Instance maps as an organising concept for complex experimental workflows as demonstrated for (nano)material safety research

• Benjamin Punz,
• Maja Brajnik,
• Joh Dokler,
• Jaleesia D. Amos,
• Litty Johnson,
• Katie Reilly,
• Anastasios G. Papadiamantis,
• Amaia Green Etxabe,
• Lee Walker,
• Diego S. T. Martinez,
• Steffi Friedrichs,
• Klaus M. Weltring,
• Nazende Günday-Türeli,
• Claus Svendsen,
• Christine Ogilvie Hendren,
• Mark R. Wiesner,
• Martin Himly,
• Iseult Lynch and
• Thomas E. Exner

Beilstein J. Nanotechnol. 2025, 16, 57–77, doi:10.3762/bjnano.16.7

• of Geological and Environmental Sciences, Appalachian State University, Boone, USA Seven Past Nine GmbH, Rebacker 68, 79650 Schopfheim, Germany 10.3762/bjnano.16.7 Abstract Nanosafety assessment, which seeks to evaluate the risks from exposure to nanoscale materials, spans materials synthesis and

• which controls), as part of good research output management, is necessary to maximise the reuse potential and value of the data. Instance maps have been developed and evolved to visualise experimental nanosafety workflows and to bridge the gap between the theoretical principles of FAIR (Findable

• batch similarity to be assessed by users wishing to integrate datasets. However, it is not clear whether characterisation data is added in practice, or whether any of the approaches suggested to date have been applied in a practical sense by the nanosafety research community. This could in part be due

Identifying diverse metal oxide nanomaterials with lethal effects on embryonic zebrafish using machine learning

• Richard Liam Marchese Robinson,
• Haralambos Sarimveis,
• Philip Doganis,
• Xiaodong Jia,
• Marianna Kotzabasaki,
• Christiana Gousiadou,
• Stacey Lynn Harper and
• Terry Wilkins

Beilstein J. Nanotechnol. 2021, 12, 1297–1325, doi:10.3762/bjnano.12.97

• these modelling results are on truly external data, which were not used to select the single descriptor model. This will require further laboratory work to generate comparable data to those studied herein. Keywords: data augmentation; embryonic zebrafish; machine learning; nanosafety; nano-QSAR

• delivery vehicles), diagnostic tools and medical devices, is a key application area [2][3]. However, as well as recognising the benefits associated with nanotechnology, it is also important to address potential negative impacts upon human health and the environment. Nanosafety concerns are reflected in

• international research efforts, such as the European Union’s NanoSafety Cluster [4] and associated research projects, such as BIORIMA [5], which has proposed a risk management framework for nanomaterials used in advanced therapeutic medicinal products and medical devices [6]. Indeed, in 2008, an iron oxide ENM

Interactions at the cell membrane and pathways of internalization of nano-sized materials for nanomedicine

• Valentina Francia,
• Daphne Montizaan and
• Anna Salvati

Beilstein J. Nanotechnol. 2020, 11, 338–353, doi:10.3762/bjnano.11.25

• problem has gotten much attention in the nanomedicine field [166][167][180]. Within the nanosafety community, dedicated to the study of potential hazards of nanotechnologies, several efforts have been focused on the establishment of standardized procedures for nanomaterial handling and for cell

• interaction studies in order to ensure quality in nanosafety testing [181][182][183]. Some of the knowledge gained there could be helpful also in developing similar standards for studies aimed at characterizing how nano-sized objects, including nanomedicines, enter cells. In the following sections, we will

Toxicity and safety study of silver and gold nanoparticles functionalized with cysteine and glutathione

• Barbara Pem,
• Igor M. Pongrac,
• Lea Ulm,
• Ivan Pavičić,
• Valerije Vrček,
• Darija Domazet Jurašin,
• Marija Ljubojević,
• Adela Krivohlavek and
• Ivana Vinković Vrček

Beilstein J. Nanotechnol. 2019, 10, 1802–1817, doi:10.3762/bjnano.10.175

• . Keywords: biocompatibility; cysteine; ecotoxicity; glutathione; nano–bio interactions; nanosafety; nanotoxicity; Introduction Metallic nanoparticles (NPs) such as silver and gold have been employed in a wide range of products and applications in the biomedical field owing to their remarkable physico

Low uptake of silica nanoparticles in Caco-2 intestinal epithelial barriers

• Dong Ye,
• Mattia Bramini,
• Delyan R. Hristov,
• Sha Wan,
• Anna Salvati,
• Christoffer Åberg and
• Kenneth A. Dawson

