State General Laboratory of Cyprus (SGL) Agathi Anastasi, Militsa Hadjigeorgiou, Spyroula Constantinou

Transcription

1 EXTERNAL SCIENTIFIC REPORT APPROVED: 16 May 2017 doi: /sp.efsa.2017.en-1238 Pilot project on the implementation of SSD2 in the frame of the electronic transmission of harmonised data collection of analytical results to EFSA: Cyprus State General Laboratory of Cyprus (SGL) Agathi Anastasi, Militsa Hadjigeorgiou, Spyroula Constantinou Abstract This document is the Report on SSD2 pilot results which is the final deliverable of the project OC/EFSA/DATA/2015/02: Pilot project on the implementation of SSD2 in the frame of the electronic transmission of harmonised data collection of analytical results to EFSA. The report describes the adaptation of the software and databases already developed as part of the project OC/EFSA/DCM/2013/05 for the implementation of SSD2 in the domains of Pesticide residues, Contaminants and Food Additives, to extend their applicability to the domain of Residues of Veterinary Medicinal Products (under Council Directive 96/23/EC). The report also describes the challenges encountered and provides recommendations to EFSA. European Food Safety Authority, 2017 Key words: (SSD, LIMS, FOODEX, data, veterinary) Question number: EFSA-Q Correspondence: EFSA Supporting publication 2017: EN-1238

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 Acknowledgements: The author would like to thank the Department for Veterinary Medicinal Products, Hormones and Contaminants (AGES) for the scientific support. Suggested citation: State General Laboratory of Cyprus (SGL), Anastasi A., Hadjigeorgiou M., Constantinou S., Pilot project on the implementation of SSD2 in the frame of the electronic transmission of harmonised data collection of analytical results to EFSA: Cyprus. EFSA supporting publication 2017:EN pp. doi: /sp.efsa.2017.en-1238 ISSN: European Food Safety Authority, 2017 Reproduction is authorised provided the source is acknowledged. 2 EFSA Supporting publication 2017:EN-1238

3 Summary This document is the Report on SSD2 pilot results which is the final deliverable of the project OC/EFSA/DATA/2015/02: Pilot project on the implementation of SSD2 in the frame of the electronic transmission of harmonised data collection of analytical results to EFSA. The report describes the adaptation of the software and databases already developed as part of the project OC/EFSA/DCM/2013/05 for the implementation of SSD2 in the domains of Pesticide residues, Contaminants and Food Additives, to extend their applicability to the domain of Residues of Veterinary Medicinal Products (VMPR), under Council Directive 96/23/EC. In particular the additional elements required for the VMPR domain are listed and their mapping and integration in the SGL LIMS is described. The various phases of the project are described which comprise design, mapping of data, training, recording and submission of data. An overview of the results submitted is presented and the challenges encountered during submission as well as issues related to specific elements are discussed. The project has run smoothly and the successful submission of the data in the SSD2 standard indicates that it is a suitable model for the VMPR domain. Some conflicts were detected between the Guidelines for reporting data on residues of veterinary medicinal products and the business rules applied by EFSA when the data was uploaded. It was found that the terminology of some elements should be defined more clearly. Foodex2 coding was a challenging task for which the trainings provided by EFSA were extremely useful. The introduction in the SGL LIMS of some new elements as well as the improvement of the LIMS Food list was beneficial to the SGL, as they provide useful information. As a result of the challenges encountered, some recommendations are provided. 3 EFSA Supporting publication 2017:EN-1238

4 Table of Contents Abstract... 1 Summary Introduction Background Terms of Reference Methodology and Data Software used and developed Project team Project plan Phase 1 Data mappings and development of LIMS modules Phase 2 Training and recording of data Phase 3 - Submission of Data Results/ Assessment Overview of the results submitted Issues with specific elements Conclusions/ Recommendations References Abbreviations Appendix A Data structure and Terminology mappings EFSA Supporting publication 2017:EN-1238

5 1. Introduction 1.1. Background In the context of its mandate to collect, collate, analyse and summarise relevant scientific and technical data in the fields within its mission, EFSA developed the Standard Sample Description (SSD), which is a standardised model for the reporting of harmonised data on analytical measurements of chemical substances occurring in food, feed and water. In its effort to facilitate reporting of occurrence data from several food safety domains, EFSA extended the SSD to cover additional data collection domains and developed a new standard called SSD2. The SSD2 model was tested to see if it is a suitable and effective tool for reporting data to EFSA in different data collection domains by eight countries (including Cyprus) which participated in the project OC/EFSA/DCM/2013/05: Pilot project on the implementation of SSD2 in the frame of the electronic transmission of harmonised data collection of analytical results to EFSA. The current project OC/EFSA/DATA/2015/02: Pilot project on the implementation of SSD2 in the frame of the electronic transmission of harmonised data collection of analytical results to EFSA is a continuation to the previous one and it includes a new domain, Residues of Veterinary Medicinal Products (VMPR), in order to facilitate the future adoption and implementation of SSD2 as a unique data model for different collections. Regarding VMPR, Council Directive 96/23/EC requires EU Member States to implement a national residue monitoring plan for specific groups of residues specified in its Annexes I and II. Currently, these data are collected annually in a database maintained by the European Commission (EC) in an aggregated format. On 12 December 2013, EFSA received a mandate from the EC to develop a sample-based data collection system which would allow direct data submission by Member States to EFSA of data obtained in accordance with the framework of Council Directive 96/23/EC, and to prepare an annual report describing these data. A working group was set up to address the terms of reference of the EC mandate, taking into account the experiences of EFSA in setting up harmonised sample-based data collections in other data domains. The main tasks of the working group were to define a data model and corresponding guidelines for reporting on sample-based VMPR data in order to support data providers. The working group proposed that the data model for VMPR data collection is based on the SSD2. In addition, implementation of SSD2 will help Member States to adopt a unique data model for different collections with consequent reductions in time needs and resource allocation for both data collection and data transmission phases. The State General Laboratory of Cyprus (SGL) participated in the above working group and was awarded the current contract by EFSA for the VMPR domain. The SGL is a department of the Ministry of Health, the National Reference Laboratory for the analysis of all substances in food of animal origin and one of the two Governmental departments involved in the implementation of the Council Directive 96/23/EC since 1995, the other department being the Veterinary Services of the Ministry of Agriculture, Rural Development and Environment. 5 EFSA Supporting publication 2017:EN-1238

