Mapping Tool User Manual

TECHNICAL REPORT
APPROVED: 14 February 2017
doi:10.2903/sp.efsa.2017.EN-1181
User manual for data providers

for mapping Member State standard terminology
to EFSA standard terminology
European Food Safety Authority
Abstract
The European Food Safety Authority (EFSA) is tasked with coordinating the reporting of zoonoses,
zoonotic agents, animal populations, antimicrobial resistance and food-borne outbreaks in the
European Union (EU) under Directive 2003/99/EC, as well as analysing and summarising the data
collected. For data collection purposes, EFSA created a simple Microsoft Office Excel-based mapping
tool to allow Member States (MSs) to map their standard terminology to EFSAs standard terminology.
This technical report is a user manual for data providers (reporting officers and reporters) that
describes how to map terms and generate extensible markup language (XML) for submission of 2016
data to EFSA, according to Zoonoses data models: prevalence, antimicrobial resistance, food-borne
outbreak, animal population, disease status and text forms.
European Food Safety Authority, 2017
Key words: zoonoses data models, Excel, XML, XSD, DCF

Requestor: European Food Safety Authority
Question number: EFSA-Q-2016-00786
Correspondence: zoonoses_support@efsa.europa.eu
www.efsa.europa.eu/publications EFSA Supporting publication 2017:EN-1181

Mapping tool user manual for the 2016 data
Acknowledgements: EFSA wishes to thank the members of the Scientific Network for Zoonoses
Monitoring Data that reviewed this report, and EFSA staff members: Kenneth Mulligan, Doreen
Dolores Russell and Anca-Violeta Stoicescu for the preparatory work on this technical output.
Suggested citation: EFSA (European Food Safety Authority), 2017. User manual for data providers
for mapping Member State standard terminology to EFSA standard terminology. EFSA supporting
publication 2017:EN-1181. 26 pp. doi:10.2903/sp.efsa.2017.EN-1181
ISSN: 2397-8325
European Food Safety Authority, 2017
Reproduction is authorised provided the source is acknowledged.
www.efsa.europa.eu/publications 2 EFSA Supporting publication 2017:EN-1181

Summary
This user manual provides guidance to data providers on the use of the Microsoft Office Excel-based
mapping tool for the submission of 2016 data by Member States (MSs) and other reporting countries.
This tool was developed by the Evidence Management Unit (DATA) in order to help MSs to report
electronic data for zoonoses, zoonotic agents, animal populations, antimicrobial resistance, food-borne
outbreaks and text forms according to the zoonoses data models.
The manual provides a general introduction to the mapping tool and covers all aspects related to the
management and use of the mapping tool. In particular, detailed guidance is provided for the
mapping of standard terminology used at national level to EFSA standard terminology, and the
creation of a locally validated extensible markup language (XML) file for submission of data to EFSA
via the Data Collection Framework (DCF).
This manual is specifically aimed at guiding the mapping of MS-specific standard terminology to EFSA
standard terminology, thus creating a much needed centralised document on mapping of controlled
terminology.

Table of contents
Abstract.........................................................................................................................................1
Summary .......................................................................................................................................3
1. Introduction........................................................................................................................5
2. Introducing the mapping tool...............................................................................................6
2.1. How the coded sheet works...............................................................................................10
2.2. General points on Excel worksheets ...................................................................................11
3. Getting started by profiling your data .................................................................................11
3.1. Mapping your profiled terms ..............................................................................................13
3.2. Steps in the mapping process ............................................................................................14
3.3. The catalogue/hierarchy search functionality ......................................................................15
4. Refreshing and changing views on data..............................................................................17
4.1. The adding and removing of formula rows..........................................................................17
4.2. The refreshing of data.......................................................................................................18
4.3. Different views on the codified data ...................................................................................18
5. Generating XML file ...........................................................................................................20
6. Rebuilding a broken coded file ...........................................................................................21
7. Particularities of the manual mapping tool ..........................................................................21
7.1. Adding rows with dropdowns in the ZOO_MAN worksheet ...................................................23
7.2. Rebuilding rows with dropdowns in the ZOO_MAN worksheet ..............................................23
7.3. Reporting repeatable data element ....................................................................................23
8. Text forms Manual Mapping Tool .......................................................................................23
References...................................................................................................................................25
Abbreviations ...............................................................................................................................26

