RAKIP-Web model repository Curation and Publication Policy

  1. Background:

The efficient transfer and re-use of existing data, models and software tools is a significant bottleneck in the area of risk assessment. On the basis of the lessons learned from the development of a prototypical QMRA food and feed safety model repository “FSK-Web”[1] (https://doi.org/10.2903/sp.efsa.2021.EN-7063), the RAKIP-Web model repository has been developed to support risk assessors in EU Member States. The RAKIP-Web model repository will allow any user to search and download FSKX-formatted data and model files. Members of risk assessment authorities and research organisations can register to get access to additional web-based services, like the web-based execution of models with default or user defined input parameters.

The RAKIP-Web model repository curation and publication policy defines all steps that will be performed before a FSKX file is made available in the RAKIP-Web model repository. The curation and publication policy is established and maintained by the RAKIP Initiative (https://foodrisklabs.bfr.bund.de/rakip-initiative/[M(1] ). The RAKIP Initiative establishes a Curation Board (CB) where employees of any RAKIP Initiative member organization can become a member. The CB elects annually by majority vote a Chair of the Curation Board (CCB).

  • General aspects:

Any researcher/modeler registered at the RAKIP-Web model repository can submit a FSKX model or FSKX data file via a dedicated FSKX submission web service (link_will_follow). On submission via this web service the user submitting the FSKX file confirms:

  1. that license conditions linked to underlying work were respected, specifically when the submitted files were created by re-using or re-implementing existing digital objects (underlying work).
  2. that the FSKX file does not contain harmful code.

Further, any FSKX file creator whose file is submitted  to the RAKIP-Web model repository must have followed the  following RAKIP  Code-of-Conduct:

  1. 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.
  2. 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.
  3. 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”.
  4.  
  5. Curation and publication procedure:

The curation process will be performed according to the following procedure:

Basic Quality Control (BQC): the CCB performs BQC checks (see section 3.1)  – if the FSKX file fulfils all BQC criteria, the file will be forwarded to one curator from the CB to perform the Advanced Quality Control (AQC) checks (see below); if the FSKX file does not pass all BQC criteria, the file is rejected and the user who submitted the FSKX file is informed.

Advanced Quality Control (AQC): the curator from the CB performs and documents the AQC (see section 3.2); if the FSKX file passes all AQC criteria, the curator notifies the CCB and user submitted the FSKX file that he/she can upload the FSKX file via a dedicated “Upload” web service into the RAKIP-Web model repository.

After successful integration, the user who submitted the FSKX file and all CB members receive a notification via email; if the file does not pass all AQC criteria the findings are reported back to user submitted the FSKX file.

3.1 Basic Quality Control (BQC) checks:

  1. the FSKX file needs to pass an online FSKX sanity check (as soon this is available).
  2. the FSKX file is compliant to the Minimum Information Required to Annotate Food Safety Risk Assessment Models (MIRARAM) guidelines[2] (https://doi.org/10.1016/j.foodres.2020.109952)
  3. The registered user who submitted the FSKX file has assured during submission that the provided FSKX file does not violate rights linked to underlying work AND that it does not contain harmful code. Specifically, the user had confirmed that the license conditions linked to the underlying work are respected, e.g. the conditions under which derivative work can be shared. NOTE: the creation of an FSKX file from any other digital asset can be considered as “derivative work”, as this process is always linked with significant customization efforts.
  4. the FSKX file annotation is compliant to the RAKIP  Code-of-Conduct (see chapter 2)

3.2 Advanced Quality Control (AQC) checks that:

  1. the FSKX file can be executed with all provided simulation scenarios in a protected computational environment
  2. the simulation with default parameters create similar results to those described in the model’s reference publication. This step could be skipped if the FSKX model file has already been under a peer review process.
  3. the execution with various new user defined simulation settings results in reasonable simulation results (e.g. check if unrealistic high output values are predicted). This step could be skipped if the FSKX model file has already been under a peer review process.
  4. the provided annotation of the model is sufficiently detailed (e.g. units for parameters, upper and lower limits for input parameters, model scope, description of each simulation scenario). This step could be skipped if the FSKX model file has already been under a peer review process.
  5. the model can be executed on the RAKIP-Web KNIME server
  • Technical aspects of the FSKX file “Upload”

The “Upload” web service makes sure that any curated FSKX file is first registered into EFSA’s KJ with all required metadata. After EFSA’s KJ curation team approved the FSKX file, it will be integrated into the public RAKIP-Web model repository under preservation of EFSA’s KJ DOI.

Glossary

CB:                                                RAKIP-Web model repository Curation Board

CB member:                               a person willing to work as curator for the RAKIP-Web model repository. CB members must be employed by any of the RAKIP Initiative member organizations. CB members perform the AQC on submitted FSKX files.

CCB:                                             Chair of the Curation Board – elected annually by the CB. The CBB performs the BQC on submitted FSKX files

FSKX:                                            Food Safety Knowledge eXchange format (https://foodrisklabs.bfr.bund.de/fskx-food-safety-knowledge-exchange-format/ )

FSKX file Creator:                      the person who creates and submits an FSKX file to the RAKIP-Web model repository. This person is responsible for the content in the submitted FSKX file.

