Database of exposure-related and ancillary data for priority substances

49 Pages·2017·2.23 MB·English

by  Kobosil, Nicole

HORIZON2020 Programme
Contract No. 733032 HBM4EU

Database of exposure-related and ancillary data
for priority substances
Deliverable Report
AD 12.1
WP 12 - From HBM to exposure
Deadline: 31 July, 2017
Upload by Coordinator: 31.07.2017

Entity Name of person Short name of institution Received
responsible [Date]
Coordinator Marike KOLOSSA- UBA 27 July 2017
GEHRING
Grant Signatory Alessandro ISS 17 July 2017
ALIMONTI
Pillar Leader Robert BAROUKI INSERM 27 July 2017
Work Package Denis AUTH 27 June 2017
Leader SARIGIANNIS
Task leader Denis AUTH 30 June 2017
SARIGIANNIS

Responsible author Alberto GOTTI, E-mail [email protected]
Denis SARIGIANNIS
[email protected]
IUSS, AUTH
Short name of Phone [phone]
institution
[phone]
Co-authors Evangelos HANDAKAS, Spyros KARAKITSIOS
AD 12.1 Database of exposure-related and ancillary data for priority substances Security: Public
WP 12 - From HBM to exposure Version: 7.2
Authors: Alberto GOTTI, Denis SARIGIANNIS Page: 2

Table of contents
Table of contents ............................................................................................................................ 2
1 Authors and Acknowledgements .............................................................................................. 5
2 Introduction .............................................................................................................................. 6
2.1 Aims, approach, scope and audience of the HBM4EU exposure database ....................... 6
2.2 Document Organisation .................................................................................................... 7
3 Design Overview ...................................................................................................................... 8
3.1 Approach .......................................................................................................................... 8
3.2 Architectural Goals and Constraints .................................................................................. 8
3.3 Maintain and Operate Database ....................................................................................... 8
3.4 Additional Considerations ................................................................................................. 8
3.4.1 Language................................................................................................................... 8
3.4.2 Requests for Technical Assistance and Information ................................................... 8
3.5 Database conceptual design ............................................................................................. 9
4 Application Architecture ......................................................................................................... 10
4.1 Technical Design Diagram .............................................................................................. 10
4.2 Server infrastructure ....................................................................................................... 10
4.3 Development tools/languages ......................................................................................... 11
4.4 Process view .................................................................................................................. 11
4.5 Logical view .................................................................................................................... 11
4.6 Web Controls Modules .................................................................................................... 12
4.6.1 Controller Administrator Module ............................................................................... 12
4.6.2 Controller Operations Module .................................................................................. 12
4.6.3 Controller Authentication Module ............................................................................. 12
4.6.4 User interface .......................................................................................................... 13
5 Description of data ................................................................................................................. 14
5.1 Type of data .................................................................................................................... 14
5.1.1 Compound – Environmental matrix .......................................................................... 15
5.1.2 Compound - Dietary ................................................................................................. 15
5.1.3 Compound – Consumer products ............................................................................ 15
5.1.4 Exposure related data .............................................................................................. 15
5.1.5 Time Activity ............................................................................................................ 15
AD 12.1 Database of exposure-related and ancillary data for priority substances Security: Public
WP 12 - From HBM to exposure Version: 7.2
Authors: Alberto GOTTI, Denis SARIGIANNIS Page: 3

5.1.6 Dietary behaviour ..................................................................................................... 16
5.1.7 Consumer behaviour ............................................................................................... 16
5.1.8 Exposure data ......................................................................................................... 16
5.2 Data included in the database ......................................................................................... 16
5.2.1 Compound – Environmental matrix .......................................................................... 16
5.2.2 Compound - Dietary ................................................................................................. 16
5.2.3 Compound – Consumer products ............................................................................ 16
5.2.4 Exposure related data .............................................................................................. 16
5.2.5 Time Activity data .................................................................................................... 17
5.2.6 Dietary behaviour ..................................................................................................... 17
5.2.7 Consumer behaviour ............................................................................................... 17
5.2.8 Exposure data ......................................................................................................... 17
5.2.9 Link to IPCheM ........................................................................................................ 17
6 Use cases analysis ................................................................................................................ 19
6.1 Use cases ....................................................................................................................... 19
6.1.1 Create an Account ................................................................................................... 19
6.1.2 Login ........................................................................................................................ 20
6.1.3 Logout ..................................................................................................................... 21
6.1.4 Reset Password ....................................................................................................... 22
6.1.5 Retrieve Username .................................................................................................. 23
6.1.6 Edit Account ............................................................................................................ 23
6.1.7 Download data ......................................................................................................... 24
6.1.8 Print data ................................................................................................................. 24
6.1.9 Copy data ................................................................................................................ 25
6.1.10 Search dataset ........................................................................................................ 26
6.1.11 Filtering by multiple search ...................................................................................... 26
6.1.12 Column visibility ....................................................................................................... 26
6.1.13 Contact us ............................................................................................................... 27
6.1.14 Import data .............................................................................................................. 28
6.1.15 Import data via excel file .......................................................................................... 29
7 Requirements ........................................................................................................................ 29
7.1 Computer and smart mobile devices specifications ......................................................... 29
7.2 Browser specification ...................................................................................................... 29
AD 12.1 Database of exposure-related and ancillary data for priority substances Security: Public
WP 12 - From HBM to exposure Version: 7.2
Authors: Alberto GOTTI, Denis SARIGIANNIS Page: 4

