EFSA supporting publication 2013:EN-444

TECHNICAL REPORT

Data Collection Framework (DCF) guidelines for Data Providers

for the 2013 Reporting Season1
European Food Safety Authority2,3
European Food Safety Authority (EFSA), Parma, Italy

ABSTRACT
EFSA is charged with coordinating the reporting of zoonoses, zoonotic agents, animal population, antimicrobial
resistance and foodborne outbreaks in the European Union under the Directive 2003/99/EC as well as analysing
and summarising the data collected. For data collection purposes EFSA has created the DCF application. This
document describes the main steps in using the DCF application.
European Food Safety Authority, 2013.

KEY WORDS
Zoonoses, DCF, XML, transmission.

1
2
3

On request from EFSA, Question No EFSA-Q-2013-00206, approved on 12 June 2013.

Correspondence: zoonoses@efsa.europa.eu
Acknowledgement: EFSA wishes to thank EFSA staff members: Francesca Riolo,
Pierre-Alexandre Beloeil and Ilaria Inverardi for the preparation work on this technical output.

Kenneth

Mulligan,

Suggested citation: European Food Safety Authority, 2013; Data Collection Framework (DCF) guidelines for Data Providers
for the 2013 Reporting Season. EFSA supporting publication 2013:EN-444. 21 pp.
Available online: www.efsa.europa.eu/publications

European Food Safety Authority, 2013

DCF guidelines for Data Providers for the 2013 Reporting Season

SUMMARY
This user manual provides brief guidance on the use of the DCF Application for the submission of
2012 data by the Member States and other reporting countries.
The manual provides a general introduction to the DCF Application. Instructions are also given on
how to request user profile and on the way to access the system.
Information about the data transfer from DCF to the Zoonoses Web Reporting Application is also
given.
This manual is specifically aimed to guide the reporting of the information deriving from the year
2012.

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TABLE OF CONTENTS

Abstract .................................................................................................................................................... 1
Summary .................................................................................................................................................. 2
1
Introducing the Data Collection Framework (DCF) ...................................................................... 4
1.1
Prerequisite: EFSA users database (LDAP) profile availability ............................................. 4
1.1.1
Request a LDAP user profile ........................................................................................ 4
1.1.2
Retrieve your LDAP Username.................................................................................... 4
1.1.3
Retrieve your LDAP Password .................................................................................... 4
1.2
Prerequisite: data files to be uploaded .................................................................................... 5
2
Working with DCF ........................................................................................................................ 9
2.1
Selection of Data Collection ................................................................................................. 10
2.2
Uploading data files .............................................................................................................. 11
2.3
Managing transmissions........................................................................................................ 13
2.3.1
Transmission status .................................................................................................... 14
2.3.2
Accepting a transmission............................................................................................ 14
2.3.3
Replacing a transmission ............................................................................................ 14
2.3.4
Rejecting a transmission ............................................................................................. 15
2.3.5
Transmission details ................................................................................................... 16
2.3.6
Error Report download ............................................................................................... 17
2.4
Logging out from the application.......................................................................................... 20
3
Abbreviations ............................................................................................................................... 21

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Introducing the Data Collection Framework (DCF)

The Data Collection Framework (DCF) application is constituted of an interactive web-based

application that aims at:

Simplifying the zoonoses data collection procedure between parties.

Facilitating data exchange, data extraction and data reusability.

1.1

Prerequisite: EFSA users database (LDAP) profile availability

IMPORTANT PREREQUISITE!

In order to access to the DCF Application Data Providers need to have a LDAP user
profile registered within the EFSAs IT system(s).
1.1.1

Request a LDAP user profile

The LDAP is the EFSA users database where all people collaborating with EFSA needs to be defined
in order to have access to the EFSA applications.
In case you do not have a LDAP user profile, you need to register by asking your National Reporting
Officer to send a specific request to define you as Data Provider for your country to the Zoonoses Help
Desk at:
zoonoses_support@efsa.europa.eu
In the request, your Reporting Officer should specify your name, surname, organisation, email address
and, optionally, your telephone number.
EFSA will create a LDAP user profile and a Data Provider account into the Data Collection
Framework (DCF) and send you the username you need to use to access the system and a link where
you can generate and activate the password.
1.1.2

Retrieve your LDAP Username

In case you have a LDAP user profile within EFSAs system(s) but you do not remember your
username, please send an email to:
servicedesk@efsa.europa.eu
1.1.3

Retrieve your LDAP Password

In case you have a LDAP user profile within EFSAs system(s) but you do not remember your
password, please recover or reset your password at the following address:
https://sciencenet.efsa.europa.eu/sumt/pages/lostPassword.jsp

