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An example of the advantages and disadvantages related to producing a protocol database for nanoscience. Dr. Ilse Gosens National Institute for Public Health and the Environment, Bilthoven, The Netherlands Joint JRC Nano-event and 2nd ENPRA Stakeholder Workshop 10 th -12 th May 2011

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An example of the advantages and disadvantages related to producing a protocol database for nanoscience

Dr. Ilse Gosens

National Institute for Public Health and the Environment, Bilthoven, The Netherlands

Joint JRC Nano-event and 2nd ENPRA Stakeholder Workshop

10th-12th May 2011

Somma Lombardo, Italy


It has been suggested that in order for a harmonised approach towards understanding the potential risks associated with exposure to nano-objects (a material with one, two or three external dimensions in the nanoscale (1-100nm) (ISO/TS 27687: 2008)) that the consistent use of standardised experimental protocols should be implemented in order to obtain reliable information quickly and efficiently.

Over the past three years therefore, the FP7 EU project ‘NanoImpactNet’ (NIN) (Grant Agreement 218539) has constructed an online-space ( for sharing research protocols with other members within NIN.

Please note that all the information contained within this presentation are available at

aim of protocol database
Aim of protocol database

The aim of the protocol database is so that laboratories may easily compare their methods and subsequently develop common protocols and strategies for the testing of nanomaterials in regards to their interaction with biological systems and their numerous physical characteristics.

In addition, a secondary aim of NIN for the protocol database is to share all of its protocols with the entire nanoscience field.

outline for producing protocols from nin
Outline for producing protocols from NIN
  • Members of NIN submitting their protocol to the NIN protocol database using the agreed protocol template.
  • NIN members are then able to view these submitted protocols, test them within their own laboratories and then comment upon the protocol itself. These comments are then available to all NIN members for an open discussion.
  • After NIN members decide to apply a specific protocol, either in its original format or slightly modified, the protocol is then upgraded to a ‘protocol recommended by NIN’.
  • The protocol is then further scrutinized by NIN members, and then if adequate becomes an ‘officially recommended protocol by NIN’ and highlighted throughout the field and international bodies as a ‘recommended protocol’ for nanoscience.

NanoImpactNet has produced a nomenclature database for the consistent use and understanding of ‘nanoscience’ terms within all of its documents – including the protocol database.

Currently, the third version is published, although a forth and final version is in preparation.

This document contains internationally recognised definitions for ‘nanoscience’ (as put forward by ISO, BSI and OECD (permissions obtained for reproduction)) as well as additional definitions for additional ‘nanoscience’ terms not covered by these bodies.


The database currently consists of 48 terms for the most common ‘nanoscience’ terms to the less known.

This database has been extremely successful in providing the basis for the use of ‘nanoscience’ terminology in NIN documents.

It has also enabled the terminology contained within the ISO database and documents to become publically available.

NIN obtained permission to reproduce ISO information, subsequently publishing it in its nomenclature database, thus making it publically available.

interaction with authors and laboratories
Interaction with authors and laboratories

In order to have a ‘home’ for the submission of any protocols to the database, as well as for any individual to forward questions, concerns, queries or comments regarding the database, a specific email address was formed;

In addition, a similar email address was formed for the nomenclature database;

Additionally, on the webpage for the protocol database, for each protocol, a comment box was made available for input regarding each specific database (i.e. ‘blog-type’ idea).

protocol template
Protocol template

All details on cover page are for both informative and legal reasons.

Title and description of assay.

Authors and their institutions of the paper from which the protocol is taken are identified.

Individuals whom adapt/edit the protocol into the NIN template are deemed editors and acknowledged as so.

protocol template1
Protocol template

The ‘contents’ page provides and easy and informative basis for the reader to obtain any ‘method-specific’ information.

The entire template is set-out to provide as much information as possible to the reader/end-user.

