Results of the pilot project on SSD2 implementation

Transcription

1 EXTERNAL SCIENTIFIC REPORT APPROVED: 23 November 2016 doi: /sp.efsa.2016.en-1128 Results of the pilot project on SSD2 implementation Roberta Ion, Ioana Neghirla, Iulian Paraian National Sanitary Veterinary and Food Safety Authority (NSVFSA) - Romania Abstract The present document represents the final report created by the team of the National Sanitary Veterinary and Food Safety Authority and Gama IT to address the task 4 from the project on the implementation of SSD2 in the frame of the electronic transmission of harmonised data collection of analytical results to EFSA. European Food Safety Authority, 2016 Key words: Mapping, standard terminologies, software, data models, data collecting, validation, electronic transmission, LIMS, SSD1, SSD2, Zoonoses Question number: EFSA-Q Correspondence: data.collection@efsa.europa.eu EFSA Supporting publication 2016: EN-1128

2 Disclaimer: The present document has been produced and adopted by the bodies identified above as author(s). This task has been carried out exclusively by the author(s) in the context of a contract between the European Food Safety Authority and the author(s), 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: Ion R., Neghirla I., Paraian I., Results of the pilot project on SSD2 implementation. EFSA supporting publication 2016:EN pp. doi: /sp.efsa.2016.en ISSN: European Food Safety Authority, 2016 Reproduction is authorised provided the source is acknowledged. 2 EFSA Supporting publication 2016: EN-1128

3 Summary The project Pilot project on the implementation of SSD2 in the frame of the electronic transmission of harmonized data collection of analytical results to EFSA had the objectives to test whether the SSD2 is a suitable and effective tool for the reporting data to EFSA in different data collection domains, in response to the EFSA public tender OC/EFSA/DCM/2013/05. NSVFSA developed a LIMS Automated Export System (LIMS AES) to export data from the Romanian national data repositories in compliance with the EFSA data models and control terminologies for Zoonoses data models and SSD1. This pilot project extended the LIMS AES for compliance with SSD2 standard and also targeted the submission of the datasets via EFSA s DCF in XML transmission formats and verification of the data transmission. To achieve an automatic electronic transmission system for XML files, it was necessary to collect data in the format specified by EFSA. This was achieved through the existing LIMS applications from each SVFSL (Sanitary Veterinary and Food Safety Laboratory) and aggregating all the national data into one central data repository. At the moment of project start, in Romania NSVFSA owned a national integrated system based on a LIMS application at laboratories level and a central application at national authority level. In this project we extended the exporting system over the current national wide LIMS system and not as a separate application. The objective was to enter data only once and be available for any type of report is needed. As a final result of the project, the data files exported were compliant with the data models, with the standard terminologies and with the validation rules as defined by EFSA. 3 EFSA Supporting publication 2016: EN-1128

4 Table of contents Abstract... 1 Summary Introduction Background and Terms of Reference as provided by the requestor Data and Methodologies Software and tools used and/or developed Terminology mapping software components Product Types mapping to FoodEx2 (base categories) Analytical method mapping Developing LIMS components Submitting compliant datasets to EFSA Verifying the data transmission operability and testing the system Experts training and review Assessment/Results Challenges encountered in migrating data structure from SSD1 to SSD2 in the national data repositories Conclusions Recommendations Glossary [and/or] Abbreviations EFSA Supporting publication 2016: EN-1128