8 References ............................................................................................................................ 30
9 Appendix ................................................................................................................................ 31
9.1 Annex 1 – web database screenshots ............................................................................ 31
9.2 Annex 2 – Data type required in the database ................................................................ 48
AD 12.1 Database of exposure-related and ancillary data for priority substances Security: Public
WP 12 - From HBM to exposure Version: 7.2
Authors: Alberto GOTTI, Denis SARIGIANNIS Page: 5

1 Authors and Acknowledgements
Lead authors
Alberto GOTTI, Denis SARIGIANNIS
IUSS, AUTH

Contributors
Evangelos Handakas, Spyros Karakitsios (AUTH)
AD 12.1 Database of exposure-related and ancillary data for priority substances Security: Public
WP 12 - From HBM to exposure Version: 7.2
Authors: Alberto GOTTI, Denis SARIGIANNIS Page: 6

2 Introduction
2.1 Aims, approach, scope and audience of the HBM4EU exposure
database
The purpose of this document is:
(a) to outline the technical development of the HMB4EU web-based exposure database developed
in WP12 to support the modelling of the exposure to HBM associations, accessible at
https://hbm4eu.enve-lab.eu/ and
(b) to provide an overview of its software implementation.
The database has been created by IUSS and AUTH and several data have been already imported.
The data come from WP12 partners, as well as from available reports and scientific literature.
Overall almost 250,000 entries have been imported up to now. Details on the imported fields have
been described in the report in Chapter 5 – Description of data.
Overall, previous experience from building similar databases (such as the ones of INTERA and
INTEGRA) and review of other similar databases such as ExpoFacts, EFSA, US EPA and
Canadian exposure handbooks and RefXP, have been very useful in the design of the database
and the data collection datasheets. In terms of design, the HBM4EU exposure database uses a
similar structure to these databases (mainly RefXP) for organizing the exposure related data, but it
is implemented using a web-based user interface, thus ensuring a more user-friendly environment.
Its main purpose is to:
• Provide the link between the Functional Specifications and the Technical Design report
• Detail the functionalities provided by the individual components and to illustrate how the
various components interact.
• Provide information with regard to the available exposure and ancillary data.
The intended users are the people involved in HBM4EU and especially WP12, but not only. The
database provides a wealth of exposure related data, that are necessary for estimating exposure
and further associate them with HBM data. Given the above, the design of the database and the
type of info included, is the result of consultation among experts in exposure science involved in
WP12.
The database is fed with data from various studies, even though not all of them provide the same
amount of detail. However, the database itself requires consistent fields for data input, so when a
user is exporting data from the database, they are in a consistent format. The database is updated
automatically whenever a user is uploading new data. However, regular updates on new data
available from the consortium are scheduled to be done on a monthly basis. In addition, new data
uploaded by the HBM4EU consortium will be checked by the database administrators (data quality
control) for avoiding mistakes, duplicates etc. on a monthly basis. Update with new data arising
from the literature will be done on an annual basis.
Updates of the web based database will be done only when deemed necessary and only when
stable versions will be provided by the developers of the used javascript libraries (jquery,
dataTable, jszip).
The database will be available for all the normal duration of the project and beyond. AUTH and
IUSS will support its maintenance till the end of the project, without any additional budget than the
AD 12.1 Database of exposure-related and ancillary data for priority substances Security: Public
WP 12 - From HBM to exposure Version: 7.2
Authors: Alberto GOTTI, Denis SARIGIANNIS Page: 7

