at it tonight (unless you fix it in the meantime :P :D) 1000000000 THANKS!

The body content is Markdown-to-HTML as you can see.

Create a Footer for the Website.

Create a Footer for the EDAM website which contains a link to all the social media handles, Contacts, etc.

Co-Author: @matuskalas

Add a ReadMe File

I would like to work on this.
@matuskalas Please approve and assign this to me.

Add links to various EDAM repos on GH; add info about EDAM Bioimaging

• Add links to various EDAM repos on GH
• Add info about EDAM Bioimaging

Create a Navbar for edamontology website.

To create a navbar for edamontology website - http://edamontology.org/page.

I am working on this issue.

Co-authored under: @matuskalas

Update NCBO BioPortal links to include ?p=classes

I think it'll be great to update most of the links to browsing EDAM in the NCBO BioPortal from https://bioportal.bioontology.org/ontologies/EDAM to https://bioportal.bioontology.org/ontologies/EDAM?p=classes. In most of the places, it makes sense to point to browsing (i.e. the "Classes" tab, ?p=classes), instead of the default "Summary" tab.

Way forward: Search for all links to https://bioportal.bioontology.org, and update everywhere where it'll be better with the "Classes" tab.

(A good short mini-task for newcomers! 😉 incl. Outreachy applicants)

Update posters

• Update EDAM poster (authors)
• Update EDAM Bioimaging poster (year, authors, remove DOI...)
• Update EDAM Browser (Submit the original to F1000 if isn't, update Zenodo, CFF, ...🥵)
• Update and add EDAM + tools poster EAH (authors, ...)

Letsencrypt certificate expired

Hi,

the Letsencrypt certificate for https://edamontology.org/topic_3070
has expired two years ago, any way to kick that into working again ?
Any place where I can open that as an (github) issue ?

Yours,
Steffen

Your https certificate has expired

It appears that your certificate has expired 23 days ago according to the warnings in my browser.

Interactive poster and several links broken

Hi, I am not sure, is this repository still the place for the website? The HTML seemed to not be fully up-to-date (or the other way around), but maybe it is some Javascript magic I did not analyze yet.

Anyway, several links (like the "Hierarchy" link) are broken, and the interactive poster displays a "404 NOT FOUND" within the page for me.