Bioimaging operations, data types, formats, identifiers and topics. EDAM-Bioimaging is an extension to the EDAM ontology (edamontology.org) for bioimaging, developed in collaboration with partners from NEUBIAS (neubias.org).
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README.md

DOI representing all stable versions, resolving to the latest: 10.5281/zenodo.1149730

DOI of the latest stable EDAM-bioimaging version alpha05: 10.5281/zenodo.2557012

Poster: 10.7490/f1000research.f1000research.1116432.1

Twitter: @edamontology (follow).

EDAM-bioimaging

An ontology of bioimage informatics operations, types of data, data formats, and bioimaging topics

EDAM-bioimaging is an extension to the EDAM ontology (http://edamontology.org) for bioimage analysis, bioimage informatics, and bioimaging, developed in collaboration between partners from NEUBIAS Cost Action (Horizon 2020 CA15124) and ELIXIR-EXCELERATE WP1 (Horizon 2020 676559), in contact with partners from Euro-BioImaging PP2.

Viewing

Download

Always the last stable version:

Other versions, e.g. the current alpha05:

Contributing

This is an open community project (transparent and participatory), and thus contributions are very welcome!

The most accessible way of contributing is writing comments with suggestions or needs for clarification, and starting discussion threads. Multiple channels are avaialable:

Preferred:

  • Add comments to the live development version of EDAM-bioimaging at WebProtégé. Free registration at WebProtégé is required. Select a concept and "Start new thread" in the "Comments" widget|window (not "Comments" tab, stay in the "Classes" tab). Contribute to already open threads ibid or in the "Comments" tab.

Other options:

  • Submit or comment on an issue at GitHub
  • Add a proposal or comment to EDAM-bioimaging at the NCBO BioPortal
    • to a selected concept in the "Classes" tab by clicking the small "Notes" tab on the right (still within the big "Classes" tab)
    • on the general level in the "Notes" tab. You can include new concept proposals here.
  • Join the discussions at wg4-edam_ontology@irbbarcelona.org.glip.com (if member of, or invited to NeuBIAS on Glip). Mostly organisational stuff.
  • Add comments to the stable versions of EDAM-bioimaging at WebProtégé, such as the last stable version and especially the frozen versions (alpha05, alpha04, alpha03, alpha02) for more persistent comments. Note that comments to the live version are handled with the highest priority.

If you want to contribute in person, please join or organise a hackathon. Get in touch with wg4-edam_ontology@irbbarcelona.org.glip.com or matus.kalas@uib.no for planning. Usual hackathons for editing EDAM-bioimaging are the NEUBIAS Taggathons.

Editing

At this momentary early stage of the development, the content of EDAM-bioimaging is developed collaboratively at http://webprotege.stanford.edu/#projects/2ce704bf-83ed-4d2e-985f-84c4841fac71/edit/Classes. After one dev cycle, these developments are commited in a batch to git. Vice versa, commits from git are merged into WebProtégé.

N.B.: Due to this special setup, edit either:

  • in only git or in only WebProtégé and merge afterwards
  • or if needed in parallel, edit properties and root concepts only in git and other concepts only in WebProtégé. Merge afterwards.

N.B.: Be aware of how IDs of new concepts are assigned, and what it means for both merging into git and Comments in WebProtégé. See https://github.com/edamontology/edam-bioimaging/issues/7.

Citing

(Download BibTeX)

Before a full article is published, please cite the following when refering to EDAM-bioimaging in a scholarly publication:

The "mainline" EDAM ontology can be cited by:

EDAM-bioimaging releases are citable with DOIs too, for cases when that is needed. 10.5281/zenodo.1149730 represents all releases and resolves to the DOI of the last stable release. For the DOI of a particular release of EDAM-bioimaging, please see /releases.