Implementation and testing of electronic submission in XML format of zoonoses, antimicrobial resistance and food-borne outbreak data for Estonia

Transcription

1 EXTERNAL SCIENTIFIC REPORT APPROVED: 10 November 2016 doi: /sp.efsa.2016.en-1114 Implementation and testing of electronic submission in XML format of zoonoses, antimicrobial resistance and food-borne outbreak data for Estonia Ministry of Rural Affairs of the Republic of Estonia Abstract The present report describes the work carried out during the project OC/EFSA/DATA/2014/01 LOT 1 CT03 : building a system to export data from the national data repositories in compliance with the EFSA data models and controlled terminologies; submitting datasets via EFSA's DCF in XML transmission format and verifying the data transmission operability. The main objective of the project was the development and testing of national electronic system that will be able to transmit collected data on zoonoses in XML format electronically to EFSA. The reported data will be processed so that it will be compatible with EFSA s data models and Business rules. European Food Safety Authority, 2016 Key words: Zoonoses data, JVIS, Data Models, Data submission, EFSA, XML transmission Question number: EFSA-Q Correspondence: DATA.ADMIN@efsa.europa.eu EFSA Supporting publication 2016:EN-1114

2 Disclaimer: The present document has been produced and adopted by the bodies identified above as authors. This task has been carried out exclusively by the authors in the context of a contract between the European Food Safety Authority and the authors, awarded following a tender procedure. The present document is published complying with the transparency principle to which the Authority is subject. It may not be considered as an output adopted by the Authority. The European Food Safety Authority reserves its rights, view and position as regards the issues addressed and the conclusions reached in the present document, without prejudice to the rights of the authors. Suggested citation: Ministry of Rural Affairs of Estonia, Veterinary and Food Board, Helmes AS, Implementation and testing of electronic submission in XML format of zoonoses, antimicrobial resistance and food-borne outbreak data. EFSA supporting publication 2016: EN pp. doi: /sp.efsa.2016.en-1114 Reproduction is authorised provided the source is acknowledged. ISSN: European Food Safety Authority, EFSA Supporting publication 2016:EN- 1114

3 Summary The present final report on Implementation and testing of electronic submission in XML format of zoonoses, antimicrobial resistance and food-borne outbreak data and updating the historical datasets is the final deliverable prepared by the Ministry of Rural Affairs (former Ministry of Agriculture) of the Republic of Estonia in cooperation with Veterinary and Food Board and Helmes AS company in the scope of the EFSA procurement project OC/EFSA/DATA/2014/01, Lot 1 Building a system to export data from the national data repositories in compliance with the EFSA data models and controlled terminologies; submitting datasets via EFSA s DCF in XML transmission format and verifying the data transmission operability. The aim of the project was to develop a system able to export data from the Estonian national data repositories in compliance with the EFSA data models and control terminologies. The project was also targeting the submission of the datasets in XML format via EFSA s DCF and verifying the data transmission operability. The data files exported are compliant with the data models, with the standard terminologies and with the validation rules as defined by EFSA. The staff involved in the activity of sampling and recording data at every level (local or national) are trained in operating the software for data collection on zoonoses, antimicrobial resistance and foodborne outbreaks. 3 EFSA Supporting publication 2016:EN-1114

4 Table of contents Abstract... 1 Summary Introduction Background and Terms of Reference as provided by the requestor Additional information Data and Methodologies Data Analysis process deliverables Development of deliverables Inserting samples protocol data into JVIS Inserting analysis results data into JVIS using JVIS user interface Inserting analysis results data into JVIS using Web service Data mappings (JVIS specific pick lists versus EFSA pick lists) Generating analysis results XML files for EFSA Uploading XML file to DCF environment Assessment/Results Conclusion and recommendations Abbreviations EFSA Supporting publication 2016:EN-1114

