Model: Yersinia enterocolitica in minced meat_V2

[schuelet]

Model Information

Model Name

Yersinia enterocolitica in minced meat_V2

References

To the model! Execute uncurated model!

Model Uploaded By admin41

Curation Pipeline

Model Status

• [x] in review (publication pending)
• [ ] 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
• [ ] #517
• [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: [name]

Technical Curation

• [x] Model does not contain malicious code
• [x] #514
• [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] #513

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

[OctavioMV]

It might not be relevant but Study identifier is mandatory (i.e. *). However, the model shows no one (Data Background/study/study identifier).

[Racem-br]

From Octavio: I might be wrong but I think that in the publication "maxtimecg" and "mintimecg" are shown as "9" and "5"respectively. However, this parameters are shown in the default values as "14.114" as "-0.114". This is due to the assumption done in the paper where ∼ Pert(25% 5; 50% 7; 75% 9). There might be a reason for that but I do not know it. However values 14.114 and -0.114 where not found in the paper. Vector "prevthrs" that describes "Prevalence thresholds of Y. enterocolitica in one package of minced meat at the end of storage (just before consumption or preparation)" was also not found in the publication.

Licence: it is provided as other. It is published in an Elsevier open access paper. Therefore, content is CC BY-NC-ND

[Racem-br]

From Octavio: Density plot is shown as Probability expressed as per 10 while in publication ins expressed as per 100%. This might mislead the results. This should be annotated somewhere.

[Racem-br]

Publisher in zenodo suggestion: Maarten