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edamontology · May 4, 2023 · f24343e · f24343e
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+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 EDAM: the bioscientific data analysis ontology (update 2021) [version 1; not peer reviewed].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. DOI: 10.7490/f1000research.1118900.1 Open access
+
+@article{Kalas-etal2019b,
+  author = {Melissa Black and Lucie Lamothe and Hager Eldakroury and Mads Kierkegaard and Ankita Priya and Anne Machinda and Uttam Singh Khanduja and Drashti Patoliya and Rashika Rathi and Tawah Peggy Che Nico and Gloria Umutesi and Claudia Blankenburg and Anita Op and Precious Chieke and Omodolapo Babatunde and Steve Laurie and Steffen Neumann and Veit Schw\"{a}mmle and Ivan Kuzmin and Chris Hunter and Jonathan Karr and Jon Ison and Alban Gaignard and Bryan Brancotte and Herv\'{e} M\'{e}nager and Mat\'{u}\v{s} Kala\v{s}},
+  title = {{EDAM: the bioscientific data analysis ontology (update 2021) [version 1; not peer reviewed]}},
+  journal = {F1000Research},
+  year = {2022},
+  month = {Jan},
+  day = {1},
+  volume = {11},
+  number = {ISCB Comm J},
+  pages = {1},
+  note = {Poster},
+  access = {open},
+  doi = {10.7490/f1000research.1116432.1},
+  url = {https://doi.org/10.7490/f1000research.1116432.1},
+  eprint = {https://f1000research.com/posters/8-158}
+}
+
+
+If you refer to EDAM (Bio)imaging, including AI and machine learning, please cite:
+
+
+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(ELIXIR): 158. Poster. DOI: 10.7490/f1000research.1116432.1 Open Access
+
+@article{Kalas-etal2019b,
+  author = {Mat\'{u}\v{s} Kala\v{s} and Laure Plantard and Nata\v{s}a Sladoje and Joakim Lindblad and Moritz Alexander Kirschmann and Martin Jones and Anatole Chessel and Leandro Aluisio Scholz and Fabienne R\"{o}ssler and Alexandre Dufour and John Bogovic and Chong Zhang Dominic Waithe and Paula Sampaio and Lassi Paavolainen and David H\"{o}rl and Sebastian Munck and Ofra Golani and Josh Moore and Alban Gaignardand and Florian Levet and {participants in the NEUBIAS Taggathons} and Perrine Paul-Gilloteaux and Jon Ison and {the EDAM dev team} and Kota Miura and Julien Colombelli and {welcoming new contributors}},
+  title = {{EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (2019 update) [version 1; not peer reviewed]}},
+  journal = {F1000Research},
+  year = {2019},
+  month = {Feb},
+  day = {6},
+  volume = {8},
+  number = {ELIXIR},
+  pages = {158},
+  note = {Poster},
+  access = {open},
+  doi = {10.7490/f1000research.1116432.1},
+  url = {https://doi.org/10.7490/f1000research.1116432.1},
+  eprint = {https://f1000research.com/posters/8-158}
+}
+
+
+
+
+
+
+
+EDAM 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.
+
+@misc{Kalas-etal2016-2019,
+  author = {Mat\'{u}\v{s} Kala\v{s} and Laure Plantard and Nata\v{s}a Sladoje and Joakim Lindblad and Moritz Alexander Kirschmann and Martin Jones and Leandro Aluisio Scholz and Anatole Chessel and Jon Ison and contributors},
+  title = {edamontology/edam-bioimaging},
+  year = {2016-2019},
+  note = {Software (all versions)},
+  howpublished = {\url{https://github.com/edamontology/edam-bioimaging}},
+  doi = {10.5281/zenodo.1149730},
+  access = {open},
+  URL = {https://doi.org/10.5281/zenodo.1149730},
+  eprint = {https://zenodo.org/record/1149730}
+}
+
+@misc{Kalas-etal2018a,
+  author = {Mat\'{u}\v{s} Kala\v{s} and Contributors from NEUBIAS Taggathons},
+  title = {edamontology/edam-bioimaging: alpha03},
+  year = {2018},
+  month = {Jan},
+  day = {16},
+  note = {Software version},
+  howpublished = {\url{https://github.com/edamontology/edam-bioimaging/releases/tag/alpha03}},
+  doi = {10.5281/zenodo.1149731},
+  access = {open},
+  URL = {https://doi.org/10.5281/zenodo.1149731},