1. Introduction
Background and Terms of Reference as provided by EFSA

EFSAs mandates for the production of annual European Union (EU) Summary Reports (EUSRs): 1) on
zoonoses and food-borne outbreaks, 2) on antimicrobial resistance (AMR) and on 3) Transmissible
1
Spongiform Encephalopathies (TSE) is described in a unifying charter that is available online. These
mandates from the European Commission to EFSA also require the production of reporting manuals
which need regular updating.
The production of the two former EUSRs, being 1) on zoonoses and food-borne outbreaks and 2) on
AMR is underpinned by the Directive 2003/99/EC laying down the EU system for monitoring and
reporting of information on zoonoses, which obligates the MSs to collect data on zoonoses, zoonotic
agents, antimicrobial resistance and food-borne outbreaks. EFSA is assigned the tasks of examining
the data collected and preparing the EUSRs in collaboration with the European Centre for Disease
Prevention and Control (ECDC).
Based on the data reported each year, EFSA and ECDC will jointly produce an annual EUSR on
zoonoses, zoonotic agents and food-borne outbreaks. Similarly, the two agencies will produce a EUSR
on antimicrobial resistance. To support the MSs in their reporting, the existing reporting manuals for
zoonoses, antimicrobial resistance and food-borne outbreaks need to be updated to take into account
the latest recommendations on reporting of antimicrobial resistance data and data on zoonoses and
food-borne outbreaks. In addition, the manuals have to be revised as a result of the changed
structure of the reporting tables in the web application and changes in the relevant EU legislation.
EFSA manages a Data Collection Framework (DCF), to which MS have the possibility of submitting
data in Extensible Markup Language (XML). New XML reporting schemas are created before the start
of the reporting period in April each year, and these are supported by revised reporting manuals.
To successfully run and complete these recurrent three annual projects the BIOCONTAM and Evidence
Management (DATA) units need to meet the following objectives:
Produce and publish:
The joint annual EUSR on Trends and Sources of Zoonoses, Zoonotic Agents and Food-borne
Outbreaks, and
The joint annual EUSR on AMR in zoonotic and indicator bacteria from humans, animals and
food
The annual EUSR on TSE.
Produce and publish the National Reports on Zoonoses, Food-borne Outbreaks and AMR, containing
raw data and statistics reported to EFSA by MSs (and a few non-MSs) for the purpose of providing an
overview at the national level.
Implement annual development improvements aimed at efficiency gains as regards IT, data collection
(data models and related tools) and data analyses, so as to shorten the production cycle of these
EUSRs. For the two annual joint EFSA-ECDC scientific reports (on zoonoses, and on AMR) the
production cycle is shortened by one month during 2015 and 2016 each year.
Support MSs in their activities of monitoring and reporting on zoonoses and AMR in animals and food,
and TSE, as necessary.
The Terms of Reference prescribes the delivery of five technical reports:
Manual for reporting on zoonoses and zoonotic agents, within the framework of Directive
2003/99/EC, and on some other pathogenic microbiological agents for information deriving
from the year 2016
Manual for reporting on food-borne outbreaks in accordance with Directive 2003/99/EC for
information derived from the year 2016
1
Available online: http://registerofquestions.efsa.europa.eu/roqFrontend/questionsListLoader?mandate=M-2015-0231

Manual for reporting on antimicrobial resistance within the framework of Directive 2003/99/EC
and Decision 2013/652/EU for information derived from the year 2016
Data dictionariesguidelines for reporting data on zoonoses, antimicrobial resistance and
food-borne outbreaks using the EFSA data models for the Data Collection Framework (DCF) to
be used in 2017, for 2016 data
User manual for data providers for mapping Member State standard terminology to EFSA
standard terminology
The present technical report is the manual for the Excel mapping tools pertaining to the 2016 data
collection.
2. Introducing the mapping tool

EFSA publish guidance on data submission using XML data transfer covering the reporting of isolate-
based quantitative antimicrobial resistance data, as well as reporting of prevalence data on zoonoses
and food-borne contaminants, food-borne outbreak data, animal population data, disease status data
and text forms (EFSA, 2017d). For zoonoses data collection, EFSA has created seven data models for:
zoonoses prevalence data (PRV), antimicrobial resistance isolate-based data (AMR), specific
monitoring of ESBL-/AmpC-/carbapenemase-producing bacteria, in the absence of isolate detected
(ESBL), food-borne outbreak data (FBO), animal population data (POP), disease status data (DST) and
text forms data (TXT).
The main objective of the mapping tool is to provide a simple and useable platform for MSs to map
their country-specific standard terminology to that published by EFSA and to enable the production of
an XML file for the submission of sample or aggregated-based zoonoses monitoring data via the DCF.
The catalogues and the specific hierarchy of each data model (AMR, ESBL, PRV, FBO, POP, DST and
TXT) are already inserted into each of the specific mapping tool. Specific Excel mapping tools
correspond to each of the seven data models are available.
For each of the Excel mapping tools a manual and a dynamic mapping template has been created to
encode MSs data to EFSAs standard terminology. The exception is the text forms mapping tool which
only has a manual mapping template. The mapping tool is a solution for MSs who are currently unable
to:
implement the EFSA data models in a database;
implement standard term mapping in a database;
automatically generate XML.
The Excel mapping tool could help MSs to:
create a comprehensive mapping of MSs standard terms;
improve the quality of data submitted to EFSA (with local data validation).
This mapping tool is useful not only for MSs reporting a small number of data, but also in
understanding what is needed to report row-level data via the DCF according to Zoonoses data
models.
This user manual introduces the basic functionalities available in the mapping tool, such as:
profiling data (selecting unique values from you data sets control terminology);
mapping profiled terms explicitly;
providing lookup and encoding of explicitly mapped terms;
generating and validating XML via published Zoonoses data models XML schema definition
(XSD).

Figure 1: Default worksheets of the dynamic mapping tool
The mapping tool is an Excel workbook which has three default data processing worksheets. Outside
of these three worksheets, each model contains all the catalogues/hierarchies needed for each data
model. All the catalogue/hierarchies worksheets have CAT_ at the beginning of or as the prefix to the
catalogue/hierarchies name. In these catalogue/hierarchies worksheets data providers need to map
their own specific terms to those required by EFSA.
In Figure 1 the default worksheets are presented:
Mapping_Options;
ZOO_FACT_(DATA MODEL_NAME);
CODED.
The Mapping_Options worksheet contains all the functionality which data providers need to manage
their mapping file. The features provided there are presented in each of the sections below.
ZOO_FACT_(DATA MODEL_NAME) or ZOO_MAN_(DATA MODEL_NAME) is where data providers insert
their own data. This is the first step whereby data providers must fit their current data into
the structure of the data model in question. This worksheet is the format into which
reporting countries must organise their data for successful mapping and submission of
data to EFSA.