5 1. Introduction In Estonia the Veterinary and Food Board (VFB) is responsible for collecting and reporting the data on zoonoses, zoonotic agents, animal population, antimicrobial resistance and food-borne outbreaks to EFSA. VFB collects on an annual base all the relevant statistical data from a number of different authorities namely the state Veterinary and Food laboratories, the Health Board, the Estonian Agricultural Registers and Information Board. VFB is carrying out its tasks under the government of the Ministry of Rural Affairs and both authorities are working in a close cooperation. The IT budget and IT projects are the responsibility of the Ministry of Rural Affairs. It was decided to apply for EFSA grant for adding additional functionalities to the national database (named JVIS official control database). JVIS is used by the different institutions that are working under the government of the Ministry of Rural Affairs: mainly Veterinary and Food Board and its county departments and different laboratories. The aim of the JVIS database is to provide a central platform for gathering supervision data. Also clients access the database via central Portal where they can apply different applications. The officials review and manage the applications and decide whether the applicant will get a permission (to deal with different kinds of food or animal feed etc) or not. During the official supervision process, officials perform official control of the companies and take samples. The official control part of the JVIS is in use by the Veterinary and Food Board officials since July In the frames of the contract JVIS has been developed so that it will be easy to export all needed data from the national database to the EFSA templates in compliance with the EFSA data models and control terminologies; the data is submitted to EFSA via DCF in XML format Background and Terms of Reference as provided by the requestor This contract was awarded by EFSA to: Ministry of Rural Affairs (former Ministry of Agriculture), Lai St 39/41, Tallinn, Estonia, pm@agri.ee Contractor: Ministry of Rural Affairs of the Republic of Estonia, Lai Street 39/41, Tallinn, Estonia Contract title: Implementation and testing of electronic submission in XML format of zoonoses, antimicrobial resistance and food-borne outbreak data and updating the historical datasets, Lot 1 Contract number: OC/EFSA/DATA/2014/01 LOT 1 CT Additional information The areas of activity of the Ministry of Rural Affairs are drafting and realisation of national agricultural development plans and effectuation of corresponding measures, regulation of activities related to the processing of agricultural products, agricultural market regulation, the national stockpiles of basic grain seed and food grains, food control and supervision, plant protection, veterinary medicine, animal and plant breeding, land improvement. The Ministry provides agricultural research, education and training, and prepares relevant draft legislation. 5 EFSA Supporting publication 2016:EN-1114

6 As provided by 29 3 (1) of the Infectious Animal Disease Control Act, Ministry of Rural Affairs delegated the monitoring of zoonoses to the Veterinary and Food Board. Veterinary and Food Board is a governmental agency carrying out its tasks under the government of the Ministry of Rural Affairs, functions as a supervising body and sees to that the requirements stipulated by the legislation that governs veterinary, food safety, market regulation, animal welfare and farm animal breeding are followed and executes supervision over fulfilment of these requirements and applies enforcement by state pursuant to the procedures and in the amount prescribed by law. The Veterinary and Food Board cooperates with the Health Board regarding epidemiology of zoonoses transmissible to humans. The requirements on organisation of zoonoses monitoring are laid down in the Regulation No 79 of the Minister of Agriculture (today Minister of Rural Affairs) Requirements on Monitoring of Zoonoses, which is based on Directive 2003/99/EC of the European Parliament and of the Council of 17 November 2003 on the monitoring of zoonoses and zoonotic agents. The purpose of this Regulation is to ensure that zoonoses, zoonotic agents and related antimicrobial resistance, food borne outbreaks are properly monitored, to enable the collection of the information necessary to evaluate relevant trends and sources. The Veterinary and Food Board is collecting the data on zoonoses, zoonotic agents, animal population, antimicrobial resistance and food-borne outbreaks in Estonia. It collects on an annual base all the relevant statistical data from a number of different authorities namely the state Veterinary and Food laboratories, the Health Board, the Estonian Agricultural Registers and Information Board. The task of the Veterinary and Food Board is to gather, evaluate and submit data through the zoonoses web application reporting system or Data Collection Framework to EFSA within the predefined deadline. Ministry of Rural Affairs, through its Veterinary and Food Board has technical and professional capacity to report and submit zoonoses, antimicrobial resistance and food-borne outbreaks data to EFSA in accordance with the Directive 2003/99/EC. 2. Data and Methodologies 2.1. Data The following data categories were involved in the frames of the project: - Sample based prevalence data - Isolate-based antimicrobial resistance data - Animal populations data - Disease status data on tuberculosis and brucellosis - Food-borne outbreak data - Text form data An additional functionalities were developed for national database JVIS in order to make it possible to collect the data, to perform different kinds of data queries and to make it easier to export the data from the national database into EFSA s data models and codify them based on EFSA s standard terminologies (pick lists). The system interface between JVIS and Lab system was developed. There was careful examination of the data models, standard terminologies, validation rules and the data dictionaries that were worked out by EFSA, so the data submitted to DCF comply with all requirements. Also the changes in national terminology were defined and performed. In addition, the data collection procedure was redesigned. The additional functionalities were developed and are used at national level: - easy to use user-interface for the end user 6 EFSA Supporting publication 2016:EN-1114