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1.2

Prerequisite: data files to be uploaded

To prepare the data file that can be uploaded to the DCF you should:
1. Map your national terms with EFSA terms using the mapping tool developed by EFSA
BIOMO Unit which you can find in Sciencenet from 16 May 2013.
2. Automate this process (IT support needed) for each pick list involved in your reporting or do it
manually.
3. Prepare a data file for each data model you wish to report.
4. Check if the structure of the dataset (data file) you prepared is correct, verifying it against the
related XSD file.
5. Upload the data file as an Excel file or as an XML file (please refer to paragraph 2.2 of this
manual).
Here below follows a summary of the steps you should perform:
1. To map your national terms you could use the Mapping Tool developed by EFSA BIOMO
Unit: for each of your terms you should select from the EFSA related pick list the most
suitable term and its SSD code.
2. Use the tool to map all the terms you have for each pick list (catalogue) such as the zoonotic
agents list, the matrix, etc.
3. To prepare the data file you could create an excel file where each column corresponds to the
Short Element name in the same order as they are in the data model for which you are
preparing the file. As you can see in the figure on the next page the Short Elements of the
Animal Population data model have been transformed in columns into the excel data file.

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4. To check if the excel data file you prepared is correct, you should verify it against the related XSD
file (you can all XSD files in Sciencenet): go to the Developer tab and click on Source.

Then click on the XML Maps button and on the Add button in the XML Maps pop-up window
which opens, select the XML Source and click on the Open button (see figure below).

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The XSD file is added into the XML Maps list, click on the OK button.

Next step would be to map each element of the excel file to the correspondent element of the XML
schema through the XML source window and then to validate the file against it (see figure below).

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Then click on the Export button in the Developer menu, type a file name and click on the Export
button in the Export XML window (see figure below) and the XML file will be created in the folder
you selected.

5.

Please refer to paragraph 2.2 and followings of this manual for the instructions on how to upload
data file using the DCF Application.

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Working with DCF

You can access the DCF Application using a normal web browser. The ones compliant with the
application are:
Mozilla Firefox 9.x or later.
Internet Explore 8.x or later.
If you have a LDAP user profile within EFSAs system(s), in order to access the DCF Application
type the following URL in your browsers address field:
https://dcf.efsa.europa.eu/dcf-war/dc
You will access the following login page.

1. Type your LDAP username. Your username is case sensitive (pay attention to uppercase
and lowercase letters).
2. Type your LDAP password exactly as it was given to you. Your password is casesensitive. For security purposes, the system displays a bullet dot for each character you
type.
3. Click on the Login button.
4. Select the account from the drop-down box at the top left-handed side of the screen.

After selecting your account from the list shown in the drop-down box, you will access the DCF Data
Upload page as shown here below.

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IMPORTANT
If you do not find an account in the drop-down box, please contact the Zoonoses Support at:
zoonoses_support@efsa.europa.eu
Users working for competent organisations responsible for submitting data will have a Data
Provider profile.
The Data Provider can access the following functionalities:
The upload of new data transmissions.
The deletion of transmissions for your user profile.
The download of transmissions from their organization.
The insertion of valid transmissions into the data repository accepting them.
Access to error reports for data transmissions which have failed validation.

2.1

Selection of Data Collection

In the tree view you can find all the Data Collections that you have permission to access as Data
Provider. Clicking on the plus symbol next to the top level data collections folder will expand the
tree.

The active data collections are: 2011_BIOMO_ANNUAL_ZOO for reporting 2011 data and
2012_BIOMO_ANNUAL_ZOO for reporting 2012 data. It is possible to report through the DCF
Application data for the following data models:
o

AMR Isolate Based Data Model.

AMR Quantitative Data Model.

AMR Qualitative Data Model.

Phagetypes and Serovars Data Model.

Prevalence Data Model.

Animal Population Data Model.

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FBO - Food Borne Outbreaks Data Model.

From this year is possible to report also data for the following data models:

2.2

Text Forms Data Model.

Disease Status Data Model.

Food Sample Based Data Model (on Pilot base).

Uploading data files

To upload for the first time a data file click on the folder for the specific Data Collection you wish to
provide data for. This opens the Data Collection Data page (see below). To start the data transmission
process click on the new transmission button.

The Upload page opens. This page contains the list of fact tables (data models) for which you can
send files.

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NOTE
The system accepts only xml and xls file format. The selectable file format set in the File Type
dropdown list depends on the configuration of the data collection set up by EFSA Data Manager.
Only .xls files in Excel 97 2003 format will be accepted.
In case the file to be uploaded is an Excel file please note that only the first Excel sheet will be
parsed and that only columns and values defined in the schema provided by your Data Manager
will be accepted. Non-expected data will cause the rejection of the transmission, as well as other
formatting of the Excel sheet, such as hidden columns, grouped columns or rows.
Should you need, for example, to send prevalence data please select first the type of file from the
related combo box.