5 1. Introduction 1.1. Background and Terms of Reference as provided by the requestor This contract was awarded by EFSA to: National Sanitary Veterinary and Food Safety Authority Contractor/Beneficiary: National Sanitary Veterinary and Food Safety Authority/EFSA Contract title: Pilot project on the implementation of SSD2 in the frame of the electronic transmission of harmonised data collection of analytical results to EFSA Contract number: OC/EFSA/DCM/2013/05 In 2010 the SSD Guidance Document10 and the Guidance on Data Exchange (GDE)11 were published defining a standard format to transmit chemical occurrence analytical data in food and feed samples to EFSA. These guidance documents describe the data model and data interchange protocol12 for reporting the results of laboratory tests on food and feed samples in several food domains (contaminants, pesticides, etc.). Since 2010, the use of the SSD has been fully implemented and used in the national competent authorities and laboratories in 27 Member States and two EFTA countries (Iceland and Norway) involved in the pesticide monitoring data collection. In addition to the general SSD Guidance Document mentioned above, an EFSA Guidance Document on the use of the SSD specific for pesticide data reporting13 has been produced and is reviewed on a yearly basis. A Working Group on SSD Extension (WG-SSD2) was established in 2012 to extend the SSD to include zoonotic agents in food and animals, antimicrobial resistance and food additives, and to provide a framework for the collection of harmonised analytical measurement data on chemical and microbiological contaminants in different matrices (e.g. food, feed, animals, water, environmental samples, food contact materials). The amended standard proposed by the working group WG-SSD2 is called Standard Sample Description version 2 (SSD2). The draft amended standard is included in the call documentation (Annex 7). Since SSD is already used for submitting pesticide residue monitoring data to EFSA, the impact of switching from SSD1 (i.e. the existing version of the SSD data model) to SSD2 needs to be tested before the new format is presented to the SCoFCAH for taking note according to Comitology procedures. After evaluating the definition of the draft harmonised specific requirements for SSD2, our team was able to design the data extraction process and the automatic conversion in SSD2-XML data file. The expected outcome and deliverables of the project were the following: 1. a. Creation of the Draft harmonized specific requirements for SSD2 by amending the existing specific requirements using SSD2 data elements and terminologies: a. Use of the EFSA Standard Sample Description for the reporting of data on the control of pesticide residues in food and feed according to Regulation (EC) No 396/2005 b. Specific requirements for chemical contaminants data submission c. Call for food additives usage level and/or concentration data in food and beverages intended for human consumption 5 EFSA Supporting publication 2016: EN-1128

6 d. Data dictionaries/guidelines for reporting data on zoonosis, antimicrobial resistance and food-borne outbreaks using the EFSA Data models for the Data Collection Framework (DCF) in the Reporting Year b. Pilot of the reporting requirements proposed in the Draft harmonized specific requirements for SSD2 (deliverable 1a) through automatically generated data transmissions in SSD2 in The same data will also be transmitted in parallel using the current standards. 2. Design and implement the data extraction process performed from the National Database. a. Data structure mapping between the LIMS national database data elements and the SSD2 data elements; b. Terminology mapping between the LIMS national controlled terminologies and the SSD2 terminologies; 3. Pilot data submission in the following data domains: a. Biological monitoring b. Pesticide residues c. Chemical contaminants d. Food additives 4. Report on SSD2 pilot results 6 EFSA Supporting publication 2016: EN-1128

7 2. Data and Methodologies In 2014 National Sanitary Veterinary and Food Safety Authority started the pilot project on the implementation of SSD2 in the frame of the electronic transmission of harmonised data collection of analytical results to EFSA in the public tender OC/EFSA/DCM/2013. The project is based on the LIMS Automated Export System that was built as a system to export data from the Romanian national data repositories in compliance with the EFSA data models and control terminologies. In order to achieve an automatic electronic transmission system for XML files in SSD2 format, it was necessary to collect data that contained the specific fields in information requested by EFSA. This was achieved through the existing LIMS applications from the 41 regional SVFSL (Sanitary Veterinary and Food Safety Laboratory) and the 2 national reference institutes IDAH and IHVPH. Even if some of the data requested by EFSA reporting system exists in LIMS databases, it was necessary to map LIMS terminologies with EFSA and also adding new fields, according to the specific SSD2 model. The following phases were done in this project: 1. Analysing and designing. 2. Data structure mapping a. LIMS structure needed to be upgraded b. Product FoodEx2 Coding Interface c. LIMS mapping d. Data fields mapping 3. Terminology mapping a. Analytical method mapping b. Parameters mapping c. Sample type mapping d. Product types SSD1 mapping e. Animal types SSD1 mapping 4. Pilot data submission in the following data domains: Biological monitoring, Pesticide residues, Chemical contaminants, Food additives 7 EFSA Supporting publication 2016: EN-1128

