The SSD2 system and its use for data reporting. Valentina Rizzi Biological Monitoring Unit

Transcription

1 The SSD2 system and its use for data reporting Valentina Rizzi Biological Monitoring Unit EURL-AR Training Course 2013 Copenhagen (Denmark), 27 November 2013

2 SSD version 2 What is SSD? New mandate for SSD Major enhancements Timelines 2

3 What is SSD? A list of data elements that are standardised and can be conveniently used by both data providers and data receivers to fully describe samples and analytical parameters for assessment purposes. The SSD includes controlled terminologies and validation rules to guarantee data quality (in data export, transmission and storage) A model harmonising the collection of a wide range of analytical results in several domains of EFSA activity 3

4 What is SSD? Harmonisation activities: Pilot projects performed internally in EFSA and with Member States 2010 Publication year Production phase and usage for data collection 4

5 What is SSD? Currently implemented for: Chemical contaminants Some revisions are needed to fit the scientific needs! Pesticide residues Additives Food contact materials 5

6 What is SSD? Data Collection Framework (DCF) can be used by Data Providers to submit data. DCF data transmission supports the following formats: XML, Excel, CSV 6

7 What is SSD? An automatic feedback is sent to data providers. 7

8 What is SSD? Standard terminologies are maintained and kept up to date: 8

9 SSD version 2 What is SSD? New mandate for SSD Major enhancements Timelines 9

10 New mandate for SSD The WG was requested to: 1. Amend the guidance on Standard Sample Description in order to cover sample-based data also for the following areas: Food additives Antimicrobial isolate-based data Data on microbiological contaminants in food at single sample level Data on zoonotic agents in animals at single sample or flock/herd level 2. Fully support the new EFSA Food Classification and Description system (FoodEx2) 3. Look for improvements based on the practical user experience gained 10

11 New mandate for SSD Aggregated data of any type Veterinary drug residues Animal diseases 11

12 SSD version 2 What is SSD? New mandate for SSD Major enhancements Timelines 12

13 Major enhancements in SSD ver. 2 The structure: Sample unit section: describe batch/flock/herd Isolate section Analytical method: Support for AMR tests (disk concentration, disk diameter) Amendment of result section (Lower bound and upper bound of the working range, etc ) 13

14 Major enhancements in SSD ver. 2 The catalogues: Clean up the structure of the catalogues Support for domain specific views of the catalogues Support for repeatable and compound fields Define a common harmonised maintenance process Update parameter, analytical method for the new domains, support of FoodEx2 14

15 Major enhancements in SSD ver. 2 In the new structure, data elements are characterised by the following: Element code: An alphanumeric code providing a unique identifier for the data element. Section code: The section code describes the entity of the SSD data model. Section: The section describes the key entity of the SSD data model. Element name: unique element name is provided. Element label: The data elements are described also by a label to be used in reports, print outs or in the graphical interfaces of the software programs that will manage the SSD. Type: A data type is associated to each data element and it defines the values that it can contain. Data types will be defined using the W3C XML schemas data types specification. 15

16 Major enhancements in SSD ver. 2 S/R/C: Type of the data element. It can contain: S (Single) if the data element can be reported only once; R (Repeatable) if the data element can be repeated more than once using the symbol $ as a values separator; C (Compound) for compound fields. M: Mandatory elements are flagged in this column with the value Y. Controlled terminology: Provides the acronym of the catalogues that can be used to populate the data element. Description: Provides a short description on what the data element should contain. 16

17 Major enhancements in SSD ver. 2 17

18 Major enhancements in SSD ver. 2 Compound fields Compound fields They are fields containing additional information on the specific field depending on specific requirements of the different data collection domains. A compound field, called Additional information on the., has been created for each section. The information reported will follow a codification system still to be defined. E.g. variable1=value1$ variable2=value2$ variablen=valuen 18

