Model: Nauta consumer phase model for transfer of Campylobacter during preparation of ready-to-eat chicken salad_V2

[schuelet]

Model Information

Model Name

Nauta consumer phase model for transfer of Campylobacter during preparation of ready-to-eat chicken salad_V2

References

To the model! Execute uncurated model!

Model Uploaded By admin41

Curation Pipeline

Model Status

• [x] in review (publication pending)
• [x] ready for publication
• [ ] model has been uploaded and published in Zenodo KJ

Basic Quality Control

• By Chair of Curationboard: @Racem-br

General Check

• [x] Online Sanitation Check: validate

MIRARAM Check

• [x] Model Name
• [x] Model ID
• [x] Model Creator (different from author!)
• [x] Creation Date
• [x] License
• [x] Model Execution Metadata (script-language/tool/web-service API)
• [x] Reference Description (URI)
• [x] Scope (any)
• [x] Parameter Metadata (Input/Output)

Code Of Conduct

• [x] In case of re-implementations or re-use of digital objects without changes in the business logic of the model, the person who created the FSKX file is only listed as “Creator”. In cases where the business logic of the existing digital object was significantly modified or the Creator developed the business logic of the model himself the creator can be listed as Author as well.
• [x] The FSKX file Creator confirmed that in case of re-implementations or re-use of digital model objects the main author of the original work was contacted and did not express objections, unless the permissions given by the license of that digital model object already provides such clearance.
• [x] An “Author” of an FSKX model is the person who created the majority of the model code or, in cases where the model code was published in an online repository, the person who is listed there as primary contact person. Other persons who contributed to the model code would be referenced as an additional “Author” in the FSKX file. In those cases where Authors contributed to the FSKX file generation (e.g. by doing quality control), they would also be listed as one of the “Creators”.

Final Step

• [x] Curator assigned to this ticket

Advanced Quality Control

By Curator

• Technical Curation by: @schuelet
• Scientific Curation by: @TarGue

Technical Curation

• [x] Model does not contain malicious code
• [x] Model metadata validates against FSKX schema
• [x] Model can be executed with KNIME FSK-Lab
• [x] All provided simulation scenarios can be executed
• [x] Model can be executed on RAKIP Model Repository

Scientific Curation

• [x] Default simulation results are in line with reference publication
• [x] User defined simulation settings result in reasonable results
• [x] Model annotation is sufficiently detailed

Report

Changes Made

Changes made to the model in preparation for publication (Zenodo KJ)

Additional notes

Observations or remarks about the model or its curation

[TarGue]

The Model is sufficiently described, and the end results are in line with Table 1 (minor differences). The margins described in Section 3 fit well with changed simulation settings and the default.

Following Comment is clarified below:

However, I had expected a similar visualization as in Figure 2 (https://onlinelibrary.wiley.com/doi/full/10.1111/j.1539-6924.2010.01481.x) and not the cumulative Risk, this was a bit confusing to me in the beginning.

[ganasp]

This model is of type consumer phase model, therefore it only calculates as model output the bacterial concentration of the Campylobacter contamination of chicken meat (Cretlog). Figure 2 of the paper presents as result the probability of illness, this model output will be provided if the consumer phase model will be joined with a dose-response model.

[TarGue]

@ganasp thank you for the explanation. I thought about something like that. Is there a possibility to provide such explanations in FSKX or at least a short description for the figure? This would make it more understandable for the end users.

[ganasp]

The objective and a description of the model is given in the FSKX metadata under General information.

[TarGue]

Okay, thank you for claryfication and explanation.

[maartenjnauta]

It all seems to be OK, all fine for me.

[schuelet]

@HernanGRedon : These SSI models that were created by Stylianos can be uploaded to Zenodo by you

[Racem-br]

Publisher in zenodo suggestion: Maarten

[schuelet]

https://zenodo.org/records/10410200