6 1.2. Terms of Reference This contract was awarded by EFSA to: Contractor: State General Laboratory 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/DATA/2015/02-CT8 6 EFSA Supporting publication 2017:EN-1238

7 2. Methodology and Data 2.1. Software used and developed The SGL uses an in-house LIMS, based on Visual FoxPro 9 in which all the information about samples and analyses is stored. General information about the sample is recorded at the sample reception point, based on information provided by the Sampling Officers. Further information is added by the laboratory personnel which also records the results of the analysis. The data extraction for EFSA transmissions is performed by the IT Unit. The LIMS was adapted in the framework of previous EFSA projects so that all the mandatory SSD1 and SSD2 elements required by EFSA for the domains of Pesticides, Contaminants and Food Additives are recorded. The data from the LIMS are exported as a Visual FoxPro dbf file by a data extraction procedure. In order to create the XML files required by EFSA, a software was developed using Microsoft Visual C # 2010 express, which converts the Visual FoxPro dbf to an XML file according to the required schema. During this project, the system was adapted to provide the VMPR data elements required by the SSD2 standard. The system modifications are described in section Project team The following experts compose the project team: Dr Popi Nicolaidou - Kanari, Director of SGL, Legal representative. Ms Agathi Anastasi, Head of IT Unit, Cyprus Data provider to EFSA, Project leader. Ms Militsa Hadjigeorgiou, Senior Chemist, Section of Veterinary Drug Residues, Pesticide Residues, Control of Food Contact Materials and Control of Toys, Member of the Working group for preparing the Guidelines for reporting data on residues of veterinary medicinal products, Member of the Network on Veterinary Medicinal Products Residues Data Collection. Ms Spyroula Constantinou, Chemist, Supervisor of the Laboratory of Veterinary Drug Residues, Member of the Network on Veterinary Medicinal Products Residues Data Collection. Ms Eleni Andreou, Chemist, Analyst in the Laboratory of Veterinary Drug Residues, recording data in the SGL LIMS Project plan Phase 1 Data mappings and development of LIMS modules Data mappings After studying the document Guidelines for reporting data on residues of veterinary medicinal products and the corresponding SSD2 Structure table provided by EFSA, the Data structure and 7 EFSA Supporting publication 2017:EN-1238

8 Terminology mappings (see Appendix A) were designed. These mappings constituted Deliverable 1- Data Standardisation document of the project. The Data structure and Terminology mappings designed in this project were a modification of the corresponding mappings already designed during the previous project (OC/EFSA/DCM/2013/05). The VMPR domain requires some elements which are not required by the Pesticides and Contaminants domains. The new elements required for VMPR are: Table 1: Elements required for VMPR data which are not required for Pesticides or Contaminants data Element Element Element label Controlled VMPR code name terminology B.06 sampler Sampler SAMPLR mandatory C.02 sampunittype Sampling unit type SAMPUNTYP mandatory C.05 sampunitids Other sampling unit mandatory identifications L.03 anmethtype Analytical method type ANLYTYP mandatory N.06 evalinfo Additional information on mandatory the evaluation D.11 sampinfo Additional Sample taken information dependent mandatory M.08 CCalpha CC alpha dependent mandatory M.09 CCbeta CC beta dependent mandatory M.15 resqualvalue Result qualitative value POSNEG dependent mandatory M.18 resvaluncertsd Result value uncertainty Standard deviation N.01 evallowlimit Limit for the result evaluation dependent recommended dependent recommended The above elements were added to the SGL LIMS database structure except for M.18 Result value uncertainty Standard deviation because the element M.17 Result value uncertainty (resvaluncert) was used to record uncertainty. Development of LIMS modules SGL LIMS has a different data entry module for each domain and consequently the data entry module for the VMPR laboratory was modified to include the EFSA elements. 8 EFSA Supporting publication 2017:EN-1238

