references.bib

@article{knuth84,
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}



@book{microbio2021,
	title = {Microbiological Risk Assessment {\textendash} Guidelines for food},
	year = {2021},
	month = {06},
	date = {2021-06-06},
	publisher = {FAO and WHO},
	doi = {10.4060/cb5006en},
	url = {http://dx.doi.org/10.4060/cb5006en}
}

@article{koutsoumanis2016,
	title = {Moving towards a risk-based food safety management},
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	year = {2016},
	month = {12},
	date = {2016-12},
	journal = {Current Opinion in Food Science},
	pages = {36--41},
	volume = {12},
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	url = {http://dx.doi.org/10.1016/j.cofs.2016.06.008},
	langid = {en}
}

@article{efsa2022,
	title = {Zoonoses and foodborne outbreaks guidance for reporting 2021 data},
	author = {{European Food Safety Authority (EFSA)} and Amore, Giusi and Boelaert, Frank and Gibin, Davide and Papanikolaou, Alexandra and Rizzi, Valentina and Stoicescu, {Anca{-}Violeta}},
	year = {2022},
	month = {01},
	date = {2022-01},
	journal = {EFSA Supporting Publications},
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	number = {1},
	doi = {10.2903/sp.efsa.2022.EN-7131},
	url = {https://data.europa.eu/doi/10.2903/sp.efsa.2022.EN-7131},
	langid = {eng}
}

@article{prevalen2022,
	title = {Prevalence sample{-}based guidance for reporting 2021 data},
	author = {{European Food Safety Authority (EFSA)} and Boelaert, Frank and Gibin, Davide and Papanikolaou, Alexandra and Rizzi, Valentina and Stoicescu, {Anca{-}Violeta}},
	year = {2022},
	month = {01},
	date = {2022-01},
	journal = {EFSA Supporting Publications},
	volume = {19},
	number = {1},
	doi = {10.2903/sp.efsa.2022.EN-7129},
	url = {https://data.europa.eu/doi/10.2903/sp.efsa.2022.EN-7129},
	langid = {eng}
}

@misc{jdom_2022,
  author       = {Juliana De Oliveira Mota and
                  Laurent Guillier and
                  Henk Aarts and
                  Virginie Desvignes},
  title        = {{Deliverable D.4.1.3. Report on the survey related 
                   to the availability and quality of data used for
                   risk assessment}},
  month        = jan,
  year         = 2022,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.5882651},
  url          = {https://doi.org/10.5281/zenodo.5882651}
}


@article{Haberbeck2018,
title = {Harmonized terms, concepts and metadata for microbiological risk assessment models: The basis for knowledge integration and exchange},
journal = {Microbial Risk Analysis},
volume = {10},
pages = {3-12},
year = {2018},
note = {Special issue on 10th International Conference on Predictive Modelling in Food: Interdisciplinary Approaches and Decision-Making Tools in Microbial Risk Analysis},
issn = {2352-3522},
doi = {https://doi.org/10.1016/j.mran.2018.06.001},
url = {https://www.sciencedirect.com/science/article/pii/S2352352218300100},
author = {Leticia Ungaretti Haberbeck and Carolina Plaza-Rodríguez and Virginie Desvignes and Paw Dalgaard and Moez Sanaa and Laurent Guillier and Maarten Nauta and Matthias Filter},
keywords = {QMRA modelling, Information exchange format, Metadata schema, Controlled vocabularies, Model annotation}
}

@article{richardson2017,
  title={An updated scheme for categorizing foods implicated in foodborne disease outbreaks: a tri-agency collaboration},
  author={Richardson, LaTonia Clay and Bazaco, Michael C and Parker, Cary Chen and Dewey-Mattia, Daniel and Golden, Neal and Jones, Karen and Klontz, Karl and Travis, Curtis and Kufel, Joanna Zablotsky and Cole, Dana},
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}

@article{sanaa2019,
  title={GenomeGraphR: a user-friendly open-source web application for foodborne pathogen whole genome sequencing data integration, analysis, and visualization},
  author={Sanaa, Moez and Pouillot, R{\'e}gis and Vega, Francisco Garces and Strain, Errol and Van Doren, Jane M},
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  year={2019},
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}

@article{balkey2021,
  title={Standardizing the Isolation Source Metadata for the Genomic Epidemiology of Foodborne Pathogens Using LexMapr},
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  journal={IAFP 2021},
  year={2021},
  publisher={IAFP}
}