Figure 2: ZOO_FACT worksheet displays mandatory, compound, facet and optional data elements
Each ZOO_FACT_(DATA MODEL_NAME) (Figure 2) worksheet displays:

the mandatory data elements (highlighted in red- ), that must be inserted into the model for
a valid submission to the DCF;
the optional data elements (highlighted in grey or yellow). Some of grey or yellow data
elements are mandatory in certain reporting conditions; as stipulated in the reporting manuals
and guidelines (EFSA, 2017 a, b, c, d);
the compound data element (highlighted in brown, column E in Figure 2) have been
introduced to allow the reporting of VTEC and MRSA using the facets (highlighted in yellow,
columns G, H and I in Figure 2);
The mapping tool supports three types of element types:
compound elements;
repeatable elements;
standard elements.
The compound data element (highlighted in brown, column E, zoonosis in Figure 2) produces a
coded value based on a collection of predefined elements known as facets (highlighted in yellow,
zoonosis_CC, zoonosis_ST and zoonosis_t in Figure 2), where each of these facets contributes to
the compound final code. When a facet value is mandatory, the data element is highlighted in red, but
its text is yellow (zoonosis_param in Figure 2).
Example: in the Figure 3, the code for zoonosis data element is automatically created in the CODED
worksheet using the combination of codes from zoonosis_param and zoonosis_CC facets for which
values were entered in the ZOO_FACT_(DATA MODEL_NAME) worksheet for the compound field
Zoonosis is RF-00000510-MCG#CC=3 which is.
Figure 3: The compound data element as displayed in CODED worksheed
The repeatable data elements are designed to allow the user to enter in multiple values for the
same data element; to do this, the mapping tool requires that each value to be separated with an
asterix * (without space).
In Figure 4 is an example of how a repeatable value can be reported using the dynamic mapping tool.
The value entered for the esbl element in the ZOO_FACT_AMR_ISOLATE_AST should be delimited
with *. When the mapping of the values inserted in the esbl data element is realised (in the

hierarchy CAT_PARAM_esbl) each of the value should be mapped to their corresponding EFSA control
terminology.
Figure 4: Repeatable data elements inserted in the dynamic mapping tool in

ZOO_FACT_AMR_ISOLATE_AST worksheet
Figure 5 displays in the CODED worksheet the code produced for the repeatable element esbl.
Figure 5: The repeatable data elements in the CODED worksheet
The standard data elements are a single elements which are linked, one to one, between the
values entered for the element and the corresponding mapped element code (only if the standard
element is linked to an EFSA control terminology catalogue/hierarchy).
To further improve the tools usability, definitions for each data element have been included in the
ZOO_FACT_(DATA MODEL_NAME) worksheet (Figure 6). To observe the definition, data providers can
simply place the mouse over the element name displayed in row one of the worksheet and that
elements definition will be displayed (Figure 6). By clicking on the element name, data providers will
be transferred to that elements catalogue/hierarchy and can see the terms that are permissible and
the mappings that have been made between the data providers data and EFSAs standard
terminologies.
Figure 6: ZOO_FACT worksheet displays the definitions for each data element

The CODED worksheet (Figure 7) reads the data inserted into the ZOO_FACT_(DATA MODEL_NAME)
or ZOO_MAN_(DATA MODEL_NAME) worksheet and then searches for the correct mapped term in the
various catalogue worksheets (this is presented in more detail in section 2.1).
Figure 7: CODED worksheet
Figure 7 shows that any terms that are not mapped are highlighted in red and display the text Not
Mapped and the value of the term in the ZOO_FACT_(DATA MODEL_NAME). All terms have to be
mapped correctly before data providers can produce a valid file to be submitted in the DCF.
2.1. How the coded sheet works
Figure 8: CODED worksheet containing LookUpDicTerm function
The worksheet CODED, Figure 8, contains the LookUpDicTerm function that will query the mapping
that data providers will create in each of the catalogue worksheets. The function will return a mapped
EFSA code. It is therefore important to make sure that the mappings created by data providers are
correct.
In Figure 8, highlighted by number (2), the value RF-00002560-MCG can be seen. This is the code
returned for a valid mapped term, found by the LookUpDicTerm function highlighted by the number
(3) in Figure 8.