7 - record all the data that are required by EFSA so the reports submitted to EFSA to be complete - flexible and able to absorb potential changes in regulations or technological and scientific developments Analysis process deliverables The main deliverables of the process analysis were already listed in the interim report. During the execution of the project (implementation and testing) these deliverables were updated. The following is the final list of the analysis deliverables: - Physical data model - tables that hold sample analysis protocol and analysis results data - Graphical HTML prototype (JVIS system screen forms) - inserting samples protocol data and samples analysis results data into JVIS system. - Specification of the web service - web service in JVIS for receiving sample analysis results from VTL labsystem: Process flows Description of the classifiers used in JVIS system and VTL labsystem. Description of the synchronisation of the classifiers. Description of data elements Validation rules in JVIS - Requirements and business rules descriptions for the developer. The detailed specifications are held in the Ministry of Agriculture s JIRA task management system and these are written in Estonian. The specification relies on the physical data model and the graphical HTML prototype Development of deliverables Inserting samples protocol data into JVIS The functionality in JVIS was developed according to the analysis specification. Figure 1 and 2 describe the main screen forms that officials use to insert samples data. Figure 3 and 4 describe the PDF file that is generated from the samples protocol data. This pdf file is also sent automatically through JVIS to VTL labsystem. 7 EFSA Supporting publication 2016:EN-1114

8 Figure 1: Main screen form EFSA Supporting publication 2016:EN-1114

9 Figure 2: Main screen form EFSA Supporting publication 2016:EN-1114

10 Figure 3: PDF page EFSA Supporting publication 2016:EN-1114

11 Figure 4: PDF page Inserting analysis results data into JVIS using JVIS user interface The analysis results may be sent to Veterinary and Food Board through different channels. Some laboratories send the results using ordinary post (paper). The official can then manually insert analysis results data into JVIS using JVIS user interface. The more favoured alternative is to use the web service (described in the next chapter) EFSA Supporting publication 2016:EN-1114

12 Figure 5. describes the main screen form that is used to insert the analysis results into JVIS system. Figure 6. describes the screen form where all the analysis results are listed. The official uses the same screen form for inserting assessments (figure 7.) for all the analytical parameter (for example for Microbiology - Bacillus cereus). Figure 5: Screen form that is used to insert the analysis results into JVIS system 12 EFSA Supporting publication 2016:EN-1114

13 Figure 6: Screen form where all the analysis results are listed Figure 7: Screen form for inserting assessments 13 EFSA Supporting publication 2016:EN-1114

14 Inserting analysis results data into JVIS using Web service When the Samples Protocol (PDF file) is sent by JVIS to VTL labsystem then the work in the laboratory can begin. In VTL laboratory the lab workers insert the analysis results data for specific analytical parameter ordered by the Veterinary and Food Board. The results data is saved in VTL system and also sent to JVIS system using web service. Example of a message is shown in figure h. JVIS validates the incoming message and applies all the necessary business rules. When there are errors in the message, then a specific error message is sent back to VTL system. If the message and data is correct then the analysis results are saved into JVIS system. The results from VTL systems can then be seen in JVIS system (in figure 6.), also an involved official from Veterinary and Food Board will get an e- mail message that analysis results from VTL system have been inserted into JVIS. The official can then start assessment of the results. Figure 8: XML file Data mappings (JVIS specific pick lists versus EFSA pick lists) Data mapping is done in JVIS through JVIS administrator menu. All the lists that are used in JVIS (countries, analysis parameters etc) can be administered through JVIS classifier management. Figure 9. shows a list of food groups that are used in JVIS system. A proper EFSA pick list item s code must 14 EFSA Supporting publication 2016:EN-1114

15 be attached to each of the JVIS pick list item. Figure 10. shows how EFSA code A025481A (from EFSA picklist ZOO_CAT_MATRIX) is linked to a specific JVIS pick list item. Figure 9: List of food groups Figure 10: Link to EFSA picklists 15 EFSA Supporting publication 2016:EN-1114