@article{efsa2015,
author = {European Food Safety Authority (EFSA)},
title = {The food classification and description system FoodEx 2 (revision 2)},
journal = {EFSA Supporting Publications},
volume = {12},
number = {5},
pages = {804E},
keywords = {food classification, food description, food groups, food categories, core list, extended list, facets},
doi = {https://doi.org/10.2903/sp.efsa.2015.EN-804},
url = {https://efsa.onlinelibrary.wiley.com/doi/abs/10.2903/sp.efsa.2015.EN-804},
eprint = {https://efsa.onlinelibrary.wiley.com/doi/pdf/10.2903/sp.efsa.2015.EN-804},
year = {2015}
}

@dataset{efsa_2022,
  author       = {European Food Safety Authority},
  title        = {Harmonized terminology for scientific research},
  month        = feb,
  year         = 2022,
  note         = {EU; XLSX; data.collection@efsa.europa.eu},
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.5949025},
  url          = {https://doi.org/10.5281/zenodo.5949025}
}

@article{tenenhaus2015,
  title={Software for predictive microbiology and risk assessment: a description and comparison of tools presented at the ICPMF8 Software Fair},
  author={Tenenhaus-Aziza, Fanny and Ellouze, Mariem},
  journal={Food microbiology},
  volume={45},
  pages={290--299},
  year={2015},
  publisher={Elsevier}
}


@misc{mangone2021,
  author       = {Iolanda Mangone and
                  Nicolas Radomski and
                  Adriano Di Pasquale and
                  Andrea Santurbano and
                  Paolo Calistri and
                  Cesare Cammà and
                  Kitty Maassen},
  title        = {{Refinement of the COHESIVE Information System 
                   towards a unified ontology of food terms for the
                   public health organizations  (COHESIVE)}},
  month        = sep,
  year         = 2021,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.5482422},
  url          = {https://doi.org/10.5281/zenodo.5482422}
}

@article{guillier2021,
  title={Risk factors for sporadic salmonellosis: a systematic review and meta-analysis},
  author={Guillier, Laurent and Th{\'e}bault, Anne and Fravalo, Philippe and Mughini-Gras, Lapo and Jourdan-da Silva, Nathalie and David, Julie and Kooh, Pauline and Cadavez, Vasco and Gonzales-Barron, Ursula},
  journal={Microbial Risk Analysis},
  volume={17},
  pages={100138},
  year={2021},
  publisher={Elsevier}
}

@article{pires2021,
  title={Burden of foodborne diseases: Think global, act local},
  author={Pires, Sara M and Desta, Binyam N and Mughini-Gras, Lapo and Mmbaga, Blandina T and Fayemi, Olanrewaju E and Salvador, Elsa M and Gobena, Tesfaye and Majowicz, Shannon E and Hald, Tine and Hoejskov, Peter S and others},
  journal={Current Opinion in Food Science},
  volume={39},
  pages={152--159},
  year={2021},
  publisher={Elsevier}
}

@article{pouillot2012,
  title={A risk assessment of campylobacteriosis and salmonellosis linked to chicken meals prepared in households in Dakar, Senegal},
  author={Pouillot, Régis and Garin, Benoit and Ravaonindrina, Noro and Diop, Kane and Ratsitorahina, Mahery and Ramanantsoa, Domoina and Rocourt, Jocelyne},
  journal={Risk Analysis},
  volume={32},
  pages={1798--1819},
  year={2012}
}

@article{filter2022,
  title={Towards efficient use of data, models and tools in food microbiology},
  author={Filter , Matthias and Nauta , Maarten and Pires , Sara M. and Guillier, Laurent and Buschhardt , Tasja },
  journal={Current Opinion in Food Science},
  volume={46},
  year={2022},
  publisher={Elsevier}
}

@article{cubero2019,
  title={‘MicroHibro’: A software tool for predictive microbiology and microbial risk assessment in foods},
  author={Salvador Cubero González and
  Arícia Possas and
  Elena Carrasco and 
  Antonio Valero and 
  Araceli Bolívar and 
  Guiomar Denisse Posada-Izquierdo and 
  Rosa Maria García-Gimeno and 
  Gonzalo Zurera and 
  Fernando Pérez-Rodríguez},
  journal={International Journal of Food Microbiology},
  volume={290},
  pages={226--236},
  year={2019},
  publisher={Elsevier}
}