Published March 3, 2020 | Version alpha06
Software Open

EDAM Bioimaging: The ontology of (bio-)image informatics and machine learning

Creators

  • 1. Centre for Image Analysis, Uppsala University, Sweden
  • 2. Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
  • 3. Francis Crick Institute, London, UK
  • 4. Deutsches Krebsforschungszentrum, Heidelberg, Germany
  • 5. Universidad Carlos III de Madrid, Spain
  • 6. Company of Biologists Ltd., Cambridge, UK
  • 7. Delft University of Technology, Netherlands
  • 8. Institut Curie, Paris, France
  • 9. Medical Research and Occupational Health, Zagreb, Croatia
  • 10. Biomedical Imaging Group, École Polytechnique Fédérale de Lausanne, Switzerland
  • 11. Computational Biology Unit, Department of Informatics, University of Bergen, Norway; @edamontology

Contributors

Contact person:

  • 1. Computational Biology Unit, Department of Informatics, University of Bergen, Norway; @edamontology

Description

The next alpha release of EDAM-bioimaging, alpha06.

  • Added and refined topics and synonyms in sample preparation and tomography, and finalised coverage of imaging techniques (all of these to the high-level extent that influences choices of downstream analysis)
  • Created a concise but comprehensive ontology of Machine learning, Artificial intelligence, and Clustering (to the level relevant in particular in bioimaging, biosciences, but also scientific data analysis in general; left todo: operations related to training/parameter optimisation)
  • A couple of other editions - and a lot of refined annotation - in operations and topics
  • Work in progress (WIP) on definitions, rdfs:comments, and seeAlso links

Major contributions are from the members and guests of the COMULIS & NEUBIAS COST Actions. Editors and the main contributors to this particular version alpha06 are listed in #18. All contributors are listed on the top of the OWL file.

Permanent location for browsing EDAM-bioimaging version alpha06: https://webprotege.stanford.edu/#projects/c149e738-4437-456c-843c-eb5861a36854/edit/Classes. Free registration required, and commenting enabled (see the brief contribution guidelines or CONTRIBUTING first).

The bulk of the work on alpha06 is in #18. All commits can be seen at alpha06 tag.

Notes

For referring to EDAM Bioimaging, please use the latest poster and abstract https://doi.org/10.7490/f1000research.1117826.1 -- For referring concretely to version alpha06 of EDAM Bioimaging, please use https://doi.org/10.5281/zenodo.3695725 -- And for referring to all versions, please use https://doi.org/10.5281/zenodo.1149730

Files

edamontology/edam-bioimaging-alpha06.zip

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Additional details

Compiles
https://edamontology.org/EDAM-bioimaging_alpha06.owl (URL)
https://edamontology.org/EDAM-bioimaging_alpha06.tsv (URL)
https://edamontology.org/EDAM-bioimaging_alpha06.csv (URL)
Is cited by
Poster: 10.7490/f1000research.1117826.1 (DOI)
Is described by
Poster: 10.7490/f1000research.1117826.1 (DOI)
Is supplement to
https://github.com/edamontology/edam-bioimaging/tree/alpha06 (URL)