Beilstein J. Nanotechnol. 2017, 8, 1396–1406, doi:10.3762/bjnano.8.141

• capacity of nanoparticles to enter cells, although promising for nanomedicine [4][5][6][7][8][9], has caused concerns of nanosafety in relation to unintended exposure to nanoparticles used in different technological applications (food additives, paintings, and others) [10][11][12][13]. Along different

• into the Caco-2 barrier. In the context of nanomedicine, the low internalisation could suggest that oral administration routes may lead to poor transport across the intestinal epithelium. For nanosafety, toxic responses measured for single cell cultures (where internalisation is usually substantial

An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology

• Richard L. Marchese Robinson,
• Mark T. D. Cronin,
• Andrea-Nicole Richarz and
• Robert Rallo

Beilstein J. Nanotechnol. 2015, 6, 1978–1999, doi:10.3762/bjnano.6.202

• potential risk posed by nanomaterials to human health and the environment [3][4][7]. Various research initiatives have been (and are being) funded to advance scientific understanding of nanotechnology and nanosafety and to enable the appropriate selection, design and regulation of nanomaterials for

• physicochemical characterisation data which the templates were designed to capture were based upon considering the well-known MINChar Initiative Parameters List [53], the provisional recommendations developed within the NanoSafety Cluster Databases Working Group [26], other resources developed within the context

• of the NanoSafety Cluster projects PreNanoTox [54] and MARINA [55] as well as discussions with nanotoxicology researchers and consideration of the published literature regarding toxicologically significant physicochemical characterisation parameters (for nanomaterials) and experimental variables

NanoE-Tox: New and in-depth database concerning ecotoxicity of nanomaterials

• Katre Juganson,
• Angela Ivask,
• Irina Blinova,
• Monika Mortimer and
• Anne Kahru

Beilstein J. Nanotechnol. 2015, 6, 1788–1804, doi:10.3762/bjnano.6.183

• that the available data on nanomaterials in environmental, health and safety databases and online chemical databases were very scarce [14]. Recently, a databases working group was established in the framework of European Union NanoSafety Cluster [15] which highlights the importance of development of in

The Nanomaterial Data Curation Initiative: A collaborative approach to assessing, evaluating, and advancing the state of the field

• Christine Ogilvie Hendren,
• Christina M. Powers,
• Mark D. Hoover and
• Stacey L. Harper

Beilstein J. Nanotechnol. 2015, 6, 1752–1762, doi:10.3762/bjnano.6.179

• called for in various ways by the NRC, the NNI and the EU Nanosafety Cluster. Multiple focal areas and driving goals must be considered across the data life cycle; multiple roles exist as well, with different orientations toward the data including creators, customers, curators, and analysts. At this

The eNanoMapper database for nanomaterial safety information

• Nina Jeliazkova,
• Charalampos Chomenidis,
• Philip Doganis,
• Bengt Fadeel,
• Roland Grafström,
• Barry Hardy,
• Janna Hastings,
• Markus Hegi,
• Vedrin Jeliazkov,
• Nikolay Kochev,
• Pekka Kohonen,
• Cristian R. Munteanu,
• Haralambos Sarimveis,
• Bart Smeets,
• Pantelis Sopasakis,
• Georgia Tsiliki,
• David Vorgrimmler and
• Egon Willighagen

Beilstein J. Nanotechnol. 2015, 6, 1609–1634, doi:10.3762/bjnano.6.165

• , Lucca, Italy in silico toxicology Gmbh (IST), Basel, Switzerland 10.3762/bjnano.6.165 Abstract Background: The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials

• interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure–activity relationships for nanomaterials (NanoQSAR). Keywords: database; EU NanoSafety Cluster; nanoinformatics; nanomaterials; nanomaterials ontology; NanoQSAR; safety

• Characterisation Laboratory (http://ncl.cancer.gov/), EC JRC NanoHub (http://www.napira.eu/), the DaNa Knowledge Base (http://nanopartikel.info/) [8], and NanoWerks Nanomaterial Database (http://www.nanowerk.com/). The EU NanoSafety Cluster alone (http://www.nanosafetycluster.eu/) has many projects with database

Experiences in supporting the structured collection of cancer nanotechnology data using caNanoLab

• Stephanie A. Morris,
• Sharon Gaheen,
• Michal Lijowski,
• Mervi Heiskanen and
• Juli Klemm

Beilstein J. Nanotechnol. 2015, 6, 1580–1593, doi:10.3762/bjnano.6.161

• area have included development and enhancement of the NPO and ISA-TAB-Nano. ISA-TAB-Nano is currently used by NCI, the NBI Knowledgebase (http://nbi.oregonstate.edu/), and the EU NanoSafety Cluster (http://www.nanosafetycluster.eu/) to enable interoperability between databases. Most recently, the Nano