16 Generating analysis results XML files for EFSA The generation of XML files (that are later uploaded to DCF - see next chapter) is done in JVIS database using standard PostgreSQL XML functionality. The XML generation procedure does the following: - Reads in the specific parameters (period, type of analysis data) - Queries the specific analysis results data from the database. The query already returns the data that is EFSA specific (meaning that it returns the EFSA specific codes that are configured using screen form shown in figure j). - Constructs an XML file according to the schema file (SSD2_schema.xsd) NB! If the structure and business rules for reporting data to EFSA will change in the future, then all the mappings and logic behind the generation of the XML files must be revalidated. Any changes in the structure of the XML also mean that the code that is used for XML generation must be updated accordingly. At the moment all this functionality is implemented in database level using procedures written in pgplsql procedural language. Figure 11. shows an example of the generated XML file. Figure 11: Example of the generated XML file 16 EFSA Supporting publication 2016:EN-1114

17 Uploading XML file to DCF environment The generated XML files (containing the data) are manually uploaded to DCF ( This is done by the official who is responsible for reporting data to EFSA (data provider). If the uploaded XML files are in incorrect format or in conflict with some business rule, then the mappings and/or the analysis results data in JVIS must be reviewed and corrected by the data provider. 3. Assessment/Results The project objectives were successfully achieved and 2016 data was submitted to EFSA using final automatic system that didn t rely on the maintenance of the EFSA Excel mapping tool. The data submitted to EFSA was compliant with the data models, standard terminologies and business rules EFSA Supporting publication 2016:EN-1114

18 4. Conclusion and recommendations We would like to thank EFSA for help and support provided to us in the frames of the contract. 1. While we understand that documentation for the data collections is updated every year and published as agreed by the Network on Zoonoses Data Collection at the end of January each year, EFSA shall better communicate updates to the documentation not directly related to the current reporting season such as those that was related to the procurement on sample based prevalence and possibly have the documentation ready well before the launch of the procurement. 2. We hope that in the future we could agree with the Network to make the documentation for all data collections available a year in advance rather than on the same year. 3. We recommend to review the report Guidelines for reporting sample based data on prevalence in accordance with Council Directive 2003/99/EC, SSD2 data model. 4. Due to the diagnostic specificity of Trichinella spp. and Ehinococcus spp. there is a need to review the type of data that should be reported on Echinococcus and Trichinella. Investigations on Echinococcus are not registered in the national database (post-mortem control is performed as visual inspection, samples are taken and laboratory investigation is performed only in suspect cases), so this data could not be extracted from the national database. It will be time consuming procedure to report all the examined carcases manually at sample/animal based level, as it means the manual reporting of data rows (in Estonia the number of susceptible slaughtered animals is not so big due to the country s small size). Moreover in 99,99% the results are negative in Estonia. Trichinella analyses should be performed in all animals slaughtered with exception of pigs raised under controlled housing conditions. Trichinella examination is performed as following: in most cases it is a pooled sample, which consists of 10 sub-samples taken from 10 animals. When this pooled sample is positive for Trichinella 2 -samples (5 animals in each sample) are made and analysed. When one of these samples is positive, the individual samples are analysed. In case the samples are negative, we have no data at animal level. We have statistics on the number of animals tested/slaughtered, but the number of samples tested is not the same. It is not possible to report data at animal s level. Moreover in Estonia all farmed animals are negative, so we think that there is no reason for reporting sample based data on Trichinella. 5. We propose to review the SSD2 data model regarding reporting the data on method used for Listeria monocytogenes in food. It is mandatory to report data on method used in 3 different columns: anmethrefid, anmethtype, anmethcode-meth. The data is mostly the same. 6. In the future the volume of data reported to EFSA will decrease, as some clinical investigations, investigations of zoo and farm animals on the initiative of the owner and investigations of wild animal s meat for Trichinella presence are not registered in the national database JVIS. This data could not be automatically reported, as the data on samples is only present in laboratory system EFSA Supporting publication 2016:EN-1114

19 7. There are difficulties with reporting of Salmonella spp. data according to the Commission Decision 218/2014. In Estonia our authority collects the information on samples taken by food business operators (Article 2 (4) G.Salmonella (b) of the Decision 2018/2014). This data is not registered in the national database as these samples are taken and analysed on the initiative of the food business operator and the samples are analysed in whatever laboratories (incl. private laboratories). 8. There is a need to decide what data and at what level (sample, herd/flock) should be reported on animals as each country can interpret it individually and the data will not be comparable between countries. Abbreviations EFSA DCF VFB VTL JVIS XML European Food Safety Authority Data Collection Framework Veterinary and Food Board Veterinary and Food Laboratory Official Control Database Extensible Markup Language SSD2 Standard Sample Description ver EFSA Supporting publication 2016:EN-1114