8 In the analysis and design phase we identified all the necessary fields that needed to be added to the current LIMS database tables and also the new terminologies tables that need to be added from SSD2. We also identified and gathered all the business rules that are needed to be implemented in the system in order to export correct data. Analysing the method of collecting data, which was used by NSVFSA, there were revealed some necessities to improve the system regarding Data structure mapping and Terminology mapping. The outcome and deliverables of the project were the following: 1. The Draft harmonised specific requirements for SSD2 data transmission as specified in task 1a. 2. Data files (manually or automatically generated) in SSD2-XML format transmitted to the EFSA Data Collection Framework (DCF) as described in task 1b. 3. The Data standardisation document as described in task Data transmitted to the EFSA Data Collection Framework (DCF) according to SSD1 XML format for chemicals or other existent standard format for microbiological data as specified in task Data transmitted to the EFSA DCF according to the SSD2-XML file format as specified in task Deliver a draft version of the Report on SSD2 pilot results as described in task 4. Current document 7. Deliver the final version of Report on SSD2 pilot results described in task 4, addressing EFSA comments on the draft report Software and tools used and/or developed In 2014, when this project started, in Romania all laboratory tests were stored in LIMS databases at local laboratory level and all data was aggregated in a national repository at central level. The data was collected via automated nightly tasks from all the 42 counties of Romania. Analysing the method of collecting data, which was used by NSVFSA, there were revealed some necessities to improve the system regarding Data structure mapping and Terminology mapping Terminology mapping software components Current LIMS database tables needed to be upgraded with fields that were added in SSD2 and according with the specified XML schema type. 8 EFSA Supporting publication 2016: EN-1128

9 Product Types mapping to FoodEx2 (base categories) Current database contained assigned codes and controlled terminology for the product types used in laboratories and mapping with SSD1 terminology. The improvements were regarding the import of EFSA FoodEx2 terminology and mappings with the current LIMS product types database and the development of a mapping component and user interface: Figure 1: Product types and FoodEx2 mapping 9 EFSA Supporting publication 2016: EN-1128

10 The same mapping processes were used EFSA FoodEx2 terminology mapping with the current LIMS animal types database and the development of a mapping component and user interface: Figure 2: Animal types and FoodEx2 mapping 10 EFSA Supporting publication 2016: EN-1128

11 Part of the new LIMS structure we integrated the new Product FoodEx2 Coding interface. Using this interface at analysis request level, by the persons responsible for sampling, will allow a high grade of accuracy in describing the products using the FoodEx2 coding standard. Figure 3: Product description FoodEx2 interface 11 EFSA Supporting publication 2016: EN-1128

12 Figure 4: Product description FoodEx2 interface contextual menu Figure 5: Product description FoodEx2 interface adding descriptions 12 EFSA Supporting publication 2016: EN-1128

13 Analytical method mapping Current database contained assigned codes and controlled terminology for the analytical methods used in laboratories. The improvements were regarding the import of EFSA analytical methods terminology in LIMS database and the development of a mapping component and user interface. Figure 6: Analytical methods mapping Figure 7: SSD2 terms searching and mapping tool for analytical methods 13 EFSA Supporting publication 2016: EN-1128

14 LIMS database contained assigned codes and controlled terminology for the sample types used in laboratories. The improvements were regarding the import of EFSA sample type s terms in LIMS database and the development of a mapping component and user interface. Figure 8: Sample types mapping Figure 9: SSD2 terms searching and mapping tool for sample types 14 EFSA Supporting publication 2016: EN-1128

15 LIMS database contained assigned codes and controlled terminology for the testing parameters used in laboratories. The improvements were regarding the import of EFSA SSD2 Parameters terminology in LIMS database and the development of a mapping component and user interface. Figure 10: Testing parameters and SSD2 parameters Figure 11: SSD2 terms searching and mapping tool for SSD2 parameters 15 EFSA Supporting publication 2016: EN-1128

