FoodEx2 Browser user s guide. European Food Safety Authority (EFSA), Francesco Vernazza and Valentino Avon

Transcription

1 TECHNICAL REPORT APPROVED: 30 August 2017 doi: /sp.efsa.2017.en-1291 Abstract FoodEx2 Browser user s guide European Food Safety Authority (EFSA), Francesco Vernazza and Valentino Avon FoodEx2 is a comprehensive and flexible food classification and description system developed by EFSA to support exposure assessment and data collection and exchange in different food safety-related domains. In connection to the classification, EFSA has developed the FoodEx2 browser, an open source tool for European data providers and international organisations like FAO to support the use of FoodEx2. The browser has progressively been enhanced based on the comments of the users of FoodEx2. The latest revision of the browser is available on EFSA s website and is freely available for download. The present report is a guide for the installation and use of the latest version of the browser and is also available for free download in the EFSA website. This report has been developed as partial fulfilment of a traineeship in the Evidence Management unit at EFSA. European Food Safety Authority, 2017 Key words: food classification, browser, FoodEx2 Requestor: EFSA Question number: EFSA-Q Correspondence: data.collection@efsa.europa.eu EFSA Supporting publication 2017:EN-1291

2 Acknowledgements: EFSA wishes to thank the EFSA Evidence Management (DATA) unit for the support provided to this report. Suggested citation: EFSA (European Food Safety Authority), Vernazza F and Avon V, FoodEx2 Browser user s guide. EFSA supporting publication 2017: EN pp. doi: /sp.efsa.2017.en-1291 ISSN: European Food Safety Authority, 2017 Reproduction is authorised provided the source is acknowledged. 2 EFSA Supporting publication 2017:EN-1291

3 Summary FoodEx2 is a powerful and flexible food classification system developed by EFSA in 2011 to support several food safety-related activities, in particular for performing exposure assessment from food and feed and for collecting the data needed to this purpose. A browser to support navigating the classification and encoding was developed for users of the system 1 and has been progressively improved based on suggestions received by the users of FoodEx2 in the European Member State (MS) organisations providing data to EFSA or in international organisations like FAO, as well as EFSA staff. The latest revision of the FoodEx2 browser is made available for free download in the EFSA website. The present guide, also available for free download on the EFSA website, explains how to install the FoodEx2 Browser and the functionalities it offers to the users. Apart from the menus and the different navigation functions, of particular interest are the sections on search and those allowing to compose a complex FoodEx2 code (the describe function). The guide is an introduction for beginners to the functionalities of the browser and also represents a reference guide for all features of the program for more experienced users. This report has been developed as partial fulfilment of a traineeship in the Evidence Management unit at EFSA. 1 Download link available at EFSA Supporting publication 2017:EN-1291

4 Table of contents Abstract... 1 Summary Background and Terms of Reference as provided by the requestor How to install and execute the tool Features of the tool Main menu Navigation Search Navigation tree browsing Navigation information on the elements Describe feature: building a FoodEx2 code References Glossary and Abbreviations EFSA Supporting publication 2017:EN-1291

