As a first step, HBM4EU will identify and collate existing human biomonitoring data that is held by our broad range of partners in 28 countries across Europe. We will review this data against current policy questions, to determine what questions might be addressed by currently available data.
Where we identify gaps in the available evidence, we will generate new human biomonitoring data through the implementation of targeted surveys and the analysis of biobanked samples.
Please find below relevant information on:
- HBM4EU Data Management Plan and Data Policy
- Multiplying the benefits of data
- How to prepare and transfer the data and metadata into the HBM4EU Data Repository, step by step
- How to make the data available in IPCHEM
- Summary of instructions for data transfer & relevant documents
HBM4EU Data Management Plan and Data Policy
In order to ensure that our work with data respects all relevant ethics and legal requirements at both national and European level, we have developed a Data Management Plan and a Data Policy.
The Data Management Plan describes the data management life cycle for all datasets collected, processed and generated under the project. It describes:
- How research data is handled during and after the project
- What type of data will be collected, processed and used
- What methodologies and standards will be applied
- Whether and how the data will be made accessible
- How the data are stored
The Data Policy describes the data management procedures to be followed by the consortium. These procedures ensure that data on human subjects are transferred and used in a secure setting, in compliance with ethico-legal requirements.
Requirements are set under:
- Consent forms signed by survey participants
- Ethics approvals at national level
- Data protection laws at national level
- The EU General Data Protection Regulation
- The HBM4EU Data Transfer Form signed by the data owner or provider
Data use requires the explicit consent of the data owner and/or data provider.
Please also find here the Commission guidance on the direct application of the General Data Protection Regulation as of 25 May 2018.
A step by step guide for the data owner/data provider to transfer data to HBM4EU is provided below under the title – How to prepare and transfer the data and metadata into the HBM4EU Data Repository, step by step.
A step by step guide for data users is provided below under the title – “How to make the data available in IPCHEM”
Multiplying the benefits of data
It is a principle aim of the project to increase the availability of human biomonitoring data to policy makers, stakeholders and the broader research community, in order to multiply the benefits that can be generated through its use.
As such, all human biomonitoring data generated under the project will be made available to policy makers and all metadata will be accessible via IPCHEM – the Information Platform for Chemical Monitoring. Existing data used under HBM4EU may also be made available via IPCHEM to the extent possible while respecting all ethics and legal restrictions that might apply.
IPCHEM is the reference access point for discovering chemical monitoring data collections which are managed by and are available to European Commission bodies, Member States, international and national organisations and research communities.
The Platform aims to support a more coordinated approach for collecting, storing, accessing and assessing data related to the occurrence of chemicals and chemical mixtures, in relation to humans and the environment. This responds to the need identified in the European Commission’s 2012 Communication on the combination effects of chemicals.
IPCHEM is designed and implemented as a de-centralised system, providing remote access to existing information systems and data providers.
How to prepare and transfer the data and metadata into the HBM4EU Data Repository, step by step
Guideline to support HBM4EU consortium partners in preparing and providing their data collection, the accompanying metadata and documentation, as requested by the HBM4EU Data Management Plan and Data Policy.
Questions can be submitted via the helpdesk for data management.
Step 1: compilation and provision of the data transfer documentation
The data transfer documentation is to be completed by Data Owner or Data Provider. In case a Data Provider is assigned by the Data Owner, the Data Provider will be responsible for implementation of the procedures described in the HBM4EU data management plan and data policy and is mandated by the Data Owner to complete and sign the transfer documentation and forms.
According to the HBM4EU Data Policy and HBM4EU Data Management Plan the Data Owner/Data Provider fills in and signs:
a) The HBM4EU Data Transfer Form for the data transfer to HBM4EU and integration into IPCHEM, compiled of:
- Description of the purpose of form and signature section
- Part A: General Part: contact details, study information, indicate variables to which the agreement applies …
- Part B: HBM4EU Data Transfer Agreement
- Part C: IPCHEM Participation form for HBM4EU project
The Data Owner/Data Provider is requested to send the completed and signed (ink signature) form to: Umweltbundesamt, Marike Kolossa-Gehring (Project Coordinator HBM4EU), P.O. Box 33 00 22, 14191 Berlin, Germany.
