An ontology of bioimage informatics operations, types of data, data formats, and bioimaging topics
Please see README.md for more details, including viewing and download.
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
- Create a pull request to https://github.com/edamontology/edam-bioimaging
- 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 (alpha06, 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.
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 #7.