5 1. Introduction 1.1. Background and Terms of Reference as provided by the requestor 2 In 2010, the first version of the Guidance on Standard Sample Description (SSD1) (EFSA, 2010) was published by EFSA aiming at harmonising the collection of analytical data on the occurrence of chemical substances in food and feed. In 2013, the data model was extended to cover additional data collection domains such as zoonotic agents in food and animals, antimicrobial resistance and food additives (EFSA, 2013). The revised model (Standard Sample Description ver. 2.0, SSD2) specifies the data elements and the data structure to describe the characteristics of several samples and analytical results transmitted from data providers to EFSA in support to its risk assessments. In order to estimate consumer exposure to hazards in food, EFSA needs to combine occurrence data with data on food consumption across the EU Member States. The food consumption data have been gathered by EFSA in the Comprehensive European Food Consumption Database; the data in this database have been collected with different methodologies in different countries. Since 2011, EFSA has launched the EU Menu project, which, based on the guidance on the EU Menu methodology (EFSA, 2014), aims at harmonizing the European Food consumption survey methodology across European countries, thus improving the comparability of the data for exposure assessment. A key element needed to collect, collate, compare and combine data for food safety and to allow dietary exposure assessment is a precise and harmonised description of the food matrix analysed or consumed. The first standardised detailed Food Classification and Description System (initially referred to as FoodEx (EFSA, 2011a), now as FoodEx1) was developed by EFSA at the end of 2008 within the SSD1 framework. It consists of about 1,700 terms (food groups) organized in a hierarchical system based on 20 main food categories that are further divided into subgroups up to a maximum of 4 levels; each term is identified by a unique code. FoodEx1 is the classification used in the Comprehensive European food consumption database project started by EFSA in In the following years, based on the experience gathered in the use of FoodEx1, a more detailed Food Classification and Description System (named FoodEx2 revision1) was developed and released in 2011 (EFSA, 2011b,c). The new system was tested during three years in 20 pilot projects granted by EFSA to Member State organisations (M , M , M ), whereby areas for improvement were highlighted. Considering the outcome of the testing phase, in 2015 FoodEx2 revision 2 was published by EFSA (EFSA, 2015). FoodEx2 is a comprehensive Food classification and description system for exposure assessment applicable across different food safety domains including food consumption, chemical contaminants, pesticide residues, zoonoses and food composition. The system is based on detailed food groups and different facets. Facets are collections of descriptors, each providing different options to describe a particular aspect of a food group (e.g. treatment, production method, fat content, packaging material, etc.). FoodEx2 is organized in different hierarchies for each relevant food safety domain such as the Exposure hierarchy, the Zoonoses hierarchy or the Pesticides hierarchy. In particular, the Exposure hierarchy was especially developed for the collection of food consumption data and the estimation of dietary exposure to chemical hazards. The flexibility and comprehensiveness of FoodEx2 requires tools to support the creation of the codes and the use of the classification. In particular, a browser for navigating the structures of FoodEx2 and creating the complex code of a food item was developed by EFSA in Java. This tool was provided as is without any specific guarantee regarding its functioning or maintenance; however, it was used by most of the scientists working on FoodEx2 until now and it proved very useful though the software only had basic functionalities. The browser, together with the related database containing the terminology and a short instruction for use, was made freely available on the EFSA website 3 ; however, both tools are now replaced by the latest version of the browser (EFSA, 2017) and the detailed user s guide represented by this report. 2 Mandate M : Full implementation of FoodEx2 food classification system, including amendments based on the outcome of pilot studies with Member States, training on FoodEx2 for Member States, and annual maintenance of the system. 3 Made available online at EFSA Supporting publication 2017:EN-1291

6 The further development of this tool was suggested by users of FoodEx2 in the MS organisations providing data to EFSA and many possible enhancements were identified. Now, in the framework of a traineeship in the Evidence management unit in EFSA, all the pending improvements were implemented and brought to the release of an improved browser (EFSA, 2017); The present guide, also available for free download on the EFSA website together with the browser 4, explains how to install the FoodEx2 Browser and the functionalities it offers to the users. Apart from the menus and the different navigation functions, of particular interest are the sections on search and those allowing to compose a complex FoodEx2 code (the describe function). The guide is an introduction for beginners to the functionalities of the browser and also represents a reference guide for all features of the program for more experienced users. This report has been developed as partial fulfilment of a traineeship in the Evidence Management unit at EFSA. 2. Data and Methodologies This user s guide refers to the latest version of the browser (EFSA, 2017); it presents to the user different features available in the browser for searching terms, navigating the system and composing complex FoodEx2 codes. The guide provides pictures of the different menus and windows of the browser and descriptions to drive the user through the available menus and the way they work. 4 Download link available at EFSA Supporting publication 2017:EN-1291

7 3. Guide If you are a user approaching the FoodEx2 browser for the first time, the following chapter will show how to install and run the browser. For more experienced users, this guide provides a quick reference to functions that are rarely used How to install and execute the tool Installing the Foodex Browser is a simple procedure, not requiring much effort. In particular, perform the following operations: 1. Extract the zip file in the folder where you want to install the Foodex Browser. 2. Once that the extraction procedure is terminated, open the DefaultProperties.xml file (located in the User Files directory) with a generic text editor program. 3. Search in the file the line related to the key Application.Dir : 4. Change the content of the entry path (in the example the D:\FoodexBrowserHome ) with the path of the directory which will contain the Foodex database in your PC. You can easily do this by opening the folder which contains the Tool and copying the address as text from the Windows Explorer, and pasting the address in the DefaultProperties file in Notepad 7 EFSA Supporting publication 2017:EN-1291