The aim, as with any written method (i.e. in peer-review journal articles), is for any user to be able to perform the protocol precisely from the information contained in the document in any laboratory.

outlook for obtaining protocols
Outlook for obtaining protocols

With the protocol template and nomenclature established, as well as various forms for communication (email/online commentary availability) regarding the protocols and the database itself, a call for protocols was announced to all members of NIN (this was officially performed at the 1st Integrating Conference, March 2009).

Additional calls were also given via email, newsletters and at NIN meetings/workshops

It was assumed that all members would take part in this exercise and submit at least 1 protocol from their laboratory.

It was assumed that protocols covering all areas of ‘nanoscience’ would be submitted due to the depth and variety of expertise within the NIN consortium and member-base.

However, after 1 year, it seemed as though all this preparatory work was ineffective………

problems encountered
Problems encountered

After 1 year, only 3 protocols had been submitted to the database, by members of the NIN scientific committee.

The reason for this was that all members were not happy, motivated or interested in submitting their protocols to this database.

Therefore, a call was given specifically to the NIN management and scientific committee members to submit at least one protocol that had previously been published in a peer-review journal.

This was ineffective however, with only 8 protocols being submitted and transferred into the NIN protocol template in the first 2 years of NIN.

Again, it was evident that NIN members did not want to submit protocols due to a number of reasons (namely, does this outlook inhibit scientific thought and progress?).

attempts to kick start the protocol database
Attempts to ‘kick-start’ the protocol database

In an attempt to increase the number of protocols submitted to the NIN protocol database the following occurred;

(1) Strong collaborations between previous and existing EU projects:

e.g. ENPRA, NanoInteract and NanoCare

Due to the collaboration/interaction between the members of NIN and those of other EU projects (since many individuals were part of all/some of these EU projects), there was a significant increase in the number of protocols published on the NIN protocol database website.

(2) Connections with institutions in the United States of America (i.e. NIST) also facilitated a further increase in the protocols submitted to NIN.

current situation
Current situation

With the help of the other EU projects and NIST, 20 protocols are now available on the NIN protocol database cover the following areas;

  • Eco-nanotoxicology
  • Genotoxicity
  • NP preparation and characterisation
  • NP usage
  • Oxidative stress
  • Cell death
  • Cell culture
current situation2
Current situation

An additional 16 protocols are also in preparation. The topic areas highlighted above are covered in more depth with these additional protocols (i.e. different protocols for different endpoint testing).

New outline for obtaining and producing protocols for NIN;

  • Protocols are submitted to NIN and immediately uploaded to the webpage as a ‘protocol submitted to NIN’.
  • Protocols are then placed into the template and uploaded as a ‘protocol put forth by NIN’.
  • After a thorough testing and examination, the protocol will then be placed as a ‘protocol recommended by NIN’ if deemed appropriate by the NIN scientific committee.
summary and outlook
Summary and outlook

After a slow start, the NIN protocol database now has 20 published protocols on its website in harmony with its nomenclature document.

An additional 21 protocols are in preparation for publication in the database (due to collaboration with EU projects past and present).

The infrastructure for formatting and sharing protocols is set-up and fully functional.

Since the collaboration between other EU projects and NIST, no further protocols have been submitted to NIN (since December 2010).

Whilst NIN will promote, at least, 41 different protocols, the outlook for the protocol database seems to be disadvantaged due to the lack of motivation and (good) reason for individuals to submit their protocols.

During the last year of NIN, efforts will continue to try and obtain more protocols and promote the continuation of the database within subsequent EU projects.


This presentation was kindly performed by Dr. I. Gosens on behalf of;

Martin J. D. Clift, Nathalie Boschung, Vicki Stone, Thomas Kuhlbusch, Peter Gehr, Iseult Lynch, Flemming R. Cassee, Michael Riediker and Barbara Rothen-Rutishauser

All authors would like to acknowlegde the following individuals and institutions for their input, help and advice;

EU Commission

EU FP7 Research Programme Network

NanoImpactNet Steering Committee ENPRA Consortium

NanoImpactNet Scientific Committee NanoInteract Consortium

NanoImpactNet Consortium NanoCare and NIST

thank you for your attention

Thank you for your attention

For additional information: