Beneris deliverables

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Deliverable list

All deliverables can also be found from the Beneris page in Heande (password-protected).

Deliverables list (full duration of project)
Deliverable name WP no. Dissemination level Success of completion Comments
D1_Workplan_pyrkilo WP1 RE Successful. Introduction of the method.
Beneris WP5 PU Successful. First project website.
D3 Kickoff meeting WP6 RE Successful. Arranged together with Qalibra 23rd-24th May, 2006
D4_poster2 D4_brochure_cover D4_brochure WP7 PU Successful. D4 Poster + 4 page brochure
D5_-_Beneris_&_Qalibra_dissemination_strategy WP6 RE Finalised at a late stage. Very active dissemination during the project was not possible because the method and case studies were still under development. The disseminating strategy that was accepted during the last year is ambitious and will be applied for a long time after the project. It is not yet possible to evaluate the success. For example, several publications are under preparation.
D6_Health_Benefits_Fish WP3 PU Successful. Summary tables and references about health impacts of fish.
D7_Database_review_-_Contaminant_food_intake WP2 PU Successful. 28 pages containing tables and introduction.
D8_Generalized_Method_and_its_application_to_the_BENERIS_project WP1 RE Successful. Taylor expansion paper, 28 pages
D9_Beneris_ethical_issues_revision2 WP2 RE Technical report.1 Signed study approval papers from the respective ethics committees.
D10_Food_diaries WP2 PU Successful. Excel file containing the desired data.
D11_Food_intake_data WP2 PU Successful. Excel file containing the desired data.
D12_Contaminant_levels_in_fish D12_Data WP2 PU Successful. Excel sheet containing the desired data.
D13_First_year_report WP7 PU Technical report. A PDF report of 48 pages.
D14_Dietary_Patterns WP2 PU Successful. Dietary patterns described as correlation tables.
D15_Pyrkilo_guide_2 WP1 PU Successful. Jouni T. Tuomisto, Mikko Pohjola: Open Risk Assessment - A new way of providing scientific information for decision-making (a report)[1]
D16_Cardiovascular_disease_benefit_meta-analysis WP3 PU Successful. A review, 23 pages.
D17_Internet_interface WP5 PU Successful. Two new wiki websites, Beneris and Heande wikis were launched.
D18_Subpopulation_intakes WP2 PU Successful. Food intake in children of 1,3, or 6 years
D19_Contaminants_in_placenta WP2 PU Successful. Table about 117 contaminants in placenta. Additionally, a manuscript under finalization.
D20_Intake_of_contaminants_in_children WP2 PU Successful. Exposure to PCDD/F, PCB, and mercury in children.
D21_Intake_of_contaminants_-_national_registries WP2 PU Successful after narrowing down the scope. A manuscript (Karjalainen et al.) that is based on the deliverable work is under finalization. It is not openly available before publishing. The deliverable has been adjusted to include only Finnish data, because we failed to receive the PCDD/F concentration data that had been requested from the Commission during P2. This change is not important for the main outcome of Beneris, namely open assessment method and Opasnet workspace.
D22_Preliminary_benefit-risk_analysis_of_fish WP3 PU Successful. Leino et al., Risk Analysis: 2008 Feb;28(1):127-40.
D23 Second project meeting WP6 RE Succesful. Minutes and information published.
D24_Midterm_review_report WP7 PU Successful. 1) Presentations, discussions, feedback. 2) Mid term review, 32 pages. 3) Reviewers' report, with response from the Beneris partners
D25_Decision_support_system WP1 RE Successful. The product itself is the improved software Uninet (downloadable from the Web). The deliverable contains a brief description of the method.
D26_Evaluation_of_patterns WP2 PU Successful but only for Finland. Problems to receive data, see D21. The new version of D26 manuscript is now in press: Tero Hirvonen, Harri Sinkko, Anja Hallikainen, Hannu Kiviranta, Pirjo Pietinen, Liisa Valsta, Jouni T. Tuomisto: Modelling the intake of polychlorinated dibenzo-p-dioxins and dibenzofurans: impact of energy under-reporting and number of reporting days in dietary surveys. Food Additives and Contaminants (in press).