16 Error checking and correction was done manually by a task responsible, selected from the NSVFSA staff. The improvements were regarding the automatically checking of the items' coding or correlation and data validation based on EFSA rules. In this context, the grant proposed by EFSA was a good opportunity for initiating a project for improving the national database repository in the domains of food additives, chemicals, pesticides and microbiological testing in Romania. Moreover, thanks to EFSA guidance, it was possible to organize information in compliance with the SSD2 Data Models and EFSA's requirements Developing LIMS components SSD2 is the reporting component for isolate-based antimicrobial data resistance. Users responsible for reporting have the option to load results from LIMS aggregated database and then review and validate each row. If any validation errors or warnings are found in data model, the system will automatically generate an excel file with all the validation messages and the user can open it and review the errors. After validating the data, user can chose to automatically transmit the data through web services in EFSA database. Figure 12: Fig. 3 SSD2 reporting component 16 EFSA Supporting publication 2016: EN-1128

17 2.3. Submitting compliant datasets to EFSA For the automated transmission process we implemented the following procedures as described in GDE: Authentication: The application will allow each user to configure their own EFSA credentials used for submitting data in the DCF framework. The data message will be authenticated using these credentials. After the authentication the user must validate the data to be transmitted. The system has implemented a set of business rules to validate the data to be transmitted. If the data passes all the validation rules it will change the status to Validated and now it can be submitted. If the data contains validation errors, the user must check and correct the fields that are invalid. When sending data with web services the system automatically creates the SOAP message that contains all the data necessary information to be accepted by the EFSA web services (header information, authentication information, dataset information, etc.) as described in the web service description (WSDL) provided by EFSA. After sending the data message the messageid returned in the Receipt message will be stored in the database. After a time that can be configured in the application (minimum 5 minutes), the system will automatically try to download the acknowledgement message. If the acknowledgement message is not ready, the system will wait until the acknowledgment message is ready. If the acknowledgment message is ready, it will be downloaded and the datasetids will be stored in the database. If the acknowledgment message contains errors, the user will correct the invalid fields and the dataset containing those fields will be retransmitted to EFSA. Figure 13: LIMS AES to DCF transmission protocol 17 EFSA Supporting publication 2016: EN-1128

18 2.4. Verifying the data transmission operability and testing the system As part of verifying the data transmission operability and testing the system of automated electronic transmission system (web service) for XML files we covered the two sub-tasks - We ve conducted a preliminary test of the transmission protocol with dummy files provided by EFSA; - We ve conducted a data submission test: exporting the data from the LIMS national data repositories, codified and transmitted them to EFSA in electronic format in a Test database in accordance with the data models defined by EFSA. - Data submission tests were performed for each data category in Zoonoses databases. The following XML files were uploaded in DCF: Figure 14: AMR dataset submission 18 EFSA Supporting publication 2016: EN-1128

19 Figure 15: Prevalence dataset submission 19 EFSA Supporting publication 2016: EN-1128

20 Figure 16: Additives dataset submission Figure 17: Chemical contaminants dataset submission 20 EFSA Supporting publication 2016: EN-1128

21 Figure 18: Pesticide dataset submission 2.5. Experts training and review The Project Team organized training sessions for the staff involved in collecting, mapping and transmitting the data in SSD2 format. At the session, 6 persons were trained. The training session had two parts: a general presentation of the database and the responsibilities of the county structures regarding the data input, and a handson session in order to train people for reviewing, introducing data into the database and to transmit them. Each report component was presented and used in practical work. The participants received individual usernames and passwords to access the reports EFSA Supporting publication 2016: EN-1128

