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Published February 5, 2019 | Version alpha05
Software Open

edamontology/edam-bioimaging: alpha05

  • 1. University of Bergen, Norway
  • 2. Uppsala University, Sweden
  • 3. Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
  • 4. Francis Crick Institute, London, UK
  • 5. Federal University of Paraná, Curitiba, Brazil

Description

The next alpha release of EDAM-bioimaging, alpha05.

  • Added some missing Operations and some clean-up of the hierarchy of Operations
  • Added Topics (especially related to multimodal imaging, and also some missing|emerging modalities) and some clean-up of the hierarchy of Topics
  • Added some Data concepts
  • Added some definitions, comments, synonyms, related terms, and links to Wikipedia and articles

Permanent location for browsing EDAM-bioimaging version alpha05: https://webprotege.stanford.edu/#projects/d9f9a5b2-d746-430a-a2cd-9aa745764079/edit/Classes. Free registration required, and commenting enabled (see the brief contribution guidelines or CONTRIBUTING first).

The bulk of the work on alpha05 is in #13. All commits can be seen at alpha05 tag; the ones on 4th and 5th February 2019 are the changes between versions alpha04 and alpha05.

The changes in the OWL file between versions alpha04 and alpha05 can nicely be seen HERE.

Files

edamontology/edam-bioimaging-alpha05.zip

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Additional details

Funding

ELIXIR-EXCELERATE – ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences. 676559
European Commission

References

  • Matúš Kalaš, Laure Plantard, Nataša Sladoje, Joakim Lindblad, Moritz Alexander Kirschmann, Martin Jones, Anatole Chessel, Leandro Aluisio Scholz, Fabienne Rössler, Alexandre Dufour, John Bogovic, Chong Zhang, Dominic Waithe, Paula Sampaio, Lassi Paavolainen, David Hörl, Sebastian Munck, Ofra Golani, Josh Moore, Alban Gaignard, Florian Levet, participants in the NEUBIAS Taggathons, Perrine Paul-Gilloteaux, Jon Ison, the EDAM dev team, Kota Miura, Julien Colombelli, and welcoming new contributors (2019). EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (2019 update) [version 1; not peer reviewed]. F1000Research, 8: 158. Poster. DOI: 10.7490/f1000research.1116432.1 Open Access
  • Jon Ison, Matúš Kalaš, Inge Jonassen, Dan Bolser, Mahmut Uludag, Hamish McWilliam, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice (2013). EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics, 29(10): 1325-1332. DOI: 10.1093/bioinformatics/btt113 PMID: 23479348 Open Access