D27_Intakes_based_on_patterns_-_adults_in_Finland WP2 PU Successful. Report containing 11 pages.
D28_Review_on_other_health_benefits_of_fish WP3 PU Successful. Review containing 28 pages
D29_and_D30_Contaminant_intake_among_Finnish_adults WP2 PU Successful. PCDD/F and PCBs, 4 pages, introduction and tables
D31_Enduser_evaluation WP5 PU Successful. Based on Open assessment workshop 2009, 8 pages
D32_Critical_dietary_patterns_in_Finland WP2 PU Successful. Report containing tables and comments, 17 pages
D33_Consumer_info_on_case_results WP1 PU Successful. Focus was more on methods and less on case results than originally planned. Deliverable has been published in International Innovation.
D34 Beneris Activity report 2nd year WP7 PU Technical report. 1)Activity report, 2)Management report, 3)Distribution of the Community's contribution report, 4)Appendix pages
D35_Pyrkilo_guide_3 WP1 PU Successful. Report, 4 pages with several links to key pages in Opasnet
D36_Fetus_contaminants_from_mothers'_diet WP2 PU Successful. A report about PCDD/F and PCB intake in mothers.
D37_Internet_update WP5 PU Very successful. A report about new functionalities in Opasnet, 11 pages. See objective "To develop an internet interface for publishing risk assessment results."
D38_Full_benefit_risk_analysis_of_fish WP3 PU Successful. Benefit-risk analysis in the Opasnet workspace (partly restricted access) [2] [3]
D39_Combined_database WP2 PU Very successful. See objective "To develop an integrated repository of surveillance, nutrient and food consumption data."
D40_Full_benefit-risk_analysis_-_vegetables WP4 PU Successful, given the new scope. More emphasis was given to method development than originally planned. Therefore, the scope of this case study was reduced to one specific question, namely food fortification as an additional source of vitamins in children with low vegetable consumption.
D41 Beneris Activity report P3, Revision 2, clean version WP7 PU Technical report. 1)Activity report, 2)management report, 3)Distribution of the Community's contribution report, 4)Appendix pages
D42_VOI_analysis_of_fish WP5 PU Successful. In addition to performing the value of information analysis, we also developed the VOI analysis further especially for Bayesian belief networks (BBNs).
D43_Consumer_reactions WP5 PU Partly successful. The original plan was to study consumer reactions by using the ZMET technique. However, there was a delay in method development and case studies, and we found it infeasible to perform the study with an immature method. As a corrective action, an Internet survey was performed, and useful information from end users was obtained. Also, the technical capability to perform surveys in Opasnet was established due to this deliverable.
D44_Third_project_meeting WP6 RE Successful. Beneris wiki-page and minutes.
D45_Application_of_BRA_to_FSA WP1 PU Mixed result. See objective "To evaluate the integration methodology by all partners and develop it further."
D46_End_user_evaluation WP5 PU Successful after a change in scope. Report about usability of open assessment and actual use of Opasnet website. See also objective "To evaluate the integration methodology by all partners and develop it further."
D47_Scientific_advisory_panel WP6 RE Successful. The SAP was actively involved in the meetings and gave very good and critical comments. For example, these comments launched the development of protocols for quality assurance and quality control and peer review within Opasnet. This has proven very valuable.
D48a Beneris Activity report P4_revised and D48b Beneris Publishable final activity report_revised WP7 PU Technical report. Final revisions under preparation. D48a:1)Activity report, 2)management report, 3)Distribution of the Community's contribution report, 4)Appendix pages. D48b: 1) Publishable final activity report, 2) Final plan for using and disseminating the knowledge, 3) Final Management report, 4) Final DCC report (to be added later) (The Word/Excel files are located in the local folder N:/YTOS/Projects/BENERIS/Admin/Deliverables/D48b Final report)