Then select the file to upload by clicking on the Browse button and then click on the send button at
the top of the page.

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The acknowledgement message is displayed at the top of the page.

To check if the data file is validated please open the transmissions page.

2.3

Managing transmissions

By default the page showing only the transmission you made opens. From this page is possible to view
and manage all the transmissions by your organisation clicking on the All button at the top right-hand
side of the page.

The All Transmissions from My Organisation page opens.

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2.3.1

Transmission status

A transmission of one or more data file can have the following status:
1. Valid.
2. Rejected.
3. Accepted.
1. A transmission becomes automatically valid if it complies with the data collection schema and
the business rules. A valid transmission can be rejected or replaced by the Data Provider
who did it or by EFSA Data Managers.
2. A transmission is rejected by the system if it does not comply with the validation rules, by the
Data Provider who performed it or by EFSA Data Managers.
3. A Valid transmission can be accepted by Data Providers or EFSA Data Managers.
2.3.2

Accepting a transmission

To accept a valid transmission, tick the check-box at the beginning of the row to select the
transmission and then click on the accept button.

In few moments the status of the transmission is changed to accepted. Newly accepted transmissions
will be migrated to the Zoonoses Web Application during the following night if the status of the report
into the Zoonoses Web Application is new or active.

2.3.3

Replacing a transmission

Please use this feature to send data corrections or to upload new data files within the same
transmission. You can replace a rejected transmission or a valid transmission.
Tick the check box of the transmission you want to replace and then click on the replace button.

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A message box asking confirmation opens. Click on the OK button to continue.

The following page opens: select the file to upload by clicking on the Browse button and then on the
send button. An acknowledgement message will appear at the top of the page.

2.3.4

Rejecting a transmission

To reject a valid transmission tick the check box at the beginning of the row and then click on the
reject button.

A message box asking confirmation opens. Click on the OK button to continue.

Please note that an accepted transmission needs to be deleted before it can be replaced.

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2.3.5

Transmission details

To check the details of a transmission tick the check-box of the transmission you are interested in and
click on the details button at the top of the page.

The following page opens:

From the above page you can view the history of the transmission by clicking on the view history
button, download the uploaded data file by clicking on the file download button, and see the error
message in case of rejected transmission by clicking on the error report download button.

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2.3.6

Error Report download

We suggest you to always click on the error report download button which contains a more detailed
error message: for example when a transmission is rejected by the system, always download the error
report from the below page.

The errors you can encounter are often related to term not in dictionary or to business rules not met.
Clicking on the error report download button, you are asked to open a zip file which contains three
different types of file (xml, xslt, xsd): extract in the same folder the xml and xslt files to open the
error message (see screen-shot here below).

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If you dont have an XML editor, we suggest you to use an Internet Browser such as Internet Explorer
and/or Mozilla Firefox.

The message will look as in the following screen-shot:

Instead if you use an xml editor the message will look as in the following screen-shot:

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As you can note the description and the value affected by the error are also given. In the above
message for example is said that for reporting a weak FBO (indicated by the variable fboAgentGroup)
is used a term that is not in the dictionary: this means that the value used is not included in the list of
zoonotic agents for weak FBO reporting: you should always use the domain information in each
picklist to filter the dictionary terms that can be applied to each variable.
For example the domains to be used to filter the allowed zoonotic agents in case of FBO reporting are:
D_FBO_fboCausativeAgent for strong FBO.
D_FBO_fboCausativeAgentGroup for zoonosis for weak FBO.
In the below message another example is given: in this case a business rule is not met.
If Enumeration Method results are used also the Quantity must be specified.

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To correct the above error you should report also the Quantity: to filter the list of values allowed use
the D_PRV_Quantity domain into the ZOO_CAT_FIXMEAS catalogue. In our example a value
from the following list should be selected for the quantity field:

2.4

SSD_Code

term

R073A

<= 100

R074A

> 400

R075A

>100 to <= 200

R076A

>200 to <= 400

R077A

>100

R078A

<100

Logging out from the application

To exit the application, click on the logout button at the top right hand side of the page.

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Abbreviations

AMR

Antimicrobial Resistance

BIOMO

Biological Monitoring

CAT

Catalogue

DCF

Data Collection Framework

EFSA

European Food Safety Authority

FBO

Food Borne Outbreak

IT

Information Technology

LDAP

Lightweight Directory Access Protocol

PRV

Prevalence

SSD

Sample Standard Description

URL

Uniform Resource Locator

XML

Extensible Markup Language

XSD

Xml Schema definition

XSLT

Extensible Stylesheet Language Transformations

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