The LookUpDicTerm expects as its first value the name of a catalogue to search in, in this case
CAT_PARAM_AMR, and a value. The value will be selected from the ZOO_FACT_AMR_ISOLATE_AST,
column E row number 2 (the zoonosis data model element). The value contained in the cell E2 should
be mapped to a catalogues term in the CAT_PARAM_AMR catalogue. If the term is not mapped, the
function returns NOT MAPPED. All NOT MAPPED values must be fixed before a valid submission file
can be made.
The number (4) in Figure 8 highlights the fact that ZOO_FACT_(DATA MODEL_NAME) elements that
require an EFSA standard term (catalogue) are linked to their respective catalogue in the workbook.
To view the standard terms catalogue, the data providers can simply click the link and the catalogue
sheet will open.
By default, the CODED worksheet has only one row pre-filled with formulas. If data providers want to
extend the number of rows in the CODED worksheet to match the number of data entries (rows) in
the worksheet ZOO_FACT_(DATA MODEL_NAME), then data providers need to use the
Mapping_Options Resize Coded Sheet Formulas button.
For example, in a ZOO_FACT_(DATA MODEL_NAME) worksheet with 560 rows (Please note, that 560
is linked only to rows that have actual data, the first row, containing element names should not be
counted), only the first one (the default is one) will be visible in the CODED worksheet. Thus data
providers will need to insert 560 in the text box beside the Resize Coded Sheet Formulas button in
the Mapping_Options worksheet and then press the button Resize Coded Sheet Formulas (see
Figure 9).
Figure 9: Resize Coded Sheet Formulas functionality
After data providers have performed the resizing of sheet formulas, the number of rows in the
CODED worksheet, with formulas will match the number 560 in the ZOO_FACT_(MODEL_NAME)
worksheet. All 560 row values in the ZOO_FACT_(MODEL_NAME) worksheet will now be copied across
and coded to the CODED worksheet.
Each ZOO_FACT_(DATA MODEL_NAME) data model contains an up-to-date list of standard terms
(catalogues) and each data model contains only the catalogues that it needs to reference.
2.2. General points on Excel worksheets

As each cell in the CODED worksheet contains a formula; the more data users put in, the slower the
use of the Excel worksheet will become. It is recommended that data providers profile all of their
data, mapping all their existing terms, and then create multiple copies of the Excel workbook. Data
providers can then split the data into groups of, for example, 5,000 to 10,000 rows, thus keeping the
Excel worksheets lighter and quicker to use. The Resize Coded Sheet Formulas button is specifically
designed to help with this issue: it automatically adds and removes the formulas required by the
CODED worksheet to map terms from the ZOO_FACT_(DATA MODEL_NAME). By using this feature,
data providers can greatly reduce the size of the model file. Setting the CODED sheet value to 1 will
reduce the size of the workbook by more than 70%. Only when data providers need to check or
actually produce a valid file for submission should they change the number of rows in the CODED
worksheet to the same number of rows data providers entered into the ZOO_FACT_(DATA
MODEL_NAME).
3. Getting started by profiling your data

When data providers open any of the data models ZOO_FACT files, they must enable macros so that
the custom function LookUpDicTerm can run. Figure 10 below shows the sequence of steps to follow
in doing this.

Figure 10: Example of enable macros
If data providers do not already have a list of all the terms that need to be mapped per data model to
EFSA terms, one simple way to profile their data is to use the Profile Your Data button in the
Mapping_Options worksheet (see below).
Figure 11: Profile Data functionality
To quickly profile the data, follow these steps:

1) Insert the data in the ZOO_FACT_(DATA MODEL_NAME) worksheet.
2) Click the Profile Your Data button, and watch as all unique terms in the data are collected and
inserted into their catalogue worksheets under the MemberState_TERMS column.
Figure 12 below, shows an example of the unique terms found in a dataset for the zoonosis data
element.

Figure 12: Example of collecting and inserting of all unique terms into a specific catalogue
The profile option selects and adds only unique and new terms to the catalogues; thus, if data
providers add more new data points to the ZOO_FACT_(DATA MODEL_NAME) worksheet, data
providers can continue to use the Profile Your Data button to check for new terms to be added to
catalogues.
3.1. Mapping your profiled terms

At this point data providers have profiled their data, and the unique terms that need to be mapped
are inserted into their catalogue worksheets. The following sequence of steps will map these values to
their corresponding EFSA standard term.
All catalogues/hierarchies have the mapping sections, where mapping is performed. Figure 13
highlights the mapping sections in the CAT_PARAM_AMR hierarchy. A mapping section is linked to a
specific standard term catalogue. The column MemberState_TERMS, highlighted by the number (1)
in Figure 13, is where your reporting country-specific terms are inserted. The column EFSA_TERM,
highlighted by the number (2) in Figure 13, is where the zoonoses standard term that will match the
reporting country term is selected from the dropdown box.

Figure 13: Example of mapping section in the CAT_PARAM_AMR hierarchy
3.2. Steps in the mapping process

1) Open the CODED worksheet in the workbook. The zoonosis element name is linked to the
standard term from ZOO_CAT_PARAM catalogue. By using the hyperlinked text of the element
zoonosis in the first column of the worksheet, data providers can move to the CAT_PARAM_AMR
hierarchy.
Once data providers have selected the standard terms from CAT_PARAM_AMR hierarchy, users
should see their profiled terms under column A (MemberState_TERMS) (Figure 13). If there are
no terms under column A (MemberState_TERMS), data providers will need to return to the
Mapping_Options worksheet and select the Profile Your Data button.
2) Once data providers have their profiled terms, the mapping of their term with the term from the
Zoonoses catalogues can be performed. In column B (EFSA_TERM), there is a dropdown list of
all the standard terms in the CAT_PARAM_AMR catalogue for the element Zoonosis (see the
example in Figure 14). Data providers have to search through this list until they find a standard
term that matches their reporting country-specific standard term. When data providers find a
match, select it, and their standard term will be physically matched to EFSAs term.
The LookUpDicTerm function in the CODED worksheet will return for every occurrence of data
providers standard term; in the example in Figure 13, Salmonella S. Abortusovis the code
value is RF-00000372-MCG.
3) The above steps should be repeated until all of terms are matched for all profiled elements.