1 Technical report means that the deliverable does not contain new scientific data or understanding but rather reports what has been achieved or done. It also implies that it was successfully completed.

Project objectives

Objective Success of achieving objective Comment
The general objective of this proposal is to create a framework for handling complicated benefit-risk situations, and apply it for analysis of the benefits and risks of certain foods. The first food commodity to be used in the development of the methodology is fish. Very successful. The framework was based on a novel idea of open participation on a web workspace. Although openness was described already in the Technical Annex, the importance and prospects of this approach was only understood during the first year of the project. A shift of emphasis from case studies towards framework development occurred starting from the first year, as described in annual reports and the mid-term meeting. The ambition level in method development clearly increased during the first year. This increased the amount and complexity of things to develop, which slowed down the progress. However, the end result was worth the effort: open assessment has solid scientific foundations, and it is widely applicable in many fields of assessment.

The resulting framework will potentially contribute in a major change in the science-policy interaction in many areas, including but not limited to food. We did not promise to demonstrate a major change in real-world practices during the lifetime of the project, and as expected, we have not yet seen major changes. However, we are optimistic about this change in the near future, maybe in a few years. The web workspace and the framework developed are being and will be used in the future in new projects by Beneris partners and others, and the ideas of openness and collaboration are clearly spreading in the scientific community. This is a mega-trend and mostly independent of us, but the progress of openness has been faster in the area of benefit-risk assessment than elsewhere, thanks to the tools and methods developed in Beneris. This is because we started an active development of these methods in 2006, but the idea of openness and collaboration has only made a breakthrough in public discussion only in 2009.