one already foreseen for the activities of WP12. The database is ownership of the HBM4EU
consortium and accessible to all partners forever.
Access has been granted to all WP12 partners. The database will be enriched with data from the
partners, especially the ones from WP12, but also with newer data arising from the European
literature.
One other key aspect of the database is the link with IPCheM. Towards this aim, we have been in
close contact with the JRC team responsible for the IPCheM platform (during the last years,
participating in various relevant workshops. Up to now, all relevant requirements for ensuring
compatibility with IPCheM, have been followed.
2.2 Document Organisation
This document is organised into the following sections:
 The 1st chapter provides general information of the report and the way this is organised.
 The 2nd chapter provides an overview of the design of the web-based database.
 The 3rd chapter illustrates the architecture of the database.
 The 4th chapter presents the use case analysis.
 The 5th chapter provides the design of the database.
 The 6th chapter includes the literature references.
 The appendix illustrates the related screenshots from the web database (Annex 1) and the
requested type of data (Annex 2).
AD 12.1 Database of exposure-related and ancillary data for priority substances Security: Public
WP 12 - From HBM to exposure Version: 7.2
Authors: Alberto GOTTI, Denis SARIGIANNIS Page: 8

3 Design Overview
3.1 Approach
The following steps were followed for the database design:
• Requirements Phase: during the requirements phase a candidate architecture was
proposed to be validated in the System Design Phase.
• System Design Phase: in this phase, the evolutionary prototype was created and finalised
by establishing a sound architectural foundation for the construction phase.
• Construction Phase: in this phase, the design was updated to reflect changes in any
interface definitions.
• Transition / Training Phase: in this phase, no further additions or modifications were made.
If a new functionality is expected to be implemented, this will go through all the above
phases and this document will be updated accordingly.
3.2 Architectural Goals and Constraints
A key architectural goal is to leverage engineering and scientific best practices for designing and
developing an intuitive and user-friendly web database.
3.3 Maintain and Operate Database
Regular maintenance of the database will be carried out at least once a year. However, the
database content will be updated in the case of emerging user needs and whenever new data are
available. The methods that will be used for staying abreast with new ancillary data include:
 Periodical research of new data
 Periodical review of scientific and regulatory body databases
 Periodical communication directly with partners
During the database lifetime, project partners will modify, add, and delete content on a regular
basis. Setting up a password-protected administrative component will ensure only project partners
are able to make changes, protecting the database content. The update of the interfaces is
responsibility of the project partners.
3.4 Additional Considerations
3.4.1 Language
HMB4EU WP12 database is available only in English.
3.4.2 Requests for Technical Assistance and Information
The webmail provides technical assistance and information to the user of web-based database
through the menu “contact us”. In addition, the web site provides instruction and technical
assistance for filling the forms. It is worth mentioning that additional instructions and material are
provided by the developers through the website.
AD 12.1 Database of exposure-related and ancillary data for priority substances Security: Public
WP 12 - From HBM to exposure Version: 7.2
Authors: Alberto GOTTI, Denis SARIGIANNIS Page: 9

3.5 Database conceptual design
The conceptual design of the database is graphically illustrated in Figure 1.

Figure 1: Database conceptual design
AD 12.1 Database of exposure-related and ancillary data for priority substances Security: Public
WP 12 - From HBM to exposure Version: 7.2
Authors: Alberto GOTTI, Denis SARIGIANNIS Page: 10

4 Application Architecture
4.1 Technical Design Diagram
The diagram in Figure 2 shows all existing technical resources required for the successful
completion of the Db developments.
Web application server Firewall Data base
User/workstation

Figure 2: Interaction of software components

 Web/Application Server: Tomcat is used as web and as application server. It is responsible
for serving web pages, mostly HTML pages, via the HTTPS protocol to clients. The server
sends out web pages in response to requests from browsers. A page request is generated
when a client clicks a link on a web page in the browser.
The server hosts the business logic and the business model classes of application as well.
It serves requests for dynamic HTTP web pages from client.
 MySql Database which stores the available dataset collected by HMB4EU WP12 partner’s
user profile, credentials and account data.
 HTTP: Hyper Text Transport Protocol is the communication protocol used to connect to
servers on the World Wide Web. The primary function of HTTP is to establish a connection
with a Web server and transmit HTML pages to the user's browser.
 PHP: Database Connectivity is providing using php language
4.2 Server infrastructure
 Server: 4 CPU’s, 8 GB RAM, 200 GB Hard Disk Space
 Web data Server: 4 CPU’s, 8 GB RAM, 50 GB Hard Disk Space
 Windows Server 2008 64-bit.