22 3. Assessment/Results The project objectives planned were successfully achieved. The data files exported were compliant with the data models, with the standard terminologies and with the validation rules as defined by EFSA. Table 1: Data domain coverage Country Data domain Area of competency Transmitted data Pesticides Residues (under Regulation (EC) No 396/2005) analysis of pesticides residues under Regulation (EC) No 396/ records Contaminants (under Regulation (EC) 1881/2006 ); analysis of mycotoxin, heavy metal in food of animal origin, nitrate in vegetables 1793 records ROMANIA Food Additives (under Regulation (EC) 1333/2008); Analysis of additives in food: Sunset yellow, Tartrazine, Amaranth, Erythrosine B, Glutamic acid, Benzoic acid, Sorbic acid, Malic acid, Tartaric acid, Sulfates, Sulphur dioxide, Sodium nitrite, Saccharin, Acesulfame K, Aspartame, 3863 records Microbiological data (zoonoses, zoonotic agents and antimicrobial resistance under Directive 2003/99/EC) analysis of prevalence of Salmonella and Listeria in food and feed, analysis of prevalence of Trichinella, Campylobacter, Cronobacter, E. coli, Enterotoxina Stafilococica, Yersinia, Histamine in food,, or antimicrobial resistance (AMR) in food and feed, or food-borne outbreaks 1264 records on prevalence records on AMR 3.1 Challenges encountered in migrating data structure from SSD1 to SSD2 in the national data repositories While submitting data, we identified the following issues: - A few changes had an important impact, mainly the data model s clarity and consistency, such as: some existing element names and controlled terminology names have been changed; some new elements have been added; some elements have been removed or changed to compound elements and this is much harder for users to work in SSD2; - Because the data validation schema was not provided at least one year before data submission, some mandatory fields were missing. Because of this, the missing data had to be manually added and involved a lot of extra working time and effort. e.g.: Field B.04 could not be provided for data recorded before first half of the year 2014 because it was not a 22 EFSA Supporting publication 2016: EN-1128

23 mandatory field in our national system and it was not collected. It had to be manually filled by our teams. - While mapping values from SSD1 to SSD2, we identified deprecated values in SSD2 that prevent us from founding a correspondence between those. We mapped these values with some generic codes from SSD2. e.g.: When we tried to map PD09A ( Non-organic production ) value from PRODMD catalogue in order to use it for G.01 element, no similar match was found in SSD2 terminology catalogues. We considered the best match would be A07RV ( Farmed / cultivated / aquaculture ), so we mapped it to this value. - It was unclear at the beginning when to use quotes on compound fields for attributes with string values. We figured out we have to use quotes for free texts, but not for SSD2 codes, even if these are strings as well. e.g.: Chapter 2.1 from SSD2 documentation does not provide clear explanation regarding how attribute values should be formatted for compound types. We encountered errors when we reported attributes with text values and controlled terminology terms because we wrapped those values inside quotes. Later we figured out only text values required quotes, but not controlled terminology terms. Initially we reported N.06 values as sampanasses= J037A $com="carbendazim si benomil" and later we changed it to sampanasses=j037a$com="carbendazim si benomil". - We encountered large waiting times for data validation after submitting it to DCF. Each data modification led to one more DCF submission of the entire data collection and waiting for the entire validation summary. This validation could be improved by having a real-time validation tool that would be able to validate independent rows and not submitting it to the production data collections. - Another aspect we encountered with the validator was the errors limitation number to 100. Also, if a series of rows contained the same error, this error was repeating inside the validation summary for each of this error, preventing us to identify more than one error at a time. An improvement here would be to group the errors by type and send them all at once. - Information provided by data validator was unclear in many cases and we could not identify very well the rows where the errors occurred. 3.2 Experience gained in testing SSD2 After implementing this pilot project on SSD2 we gained a lot of experience in mapping and reporting our national repositories data in SSD2 format. Data structure was deeply understood and the benefits and flexibility of this new standard became obvious. We also learned to use FoodEx2 standard in order to transpose product and animal types to FoodEx2 terminology. To increase productivity, we developed an interface that allows users to achieve these codes using a friendlier interface by selecting required types and facets. With this tool we eliminate the need of the user to search the codes dictionaries which took a lot of time before. By assimilating this experience, we are able to store our data in SSD2 format and deploy future reports in shorter times and with better data quality. 3.3 Recommendations for EFSA on effectiveness and suitability of the SSD2 in the different domains 23 EFSA Supporting publication 2016: EN-1128