FSKX file Author:                       in the FSKX format metadata schema, the FSKX file Author is the person who generated the model code or generated the data set originally.

digital model objects:               e.g. software code

AQC:                                             Advanced Quality Control – curation steps performed after completion of BQC

BQC:                                             Basic Quality Control – curation steps performed by CCB after submission of FSKX files

MIRARAM                                   Minimum Information Required to Annotate Food Safety Risk Assessment Models guidelines.

EFSA KJ                                        European Food Safety Agency Knowledge Junction (https://zenodo.org/communities/efsa-kj/about/ ) is a curated, open repository for the exchange of evidence and  supporting materials used in food and feed safety risk assessments.

[1] Schüler, T, Ganas, P, Fuhrmann, M, de Alba Aparicio, M, Lopez de Abechuco, E, Mensching, Y, Valentin, L, Filter, M, 2021. Extension of the content, functionality and usability of the online FSK-Web model repository. EFSA Supporting Publication 2021: 18( 12):EN-7063. 36 pp doi: 10.2903/sp.efsa.2021.EN-7063

[2] Filter, M., et al., Minimum Information Required to Annotate Food Safety Risk Assessment Models (MIRARAM). Food Res Int, 2021.139: p. 109952.

the link will work when this is published. It will redirect to this page: https://foodrisklabs.bfr.bund.de/rakip-web-portal/

Controlled Vocabularies

To support harmonized annotation of food safety knowledge we established an online resource with controlled vocabularies for those metadata concepts that are not free text. Some of them are specific for the different model classes. These controlled vocabularies are based on the terms used by other sources like ontologies, standards and tools (SSD-CODE, FOODON, MIME, PMM-Lab, OpenFSMR, Bibliographic Ontology Specification, etc.)

The lists of proposed controlled vocabularies for food safety knowledge annotation:

Controlled_Vocabularies_Master_Table_V1.04

 

This resource was developed in part under the EFSA-BfR Framework Partnership Agreement Area 2   https://foodrisklabs.bfr.bund.de/safetytools-efsa-sa2/

FoodChain-Lab Online-Training, December 2020 (in German)

Dienstag, 08.12.2020

10:00-10:15
Begrüßung und Organisatorisches
BVL, BfR

10:15-10:45
Modernisierung des Austausches, der Auswertung und der Visualisierung von lagerelevanten Daten zur Konsolidierung des Lageberichtes
Andreas Kliemant, BVL

10:45-11:15
FoodChain-Lab: ein innovatives Tool zur Erhöhung der Lebensmittelsicherheit durch Warenkettenanalysen
Marion Gottschald, BfR

11:15-12:15
Rückwärts- und Vorwärtsverfolgungsanalysen mit FoodChain-Lab: Datensammlung, Datenstrukturen, Datenbedarf und Arbeitsablauf
(inklusive Übung zur Datensammlung)
Alexander Falenski und FCL-Team, BfR

12:15-13:15
Mittagspause

13:15-13:45
Einführung KNIME und FoodChain-Lab Desktopversion
Alexander Falenski, BfR

13:45-16:45
Interaktives Rückverfolgungsszenario am Beispiel eines lebensmittelbedingten Ausbruchs unter Verwendung der FoodChain-Lab Desktopapplikation
Marion Gottschald und FCL-Team, BfR

16:45-17:15
Diskussion und offene Fragen

 

Mittwoch, 09.12.2020

09:00-09:15
Zusammenfassung erster Tag und Organisatorisches 09:15-11:00
Live-Demo und praktische Übung FoodChain-Lab Webapplikation
(WebApp, Übung und Vergleich WebApp mit Desktop-Version)
Alexander Falenski und FCL-Team, BfR

11:00-11:30
ATAST – Browserbasierte Erfassung von Lieferkettendaten durch lokale Lebensmittelkontrollbehörden
Christian Gerlach und Tobias Zenkner, LANUV NRW

11:30-12:30
Mittagspause

12:30-13:00
EFSA-Visionen zur Rückverfolgung in Europa
Olaf Mosbach-Schulz, EFSA

13:00-13:30
Ein neues Tool zur geführten Extraktion von Daten aus RASFF-Meldungen – Grundprinzip, Live-Demo und geplanter Arbeitsablauf
Olaf Mosbach-Schulz, EFSA

13:30-14:15
Rapid Alert Supply Network Extractor (RASNEX): Tool zur maschinellen Extraktion und Visualisierung von Lebens- und Futtermittelwarenketten aus RASFF-Meldungen: Grundprinzip, Ausblick und Live-Demo
Marc Lorenzen, BfR

14:15-15:00
Zusammenfassung, offene Fragen und Gruppendiskussion:
– Feature requests
– Schnittstellen mit anderer Software
– Weitere Analysen, gemeinsame Fallstudie
– Feedback

15:00-15:10
Ausblick zur weiteren Zusammenarbeit und Schlusswort
BVL, BfR, EFSA