Figure 14: Example of mapping a national standard term with EFSAs term
3.3. The catalogue/hierarchy search functionality

If data providers have a large number of terms in a catalogue/hierarchy, like in CAT_PARAM_AMR
above, a search facility has been developed that will allow data providers to quickly search for terms.
The search facility allows data providers to enter a maximum of three search text elements in the
following format:
[search text1]-[search text2]-[search text3]
[search text1]-[search text2]
[search text1]
For example, if data providers want to search for the term Salmonella S. Enteritidis PT 24, the
search string could be salmon-enteri-pt 24 or pt 24-salmon-enteri; the search function will return
the first catalogue item that it finds that contains all three search strings in order of sequence. Each
search string must be separated by the - character. The more specific the search string is, the
greater the accuracy data providers will achieve in searching for their catalogue item. Figures 15 and
16 below demonstrate the search feature using the maximum three search strings as above. A match
could also have been achieved using the search string enteri-pt 24, corresponding to [search
text1]-[search text2].

Figure 15: Example of the catalogue search functionality searching
Figure 16: Example of the catalogue search functionality finding

4. Refreshing and changing views on data

The Excel tool has turned off Excels ability to automatically update cell formulas when a value linked
to the formula has been changed to improve performance. In the CODED worksheet, all cells contain
a formula to either look up/codify values entered in the ZOO_FACT_(MODEL_NAME) worksheet, or
simply copy across values that have no catalogue and therefore do not need to be coded. All this
codifying and cell value copying affects performance; the more rows of data in the
ZOO_FACT_(MODEL_NAME), the slower and larger the CODED worksheet and Excel workbook
become. If we leave Excel to look after all these cell formulas, it will continuously recalculate them,
making the use of a large file almost impossible. Instead we have switched off this recalculating and
given the user the power to recalculate the formulas in the coded sheet when it is needed, thereby
reducing the computer resources needed and speeding up the tool as a whole. We have also
introduced a feature that allows the user to add and remove formula rows in the CODED worksheet.
This feature may not seem useful, but with experience we have found that users sometimes need to
either email their data to other colleagues or simply upload their data to the DCF, and large files can
take some time to upload and are virtually impossible to send via email.
4.1. The adding and removing of formula rows

The adding and removing of formula rows becomes important when problems of file size need to be
resolved. By setting the number of formula rows to one (the minimum allowed, Figure 17), data
providers can effectively reduce the size of their working file by more than 70%.
Figure 17: Resize Coded Sheet Formulas functionalities-the default size of the coded worksheets
Data really need to be coded only when data providers are producing a dataset which data providers
wish to submit to EFSAs DCF; to do this data providers simply add as many rows to the CODED
sheet as data providers have in their ZOO_FACT_(DATA MODEL_NAME) worksheet, select the resize
coded sheet button (entering in the number of rows in the text box of course) and all the row values
data providers have in the ZOO_FACT_( DATA MODEL_NAME) will be transferred and codified into the
CODED worksheet.
Because the first row in the mapping tool contains the name of the elements, when we perform an
increase of the size of the coded worksheet, then number of rows with data is always the first row,
plus the number supplied by the Resize Coded Sheet Button, the following series of figures (Figure
18) demonstrate how the mapping tool handles the increasing of formulas in the coded worksheet.
The default size of the coded worksheets rows in set to one, if you look at Figure 18 below, you can
see the sequence for incrementing the size of then CODED worksheet to two. If you look at number
one in the sequence, you can see the default size of the coded worksheet is set to one, so only one
row of data from the ZOO_FACT_(DATA MODEL_NAME) worksheet is displayed in the coded
worksheet. In number two of the series, we are resizing the coded worksheet to two rows, the final
step in the series, 3, now shows that the coded worksheet displays two rows of data from the
ZOO_FACT_(DATA MODEL_NAME) worksheet.

Figure 18: Increasing coded worksheet size
4.2. The refreshing of data

The refreshing of data is also very important. If data providers have spotted an error or missed
mapping in their file they will want to fix it, and only when all their fixes have been made will data
providers want to refresh the CODED worksheet with those changes. This is also necessary because
we have switched off Excels ability to recalculate which gives the user total control over the
processing of their data. In the Mapping_Options worksheet, data providers will find the Refresh
Coded Sheet Formulas button, and every time data providers click this button an update of their data
in the CODED worksheet is performed.
The R e fre sh button re-calculates all formula cells and summery pivots in
2 Refresh Coded Sheet Formulas
the worksheets.
Figure 19: Refresh Coded Sheet Formulas functionality
4.3. Different views on the codified data

The tool supports the concept of different views on the codified data by which a user can change the
behaviour of the LookUpDicTerm display of coded terms. Normally in the coded sheet only the code
connected to an EFSA term is displayed (Figure 20). However sometimes during the checking of the
coded data it can be difficult to visually link a displayed code with its textual meaning. With this in
mind, EFSA designed the mapping mode feature which allows the CODED worksheet to display both
the coded term and its text together and also the user can also display their own term texts combined
with the EFSA code and term text in the CODED worksheet. This feature allows users to make sure
that the mappings that were made between the Member State term and its EFSA term are correct. It
is important to remember, that when all the data has been correctly coded and checked, the user
must change the mapping mode back to the Normal Mapping Code only displayed. This is because
only the EFSA codes are accepted in any submission of data to the DCF; XML files containing both the
term text and the code together will be rejected.