8 5. Save the text file with File->Save. 6. Run the CatalogueBrowser.exe application. A warning should be raised telling you that the database is empty. Press OK, then you should be able to see the Foodex Browser main page without any data loaded. 7. Click in the upper left menu, File -> Open. 8. Select the.catalog file (i.e. the database) which you want to load into the Foodex Browser. If everything goes fine, you will see the Foodex Browser with data loaded into it. 8 EFSA Supporting publication 2017:EN-1291

9 3.2. Features of the tool Main menu The main menu includes four tabs: File, Edit, Tools and Help. You can access several functionalities of the Foodex Browser from the Main menu. You can find it in the upper left corner of the main page. The File menu item allows you to open a Foodex catalogue in the browser (Open ) or to save the current catalogue in a.catalog file (Save as ). Moreover, you can create a simple report for visualization purposes just clicking the Report item. More precisely, you can select the terms that you want to report and you can choose if some basic statistics should be included in the report file, or not (for further details on reports see Section ). Finally, you can exit the tool with the Exit item. The Edit menu item offers to you three important features which help the Foodex navigation. In particular, you can collapse the navigation tree (i.e. all the open elements of the main tree will be closed) or you can expand or collapse a node, that is, all the terms that are under the term selected in the tree will be expanded or closed respectively. Favourite Pick List; in case you have pre-defined lists of codes (pick-lists) here you can select the pick-list that you want to use in the Foodex Browser. The Pick-lists have a specific format and must be inserted in the Picklists folder of the Foodex Browser; otherwise they will not be recognized by the tool. For more information about picklists see Section General Search Options; here you can decide the search criteria which are used in the Tool for retrieving terms with search functions (see Section for further details). User Preferences; here you can set your preferences regarding several aspects of the Foodex Browser. See Section for further information about user preferences Report Window The Report Window is accessible from the main menu (File -> Report) and allows generating a simple report for visualization purposes. You can choose the file name and format by clicking the three dots on the right. This opens an explorer window, which allows you selecting these parameters. 9 EFSA Supporting publication 2017:EN-1291

10 Here you can choose the folder which will contain the report file. Moreover, you can write the desired report name in the File name field and you can choose the report format in the Save as type field. In particular, you can choose between.txt and.htm formats. Once you have inserted the required information, click the Save button to return to the main Report Window. In the main Report Window, if you want to add statistics on the numbers of entries at the different levels check the Add statistics checkbox. You can select which hierarchies/facets lists you want to add in the report by checking them in the tree, which is located in the centre of the Report Window. Once you have checked the elements you are interested in, click the OK button in the main Report Window to generate the report. The report appears in a separate window (as preview) and is also saved in the chosen directory as file User Preferences The User preferences help you customize your user experience with the Foodex Browser. In particular, you can modify the following options: 10 EFSA Supporting publication 2017:EN-1291

11 Min search chars; this value is the minimum number of characters that has to be inserted in a search panel in order to execute the search. The default value is set to 3, since searching terms using only two letters could return too many, not related, results. Logging; this value can be either set to TRUE or to FALSE. A TRUE value means that a log file will be created while the Foodex Browser is working. This is needed only for de-bugging purposes and should be avoided during normal operations, since a new file is created each time the browser is opened Current directory; this string is the path of the directory which contains the Tool. Copy Implicit Facets; this value can be either set to TRUE or to FALSE. A TRUE value means that implicit facets codes will be shown in the full codes in the Describe Window. Unless there are specific needs, the value should be set at FALSE, since while reporting data the implicit facets shall not be reported. Max recent terms; the maximum number of recently described terms recorded by the tool (see Section for further information). Business Rules Checks; this value can be either set to TRUE or to FALSE. A FALSE value means that the business rules checks (Section ) will be disabled in the Describe Window. Domains which are related to consumption should set this value to TRUE, since these rules were created specifically for consumption data Navigation Search The Foodex Browser provides you with a powerful and flexible search function to quickly find specific terms through the catalogue. The main search function is accessible from the main page of the Foodex Browser and it allows searching several fields related to the terms How to execute a search Search Options You can execute a search in different ways, but the most common one consists in searching a term through its name or a part of it. Remember that you can also search terms through any names, codes (or a substring of them) related to the terms, such as scientific names, GEMS and pesticide codes. If you want to restrict the search to some fields (e.g. code and name) you can set the options in the General Search Options window (Section ). Another core feature which is provided by the Foodex search function is the search methodology. More precisely, you can choose among three different search strategies: 11 EFSA Supporting publication 2017:EN-1291

