TECHNICAL REPORT submitted to EFSA. Implementation of Electronic Transmission of Chemical Occurrence Data (CFP/EFSA/DATEX/2010/01) in Latvia 1

Transcription

1 TECHNICAL REPORT submitted to EFSA Implementation of Electronic Transmission of Chemical Occurrence Data 1 Prepared by Dr Dace Vilcane, Assessment and Registration Agency, PVD and Atis Saule, PVD Abstract The present report describes the results, resources used, benefits gained and challenges met in restructuring the chemical occurrence data system of Food and Veterinary Service of Latvia that forms national data bank for chemical contaminants and pesticides in order to implement and test an electronic system for the transmission of chemical occurrence data to European Food Safety Agency according to standards. Summary To support EFSA overall objective, to collect standardized data for risk assessment purposes, the Food and Veterinary Service of Latvia (PVD) has implemented and tested an electronic system for collecting, transforming and transmitting sample based results on food chemical occurrence data to EFSA. The objective of the project call is to implement this system according to EFSA standards. During the project test phase PVD has successfully transmitted occurrence data exported from the Integrated Database (IDB) to the EFSA Data Collection Framework (DCF), considering the EFSA standardization rules. The result of this exercise is that the project facilitates the harmonization of data collection and processing, with the consequence of a positive impact on the quality of data produced by the national laboratories reflecting also on the quality and efficiency of the risk assessments produced using these data. Key words: Chemical occurrence data, Residues, Data transmission, XML, Data Collection, Framework, Standard Sample Description, EFSA, PVD 1 (Question No EFSA-Q ). Accepted for Publication on 1 February The present document has been produced and adopted by the bodies identified above as author(s). In accordance with Article 36 of Regulation (EC) No 178/2002, this task has been carried out exclusively by the author(s) in the context of a grant agreement between the European Food Safety Authority and the author(s). The present document is published complying with the transparency principle to which the European Food Safety Authority is subject. It may not be considered as an output adopted by EFSA. EFSA reserves its rights, view and position as regards the issues addressed and the conclusions reached in the present document, without prejudice to

2 Table of Contents Abstract... 1 Summary... 1 Table of Contents... 2 Background... 3 Terms of reference... 3 Acknowledgements... 3 Contract/grant number: CFP/EFSA/DATEX/2010/01 Introduction and Objectives... 3 Introduction and Objectives... 4 Materials and Methods Deliverables Implementation... 6 Results... 8 Discussion Assessment of resources needed and challenges encountered in restructuring the national data repositories according to the SSD A benefit analysis Conclusions and Recommendations References Glossary / Abbreviations

3 Background Data collection is an important task of EFSA and a fundamental component of risk assessment (Articles 22 and 23 of Regulation EC No 178/2002). As a result, EFSA requests and receives an increasing volume of data from wide range of providers in support of the scientific mission. The project realization is strictly addressed to the National Competent Authorities for the collection of chemical occurrence data which are included in the list adopted by EFSA Management Board according to Article 36 of Regulation EC No 178/2002. In order to achieve the high level of harmonization and degree of detailed elaboration regarding to the chemical occurrence data for the transmission, EFSA has prepared a certain tool of standardization: Standard Data model (SM) or the Standard Sample Description model (SSD). Terms of reference Electronic Transmission of Chemical Occurrence Data, Call for proposals CFP/EFSA/DATEX/2010/01. The expected outcome and deliveries of the project according to requirements are: (1) List or lists of validation rules, (2) Document D1 Data standardization, (3) Three data transmissions to EFSA, and (4) Document D3 Final Report Acknowledgements This grant was awarded by EFSA to: Food and Veterinary Service of Republic of Latvia Peldu Street 30, Riga, LV-1050, Latvia Grant title: Electronic Transmission of Chemical Occurrence Data Grant number: CFP/EFSA/DATEX/2010/01 3