Figure 20: Functionalities of the Mapping Mode
Among the options available via the Mapping Mode section in the Mapping_Options worksheet seen
in Figure 13 above, data providers can see that, for normal mapping there is:
1) Normal Mapping: Code, only codes are displayed;
2) Normal Mapping: Code+Term, codes and terms are displayed together
And under the Display mapped data there are:
1) EFSA Terms
2) Memberstate mapped terms
These two features combined will provide us with the different views we mentioned above. For
example, if we select
1) Normal Mapping: Code only displayed, and
1) EFSA Terms
the coded term is all that we will see in the CODED worksheet:
zoonosis
RF-00000796-MCG
If we choose
2) Normal Mapping: Code+Term and
1) EFSA Terms
we get both the EFSA code and the term text:
zoonosis
RF-00000796-MCG | Salmonella - S. Montevideo
If we really want to be sure the mapping we made was correct between the reporting country term
and the EFSA term, we can also choose
2) Normal Mapping: Code+Term, and
2) Memberstate mapped terms
This will provide us the Member State term (in this example Montevideo), its mapped EFSA code and
the term text:
zoonosis
Montevideo | RF-00000796-MCG | Salmonella - S. Montevideo
This level of display flexibility should greatly help to ease the use of the tool. When the user is ready
to create and submit their data, the first example setting should be selected so that only the coded
term is displayed and not the text associated with it namely:
1) Normal Mapping Code, and
1) EFSA Terms

5. Generating XML file

The mapping tools automatically created the XML files using 3 buttons: Create DCF XML, Create
[Update] DCF XML and Create [Delete] DCF XML ((Figure 21).
Figure 21: XML generation functionalities
Create DCF XML functionality should be use for the below dataset operation:
1. Insert: The data provider sends a new dataset to be inserted into EFSAs database. A unique
identifier for the dataset (datasetId) is generated by the receiver system and assigned to the dataset
(EFSA, 2014).
2. Replace: A new dataset entirely replaces a dataset previously stored in EFSAs database. The
system uses, for the new dataset, the same datasetId previously assigned to the replaced one.
3. Partial replace: A set of records is uploaded to partially replace a target dataset present in EFSAs
database. The dataset maintains the same datasetId. This operation is recommended for only large
datasets containing just a few records to be updated. The system updates in the target dataset all the
records that have a corresponding record unique identifier. If the newly uploaded dataset also
contains records for which the record unique identifier does not exist in the target dataset, the records
are added and appended to the target dataset.
4. Partial delete: A set of records is uploaded to partially delete a target dataset present in EFSAs
database. The dataset maintains the same datasetId. The system deletes in the target dataset all the
records that have a corresponding record unique identifier. If the newly uploaded set also
contains records for which the record unique identifier does not exist in the target dataset, the
operation fails.
Create [Update] DCF XML and Create [Delete] DCF XML should be used ONLY to create XML
files to facilitate the Amendment operations. The amendments allow MSs to modify records in
datasets which are ACCEPTED DWH (EFSA, 2014). If an amendment to the dataset which was
ACCEPTED DWH is needed, the data provider shall upload a new dataset with the insert operation
to perform an amendment operation on the records already loaded in the DWH.
Amendment operations are transmitted as datasets. The field, amType (amendment type), has to be
used in order to specify which type of amendment is requested by the data provider for each of the
records to be amended included in the dataset and identified by the record unique identifier.
The amendment operations supported by the tool are:
amType = U (update), then Create [Update] DCF XML should be used
This operation is used to update records (status ACCEPTED DWH) in the EFSA database. This
operation will result in a new version of the record in the database.
amType = D (delete), then Create [Delete] DCF XML should be used
This operation is used to perform a deletion (status ACCEPTED DWH) of accepted records in
the database. The records flagged as deleted will reach their final status in the receiver DWH
and can no longer be modified.
Please note that only the records in the ZOO_MAN/ZOO_FACT_(DATA MODEL_NAME) worksheet that
have their amType set to update U or Delete D will be exported to a DCF formatted XML file.

When the data provider is satisfied that all data has been mapped, the Create DCF XML button
should be used. This action will start the full validation of the data that is in the CODED worksheet,
to produce a valid XML file containing all inserted and mapped data.
If while processing and validating the data in the CODED worksheet, and error is found,
the creation of the XML file will be stopped and an error box will display beside the cell
where the error occurred, explaining in detail what the problem is. Figure 22 below
shows the error message box, where the mandatory data element (cell highlighted in
red) (repYear) was not fill in for the cell B2. This error message box can be moved or
deleted.
Figure 22: Error Messaging in XML production
When all errors have been fixed, the data provider will be prompted to save the created
XML file, with the option to add the current time. Once the XML export is finished the file
can be uploaded in DCF.
6. Rebuilding a broken coded file

Under normal conditions, the CODED worksheet is quite robust and will not break too easily. Some
situations will arise, however, where formula references in the CODED worksheet will break. This is
normally linked to cut/delete or paste operations performed in the ZOO_FACT_(MODEL_NAME)
worksheets. When this happens it would be helpful to press a button and have all the broken formulas
fixed. This is exactly what is implemented in the tool with the button called Rebuild Coded Sheet
Formulas (Figure 23). The button can be found on the Mapping_Options worksheet, but hopefully
data providers will not need to use it too often.
Figure 23: Rebuild Coded Sheet Formulas functionality
7. Particularities of the manual mapping tool

The manual tools support only the direct entry of EFSA coded standard terminology
catalogue/hierarchies terms. What this means is that no actual physical mapping of MS terms to EFSA
coded terms is performed; the user simply selects EFSA standard terms directly from
catalogues/hierarchies embedded in the ZOO_MAN (MODEL_NAME) worksheet. The benefit of this
approach is its simplicity; the drawbacks are the time needed to fill in a large number of data and the
constant need to search for terms or select terms from the dropdown boxes in the data entry
worksheet.