Objectives in developing benefit-risk analysis methods
To develop Bayesian belief networks (BBN) to handle complicated benefit-risk situations, and to develop a decision support system (DSS) based on BBN. Successful. Uninet software was further developed for open benefit-risk assessments for food. E.g. functionalities for linking Uninet models to Opasnet assessment descriptions were added.
To develop improved methods for dose-response assessment, combining epidemiological and toxicological data, and apply them in combining epidemiological and toxicological information on fish contaminants (esp. dioxins and PCBs). Successful. An improved method was developed and utilised for dose-responses. It is based on a flexible mathematical method Taylor's expansion. In addition, reviews were performed to obtain dose-response data needed for case studies.
To develop an integrated repository of surveillance, nutrient and food consumption data that is capable of receiving, analyzing, and disseminating the accumulated data for benefit-risk analysis and to key stakeholders. Successful. The integrated repository Opasnet Base was developed with wide usability in mind. We wanted that it could contain very different kinds of information, basically anything that could be used in benefit-risk assessments. During the work (mostly second and third year) we realised that the database structure and interfaces need more work than we originally thought if the usability objective is to be met. Therefore, we put less emphasis in collecting raw data. The usability was demonstrated by the case studies.
Scientific objectives in food risks and benefits
To review the existing databases and their availability for chemical contaminant data in Europe, and integrate available data. Successful in review; problems in integration but leading to important lessons learned. The data was reviewed as planned. However, the actual integration of contaminant data was clearly smaller than originally planned. There are two reasons for this. First, it was realised that method development is the more important part of the project than data production or collection. Second, it was found out that data ownership, intellectual property rights, or practical hindrances of the persons possessing the data effectively prevented a large-scale collection of data. Instead of spending more time on collection of specific pieces of data, we tried to understand the dynamics of data production and openness to be able to overcome the problem.
To estimate average nutrient intakes and food consumption in various subgroups based on national registries in three countries and to explore the use of the data in benefit-risk analysis. Successful. Several pieces of work were performed, as can be seen from the list of related deliverables. Several age groups were looked at as planned.
To estimate the health benefits of fish, and understand the effect of fish on different population subgroups (age, health, pregnancy etc.) Successful. A large Benefit-risk analysis of fish was performed. One part of it was focussing on pregnant mothers and fetal development.
To establish the association between external dose (intake) and internal dose (concentrations in the body) by analysing contaminants (PCDD/Fs, PCBs, PBDEs, organotin compounds, PCNs and Hg/methyl-Hg) from 100-200 placentas. Successful. 130 placentas were analysed. The concentrations measured were compared to the pollutant intakes of the mothers. Pollutant exposures were estimated based on individual food intake records and measurements of pollutants in food.
To combine existing and new data from food consumption databases with data on levels of contaminants in fish. The special emphasis is on children and the developing foetus. Successful. New important chemical analyses were performed and linked with food consumption data. In this study, it was possible to link individual-level food intake to actual pollutant concentrations in the immediate environment (i.e., placenta) of the fetus.
To estimate distributions of nutrient intake and food consumption relevant to benefit-risk analysis in a number of populations, and also the variability in exposure among various subgroups in the population. Successful. Several populations in several countries were studied. Results included inter-individual variation within several age groups and both sexes separately.
To identify food consumption patterns and food choices that determine the intake of those nutrients and contaminants that are related to benefit/risk-balance of a food item. Successful. Dietary patterns were studied for Finland.
To explore the usability of these patterns in another country than in which they were developed. Successful after a shift in focus. The original plan was to to create a food consumption pattern (a list of correlations between intakes of different food items) in one country and then predict food intake in another country based on this. When the work started, we found out that it is more feasible and relevant to study total nutrient intakes based on national data rather than trying to extrapolate from another country. These intake estimates were performed for three countries in the vegetable case study: Finland, Spain, and Ireland.
To find out the effects of certain policy options on dietary habits and on intake of important nutrients and contaminants (e.g. vitamin D, n-3 fatty acids, dioxins, PCBs). As an example, does a restrictive recommendation on fish eating increase meat consumption? Successful. Food fortification was used as the policy option that was evaluated. We estimated the impacts the policy on the intakes of folate, vitamin A, and vitamin C.
Objectives in dissemination
To integrate results into updated benefit-risk assessments, and evaluate the remaining uncertainties and their importance for decision-making. Successful. Value of information analysis was performed to the results of the fish case study. It was found out that the decision about increasing total fish intake would benefit from better information about methylmercury and omega-3 fatty acids in the most popular fish species, notably salmon and Baltic herring. In contrast, information about other topics is less valuable for the decision. In addition, we developed a new practical way of doing screening analyses of value of information.
To evaluate the integration methodology by all partners and develop it further. Mixed result: important lessons learned but not the way that was planned. The methodology was presented to Beneris partners and one Qalibra partner in September 2007 in Berlin. It was discussed there. In addition, it was planned to be evaluated in more detail by FSAI. However, the methodology was found very confusing and different from traditional benefit-risk assessment. Detailed evaluation was considered impossible by FSAI, as explained in the fourth period report and D46 End user evaluation. Although the evaluation process itself was not very successful, it gave a lot of food for thought and boosted the development of the method into something more practical and understandable. It was a confusing learning experience, but in the end, we did learn many useful things that were important for the subsequent method development. The outcome did clearly improve due to the evaluation, which was, after all, its purpose.
  • End results: D46 End user evaluation, Berlin 2007 meeting, new insights of the user needs.
  • All partners, especially FSAI, THL, and TUDelft.
To develop an internet interface for publishing risk assessment results. Extremely successful. Our original objectives were rather modest here: the plan was to develop a website where stand-alone assessment models can be published together with detailed descriptions. This was originally set up by Lendac ( However, we were able to develop a web workspace where whole assessments can be initiated, designed, executed, evaluated, and disseminated, and where stakeholders can participate at any point. The actual website for publishing benefit-risk assessments was first changed to and later to Opasnet ( There is still a lot of work to be done to be able to actually run assessment models within the workspace. Other projects (e.g. Intarese) are now continuing this work.
To develop a method to publish entire benefit-risk models over the Internet using XML. Extremely successful. See also above. In the beginning of the project, we were only planning to focus on Analytica models which are in XML format. We developed a tool for automatically converting Analytica model files into model descriptions. Then we developed better practices to describe models directly in the workspace, which made a big leap towards open and collaborative modelling systems.
To develop methods to collect feedback from end-users about benefit-risk analyses. Successful. A survey functionality was developed to the Opasnet workspace. See e.g. End user evaluation.
  • End results: PollDaddy feedback system, also the commenting system at the end of each Opasnet page ("Post comment").
  • Partners: THL.
To enhance the availability of existing databases through this interface. Successful. Opasnet workspace offers a practical place to describe existing databases (e.g. WHO mortality data, IA Tools). Opasnet Base also offers a practical place to store the data itself, if it is freely available. This kind of work started in Beneris and is now ongoing in other projects. For example, Heimtsa project is using these tools to collect morbidity data for Europe.
To disseminate the results and to evaluate the relevance and usefulness of the work done in the project from the perspective of an end-user / authority. Overall successful, but changes in focus. Beneris has disseminated project and scientific information on its websites since the beginning. Also D46 End user evaluation looked at this issue. Beneris has disseminated less about the case study results but clearly more about the methodological development than originally thought. The case studies were finalised later than thought, and therefore the time to disseminate results was shorter. On the other hand, it was found out during the project that methodological results are more important than the case studies. Beneris actively discussed with other projects, notably Intarese and Heimtsa. This was a major way to obtain evaluation and comments about the usefulness of Beneris framework and workspace. So, we got a lot of feedback from assessors as end users of the framework, but not very much from authorities or others as end users of Beneris case study assessments.