4 Introduction and Objectives INTRODUCTION The project Electronic Transmission of Chemical Occurrence Data (CFP/EFSA/DATEX/2010/01) has been financially supported by EFSA according to Article 36 of the Regulation EC No 178/2002. The outcome of the project is to assist EFSA to collect, collate, analyze and summarize relevant scientific and technical data in the fields within its mission. In scope of the project, selected data from the national monitoring data system of PVD have been made available for transmission to EFSA in accordance with EFSAs SSD. Chemical contaminant groups transmitted to EFSA during the project phase are: 1) Organic contaminants (PCBs, Dioxins, Halogenated Hydrocarbons like 3-MCPD, Acrylamide, PAHs); 2) Mycotoxins (Aflatoxins, Fusarium Toxins, Ochratoxin A, Patulin); 3) Chemical elements and derivatives (Heavy metals and derivatives, Nitrogen and derivatives). During the project test phase, data from three selected areas have been transmitted to EFSA successfully by using interaction of IDB and DCF. It is important to stress that the IDB that has been developed and adopted in scope of the projects, was successfully utilized for data on pesticide residues transmission to EFSA, to report outcomes of Pesticides residue monitoring activities and present Latvia data of the EU coordinated programme, (2010). The report highlights the assessment of resources needed and challenges encountered in restructuring the national data bases and systems for chemical occurrence data, and in coding according to EFSA standards. It also contains a benefit analysis, comparing the situation, before the SM was introduced and after the implementation of the SM and the data electronic transmission. The report sums up with conclusions and recommendations obtained from our experience gained during the project. There is no doubt that the project facilitates the harmonization processes of chemical occurrence data collection and processing, and has significant impact on further risk assessment performance quality and representativeness. The project causes a great impact to data management efficiency and further improvement of data quality produced by the national risk managers and laboratories. OBJECTIVE The objective of the project is to implement and test an electronic system for the transmission of food chemical occurrence data to EFSA, according to EFSA standards. 4

5 Materials and Methods MATERIALS Chemical occurrence data: Outcomes of the monitoring programs, conducted by the structural units of PVD during the 2008 and Software, data base systems and tools: Data base system (server): MSSQL 2005 XML validation tool: Notepad, 2007 Microsoft Office Standard PC-Software Others: Human resources and intellectual contribution EFSA SSD standardization model METHODS In order to achieve the project objective the work was organized strictly following to the requirements set by EFSA in the guide for applicants, focusing on accomplishment of EFSA predefined deliverables. 1. Deliverables The following reports and tools have been developed in the framework of this project: Document: D1- Data Standardization This document describes the Encoding and mapping strategy of the database used and the necessary transformations for generating the data in accordance to the EFSA SSD. It highlights internal procedures on how these transformations or mapping tables have to be maintained. Software tools The software components analyzed, developed and used in scope of the project is by purpose accumulated in IDB and Script to export data to XML format from the IDB. It is crucial to mention that the software tools developed have been successfully tested while transmitting three data packages to EFSA upon EFSA calls for data. Report D3 - Final report The final deliverable provides the overview on findings, experience and outcomes gained in the course of realization of the project. 5

6 2. Implementation To perform the data transmission to the EFSA, data management experts have to find all the data, map the information according to the SSD structure and codify the data using EFSA catalogues. The chemical occurrence data in Latvia are stored in different databases and some mandatory information is stored only in paper documents (testing reports, inspection reports, etc.). Experts in close cooperation with IT specialists extracted data from their own database and convert it to comply with the structure of SSD. Experts had not only to map the data from their own database with the SSD structure but even to change the information manually. There has been developed a D1 document Data standardization plan that describes every type of data and it highlights the missing fields and necessary data transformations to comply with the structure of SSD. A new database called IDB was created to collect all the information and to send it to EFSA in XML file format. The database consists of 43 tables including EFSA catalogues and 21 views. Its main goal is to store all the chemical occurrence data in one place, to support the data coding according the EFSA catalogues, to support data foreign key and business rules validation and to support the data extraction to the XML file. The IDB has been created using MS SQL 2005 tools. As the data collection has to be done by data management experts and they do not have strong knowledge about MSSQL2005 tools, an MS Excel template was used to collate all the data. The second purpose of the MS Excel template is to fix all the data errors (remove spaces before and after text, replace comma with dot, convert text to number and etc.). Figure 1. Data collection The collated data are in Latvian language, so to codify the data they had to be exported from the IDB to the Excel file. Scientists found the most appropriate code for each unique data entry and the coded data has been imported back in to the IDB. To perform all the validation IT specialist has to launch the SQL queries. The SQL queries are made to return only data that do not pass the validation. There has been made 20 SQL query for business rules validation and 21 SQL query for foreign key validation. 6