24 In order to facilitate optimum use of catalogs SSD2, especially "SSD_CAT_ANYLYMD" and "SSD_CAT_PARAM", we recommend splitting their fields or create a browser similar to that used for FoodEx2., with associated terms for the different areas of data collection. For users, it would be easier if the terms in these catalogs could be splitted in two separate lists or in a more facile way, eg. zoonoses and zoonotic agents separated from other fields (substance for pesticides, chemical contaminants in food), because usually the data reporter is a person from laboratory which is trained in specific field. To avoid generating validation errors and to facilitate the selection of terms by the users, in the catalogs should be valid only terms "validto" or "lastupdate". The SSD2 should be updated with the suggestive description of the specific requirements and for collection investigation data for food-borne outbreaks (the characteristics should be described using the domain-specific hierarchies). Supplementation of the following SSD2 catalogues with known terms, as described below, in order to avoid the selection of the terms "unknown" or "other", in some cases: LEGREF (pesticides, additives, contaminants): ILAC-G8:03/2009 Guidelines on the Reporting of Compliance with Specification - used for evaluate the results; SAMPMD (additives): The national procedure food sampling for sampling procedures developed by a national competent authority; ANLYMD (additives, contaminants): Ultra Performance Liquid Chromatography (UPLC) ; Optical emission spectrometers with inductively coupled plasma (ICP-OES)" and "Chromatography/high-resolution mass spectrometry (GC/HRMS)" should be added; LMTTYP (additives): Combined maximum limit according to Reg no. 1333/2008; RESEVAL (pesticide, additives, contaminants): It is not possible to state compliance, if the measurement result plus/minus the expanded uncertainty with a 95 % coverage probability overlaps the limit, it is not possible to state compliance or non-compliance, according to ILAC-G8:03/2009; The PARAM (additives) should be completed with the common Names E 651 for Monosodium glutamate, according to Reg no. 1333/2008. It would be easier for users if the terms in the "PARAM " catalog should be alphabetically ordered (toate domeniile). The fields resllwr, resulwr ; resval and "evallowlimit" for antimicrobial resistance (AMR) should have predefined values, as it was in the old list ZOO_CAT_FIXMEAS, in order to avoid typing mistakes and to provide better accuracy in the collection and validation of data EFSA Supporting publication 2016: EN-1128

25 NSVFSA 4. Conclusions For Romania it is necessary to continue developing such system for data collection to cover all the aspects regarding different data collection domains: zoonoses, antimicrobial resistance and food-borne outbreak data or specific requirements for chemical contaminants; additives and residues of pesticides data, in order to assure national reliable data for risk assessment within EFSA. Collection of terms and recording all relevant characteristics of a food item according to FoodEx2 it is quite difficult, not being a standardized system, but flexible and allowing the users to make their own assumptions when describing a product. For users, the time needed to create a full code is too long, the combination of facets is hardly, too much details to build into the facets. Training of inspectors responsible for providing information regarding sampling and product description according to Foodex2, necessary to cover all areas for data collection, remains the main concern of NSVFSA. 5. Recommendations In order to assure national reliable data for risk assessment with EFSA rules, technical support from EFSA in this direction will speed up the process of data collection EFSA Supporting publication 2016: EN-1128

26 NSVFSA Abbreviations EFSA NSVFSA IDAH IHVPH SVFSL DCF XML LIMS LIMS AES European Food Safety Authority National Sanitary Veterinary and Food Safety Authority Institute for Diagnosis and. Animal Heath Institute of Hygiene and. Veterinary Public Health Sanitary Veterinary and Food Safety Laboratory Data Collection Framework Extensible Markup Language Laboratory Information Management System LIMS Automated Export System 26 EFSA Supporting publication 2016: EN-1128