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20 Major enhancements in SSD ver. 2 The sections: 1. Local organisation 2. Sampling programme 3. Sampling unit 4. Sample taken 5. Sample analysed 6. Sample analysed portion 7. Laboratory 8. Isolate 9. Analytical method 10. Result 11. Result evaluation 20

21 Major enhancements in SSD ver Local organisation the organisation (local competent authority or other type of local organisation) who initially requested or performed the sampling and is in charge of the implementation of the sampling programme. 21

22 Major enhancements in SSD ver Sampling programme The description of criteria, purpose, method and legislative reference used to generate a sampling event. 22

23 Major enhancements in SSD ver Sampling unit The type of sample unit the result refers to (e.g. animal, flock, herd, batch, single etc) 4. Sample taken The sample taken from the sampling unit at certain time in order to evaluate the chemical and microbiological properties of the sampling unit. 23

24 Major enhancements in SSD ver. 2 24

25 Major enhancements in SSD ver Sample analysed The portion of material which is analysed by the laboratory. 25

26 Major enhancements in SSD ver Sample analysed portion The sample analysed portion (usually / often called test portion ) is a replicate achieved by subdividing a sample analysed. It represents the repetition of the same experimental condition defined in a laboratory sample. 7. Laboratory The laboratory in which the analysis to obtain the relevant result was performed. 26

27 Major enhancements in SSD ver Isolate The isolate identifies with a unique code a culture of biological agent, which was isolated from a specific sample taken. It is used to group results of tests performed on the same isolate. 27

28 Major enhancements in SSD ver Analytical method The method of analysis used to generate the result. 28

29 Major enhancements in SSD ver Result The result of the laboratory tests, a quantitative or qualitative outcome value. Information relating to the result includes the parameter analysed, limits of detection, and, for control programmes, the legal limit used for compliance testing and the evaluation of the result. 11. Result evaluation Assessment of the sampling unit, sample or result for testing its compliance with a defined limit. 29

30 Major enhancements in SSD ver. 2 30

31 Major enhancements in SSD ver. 2 31

32 Example AMR Isolate Based Data Model 32

33 Example AMR Isolate Based Data Model 33

34 Example AMR Isolate Based Data Model 34

35 Example AMR Isolate Based Data Model 35

36 Example AMR Isolate Based Data Model 36

37 Example AMR Isolate Based Data Model 37

38 Major enhancements in SSD ver. 2 Catalogues The catalogues: All the catalogues used in zoonoses have been already mapped against the catalogues of SSD and coded, except for: Matrix: FoodEx2 will be used Analytical method: it needs a revision Sampling strategy Matrix type code ST10A ST20A ST30A ST40A ST50A ST90A STXXA name Objective sampling Selective sampling Suspect sampling Convenient sampling Census Other Not specified code S000A S019A S026A S027A S030A S031A S023A name animal sample food sample feed sample environmental sample unknown contact material food simulant 38