12 Exact Match; the Tool searches the given keywords as a single string, exactly as they are written; in this case, the order of the keywords is relevant. Any Word; the Tool searches all the terms which contain at least one of the written keywords. Note that the order of keywords is not relevant. All Word; the Tool searches all the terms which contain all the written keywords. Note that the order of keywords is not relevant. Moreover, you can choose to search terms with two different scopes using the highlighted radio buttons: Search current = search in the current hierarchy only Search dictionary = search in all the available hierarchies and facets lists (the search is performed on the complete terminology) Executing a search Example of Usage Exact match with kiwi and frui as search keywords. The Tool retrieves all the terms which contains in full kiwi and frui. This means that searching kiwi ruit (f is missing) will not find the terms called kiwi fruits. Any word with kiwi and ruit as search keywords. The tool retrieves all the terms which contain at least one of the keywords. This means that the Tool will return all the terms that contains the word kiwi or the word ruit. Note that in this case even if the f of fruit is missing, nevertheless all the terms are found, because the two keywords are searched independently. All word with kiwi and frui as search keywords. The Tool retrieves all the terms which contain both the keywords. Practically, this search method relaxes the constraint imposed by the Exact Match method Setting the search preferences The Foodex Browser provides you with a way to customize the search results. More precisely, you can choose which type of terms should be included in the results, and which fields of the terms have to be taken into consideration while searching keywords inside the terms (as previously said in Section ) EFSA Supporting publication 2017:EN-1291

13 For example, you can choose to display only results for raw primary commodities terms, and to search keywords only in a subset of additional fields of the term, as scientific names and GEMS code 5. You can access the search preferences through the main menu, clicking General Search Options in the Tools menu item. You can choose which type of terms to visualize in the search results (Search options table) and which additional fields should be analysed in the search (Additional search fields table). Note that these are general search options; therefore they will be used in each search panel of the Foodex Browser (except while searching picklists and recently described terms) Navigation tree browsing As you may know, the Foodex Browser contains a high number of terms (both list terms and facets), which are organized in several hierarchies. This chapter will explain how you can navigate this huge amount of information in an easy manner. The Tool provides you with a way to browse all the terms with an intuitive interface, which is basically a tree (i.e. a list with indented levels) that shows all the terms with their parent-child relationships. The logic is simple: A parent term is an element which includes one or more indented terms under it; The indented terms are called children of the parent term; A term could be both a parent and a child; As you open the higher levels of the tree (i.e. you go deeper in the branch ), you will get more detailed terms until you reach the last level term ( leaf ) Opening, closing and navigating the tree The tree panel is shown in the main Foodex Browser page in the frame at the centre of the screen. The picture shows you the tree panel with the terms regarding the reporting hierarchy. You can easily recognize that the main elements are Food, Feed and Non-food matrices for this hierarchy, since they are the less indented terms. You can open and see the children of a parent term simply by left clicking the white arrow placed in the left of the term name. Similarly, you can close the opened children of a parent term by 5 Global Environment Monitoring System of the World Health Organisation EFSA Supporting publication 2017:EN-1291