9 The SGL LIMS contains a data extraction procedure called LIMS-EFSA Export Module which performs the following functions: Selects records from the LIMS based on the parameter type and the year of sampling Extracts from the above records the required fields for the EFSA transmission Gives default values to some fields Gives calculated values to some fields (based on the value of other fields) Identifies the records in which a mandatory field is missing Performs some basic validation of the data according to EFSA rules and provides error messages Saves the export file as a VFP table which is manually imported into another module, the XML tool The XML tool is a Microsoft Visual C# 2010 express application which converts the exported VFP table to an XML file, applying the XML schema. During this project new versions of the LIMS-EFSA Export Module and of the XML tool were developed which include the new elements and business rules required by the VMPR domain Phase 2 Training and recording of data The samples received at the SGL are recorded in the SAMPLES database and the sample matrix is described using the Food picklist which contains food descriptions in Greek and in English and the corresponding Foodex2 code. The SAMPLES database also contains a field called Additional Foodex2 facet which enables the laboratory personnel to provide additional Foodex2 information for a particular sample, by adding facets from the Foodex2 browser (provided by EFSA) to this field, in exceptional cases, if the required detail is not found in the Food picklist. The extraction procedure LIMS-EFSA Export Module combines the Foodex2 code from the Food picklist with the facet codes derived from the Additional Foodex2 facet field and copies this value into the compound element E.02 (sampmatcode). The SGL LIMS Food picklist is common to all domains and consequently many foods were already coded during the previous project (OC/EFSA/DCM/2013/05) for the Pesticides and Contaminants domains. However most of the samples analysed for VMPR are different and a major task was to select and record the correct Foodex2 code in the Food picklist. The Project Team attended a web training on Foodex2 coding. In April 2016 an SSD2 and Foodex2 training was arranged at the SGL premises which was attended by the Project Team, other laboratory personnel and the Sampling Officers. This training resolved some uncertainties about the use of the SSD2 and especially Foodex2. The Food picklist was exported from the LIMS to an excel table on which the Foodex decoder provided by EFSA was installed. The project team selected the Foodex2 code by using the Foodex Browser tool provided by EFSA and recorded it in the Foodex decoder to provide full description of the Foodex2 code for validation. The code was then copied into the LIMS Food picklist. Most other SSD2 elements which are in controlled terminology catalogues have been mapped in the SGL LIMS from the previous project. The element C.02 Sampling unit type was not required by the other domains and a new picklist was created and added to the database. The element L EFSA Supporting publication 2017:EN-1238

10 Analytical method type was added to the existing p_tests picklist. The element B.06 Sampler is recorded with a default value as it is the same for all the SGL data. The element M.15 Result qualitative value is recorded manually. The mapped picklists were updated to include the codes required for the VMPR domain. During this phase the data in the LIMS system was examined to ensure that all the mandatory elements were recorded and the various validation procedures were correctly applied Phase 3 - Submission of Data After exporting the SGL LIMS data using the software LIMS-EFSA Export Module and converting them to XML using the XML Tool, they were uploaded to the EFSA Data Collection Framework (DCF). This procedure was repeated several times after making corrections indicated by the error messages. At this stage some additional business rules were applied by EFSA which changed the requirement for some elements from optional to mandatory or dependent mandatory. The problem was resolved by modifying the software so that the elements B.01, C.01, F.01, J.01 and L.01 were given values already recorded in other relevant elements. This is further explained in section 3.2. The VMPR data for the year 2015 were submitted to EFSA as Deliverable 2 of the project. An overview of the results submitted is presented in Table Results/ Assessment 3.1. Overview of the results submitted The total number of results submitted was and the Table 2 provides information about the Analytes and Matrices. Table 2: Numbers of data submitted by the SGL for VMPR Analyte Matrix No. of results Anabolic steroids Farm water 300 Anabolic steroids Urine 150 Anthelmintics Eggs 205 Anthelmintics Fish 62 Anthelmintics Milk 630 Anthelmintics Muscle 435 Antibiotics Eggs 1550 Antibiotics Fish 624 Antibiotics Honey EFSA Supporting publication 2017:EN-1238

11 Antibiotics Milk 3943 Antibiotics Muscle Avermectines Fish 18 Avermectines Liver 66 Avermectines Milk 234 Avermectines Muscle 48 B-Agonists Farm water 360 B-Agonists Muscle 1 B-Agonists Perirenal fat 14 B-Agonists Urine 144 Carbadox/ Olaquindox metabolites Muscle 38 Chloramphenicol Eggs 10 Chloramphenicol Farm water 30 Chloramphenicol Fish 12 Chloramphenicol Honey 12 Chloramphenicol Milk 36 Chloramphenicol Muscle 64 Coccidiostats Eggs 1148 Coccidiostats Liver 858 Coccidiostats Muscle 260 Corticosteroids Milk 210 Corticosteroids Muscle 70 Dapsone Eggs 10 Dapsone Fish 6 Dapsone Milk 20 Dapsone Muscle 31 Dyes Fish 24 Gestagens Muscle 3 Gestagens Perirenal fat 42 Nitrofuran metabolites Eggs 40 Nitrofuran metabolites Fish 60 Nitrofuran metabolites Milk 144 Nitrofuran metabolites Muscle 224 Nitrofurans Farm water 120 Nitroimidazoles Eggs 60 Nitroimidazoles Farm water 120 Nitroimidazoles Fish EFSA Supporting publication 2017:EN-1238