Furthermore, it is requested to submit the completed electronic form using the “Submit form” button. In case of technical issues submitting the form, please send it via e-mail to HBM4EU.DATAMANAGEMENT@vito.be. Including e-signature will enable to progress faster to the process of transfer of the data. However, the print version with ink signature shall arrive no later than 4 weeks upon submission of the electronic form at the above mentioned address. Please note that the print version with ink signature is the binding one.
The form for data transfer to HBM4EU and integration into IPCHEM can be downloaded here.
In parallel, the Data Owner/Data Provider collects and provides the Ethics and/or Data Protection documents:
b) Instructions are available at https://c.deic.dk/hbm4euethics
In short, HBM4EU Ethics Template (v. 28.05.2018) shall be filled out and copies in pdf format of all required documents shall be provided.
Documents a) and b) must be sent together and named using the following rules:
- Acronym of the organisation_Acronym/short name of the data collection_HBM4EU_Data TransferForm
- Acronym of the organisation_Acronym/short name of the data collection_ HBM4EU_EthicsTemplate
- Acronym of the organisation_Acronym/short name of the data collection_Ethics document1
Step 2: provision of the HBM4EU-IPCHEM metadata fiche
The Data Owner/Data Provider fills in the HBM4EU-IPCHEM metadata template, which reports the general information of a data collection/monitoring initiative: one metadata fiche for one data collection.
The HBM4EU-IPCHEM metadata template can be downloaded here.
Please Note: In this first data and metadata collection phase for the HBM4EU project, the request of compiling the metadata has been anticipated. In the future the metadata fiche will be compiled and collected shortly after the data owner/provide has signed and provides the aforementioned documents: a) and b) (Step 1)
Exceptions / special cases
A data collection may be composed by a series of sub-studies. It is a decision of all the Data Owners/Data Providers of the sub-studies, to structure, merge the data and propose a unique data collection. This will be handled during the HBM4EU project (and, if agree, also inside IPCHEM) as a single data collection; however the data owners can describe/report the main information of the sub-studies in the metadata template.
The Data Owner/Data Provider sends the metadata fiche to: HBM4EU.DATAMANAGEMENT@vito.be
Each metadata fiche will be stored into the HBM4EU-IPCHEM Data Repository, by the Data Repository managers and later available to each data owner/provider that can consequently update the file of the metadata fiche over the time, if necessary.
Note: For HBM4EU the IPCHEM metadata fiche has been updated and the data are to be provided in a harmonized manner (step 4). This was needed to allow the analyses that are scheduled. However, for data collections that have been integrated into IPCHEM before, it may be made possible by HBM4EU data management team to not have to provide the same information again. HBM4EU data management team proposes to provide the templates (metadata fiche and data template) with the information that has been provided in the past already filled out. Please contact HBM4EU data management team via the helpdesk for data management if you would like this for a particular data collection.
Step 3: creation of the EU Login Account
In parallel, the Data Owner/Data Provider creates an EU LOGIN from this link: https://ecas.ec.europa.eu/cas
This is an individual account, therefore each member, of each organisation acting as owner/provider of the data (i.e. data responsible declared into the metadata fiche and data transfer agreement) creates an individual account.
The Steps to create the EU Login account are available at: https://webgate.ec.europa.eu/cas/manuals/EU_Login_Tutorial_1.1.pdf
Once created the EU Login account, the Data Owner/Data Provider opens IPCHEM (https://ipchem.jrc.ec.europa.eu) and Log-in. An email notification will inform the Data Owner/Data Provider when authorised to access to HBM4EU Data Repository.
Why the EU Login
The EU Login is the European Commission authorisation and authentication service and it ensures secure access both the HBM4EU Data Repository and restricted data in IPCHEM. Once the data owner/provider has signed and sent all the documents summarised in Step 1 and created the EU Login Account, the IPCHEM team can proceed with the management of the accounts to access to the HBM4EU Data Repository. Only authorised accounts get the access to it.