14 left clicking again the black arrow. Remember that you can browse the tree also using the Expand Node, Collapse Node and Collapse Tree functions in the Tools menu item. In the case of Expand node or Collapse node, the highlighted node is intended; more than one node may be opened with a single click by highlighting them all keeping CTRL pressed. Using the tree panel you can browse both hierarchies and facets. More precisely, you have to select the correct radio button highlighted in red colour, and then you can open the list box and choose the hierarchy/facet list you want. You can also filter the tree terms by their applicability. In fact, you can choose to see either the terms that are in use in the domain or those which were in use previously but were dismissed, or both. A dismissed term is easily recognizable, since it contains a [DISMISSED] flag at the end of its name. Non reportable terms are always shown instead, and they contain a [NON REPORTABLE] flag at the end of their name. Non reportable terms are for example the hierarchy terms (blue pyramids) What if you have found the term that you are interested in, but in the wrong hierarchy/facet list? You can right click the term to open the contextual menu and select the See in other hierarchies menu item. This item will show you all the hierarchies/facet lists where the selected term is in use and allow changing the hierarchy/facet list maintaining the selected term opened Connection with search Browsing the tree through the parent-children exploration is easy, but can become a quite long procedure if you do not know where the term that you are searching is. For this reason, the search panel of the main page was connected to the tree panel. In fact, if you select a term contained in the search results box, the tree will show it in the current hierarchy (if present) EFSA Supporting publication 2017:EN-1291

15 If the term is not present in the current hierarchy, no automatic action is performed. Nonetheless, you can right click in the search results box the term that you are interested in to open a contextual menu, which will allow you to open the term in any of the hierarchies/facet lists where it is in use Contextual menu of the tree You can access the contextual menu of the tree by right clicking one element of it. In particular, here you can do the following: See in other hierarchies; open the selected term in one of the hierarchies which contain it Copy; copy the code of the term in the clipboard Copy code and name; copy the term code and its name (tab-separated) in the clipboard Copy full code and name; copy the term full code (i.e. the code also includes the implicit facets codes) and its name (tab-separated) in the clipboard The other menu items provide more complex functions and therefore are explained in a subsequent specific Section (Section 3.2.5) Navigation information on the elements The name of a term could be not sufficient to precisely identify the type of food it represents. Moreover, you could encounter some terms which are named with a specific convention that you do not know. For these reasons, the Tool provides near the tree frame a frame which helps to better understand the nature and the scope of terms EFSA Supporting publication 2017:EN-1291

16 The frame we are talking about is located in the right side of the main page. As the snapshot shows, the Tool provides all the data needed to define a term. In particular, the Term naming and definition tab shows the following information: State: the term type (raw commodity, derivative etc.). Corex: a flag which indicates how detailed is the food group defined by the term. Term Name Correlated Codes: some relevant codes for the same food group in other classification, e.g. the pesticide code. Scientific Names: the names used in official taxonomies in relation to the selected term. Alias Included terms: synonyms of the term name or name of similar items which are all included in the scope of the chosen group. Scope notes: textual information helping describing the selected term. Links: URL links which guide you to web sites providing more specific information related to the term. The Implicit facets tab, instead, shows you the implicit facet descriptors for the selected term. These descriptors are organised by facet and the header of the facet is also given EFSA Supporting publication 2017:EN-1291

17 The tabs are updated each time you select a term in the tree panel. An important feature of the scope notes is the interactive search in the web. To do this, select some interesting text which you want to analyse better, and right click it. This will open a contextual menu providing the option to search the selected text in Google, Google Images and Wikipedia. Moreover, you can directly translate a phrase through Google Translate. Note that you can easily auto-select a single word directly right-clicking it; the Tool will recognize the clicked word and will open the contextual menu on that word Describe feature: building a FoodEx2 code The describe feature is the main function of the Tool, since it allows building the full complex FoodEx2 code of a given food. In particular, this procedure implements all the rules described in the Chapter 5 of the report The food classification and description system FoodEx2 (revision 2) (EFSA, 2015) Description starting from the base term Once you have decided which base term from the tree panel needs to be described (by adding facet descriptors), you can right click it and choose the menu item Describe, in order to open the Describe Window. Alternatively, you can simply double click the term of interest. The selected element will be treated as base term for the describe function, and its code will automatically be loaded into the Describe window. The following snapshot shows the Describe Window: 17 EFSA Supporting publication 2017:EN-1291