12 Nitroimidazoles Milk 138 Nitroimidazoles Serum 192 NSAIDs Milk 340 NSAIDs Muscle 396 Stilbenes Urine 48 Thiamphenicol Milk 36 Thiamphenicol Muscle 6 Thyreostats Blood 6 Thyreostats Urine 72 Tranquilizers Kidney 152 Tranquilizers Muscle 24 Zeranols Urine Issues with specific elements The main objective of this project was to design the data extraction process and define the automatic conversion in SSD2-XML data file by: improving the reporting guidelines documents (applicable only if applying for residues of veterinary medicinal products domain); improving the SSD2 data model for the specific domain(s) for which the tenderer will apply for (e.g. proposing the addition or removal of compound fields attributes); improving the SSD2 catalogues (propose new structures/new terms and add/improve the scope notes) for the specific domain(s) for which the tenderer will apply; improving the specific requirements and the business rules for the specific domain(s) for which the tenderer will apply; In view of the above objective, the challenges encountered are described below. B.01 Sampling programme identification code, B.02 Programme legal reference Although B.01 is optional according to the document Guidelines for reporting data on residues of veterinary medicinal products, 2015, business rule GBR8a converts it to dependent mandatory. The value of B.02 was copied to B.01 to avoid the error. After reconsidering, we concluded that recording a combination of the Programme type (B.04) and the Laboratory identification code (J.01) would be a more appropriate value for this element. We cannot see the reason why this element should be mandatory EFSA Supporting publication 2017:EN-1238

13 C.01 Sampling event id code, D.01 Sample taken id code, F.01 Sample analysed id code Although only D.01 is mandatory according to the document Guidelines for reporting data on residues of veterinary medicinal products, 2015, C.01 and F.01 are converted to mandatory by the business rules GBR2a and GBR4a. The value of D.01 was copied to C.01 and F.01 to avoid the error. For the SGL there is no need for different identification codes in these elements. The sample analysed is the same as the sample taken. Sampling event information may be extracted from the elements C.05 (other sampling unit identifications), where we record animal or holding id, and D.06, D.07, D.08 (date of sampling). We cannot see the reason why C.01 and F.01 should be mandatory. C.02 Sampling unit type This element was difficult to record because the description of the various choices in the controlled terminology was not very clear to us. For example we recorded samples of imported shrimps in packs as single but the classification batch also seems to fit. Similarly for samples of honey which we recorded as single could also be recorded as batch. A clearer description of the terminology is required so that the terms are mutually exclusive. C.05 Other sampling unit identifications In this element we recorded either animal id or batch id or holding id. The information was provided to us by the Sampling Officers and it was not difficult to obtain it. In most cases a code was recorded for the protection of commercial interests. In some cases the batch id contains the name of the producer. D.11 Additional Sample taken information This element was used to provide the link to original sample to report any links between samples taken during follow-up investigations. This attribute contains the identification code of the original sample taken, as provided in the D.01 (Sample taken identification code) element for the original sample. The addition of this field in our LIMS was beneficial to us because it is useful information. E.02 Foodex2 Foodex2 coding was a challenging task. The on-line and physical trainings were very helpful to ensure correct coding. One of the difficulties was to find the code for Farm water which we could not locate in the VetDrugRes hierarchy of the Foodex2 Browser Tool. With the help of EFSA we located the code in the Reporting hierarchy, Non-food matrices, Environment section. Another difficulty was to code the perineal fat, for which we had two options, one starting from Mammals fat tissue (for example Cattle fresh fat tissue, PART=Visceral fat ) and the other starting from Animal offal (for example Bovine kidney, PART=Visceral fat ). With the help of EFSA we concluded that the first option was best. The advice of the Veterinary Services sampling officers was required in order to select the correct agegroup of the animals EFSA Supporting publication 2017:EN-1238

14 Recording Foodex2 gave us the opportunity to improve our LIMS Food list providing more information (for example animal age group) and a clearer and more uniform description of the sample. J.01 Laboratory identification code Although J.01 is a recommended element, according to the document Guidelines for reporting data on residues of veterinary medicinal products, 2015, business rule GBR10a converts J.01 to dependent mandatory. A default value is recorded for this element since the laboratory for all the results is the SGL. K.02 Coded description of the parameter The following parameters were not found in the Catalogue SSD_CAT_PARAM downloaded from the EFSA DMS. EFSA was informed by sending the request for new terms in the appropriate template. Clopidol, CAS Number Desoxycarbadox, CAS Number Methyl-3-quinoxaline-2-carboxylic acid, CAS Number Quinoxaline-2-carboxylic acid, CAS Number Triclabendazole-Sulfoxide, CAS Number The Catalogue SSD_CAT_PARAM contains the following parameters twice, with different paramcodes. RF VET RF VET RF VET RF VET Cefoperazon Cefoperazone Betamethasone Betamethasone We recorded RF VET and RF VET. L.01 Analytical method identification Although L.01 is optional according to the document Guidelines for reporting data on residues of veterinary medicinal products, 2015, business rule GBR11a converts it to mandatory. L.01 was given the value of L.03 + L.04 to avoid the error. We cannot see the reason why this element should be mandatory EFSA Supporting publication 2017:EN-1238

15 M.04 LOD, M.05 LOQ, M.08 CCA, M.09 CCB, M.16, N.04 The laboratory implements confirmatory methods. For substances with no Permitted Limit: the CCα was reported where the substance was not detected the result type was CCA where the substance was quantified the result type was VAL For substances with Permitted Limit the LOD, LOQ, CCα and CCβ values were calculated and the following were reported: Where a substance was not detected then the LOD value was reported and the result type was LOD Where a substance was detected but the result was lower than the LOQ then the LOQ was reported and the result type was LOQ Where a substance was quantified higher than the MRL then the uncertainty value was reported, the result type was VAL and the result evaluation was either J003A (>maximum permissible quantities) or J031A (compliant due to measurement uncertainty) Our opinion is that the result evaluation could be derived by comparing the result value to the CCα value, as it is required by Decision 657/2002, and the uncertainty should not be required. N.06 Additional information on the evaluation The only evaluation information provided is the sample taken assessment and therefore N.06 is given the value "samptkasses="+n.04. We cannot see the reason why this element should be mandatory EFSA Supporting publication 2017:EN-1238

16 4. Conclusions/ Recommendations The successful submission of the data in the SSD2 standard indicates that it is a suitable model for the VMPR domain. One of the problems encountered was that, while the data was prepared according to the Guidelines for reporting data on residues of veterinary medicinal products, several new business rules were applied at the time of data transmission which required some redesigning of the data and software. It is recommended that the new business rules are discussed with MS and that the Guidelines for reporting data on residues of veterinary medicinal products are modified to reflect the changes resulting from the new business rules to avoid conflict. In particular, it is recommended that the business rules are modified so that the following elements are not mandatory: «Sampling programme identification code», «Sampling event identification code», «Sample analysed identification code», «Analytical method identification», «Additional information on the evaluation». Another element which posed difficulty was the «Sampling unit type». It is recommended to make the terms of the controlled terminology more clearly defined and mutually exclusive. The introduction in the SGL LIMS of the element «Additional sample taken information», providing the link to original sample in follow-up investigations, was beneficial to the SGL, as this is a very useful information. Foodex2 coding was a challenging task and the trainings provided were extremely useful. It is recommended that all MS have the opportunity to attend Foodex2 trainings to ensure correct coding. The data submission environment is quite friendly and the error messages quite informative. It is recommended to have the following improvements: a) a column with the original file name of the MS in the datasets section (it is shown only in the messages section) and b) to provide a line break after each error in the message EFSA Supporting publication 2017:EN-1238

17 References EFSA (European Food Safety Authority), Standard Sample Description ver.2.0. EFSA Journal 2013; 11(10):3424, 122pp. EFSA (European Food Safety Authority), The food classification and description system FoodEx2 (revision 2). EFSA supporting publication 2015:EN-804, 90pp. EFSA (European Food Safety Authority), Guidelines for reporting data on residues of veterinary medicinal products. EFSA supporting publication 2015:EN-783, 77pp. EFSA Information Technology Unit, DCF Data Provider User Guide Ver.3. 97pp. SSD_STRUCTURE excel tables provided by EFSA. Foodex2 browser tool provided by EFSA (Foodex 2.0 win s7). Cyprus Data Standardisation Document, 2015 (Deliverable 1 of this project), 23pp EFSA Supporting publication 2017:EN-1238

18 Abbreviations VMPR DCF LIMS SGL SSD VFP XML Veterinary Medicinal Products Residues Data Collection Framework Laboratory Information Management System State General Laboratory Standard Sample Description Visual Foxpro Extensible Markup Language 18 EFSA Supporting publication 2017:EN-1238

19 Appendix A Data structure and Terminology mappings 19 EFSA Supporting publication 2017:EN-1238

20 1. Data structure mapping The following table presents the Mandatory and/or Recommended SSD2 elements, as well as some optional elements which are submitted for the VMPR data, the corresponding LIMS field if available, the calculated and default values as well as rules applied. Thereafter a more detailed description of each field is given. Elements marked with * in the column M/R are those for which the requirement was modified by the GBR business rules. Table 3: Mapping of SGL LIMS fields to SSD2 elements SSD2 element label SSD2 element code SSD2 controlled terminology M/R LIMS field LIMS table Calculation / Default / Rule Sampling programme identification code B.01 DM* Same value as B.02 BR: GBR8a Programme legal reference B.02 LEGREF R Efsa_s32 P_LEGREF Sampling strategy B.03 SAMPSTR M Efsa_s33 P_SAMSTR Programme type B.04 PRGTYP M Efsa_s34 P_PROGTY Sampler B.06 SAMPLR M Default: CX02A (Official sampling) Sampling point B.07 SAMPNT M Efsa_s39 P_SPTYPE 20 EFSA Supporting publication 2017:EN-1238 out exclusively by the author(s) in the context of a contract between the European Food Safety Authority and the author(s), awarded 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