7 Figure 2. Data coding and validation An additional SQL query returns well-formed XML file including all the data but without massage header. The massage header has been added using tool Notepad ++. The XML file validation against XSD schema has been performed using XML Notepad 2007 tool. Figure 3. Data export, validation and insert to DCF As the IDB has been created using the internal IT resources, the database is more flexible against any changes in the SSD. The IDB can be used to structure and codify any other data like pesticide residues, zoonoses etc as long as the necessary data format is flat table and it comply the SSD structure. Any new mandatory fields can be added in to the main table, any new catalogues can be introduced creating new tables and the business and foreign key validation can be changed modifying SQL queries. The gained experience will be used during the foreseen Laboratory and PVD system connection. It will allow importing the data in to the IDB directly from these two systems. 7

8 Results The software function established and the IT technological process developed formed a sound base for data transmission tests that were successfully performed during three data calls. All data transmissions from IDB were performed in XML to the DCF system. The 1.Table contains summary of all data requested by EFSA and submitted by PVD during the test phase. Table 1. Summary of the data submitted to EFSA in scope of the Test phase Chemical occurrence data Year of sampling PARAM_TYPE_DESC PARAM_GROUPHLT_DESC N n Chemical elements and derivatives Cadmium and derivatives Lead and derivatives Mercury and derivatives 27 1 Nitrogen and derivatives Mycotoxins Aflatoxins Fusarium Toxins Ochratoxin A Patulin Organic contaminants Dioxins and PCBs Halogenated Hydrocarbons (3-MCPD 5 7 Acrylamides 40 - Polycyclic aromatic hydrocarbons In addition, it is important to stress that the interaction of IDB and DCF that has been developed and adopted in scope of the Projects, was successfully used to transmit data on pesticide residues to EFSA, to report outcomes of Pesticides residue monitoring activities and present Latvia data of the EU co-ordinated programme, (2010). 8

9 Discussion The Chapter in brief highlights the assessment of resources needed, challenges met and the benefits gained from the implementation of the project. 1. Assessment of resources needed and challenges encountered in restructuring the national data repositories according to the SSD. The assessment of resources needed to develop the project was done accurately and prudently before to submit the project proposal with reference to call of the project: CFP/EFSA/DATEX/2010/01. Based on the analysis of the resources and capabilities it is clear that the PVD possesses the necessary technical, intellectual and managerial resources to guarantees high level of science output of the project as: The PVD is a National Competent Authority for the collection of chemical contaminant data and the approved competent organizations from the list of competent organizations designated by the Member States which may assist EFSA according to Article 36 of EFSA s Founding Regulation The chemical contaminants database of PVD includes data on monitoring programs: - covering almost all the chemicals included in Regulation No. 1881/2006 and subsequent amendments, except Tin, fumonisin, and toxins T-2 and HT-2. - pesticides; - veterinary drug residues; - acrylamide. The database includes data belonging to almost all of the 20 macro-categories of the EFCS, except samples referring to 10, 13-15, 18, and 19 macro-categories of the EFCS. The target samples selection were carried out by qualified, trained staff according to the procedures and guidelines. PVD has the Quality management system that is accredited according to requirements of LVS EN ISO 9001, LVS EN ISO and LVS EN ISO/IEC The target samples were examined in accredited laboratory (pursuant to requirements of the standard LVS EN ISO/IEC according to Latvian national accreditation system; compliance of separate structural units with this Standard has been confirmed also by German and Russian accreditation systems. In September of 2005, international certification institution Det Norske Veritas approved the quality management system of the laboratory that has performed the analysis as compliant to requirements of LVS EN ISO 9001). IT system to collect and process the chemical occurrence data consists of two modules: Laboratory testing results recording and control system Junda with Database (developed under Oracle Database and applications developed in Java). PVD is well experienced concerning participation in EU funded scientific and risk management type activities. The project team was composed of risk managers, risk assessors and IT specialists of the PVD. The involvement and cooperation of risk managers and risk assessors is facilitating the 9