39 sortingcod code name status validfrom validto lastupdate parentcode e K005A Official (National) programme A 01/01/2010 ROOT Z001 K009A Official (EU) programme A 01/01/2010 ROOT Z002 K018A Official (National and EU) programme A 01/01/2010 ROOT Z003 microprgtyppare microprgtypsor ntcode tingcode K010A Diet study A 01/01/2010 parentco ROOT Z004 microprgtypparent microprgtypsorti code name status validfrom validto lastupdate de sortingcode Code ngcode K012A Industry/ private programme A 01/01/2010 ROOT Z005 K013A Survey A 01/01/2010 ROOT Z006 ROOT Z001 K013A K020A Survey Clinical investigations A A 07/02/ /01/2010 ROOT ROOT Z009 Z006 ROOT ROOT Z002 Z001 A K014A Other/ Control Combination and of eradication several programmes A 01/01/2010 ROOT Z007 K021A programmes 07/02/2012 ROOT Z010 ROOT Z003 EU increased control programme on imported A K019A K022A food Monitoring A 07/02/ /12/2011 ROOT ROOT Z011 Z008 ROOT Z004 A K020A K023A Clinical Monitoring investigations - active A 07/02/ /02/2012 ROOT ROOT Z012 Z009 ROOT ROOT Z005 Z002 A A K021A K024A Control Monitoring and eradication - passive programmes 07/02/ /02/2012 ROOT ROOT Z013 Z010 ROOT ROOT Z006 Z003 Monitoring - EFSA A A K022A K025A Monitoring specifications 07/02/ /02/2012 ROOT ROOT Z014 Z011 ROOT ROOT Z007 Z004 A A K023A K026A Monitoring Surveillance - active 07/02/ /02/2012 ROOT ROOT Z015 Z012 ROOT ROOT Z008 Z005 A K024A K030A Monitoring Surveillance - passive active A 22/04/ /02/2012 K026A ROOT Z Z013 K026A ROOT Z012 Z006 A K031A Surveillance passive A 22/04/2013 K026A Z K026A Z013 K025A Monitoring - EFSA specifications 07/02/2012 ROOT Z014 ROOT Z007 A K027A Survey - EU baseline survey A 07/02/2012 ROOT Z016 ROOT Z009 K026A Surveillance 07/02/2012 ROOT Z015 ROOT Z008 K028A Survey - national survey A 07/02/2012 ROOT Z017 ROOT Z010 K030A K029A Surveillance Unspecified active A A 07/02/ /04/2013 ROOT K026A Z018 Z ROOT K026A Z011 Z012 K031A Surveillance passive A 22/04/2013 K026A Z K026A Z013 A K027A Survey - EU baseline survey 07/02/2012 ROOT Z016 ROOT Z009 K028A Survey - national survey A 07/02/2012 ROOT Z017 ROOT Z010 K029A Unspecified A 07/02/2012 ROOT Z018 ROOT Z011 39

40 Major enhancements in SSD ver. 2 Catalogues There is a plan for an annual revision of the catalogues Data Collection Domain Annual Reporting Deadline Deadline for terms to include in next release Deadline for discussion within the network Submission of updates from the network Submission of updated version for final comments Deadline for SSD Revision Publication Biological Monitoring 31 st May Pesticides 31 st August Chemical Contaminants 1 st October 15 October Up to the networks No later than 30 Nov 31 Jan 28 Feb Additives Ad-hoc basis Food contact materials Ad-hoc basis 40

41 Major enhancements in SSD ver. 2 Catalogues Urgent request In addition, there may be instances where unplanned calls for data are launched which require catalogue revisions or new terms need to be added with urgency to the catalogue to enable the transmission of the data of an existent data collection. In this case, preliminary terms can be added. These terms are made immediately available for the reporters. Then they will be evaluated in the annual revision (according to the agreed timelines) and it will be decided if either they could be accepted or should be rejected. 41

42 SSD version 2 What is SSD? New mandate for SSD Major enhancements Timelines 42

43 Timelines SSD2 guidance The Guidance Standard Sample Description ver. 2.0 was published on the EFSA website on 31 October Available on the web site: Guidance Catalogues Structure of the system 43

44 Timelines SSD2 guidance Implementation: Support of current available standard for a period of time to be decided by the competent networks Support of SSD ver. 1 Pilot activities to support and test the implementation of the SSD ver. 2 Set up of joint maintenance group for the controlled terminology maintenance Implementation plan of SSD ver. 2 to be decided by the competent networks 44

45 Timelines GDE Work plan for the publication of the Guidance on data exchange (GDE) - Finalisation by the WG - Last WG meeting in December - Consultation in January Publication in February

46 Recommendations The WG-SSD2 experts agreed on the need to have a short guidance like a Practical guidance on classification of food using the FoodEx2 system describing: the procedure for the correct coding of the food/feed/other elements, presence of implicit facets, the choice of explicit facet using the option Describe in the web browser, how to report the food/feed code in the National database and to EFSA (short code, full code). The WG agreed to add a recommendation in the SSD2 guidance regarding this topic. 46

47 Thank you! 47