21 SSD2 element label SSD2 element code SSD2 controlled terminology M/R LIMS field LIMS table Calculation / Default / Rule Sampling event identification code C.01 M* Same value as D.01 BR: GBR2a Sampling unit type C.02 SAMPUNTYP M Efsa_c02 P_SUTYPE Other sampling unit identifications Sample taken identification code C.05 M Efsa_c05 SAMPLES D.01 M Ga_no SAMPLES Reporting country D.02 COUNTRY O Default: CY Country of sampling D.03 COUNTRY M Default: CY Reporting year D.05 Date_rec SAMPLES Year (date_rec) Year of sampling D.06 M Date_samp SAMPLES Year (date_samp) Month of sampling D.07 O Date_samp SAMPLES Month (date_samp) Day of sampling D.08 O Date_samp SAMPLES Day (date_samp) 21 EFSA Supporting publication 2017:EN-1238 out exclusively by the author(s) in the context of a contract between the European Food Safety Authority and the author(s), awarded 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

22 SSD2 element label SSD2 element code SSD2 controlled terminology M/R LIMS field LIMS table Calculation / Default / Rule Additional Sample taken information D.11 DM Efsa_d11 SAMPLES origsampid= + D.01 Type of matrix E.01 MTXTYP M matrixtype P_STYPE Coded description of the matrix of the sample taken E.02 MTX M Foodex2 Foodex2m P_STYPE SAMPLES See detailed description below Text description of the matrix of the sample taken Country of origin of the sample taken Sample analysed identification code E.03 R S_type3e P_STYPE E.04 COUNTRY Efsa_s06 P_COUNT F.01 M* Same value as D.01 BR: GBR4a Year of analysis F.03 M date_anal SAMPLES Year(date_anal) 22 EFSA Supporting publication 2017:EN-1238 out exclusively by the author(s) in the context of a contract between the European Food Safety Authority and the author(s), awarded 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

23 SSD2 element label SSD2 element code SSD2 controlled terminology M/R LIMS field LIMS table Calculation / Default / Rule Coded description of the analysed matrix G.01 MTX M Foodex2 Foodex2m P_STYPE SAMPLES See detailed description below Text description of the matrix analysed Laboratory identification code G.02 DR S_type3e P_STYPE J.01 R/ DM* Default: SGL_CYPRUS BR: GBR10a Laboratory accreditation J.02 LABACC M Default: L001A Laboratory country J.03 COUNTRY O Default: CY Type of parameter K.01 PARAMTYP M paramtype P_TESTS Coded description of the parameter K.02 PARAM M paramcode P_TESTS Parameter text K.03 DM T_eng P_TESTS Analytical method L.01 M* L.03 + L.04 BR: GBR11a 23 EFSA Supporting publication 2017:EN-1238 out exclusively by the author(s) in the context of a contract between the European Food Safety Authority and the author(s), awarded 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

24 SSD2 element label SSD2 element code SSD2 controlled terminology M/R LIMS field LIMS table Calculation / Default / Rule identification Analytical method type L.03 ANLYTYP M methtyp P_TESTS Analytical method code L.04 M methcode P_TESTS Analytical method text L.05 DM Result identification code M.01 M Ga_no + test_no RESULTS See detailed description below Accreditation procedure for the analytical method M.02 MDACC M accredproc P_TESTS Result unit M.03 UNIT DM unitcode P_TESTS Result LOD M.04 DM Detect_lim P_TESTS Result LOQ M.05 R Determ_lim P_TESTS CC alpha M.08 DM Cc_alpha P_TESTS 24 EFSA Supporting publication 2017:EN-1238 out exclusively by the author(s) in the context of a contract between the European Food Safety Authority and the author(s), awarded 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

25 SSD2 element label SSD2 element code SSD2 controlled terminology M/R LIMS field LIMS table Calculation / Default / Rule CC beta M.09 DM Cc_beta P_TESTS Result value M.10 DM Res_num RESULTS Expression of result percentage M.13 DR Perc_moist, perc_fat SAMPLES See detailed description below Result qualitative value M.15 POSNEG DM Type of result M.16 VALTYP M Calculated See detailed description below Result value uncertainty M.17 DR uncertain RESULTS Result value uncertainty Standard deviation Limit for the result evaluation Type of limit for the result evaluation M.18 DR Not used by SGL N.01 DR limitlow RESULTS N.03 LMTTYP DR Limtype RESULTS 25 EFSA Supporting publication 2017:EN-1238 out exclusively by the author(s) in the context of a contract between the European Food Safety Authority and the author(s), awarded 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

26 SSD2 element label SSD2 element code SSD2 controlled terminology M/R LIMS field LIMS table Calculation / Default / Rule Evaluation of the result N.04 RESEVAL M Eval RESULTS Action Taken N.05 ACTION DM action SAMPLES Additional information on the evaluation N.06 M samptkasses= + N EFSA Supporting publication 2017:EN-1238 out exclusively by the author(s) in the context of a contract between the European Food Safety Authority and the author(s), awarded 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