+  eprint = {https://zenodo.org/record/1149731}
+}
+
+@misc{Kalas-etal2018c,
+  author = {Mat\'{u}\v{s} Kala\v{s} and Laure Plantard and Nata\v{s}a Sladoje and Joakim Lindblad and Moritz Alexander Kirschmann and Martin Jones and Leandro Aluisio Scholz and Anatole Chessel and Jon Ison and contributors},
+  title = {edamontology/edam-bioimaging: alpha04},
+  year = {2018},
+  month = {Oct},
+  day = {17},
+  note = {Software version},
+  howpublished = {\url{https://github.com/edamontology/edam-bioimaging/releases/tag/alpha04}},
+  doi = {10.5281/zenodo.2556019},
+  access = {open},
+  URL = {https://doi.org/10.5281/zenodo.2556019},
+  eprint = {https://zenodo.org/record/2556019}
+}
+
+@misc{Kalas-etal2019a,
+  author = {Mat\'{u}\v{s} Kala\v{s} and Nata\v{s}a Sladoje and Laure Plantard and Martin Jones and Leandro Aluisio Scholz and Joakim Lindblad and contributors},
+  title = {edamontology/edam-bioimaging: alpha05},
+  year = {2019},
+  month = {Feb},
+  day = {5},
+  note = {Software version},
+  howpublished = {\url{https://github.com/edamontology/edam-bioimaging/releases/tag/alpha05}},
+  doi = {10.5281/zenodo.2557012},
+  access = {open},
+  URL = {https://doi.org/10.5281/zenodo.2557012},
+  eprint = {https://zenodo.org/record/2557012}
+}
+
+
+
+Older publications:
+
+Matúš Kalaš, Laure Plantard, Moritz Alexander Kirschmann, Joakim Lindblad, Anatole Chessel, Nataša Sladoje-Matić, Leandro A. Scholz, Chong Zhang, Fabienne Rössler, Alexandre Dufour, John A. Bogovic, Martin Jones, Josh Moore, Alban Gaignard, Lassi Paavolainen, David Hörl, Ofra Golani, Participants in the NEUBIAS Taggathons, Perrine Paul-Gilloteaux, the EDAM dev team, Kota Miura, Julien Colombelli, and welcoming contributors (2018). EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats [version 1; not peer reviewed]. F1000Research, 7(ELIXIR): 180. Poster. DOI: 10.7490/f1000research.1115257.1 Open access
+
+@article{Kalas-etal2018b,
+  author = {Mat\'{u}\v{s} Kala\v{s} and Laure Plantard and Moritz Alexander Kirschmann and Joakim Lindblad and Anatole Chessel and Nata\v{s}a Sladoje-Mati\'{c} and Leandro A. Scholz and Chong Zhang and Fabienne R\"{o}ssler and Alexandre Dufour and John A. Bogovic and Martin Jones and Josh Moore and Alban Gaignard and Lassi Paavolainen and David H\"{o}rl and Ofra Golani and {Participants in the NEUBIAS Taggathons} and Perrine Paul-Gilloteaux and {the EDAM dev team} and Kota Miura and Julien Colombelli and {welcoming contributors}},
+  title = {{EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats [version 1; not peer reviewed]}},
+  journal = {F1000Research},
+  year = {2018},
+  month = {Feb},
+  day = {12},
+  volume = {7},
+  number = {ELIXIR},
+  pages = {180},
+  note = {Poster},
+  access = {open},
+  doi = {10.7490/f1000research.1115257.1},
+  url = {https://doi.org/10.7490/f1000research.1115257.1},
+  eprint = {https://f1000research.com/posters/7-180}
+}
+
+
+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
+
+@article{Ison-etal2013,
+  author = {Ison, Jon and Kala\v{s}, Mat\'{u}\v{s} and Jonassen, Inge and Bolser, Dan and Uludag, Mahmut and McWilliam, Hamish and Malone, James and Lopez, Rodrigo and Pettifer, Steve and Rice, Peter}, 
+  title = {{EDAM: An ontology of bioinformatics operations, types of data and identifiers, topics, and formats}},
+  journal = {Bioinformatics},
+  volume = {29},
+  number = {10},
+  pages = {1325-1332},
+  year = {2013},
+  month = {Mar},
+  day = {11},
+  doi = {10.1093/bioinformatics/btt113},
+  access = {open},
+  pmid = {23479348},
+  pmcid = {PMC3654706},
+  URL = {https://doi.org/10.1093/bioinformatics/btt113},
+  eprint = {https://academic.oup.com/bioinformatics/article/29/10/1325/255660},
+  PDF = {https://academic.oup.com/bioinformatics/article-pdf/29/10/1325/710075/btt113.pdf}
+}