18 On the left of the window all the facets for the described term are listed grouped by their type (the implicit facets were automatically added by the Tool), while on the upper right the codes related to the described term are shown. In particular, you can read the full code of the term, which is generated by the base term code, concatenated with the explicit facets codes with the following syntax: BaseTermCode#FacetHeader1.FacetCode1$FacetHeader2.FacetCode2$... In the picture, Andigena was chosen as base term and the Slicing process facet was added. Moreover, the Tool provides you also an interpreted version of the full encoding. This is useful to understand which facets were added to the base term with a human-readable text. In the example, the interpreted code tells that a Slicing process facet was added to the base term Andigena. Note that if you set to TRUE the copy implicit facets preference (in the user preferences entry of the menu Tools ), the full code and the interpreted code would include the implicit facets codes also. The following pictures should clarify this concept. The Describe Window also implements a system which checks several business rules, in order to guide you to a correct encoding. If you perform a wrong encoding action, then the Log Console will warn you with a text and the overall warning level will be accordingly set (green= not an issue, 18 EFSA Supporting publication 2017:EN-1291

19 yellow= possible problem, red=probable serious problem). For further details about the business rules, see Section How can I add new facets to the description? You can add new facets simply right clicking on the facet group that you are interested in, and then clicking the Add menu item in the contextual menu. Alternatively, you can simply double click the facet group. Once you have clicked the Add menu item, the following window will appear: You can use this window to select which descriptors for the chosen facet to add to the base term. If the selected facet group allows adding more than one element, then the multiple selection will be enabled, that is, the checkboxes located on the left of the terms names will appear. You can use this checkboxes to select multiple descriptors at a time for the facet (if allowed). You can see that the interface of this window is very similar to the main page of the Tool; therefore the usage is intuitive. In fact, a tree which allows browsing the facet descriptors and a search box to search through them are provided (the global search options are used here as well as in the main page search). Moreover, all the relevant data related to the descriptors are reported (i.e. scientific names, alias and scope notes with links) EFSA Supporting publication 2017:EN-1291

20 Note that an additional box called Selected Elements is present. This box is used only in the multiple selection case and it contains all the facets which were selected until that moment and allows you to read their information and possibly to remove them from the selection. In fact, the facet descriptors will be actually added only if you click the OK button. The search panel works exactly in the same way as the main one (Section 3.2.2). The only difference lies on how the results are shown. A simple search results window is opened when you press the Go button or the ENTER key from the keyboard. Here you can see all the search results and then double click the descriptor which you want to add. In the multiple selection case, the facet will be added into the Selected Elements box. In the single selection case, instead, the facet will be immediately added to the base term, and the application will return to the Describe Window. At the end of this process you will return to the Describe Window, where you can add other facets or copy the codes. In particular, once you have added all the required facets and thus generated the final encoding, you can perform the following actions from the describe window: Copy the full code with the Copy button Copy only the interpreted code with the Copy description button Copy both the full code and the interpreted code (tab separated) with the Copy code+descr. button Close the Describe Window with the Close window button Description starting from a recently created code We have seen that a term can be described starting from the base term, but actually this is not the only way to describe a term. In fact, you can use more sophisticated functions provided by the Tool to make the description process easier and faster. In particular, you can start describing from a recently created code or from a specific pick-list created ad-hoc for your encoding needs. In this Section we focus on the former, while in Section we show the latter. For several reasons it usually happens that you need the code of a term which you have already described recently. If you start from the base term, you will have to add all the required facets again, in order to reproduce the old code. This could be a relatively long procedure. The Recently described terms function is basically a way to recover the codes of terms which you have described recently, in order to avoid the long procedure discussed above. Moreover, this functionality allows also extending their code adding other facets, if you need to make more specific encodings EFSA Supporting publication 2017:EN-1291

21 You can access the recently described terms by right clicking anywhere in the main tree panel of the Tool. This will open the usual contextual menu, which allows you selecting the Recently Described Terms menu item. A new window will be opened, from which you can access and analyse the recently encoded terms. The window shows a list of the terms which were recently described with their full and interpreted codes; you can scroll the list. Additionally, you can search through the terms using the search bar on the upper left. This search function is particular, because it is not subjected to the global search options. In fact, for efficiency reasons it relies only on term names and interpreted code. Once you have selected a recent term, you can either copy its codes or load the term into the describe window using the Load Term in Describe button. Describing a recent term allows you adding new facet descriptors or removing old ones. For example, we can reload the Andigena term with the Slicing facet in the Describe Window to modify it. It is clear that this procedure saves you a lot of time if you have to describe many similar food items with slightly different characteristics. Note that maintaining too many recent terms in memory could be useless and could hamper the efficiency of the tool, since the term list could be subjected to some slowdowns. For this reason, the default number of recently described terms which are stored is limited to ten. You can customize this number accessing the User Preference window (see Section ) Description from a pick-list Similarly to what explained in the previous Section ( ), sometimes several terms could be repeatedly encoded with the same or slightly different codes. In particular, each domain owns many complex terms which are quite commonly used; therefore it is convenient to allow personalised coding lists to help encoding common terms for a specific domain, and to standardize the encoding itself. Here comes in the concept of pick-list, which is a CSV file semicolon-separated, that may contain several complex terms which are common in a particular domain. These terms were already described; therefore you can simply load them (in analogy to the recently described terms) into the Tool to easily use the standard encoding or modifying it. How can I import and open a pick-list into the Foodex Browser? Once you have created a pick-list (e.g. by saving as.csv a spreadsheet with the appropriate structure and content), it is sufficient to locate the file into the Picklists subfolder of the folder where the Tool resides. The Foodex Browser will automatically recognize it EFSA Supporting publication 2017:EN-1291