27 B.01 Sampling Programme identification code Although B.01 is optional according to the document Guidelines for reporting data on residues of veterinary medicinal products, 2015, business rule GBR8a converts it to dependent mandatory. Presently, the value of B.02 is copied to B.01 to avoid the error. B.02 Programme legal reference This field in LIMS is extracted from the picklist P_LEGREF which includes the field efsa_s32 in which the corresponding EFSA controlled terminology code (LEGREF) is recorded. The value of this field is copied to the corresponding EFSA SSD element proglegalref. B.03 Sampling strategy This field in LIMS is extracted from the picklist P_ SAMSTR which includes the field efsa_s33 in which the corresponding EFSA controlled terminology code (SAMPSTR) is recorded. The value of this field is copied to the corresponding EFSA SSD element SampStrategy. B.04 Program type This field in LIMS is extracted from the picklist P_ PROGTY which includes the field efsa_s34 in which the corresponding EFSA controlled terminology code (STCTYP) is recorded. The value of this field is copied to the corresponding EFSA SSD element progtype. B.06 Sampler All sampling is performed under control of the competent authority, therefore the default value CX02A (Official sampling) is given to the EFSA SSD element sampler for all the records. B.07 Sampling point This field in LIMS is extracted from the picklist P_SPTYPE which includes the field efsa_s39 in which the corresponding EFSA controlled terminology code (SMPNT) is recorded. The value of this field is copied to the corresponding EFSA SSD element samppoint. C.01 Sampling event identification code Although C.01 is optional according to the document Guidelines for reporting data on residues of veterinary medicinal products, 2015, it is converted to mandatory by the business rule GBR2a. Presently, the value of D.01 is copied to C.01 to avoid the error EFSA Supporting publication 2017:EN-1238

28 C.02 Sampling unit type This field in LIMS is extracted from the picklist P_SUTYPE which includes the field efsa_c02 in which the corresponding EFSA controlled terminology code (SAMPUNTYP) is recorded. The value of this field is copied to the corresponding EFSA SSD element sampunittype. C.05 Other sampling unit identifications The value of the field SAMPLES.efsa_c05 in LIMS is copied to the SSD element sampunitids. D.01 Laboratory sample code The value of the LIMS field SAMPLES.ga_no is copied to the corresponding EFSA SSD element sampid. D.02 Reporting country The reporting country is Cyprus, therefore the default value CY is given to the optional EFSA SSD element repcountry for all the records. D.03 Country of sampling All samples are taken in Cyprus, therefore the default value CY is given to the EFSA SSD element sampcountry for all the records. D.05 Reporting year The reporting year is extracted from the field SAMPLES.date_rec in LIMS in which the date the sample was received by the lab is recorded and it is copied to the SSD element repyear. D.06 Year of sampling The year of sampling is extracted from the field SAMPLES.date_samp in LIMS in which the date of sampling is recorded and it is copied to the SSD element sampy. D.07 Month of sampling The month of sampling is extracted from the field SAMPLES.date_samp in LIMS in which the date of sampling is recorded and it is copied to the optional SSD element sampm. D.08 Day of sampling The day of sampling is extracted from the field SAMPLES.date_samp in LIMS in which the date of sampling is recorded and it is copied to the optional SSD element sampd EFSA Supporting publication 2017:EN-1238

29 D.11 Additional Sample taken information The LIMS field SAMPLES.efsa_d11 is used to provide the link to original sample to report any links between samples taken during follow-up investigations. This attribute contains the identification code of the original sample taken, as provided in the D.01 (Sample taken identification code) element for the original sample and it is copied to the SSD element sampinfo. E.01 Type of matrix This field in LIMS is extracted from the picklist P_ STYPE which includes the field matrixtype in which the type of matrix is recorded. The value of this field is copied to the corresponding EFSA SSD element sampmattype. E.02 Coded description of the matrix of the sample taken (FOODEX2) This compound SSD element sampmatcode is extracted from the picklist P_STYPE which includes the field foodex2 in which the Foodex2 code which corresponds to the sample description is recorded. Additional facets may be recorded in the LIMS field SAMPLES.Foodex2m and the code of these facets is combined with the foodex2 code in the SSD element sampmatcode. E.03 Text description of the matrix of the sample taken This field in LIMS is extracted from the picklist P_ STYPE which includes the field s_type3e in which the product description in English is recorded. The value of this field is copied to the corresponding EFSA SSD element sampmattext. E.04 Country of origin This field in LIMS is extracted from the picklist P_ COUNT which includes the field efsa_s06 in which the corresponding EFSA controlled terminology code (COUNTRY) is recorded. The value of this field is copied to the corresponding EFSA SSD element origcountry. F.01 Sample analysed identification code Although F.01 is optional according to the document Guidelines for reporting data on residues of veterinary medicinal products, 2015, it is converted to mandatory by the business rule GBR4a. Presently, the value of D.01 is copied to F.01 to avoid the error. F.03 Year of analysis The year is extracted from the field SAMPLES.date_anal in LIMS in which the date of analysis is recorded and it is copied to the SSD element analysisy EFSA Supporting publication 2017:EN-1238

30 G.01 Coded description of the analysed matrix For the analyses carried out by the SGL the matrix analysed is the same as the sample taken, therefore this field is the same as E.02. G.02 Text description of the matrix analysed For the analyses carried out by the SGL the matrix analysed is the same as the sample taken, therefore this field is the same as E.03. J.01 Laboratory identification code The default value SGL_CYPRUS is given to the EFSA SSD element labid for all the records. J.02 Laboratory accreditation All the laboratories comprising the SGL are accredited thus the default value L001A is given to the EFSA SSD element labaccred for all the records. J.03 Laboratory country The laboratory country is Cyprus, therefore the default value CY is given to the optional EFSA SSD element labcountry for all the records. K.01 Parameter type This field in LIMS is extracted from the picklist P_TESTS which includes the field paramtype in which the corresponding EFSA controlled terminology code (PARTYP) is recorded. The value of this field is copied to the corresponding EFSA SSD element paramtype. K.02 Parameter code This field in LIMS is extracted from the picklist P_TESTS which includes the field paramcode in which the corresponding EFSA controlled terminology code (PARAM) is recorded. The value of this field is copied to the corresponding EFSA SSD element paramcode. K.03 Parameter text This field in LIMS is extracted from the picklist P_TESTS which includes the field t_eng in which the parameter description in English is recorded. The value of this field is copied to the corresponding EFSA SSD element paramtext EFSA Supporting publication 2017:EN-1238