Figure 24: Mapping_Options worksheets of the manual mapping tool
The manual tool does not support all functionality (Figure 24) of the dynamic mapping tool; this is
because the LookUpDicTerm is not used in the CODED worksheet. The CODED worksheet in the
manual model simple removes the text part of an EFSA standard coded term, leaving only the code;
no dictionary lookup is needed because the values in the ZOO_MAN (MODEL_NAME) worksheet are
already coded terms selected from a pick list. Figure 25 below shows how each term is picked from a
dropdown list in the data entry worksheet.
Figure 25: Example of selection of terms from a dropdown list in the data entry worksheet
The manual tools data entry worksheet, ZOO_MAN (MODEL_NAME), supports the pick list search
functionality outlined in section 3.3. Instead of selecting directly from the pick list dropdowns as
shown in Figure 25, data providers can type in their pick list search terms.

7.1. Adding rows with dropdowns in the ZOO_MAN worksheet

The adding of new rows that will contain all the catalogues required for mapping is very simple as it is
linked to the Resize Coded Sheet Formulas button for increasing the number of formula rows in your
CODED worksheet. Whatever number data providers put into the text box will be the exact number of
rows that will be added with functioning dropdown pick lists. Alternatively, data providers could simply
highlight the entire row and drag it down to do the same thing.
7.2. Rebuilding rows with dropdowns in the ZOO_MAN worksheet

Section 7 covers the rebuilding of the CODED worksheet; for the manual tool, the process is exactly
the same. Every time data providers want to rebuild either the CODED worksheet or the dropdowns
in all of the columns of the ZOO_MAN (DATA MODEL_NAME) worksheet, select the Rebuild Coded
Sheet Formulas button on the Mapping_Options worksheet. When data providers are rebuilding a
worksheet because it has become broken or it is missing pick list dropdown boxes, enter the number
of rows wanted to rebuild. By default only the first row on the CODED and ZOO_MAN worksheets are
rebuilt. To rebuild all of the rows in the dataset, you will need to enter the number of rows in the
Resize Coded Sheet Formulas text box, and then select the Rebuild Coded Worksheet Formulas
button.
For example, in Figure 26 below, if data providers were to press the Rebuild Coded Sheet Formulas,
as currently displayed, only the first 230 row records would have their formulas and dropdown pick
lists rebuilt.
Figure 26: Example of rebuilding of CODED and or any of the dropdown pick lists
7.3. Reporting repeatable data element

The repeatable data elements are designed to allow the user to enter in multiple values for the same
data element; to do this, the mapping tool requires to add all the values which should be added for
that specific data element. The mapping tool automatically will add an asterix * as separator
between values (Figure 27).
Figure 27: Repeatable data elements inserted in the FBO manual mapping tool
8. Text forms Manual Mapping Tool

For the reporting of text forms, EFSA has recently developed a manual mapping tool that data
providers can use to select EFSA standard terms directly from catalogues embedded in the
ZOO_MAN_TEXTORMS worksheet. The TXF data model was not previously supported by its own
mapping tool, but with the mandatory electronic data transmission of text forms it became necessary
to develop one. Figure 28 shows where data providers can select the available paragraphs to be
reported on.

Figure 28: Example showing a selection of terms from a drop down list from the catalogue
CAT_PARAGRAPH_TYPE
An added feature of the ZOO_MAN_TEXTORMS worksheet is the possibility to select - from a pre-
defined list - the corresponding description of the sub-titles (subTitleOrder) corresponding to the
reported paragraph which is designated by a number. In Figure 28 this aspect is illustrated: in the
column headed subTitleOrder the numbers 1 (Description of sampling designs) and 8 (Sampling
strategy used in monitoring - Methods used for collecting data) have been chosen.
The free text information for each paragraph and subtitle is inserted by the data provider manually in
column N (value) in the text box containing the number and Text Form Subtitle (see Figure 29).
Figure 29: Text box for reporting information relevant to the selected Text Form Subtitle

References
EFSA (European Food Safety Authority), 2014. Guidance on Data Exchange version 2.0. EFSA Journal
2014;12(12):3945, 173 pp., doi:10.2903/j.efsa.2014.3945
EFSA (European Food Safety Authority), 2017a. Manual for reporting on zoonoses and zoonotic
agents, within the framework of Directive 2003/99/EC, and on some other pathogenic
microbiological agents for information deriving from the year 2016. EFSA supporting publication
2017:EN-1175. 98 pp. doi:10.2903/sp.efsa.2017.EN-1175
EFSA (European Food Safety Authority), 2017b. Manual for reporting on antimicrobial resistance
within the framework of Directive 2003/99/EC and Decision 2013/652/EU for information deriving
from the year 2016. EFSA supporting publication 2017:EN-1176. 35 pp.
doi:10.2903/sp.efsa.2017.EN-1176
EFSA (European Food Safety Authority), 2017c. Manual for reporting on food-borne outbreaks in
accordance with Directive 2003/99/EC for information deriving from the year 2016. EFSA
supporting publication 2017:EN-1174. 44 pp. doi:10.2903/sp.efsa.2017.EN-1174
EFSA (European Food Safety Authority), 2017d. Data dictionariesguidelines for reporting data on
zoonoses, antimicrobial resistance and food-borne outbreaks using the EFSA data models for the Data
Collection Framework (DCF) to be used in 2017, for 2016 data. EFSA supporting publication 2017:EN-
1178. 26 pp. doi:10.2903/sp.efsa.2017.EN-1178