10 project outcome quality and contribute to development of added value to risk assessment outputs both on international and national level. The project management was well organized and focused. The management functions were realized by the project Administrative or Management Board that includes Director General of PVD, Director of ARA (Project Manager), Head of Financial Division, Director of Informatics Division, and Deputy Director of ARA (Project Coordinator). It is important to stress that the resources possessed by PVD are crucial to meet the challenges and to successfully carry out the tasks of the project. The main challenges that our team was faced during the project realization were: a) Team building, networking and strengthening of internal cooperation; b) Additional workload focused on inventory of resources. Finally, it can be confirmed that the challenges addressed at the beginning of the project were successfully turned into project outcomes (see Chapter: A benefit analysis). The success of this project is an achievement of our team and of the close cooperation with the EFSA DCM staff. 2. A benefit analysis We would like to especially stress several significant benefits arising from implementation of the project: 1. Self - auditing of existing databases and systems; data inventory. In scope of the project, selected data from the national monitoring data system of PVD has been made available for transmission to EFSA in accordance with EFSA SSD. To perform the task, both data management experts and IT specialists of PVD, had to do remarkable preparatory work on data and information sources inventory and validation for their completeness. Finally the time consuming routine auditing activities resulted in the successful implementation of data transmission model with consequent improvement of the national monitoring data system. The project helped us significantly to evaluate the strengths and weaknesses of our some of our existing data management systems. 2. Harmonisation and optimization. Harmonisation and optimization of the data management process, resulting in improved traceability of the relevant business process of PVD. It is absolutely clear that the project facilitates the harmonisation processes of data collection and processing that has significant impact on further risk assessment performance quality and representativeness. The project impacts positively on data management efficiency and data quality, produced by the national food safety risk managers and by laboratories. 3. Improvement of professional skills. 10

11 For IT specialists involved in the project activities, the work on development of the system and tools to achieve the modernization and optimization of the IT processes supports the further improvement of their personal professional skills. The project provided an opportunity to gather knowledge and improve the practical skills on application of different IT tools, like MSSQL2005, XML and generation of XML files in MSSQL2005 media. 4. Time savings. Although at the beginning of the project implementation our team faced a considerable workload, finally the challenges were overcome and the work done is valued as highly beneficial. The system built is an efficient tool for data transmissions to be used also in the future, in case of any new data calls (mandatory or optional) that helps to save time and any relevant resources to complete the task timely and according to standards. As it was mentioned above, the interaction of IDB and DCF that has been developed and adopted in scope of the projects, was successfully utilized for data on pesticide residues transmission to EFSA, as well (to report outcomes of Pesticides residue monitoring activities and present Latvia data of the EU coordinated programme, (2010)). Outcomes of EFSA standardization initiatives, like SSD, are highly important and effective, and accomplish data transmission process to meet the harmonization and data quality requirements. 5. Practical and timely applications of the EFSA standardization tools (like, SSD model) for national data base updates. The gained experience will be used during the foreseen project that will connect the laboratory and PVD data base system. It will allow to organize the importing of the data in to the IDB directly from these two systems, (see the Chapter: Implementation), considering the EFSA standardization rules and requirements. Conclusions and Recommendations CONCLUSIONS In the scope of the project test phase, the occurrence data from the PVD database, agreed with EFSA, were transmitted successfully. It is important to highlight that the model of interaction between IDB and DCF that has been developed and adopted during the projects, can be successfully used for transmission of different type of data to EFSA, responding to different type of data collection calls, for instance, to report outcomes of Pesticides residues monitoring activities of the EU coordinated programme. The project facilitated the standardization and harmonization processes of chemical occurrence data collection and processing. It had significant impact on quality and representativeness of 11

12 further risk assessment performance in European and national level. The project improved data management efficiency and data quality. RECOMMENDATIONS Based on our experience, we would like to recommend to EFSA to develop a repository to collect together in one place and present to MS all documents that are relevant to data collection like guidelines, standards, publications, and reports. In regard to updates of SSD, it is very important to indicate the latest updated fields within the version, and to put the date and number on top of the newly updated SSD version. We supposed that it will help to save the time of experts dealing with the chemical occurrence data management and standardize the actions. We consider that it would be also helpful to send news and to organise subscription lists within the network of experts who are involved in chemical occurrence data collection and in the preparation of the data transmissions to EFSA. References EC Regulation No 178/2002; Available online: EFSA-GDE. European Food Safety Authority; Guidance on Data Exchange EFSA Journal 2010; 8(11):1895 [50 pp.]. doi: /j.efsa ; Available online: MS SQL 2005 database; Available online: XML Notepad 2007; Available online: EFSA-SSD; Available online: 12

13 Glossary / Abbreviations ARA DCF EC EFCS EFSA EU 3-MCPD MS IDB IT PAH PCBs PVD SM SSD XML Assessment and Registration Agency of PVD Data Collection Framework Europe Commission EFSAs standardized food classification and description system European Food Safety Authority Europe Union Esters of 3-chloro-1,2-propanediol Member State of the European Union Integrated database Information Technologies Polycyclic aromatic hydrocarbon Polychlorinated biphenyls Food and Veterinary Service of Latvia Standard Data Model Standard Sample Description Extensible Markup Language 13