22 Inside the Tool you can choose which pick-list you want to use from the Tools menu item. Select Tools -> Favourite Pick List ->. In this way the Tool will use the selected pick-list. You can access the pick-list terms by simply right clicking anywhere in the tree main panel and selecting the menu item Favourite Picklist. This will open a new window very similar to the one used for the recently described terms. The list of predefined terms is then loaded into the Tool and you can select the one you are interested in. The search bar works exactly in the same way as the one used in the recent terms window (i.e. it uses the term names to filter the results). Here, you can either copy the term codes or load them into the Describe Window to modify their predefined facets.? This functionality helps you saving time using standardized codes for your encodings. Moreover, it allows avoiding encoding errors, since standardized codes are used. If you are interested in creating your own pick-list, go at the end of this Section and read the How can I create my own pick-list paragraph. Advanced Search in the favourite pick-list The Tool provides you even a smarter way to execute a search inside of a pick-list. In fact, you can search which pick-list terms contain a specific term in their explicit/implicit facets. This allows you to perform searches with a different criterion, which can be useful for some purposes. The procedure is really simple. Select from the main tree panel the term which you want to search in the pick-list, and right click it. Choose from the usual contextual menu the menu item Search in favourite picklist EFSA Supporting publication 2017:EN-1291

23 The pick-lists window will appear, showing the search results in the pick-list term list. The example shows the results of a search, in which we have chosen as search term the Cattle (live animals). As you can see, the reported pick-list terms shown are only the terms which contain among their explicit/implicit facets the term Cattle (live animals). How can I create my own pick-list? A pick-list is a CSV semi-colon separated file; therefore you can generate and easily edit it using a spreadsheet. In this section, we explain how to create a correct pick-list by filling the right data into the right column of the CSV file. A pick-list contains three mandatory columns and an optional one. In particular, the mandatory fields are: Level: this is an integer which can take any value greater or equal than 1. This column is used for visualization purposes only. In fact, its value means how much should this term be indented in the pick-list?. This feature is useful to distinguish groups of terms with a sort of hierarchy. The default value is 1, which means no indentation. Pick-list elements: this is the name which will be visualized in the Pick-list Window to identify the term. Note that this name is not only used for visualization purposes, since the search inside the Pick-list window uses only this name as search field. Therefore, it could be useful to insert in the name keywords or codes which discriminate the terms, in order to be able to find what you need simply using the search bar function. Pick-list code: this is the foodex2 encoding which contains the base term and all the explicit facet descriptors following the FoodEx2 code standard pattern (basetermcode#facetheader1.facetcode1$facetheader2.facetcode2$...). Note that as usual you should not include the implicit facet descriptors in this encoding, because they are already present in the classification system. This field is used to load the base term and all the added facet descriptors into the Describe Window. The optional column is: allfacets: this is the full code of the base term related to the pick-list term. This encoding follows the usual syntax of full codes (the same mentioned in the above point), but it contains only the codes of the implicit facet descriptors. This field was created for a more technical reason. In fact, the implicit facet extraction from the database would take a long time, if the pick-list is very long. This column provides this information directly without interacting with the database, therefore the search function results less computational intensive. If the column is not present, it is simply ignored by the program; if it is present, the search function searches the selected term also in the implicit facets of the picklist terms. A picklist term with an empty value in the allfacets column will results as if it would have no implicit facets. Once you have created your own pick-list, you can save it into the Picklists folder of the FoodEx Browser as a CSV file (semi-colon separated) using the export function of Excel save as CSV. At this point the picklist is ready to be chosen as favourite pick list and used by the browser EFSA Supporting publication 2017:EN-1291