Abbreviations
AMR antimicrobial resistance
DCF Data Collection Framework
EC European Commission
ECDC European Centre for Disease Prevention and Control
EFSA European Food Safety Authority

EMA European Medicines Agency
EU European Union
MS Member State of the European Union

XML extensible markup language
XSD schema definition language
Abbreviations used in codes of data elements that refer to a data model:

AMR AMR isolate based-data model
specific monitoring of ESBL-/AmpC-/carbapenemase-producing
ESBL
bacteria, in the absence of isolate detected data model
POP animal population data model
DST disease status data model
FBO food-borne outbreaks data model

PRV prevalence data model
TXF text forms data model

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TECHNICAL REPORT

APPROVED: 14 February 2017

User manual for data providers

Key words: zoonoses data models, Excel, XML, XSD, DCF

www.efsa.europa.eu/publications EFSA Supporting publication 2017:EN-1181

www.efsa.europa.eu/publications 2 EFSA Supporting publication 2017:EN-1181

www.efsa.europa.eu/publications 3 EFSA Supporting publication 2017:EN-1181

www.efsa.europa.eu/publications 4 EFSA Supporting publication 2017:EN-1181

Background and Terms of Reference as provided by EFSA

www.efsa.europa.eu/publications 5 EFSA Supporting publication 2017:EN-1181

2. Introducing the mapping tool

www.efsa.europa.eu/publications 6 EFSA Supporting publication 2017:EN-1181

Figure 1: Default worksheets of the dynamic mapping tool

www.efsa.europa.eu/publications 7 EFSA Supporting publication 2017:EN-1181

Each ZOO_FACT_(DATA MODEL_NAME) (Figure 2) worksheet displays:

Figure 3: The compound data element as displayed in CODED worksheed

www.efsa.europa.eu/publications 8 EFSA Supporting publication 2017:EN-1181

Figure 4: Repeatable data elements inserted in the dynamic mapping tool in

Figure 5: The repeatable data elements in the CODED worksheet

www.efsa.europa.eu/publications 9 EFSA Supporting publication 2017:EN-1181

Figure 7: CODED worksheet

2.1. How the coded sheet works

Figure 8: CODED worksheet containing LookUpDicTerm function

www.efsa.europa.eu/publications 10 EFSA Supporting publication 2017:EN-1181

Figure 9: Resize Coded Sheet Formulas functionality

2.2. General points on Excel worksheets

3. Getting started by profiling your data

www.efsa.europa.eu/publications 11 EFSA Supporting publication 2017:EN-1181

Figure 10: Example of enable macros

Figure 11: Profile Data functionality

To quickly profile the data, follow these steps:

www.efsa.europa.eu/publications 12 EFSA Supporting publication 2017:EN-1181

3.1. Mapping your profiled terms

www.efsa.europa.eu/publications 13 EFSA Supporting publication 2017:EN-1181

Figure 13: Example of mapping section in the CAT_PARAM_AMR hierarchy

3.2. Steps in the mapping process

www.efsa.europa.eu/publications 14 EFSA Supporting publication 2017:EN-1181

3.3. The catalogue/hierarchy search functionality

www.efsa.europa.eu/publications 15 EFSA Supporting publication 2017:EN-1181

Figure 15: Example of the catalogue search functionality searching

Figure 16: Example of the catalogue search functionality finding

www.efsa.europa.eu/publications 16 EFSA Supporting publication 2017:EN-1181

4. Refreshing and changing views on data

4.1. The adding and removing of formula rows

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Figure 18: Increasing coded worksheet size

4.2. The refreshing of data

Figure 19: Refresh Coded Sheet Formulas functionality

4.3. Different views on the codified data

www.efsa.europa.eu/publications 18 EFSA Supporting publication 2017:EN-1181

Figure 20: Functionalities of the Mapping Mode

www.efsa.europa.eu/publications 19 EFSA Supporting publication 2017:EN-1181

5. Generating XML file

Figure 21: XML generation functionalities

www.efsa.europa.eu/publications 20 EFSA Supporting publication 2017:EN-1181

Figure 22: Error Messaging in XML production

6. Rebuilding a broken coded file

Figure 23: Rebuild Coded Sheet Formulas functionality

7. Particularities of the manual mapping tool

www.efsa.europa.eu/publications 21 EFSA Supporting publication 2017:EN-1181

Figure 24: Mapping_Options worksheets of the manual mapping tool

www.efsa.europa.eu/publications 22 EFSA Supporting publication 2017:EN-1181

7.1. Adding rows with dropdowns in the ZOO_MAN worksheet

7.2. Rebuilding rows with dropdowns in the ZOO_MAN worksheet