The Approval document folder of a data collection set up in the HBM4EU Data Repository will be later accessible to the data owner/provider, thus ensuring full transparency of the data transfer process.
Step 4: preparation of the data to be uploaded into the HBM4EU Data Repository
For the transfer of individual data, the Data Owner/Data Provider prepares the harmonised version of the individual data collection under his/her responsibility to make available for HBM4EU project. Data should be prepared according to the HBM4EU Codebook and HBM4EU data template available here.
Below, please find more information on the codebook and the data template. Do not hesitate to contact HBM4EU.DATAMANAGEMENT@vito.be if anything is not clear.
Description of the data template and codebook:
Relevant Files: Empty Data Template.xlsx; Codebook.xlsx; Biomarkerlist.xlsx; Empty_DataTemplateAdnCodebook.RData > if you prefer R, it includes the same information as the xlsx files. (Will be available soon)
1) The data shall be split over different sheets of the excel template, in order to avoid the need for replication.
In short, the data shall be put together considering the sample as the main unique identifier.
Information of the sample is provided in sheet “SAMPLE”.
Each sample shall be mapped to a group (point 2) and to a subject (point 3).
Group has been included to indicate if a collection of samples shall be considered together, e.g. relevant in repeated sampling design.
More samples may be mapped to the same subject, e.g. when blood and urine samples for a given subject are available.
In the codebook, you will find under the corresponding sheet, a description of the variables, and the format in which they need to be provided.
In the sheet “GROUP” a short description of the different groups has to be provided.
2) Information of the subject is provided in two sheets “SUBJECTUNIQUE” and “SUBJECTREPEATED”.
This has been split, to enable to capture values that may change during the course of e.g. bmi of the individual at first versus second sampling if there is some time in between the measurements.
All information that is considered unique to the person from the first sampling onwards, has been included in the table “SUBJECTUNIQUE”.
All information that may change, has been included in table “SUBJECTREPEATED”. The link with group shall be indicated in id_group referring to the GROUP table.
Please note that in the sheet “SUBJECTUNIQUE”, linkage between the subjects is also created. This enables to identify e.g. mother-child pairs.
3) The data obtained from measurements of the samples is to be provided in the sheets with prefix DATA_.
For each matrix, a separate sheet is provided. Please note that the id_sample shall be extracted for the specified matrix from the sheet “SAMPLE”.
We did not include all biomarkers and matrices in the template, since the list of possible biomarkers is quite long. Instead we ask the data provider to highlight in Biomarkerlist.xlsx which biomarkers have been measured in which matrix (put a “1” in the blue columns). This is necessary for correct interpretation of the data. This is necessary for correct interpretation of the data.
Upon receipt of this information, we will provide you a template adapted for your data collection with a column for the actual measurement value of each indicated biomarker, and two additional columns (for LOD and LOQ respectively).
Please provide us with this information in order to proceed.
Filled out example template with simulated data:
To guide the data providers, we compiled an example filled out data template: VITO_Example_DataTemplate.xlsx / –.RData .
It concerns simulated data from 50 newborn-mother pairs; and 150 samples.
Samples: 50 cord blood-whole blood samples of newborns (participant); 50 blood-whole blood and 50 morning urine samples of the mothers.
The template is provided both in excel and in R, feel free to choose the format that best suits you.
Please indicate your choice by putting a 1 in the respective field Biomarkerlist.xlsx.
Some further notes:
Please do not send the filled out data template to us via e-mail. When everything is in place and has been checked (inkt signed data transfer form, ethics template + documentation); we will provide you with instructions to upload the data to the HBM4EU repository.
Upon receipt of the annotated Biomarkerlist.xlsx (send to HBM4EU.DATAMANAGEMENT@vito.be , we will provide the personalized data template in the preferred format (Excel or R) for your data collection.