24 If you require more information about the use of pick-list inside the Tool, see the beginning of this Section Implementation of rules for coding while describing At the beginning of the Section 3.2.5, we said that the Describe Window implements a system which checks if you are making a correct encoding and provides automatic warning during the coding process. In this Section, we will provide additional information on this feature implementing the rules described in the Chapter 5 of the report The food classification and description system FoodEx2 (revision 2) (EFSA, 2015). The Tool communicates with you through two graphical elements of the Describe Window. In particular, the window includes a semaphore, which is a canvas highlighting through its colour the eventual presence of potential errors and their severity (Overall warning level). Moreover, a log console (Message Log) sends messages explaining the possible issues encountered during the encoding until now. Note that also the messages are coloured based on the severity colour scale, but are not necessarily linked to the semaphore colour. In fact, some messages can be somewhat serious, but if the Tool cannot conclude that there is a real mistake, the semaphore will not be changed. These peculiar messages usually suggest you to check some facets, because they may be one of the allowed exceptions or a serious error. Green messages and semaphores tell you that no known potential mistake was identified. Yellow and red colours tell you instead that a low level and a high level warning were raised respectively. In both cases, check accurately the possible errors following the messages of the log console EFSA Supporting publication 2017:EN-1291

25 4. Conclusions This user s guide explains in simple terms how to install and use the FoodEx2 Browser published in 2017 (EFSA, 2017) and available for free use on the EFSA website. Following the different sections of the user interface and the menus, all the functionalities of the browser are shown with examples, to introduce new users to the use of the tool. Also in the case of proficient users, the guide is useful as a reference for rarely used features of the tool. References EFSA (European Food Safety Authority), EFSA Guidance on Standard sample description for food and feed. EFSA Journal 2010; 8(1):1457, 54 pp., doi: /j.efsa EFSA (European Food Safety Authority), 2011a. Evaluation of the FoodEx, the food classification system applied to the development of the EFSA Comprehensive European Food Consumption Database. EFSA Journal 2011; 9(3):1970, 27 pp. doi: /j.efsa EFSA (European Food Safety Authority), 2011b. Report on the development of a food classification and description system for exposure assessment and guidance on its implementation and use. EFSA Journal 2011; 9(12):2489, 84 pp., doi: /j.efsa EFSA (European Food Safety Authority), 2011c. The food classification and description system FoodEx 2 (draft revision 1). Supporting Publications 2011:215, 438 pp. Available online: EFSA (European Food Safety Authority), Standard Sample Description ver EFSA Journal 2013; 11(10):3424, 114 pp. doi: /j.efsa EFSA (European Food Safety Authority), Guidance on the EU Menu methodology. EFSA Journal 2014;12(12):3944, 77 pp. doi: /j.efsa EFSA (European Food Safety Authority), The food classification and description system FoodEx2 (revision 2). EFSA supporting publication 2015:EN pp. EFSA (European Food Safety Authority); Vernazza F and Avon V, FoodEx2 Browser enhancement. EFSA supporting publication 2017:EN pp EFSA Supporting publication 2017:EN-1291

26 Glossary and Abbreviations DATA Unit DCF EFSA EU EU Menu Facets FAO Evidence Management Unit of EFSA. Data Collection Framework. European Food Safety Authority. European Union. Fully harmonised European Food consumption survey methodology. Collections of (food) descriptors from specific points of view included in FoodEx2 Food and Agriculture Organisation of the United Nations FoodEx1 Preliminary detailed food classification developed by EFSA in FoodEx2 Multi-purpose food classification and description system developed by EFSA. Revision 1 of FoodEx2 was published in 2011, while revision 2 was released in GEMS SSD SSD1 SSD2 Global Environment Monitoring System Standard sample description. Standard Sample Description rev.1. Standard sample description rev.2 (extended to different food safety domains, including Zoonoses, residues of veterinary medicines and food additives) EFSA Supporting publication 2017:EN-1291