31 L.03 Analytical method type This field in LIMS is extracted from the picklist P_TESTS which includes the field methtyp in which the corresponding EFSA controlled terminology code (ANLYTYP) is recorded. The value of this field is copied to the corresponding EFSA SSD element anmethtype. L.04 Analytical method code This field in LIMS is extracted from the picklist P_TESTS which includes the field methcode in which the corresponding EFSA controlled terminology code (ANLYMD) is recorded. The value of this field is copied to the corresponding EFSA SSD element anmethcode. L.05 Analytical method text This element is not recorded in the SGL LIMS. M.01 Result identification code The calculated value of the LIMS field SAMPLES.ga_no + _ + RESULTS.test_no is copied to the corresponding EFSA SSD element resid. M.02 Accreditation procedure for the analytical method This field in LIMS is extracted from the picklist P_TESTS which includes the field accredproc in which the corresponding EFSA controlled terminology code (MDSTAT) is recorded. The value of this field is copied to the corresponding EFSA SSD element accredproc. M.03 Result unit This field in LIMS is extracted from the picklist P_TESTS which includes the field unitcode in which the corresponding EFSA controlled terminology code (UNIT) is recorded. The value of this field is copied to the corresponding EFSA SSD element resunit. M.04 Result LOD This field in LIMS is extracted from the picklist P_TESTS which includes the field detect_lim in which the LOD is recorded. The value of this field is copied to the corresponding EFSA SSD element reslod. M.05 Result LOQ This field in LIMS is extracted from the picklist P_TESTS which includes the field determ_lim in which the LOQ is recorded. The value of this field is copied to the corresponding EFSA SSD element resloq EFSA Supporting publication 2017:EN-1238

32 M.08 CC alpha This field in LIMS is extracted from the picklist P_TESTS which includes the field cc_alpha in which the CC alpha is recorded. The value of this field is copied to the corresponding EFSA SSD element ccalpha. M.09 CC beta This field in LIMS is extracted from the picklist P_TESTS which includes the field cc_beta in which the CC beta is recorded. The value of this field is copied to the corresponding EFSA SSD element ccbeta. M.10 Result value The value of the LIMS field RESULTS.res_num is copied to the EFSA SSD element resval. This field is left blank if the Type of result (M.16) has the value LOD. M.13 Expression of result percentage This compound SSD element (exprresperc) is composed by combining the values of the LIMS fields perc_moist and perc_fat. M.15 Result qualitative value This element is not recorded in the SGL LIMS. M.16 Type of result The LIMS-EFSA Export Module gives the following values to the EFSA SSD element restype : restype= LOD if no value is recorded in M.10 restype= LOQ if res_alpha= <LOQ restype= CCA if res_alpha= <CCA restype= CCB if res_alpha= <CCB restype= VAL if M.10 is greater than M.09 (and M.09>0) or greater than M.05 (and M.05>0) M.17 Result value uncertainty The value of the LIMS field RESULTS.uncertain is copied to the EFSA SSD element resvaluncert. M.18 Result value uncertainty Standard deviation This element is not recorded in the SGL LIMS EFSA Supporting publication 2017:EN-1238

33 N.01 Limit for the result evaluation The value of the LIMS field RESULTS.limitlow is copied to the EFSA SSD element evallowlimit. N.03 Type of limit for the result evaluation The value of the LIMS field RESULTS.limtype is copied to the EFSA SSD element evallimittype. N.04 Evaluation of the result The value of the LIMS field RESULTS.eval is copied to the EFSA SSD element evalcode. N.05 Action taken The value of the LIMS field SAMPLES.action is copied to the EFSA SSD element acttakencode. N.06 Additional information on the evaluation The only evaluation information provided is the sample taken assessment and therefore N.06 is given the value "samptkasses="+n.04. This value is copied to the EFSA SSD element evalinfo. 2. Table fields and relationships SGL LIMS is based on a relational database which includes 35 tables with relationships between them. The main tables are the following: a) SAMPLES it contains information about the samples (EFSA elements C.05, D.01, D.05, D.06, D.07, D.08, D.11, E.02 (exceptional facets), F.03 and M.13). b) RESULTS it contains information about the analyses and results (EFSA elements M.01, M.10, M.17, N.01, N.03 and N.04). All other tables contain information which is related to either SAMPLES or RESULTS and are referred to as picklists. The picklists which contain EFSA related fields are the following: Table 4: SGL LIMS picklists which contain SSD2 elements LIMS table Description SSD2 element code P_LEGREF Programme legal reference B.02 P_SAMSTR Sampling strategy B EFSA Supporting publication 2017:EN-1238