When the individual data template is filled out, the Data Owner/Data Provider can use the HBM4EU -R script for launching the statistics and creating the aggregated version of each individual data collection. The R-script has been developed to ensure the same analysis protocol which enhances comparability of aggregated data between studies. The HBM4EU-R script is available here. (will be made available soon)
Once the data collection have been transformed and/or the aggregated data have been generated the Data owner/provider informs via email the HBM4EU WP 10 team: HBM4EU.DATAMANAGEMENT@vito.be
Step 5: upload of the data into the HBM4EU Repository
The HBM4EU data management team will provide information on the dedicated folder in the repository.
To upload the data into the dedicated folder set up for each data collection into the HBM4EU Data Repository the Data Owner/Data Provider shall use the following link: https://ipchem.jrc.ec.europa.eu/share or access to IPCHEM and log-in.
How to make the data available in IPCHEM
For Data owners/providers that decide to make their data available in IPCHEM
For HBM4EU research, data shall be harmonised according to the HBM4EU Data Management Plan and Data Policy by performing step 4 of these guidelines. This is needed to be able to compare different studies across the project. However, the Data Owner/Data Provider may decide to make their data “as is”, i.e. in own format, available in IPCHEM; and in later stage in harmonized format in the Repository. In this scenario, it allowed to proceed from Step 3 to Step 5; and perform Step 4 in later stage.
Upon upload of the data into the HBM4EU repository by the Data Owner/Data Provider (Step 5), the IPCHEM team will integrate the data into IPCHEM in accordance with the specifications in form C of the data transfer form (indicating the level of integration into IPCHEM). For data that are provided in own format, additional information or technical documentation may be requested by the IPCHEM team to understand the structure of the data collection and the related variables.
When the Data Owner/Data Provider decides to integrate data in own format into IPCHEM, there will be a unique data collection in IPCHEM, described by a unique metadata, with maximum 4 different related datasets (depending on the specifications in form C of the data transfer form):
- Aggregated data as created and managed by the data provider/owner (a core set of data elements are pre-harmonised according to the IPCHEM internal data model, by the IPCHEM team)
- Single measurement data as created and managed by data provider/owner (a core set of data elements are pre-harmonised according to the IPCHEM internal data model, by the IPCHEM team)
- HBM4EU Harmonised single measurement data, prepared by the data provider/owner according to the HBM4EU codebook
- HBM4EU Harmonised aggregated data, prepared by the data provider/owner according to the HBM4EU codebook and R-script
The metadata remains one, related to the data collection, the title of the datasets self-explains the type of information of each dataset, as additional information available into the metadata page.
When the Data Owner/Data Provider decides to integrate int IPCHEM only data in HBM4EU harmonised format, there will be a unique data collection in IPCHEM, described by a unique metadata, with maximum 2 different related datasets (depending on the specifications in form C of the data transfer form):
- HBM4EU Harmonised Individual data, prepared by the data provider/owner according to the HBM4EU codebook
- HBM4EU Harmonised aggregated data, prepared by the Data Owner/Data Provider according to the HBM4EU codebook and R script
The metadata remains one, related to the data collection, the title of the datasets self-explains the type of information of each dataset.
Step 6: Quality control and data integration into IPCHEM
The IPCHEM team starts the integration phase and prepares the “IPCHEM Quality and Integration Report” to share with the Data Owner/Data Provider that is invited to check, explain and/or solve all the quality issues identified during the integration phase. Type of rules launched in the integration phase are available as Annex. Unsolved quality issues are flagged into IPCHEM data interface, to facilitate the correct use of the data available in IPCHEM.
During the integration phase the data and metadata IPCHEM interfaces for a data collection are accessible only to IPCHEM team and the Data Owner/Data Provider, allowed to check the data using the own EU Login account.
The Data Owner/Data Provider at any time can check the data integration outputs (data ad metadata pages) and contact the IPCHEM team for any clarification or request of improvements at: firstname.lastname@example.org.
Step 7: data and metadata publication in IPCHEM
Data and metadata pages are published in IPCHEM only when the Data Owner/Data Provider agrees. Afterwards, the IPCHEM team makes these interface accessible to the User Groups specified into the IPCHEM Participation Form (Part C of the HBM4EU Data Transfer Form) signed by the Data Owner/Data Provider.