Development of Beneris websites

The first website opened for Beneris was, which was opened in the beginning of the project and managed by Lendac. The purpose of the website was to disseminate information about the project, because there were - naturally - not yet results produced by the project. The website had a password-protected area, but this area was used only a little. The idea about a wiki-based website already existed in the beginning of the project, but not yet during the writing of the Description of Work. The possibilities to actually use a wiki site for the needs of the project were unclear in the beginning of the project. Therefore, the development of went on for the first year or so of the project.

The project wiki website was opened soon after the project started with the name The name was later changed to, but this change did not affect the contents in any way. This website was called the "Beneris wiki", as THL was running also other wiki websites for research projects. The Beneris wiki is a password-protected website, and it only contains materials of the Beneris project. One idea was that Beneris wiki would have been a true workspace for the project so that all material would have been available there and contents would have been edited there directly. However, this never worked out in full, as few people in the project had little experience in working with wiki. Also, the functionalities of the website were not very developed in 2006. However, THL made an effort to share at least the most important materials via the Beneris website.

In September 2006, THL opened another wiki website called (originally, but the name was later changed). Opasnet was an open website for materials that researchers wanted to distribute freely. Some of the public Beneris materials were put directly to Opasnet, while most of it was kept behind the password in the Beneris wiki.

During 2006-2007, several wiki websites were opened for projects like Intarese, Heimtsa, and others. In two years, THL was maintaining 14 different wiki sites, most for a single project. This made no sense. It just caused technical burden, and it also made it difficult to find information. Therefore, THL started to promote the idea of a joint project wiki for all interested research projects. It would be password-protected, but the default would be to show all or at least most project information to researchers in other projects. It was also made possible to hide the information of one project from others, but this was discouraged. Finally, this joint wiki site for several projects, called, was opened in June 2008. Heande became the password-protected part of Opasnet for all projects.

Gradually, THL closed project-specific wikis and moved the information to either Heande or Opasnet. We started from the newest and smallest wikis because those were the easiest to move and the benefit was largest. Beneris project had only a year or so to go, and it contained a large amount of information already. It was thought that it was not worthwhile to move the information while the project was still active. This had the drawback that some protected material were split between the Beneris wiki and Heande. However, the ultimate archive of the Beneris material will be in Heande, and Opasnet for such material that can already be released. This work is slowly going on now, but the main focus is on writing manuscripts based on Beneris results. After the writing period, the Beneris material will be archived, and Beneris wiki will be closed.

The four years from spring 2006 to spring 2010 have been an intensive period of wiki development. The work started with a plain MediaWiki software with no additional help for making benefit-risk assessments. Nor were researchers familiar with the concept of mass collaboration using websites. Beneris was one of the first research projects that seriously pushed the idea of wikis as the tool to do science and assessments. As a result, there is a growing interest in these tools. Also, the tools themselves have become very sophisticated and fit for sharing, collecting, organising, and synthesising scientific information, and disseminating results to and discussing the results with interested stakeholders. Opasnet has grown into real a web workspace for mass collaboration of researchers, assessors, and stakeholders.

Projects currently using or planning to use Opasnet

Follow the links to find more details about the projects.

Projects currently using or planning to use Opasnet or Heande for research.
Project name Main funder Topic of project How Opasnet is used
Intarese EC Integrated environmental health impact assessment Project workspace, distribution of materials within and outside the project.
Heimtsa EC Integrated environmental health impact assessment Project workspace, distribution of materials within and outside the project.
Hiwate EC Benefit-risk assessment of drinking water chlorination and microbes Project workspace, benefit-risk assessments.
Plantlibra EC Health risks of plant extracts Project workspace, risk assessments (project starts in June 2010).
Claih Academy of Finland Climate change and health Project workspace, health impact assessments on climate change, distribution of materials within and outside the project.
Bioher Academy of Finland Bioenergy and health Project workspace, health impact assessments on bioenergy and climate change, distribution of materials within and outside the project.
Hitea Academy of Finland Indoor air and health Project workspace, end-user feedback and surveys.
Altti Academy of Finland Indoor air and health Population survey and feedback.
Bepraribean European project, several national funders Benefit-risk assessment for foods Writing of scientific articles.
Tapas Coca Cola Company Health impacts of active transportation Project workspace.
Hiccups Academy of Finland Climate change and health Writing of application (project not yet funded).