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Krans NA, Ammar A, Nymark P, Willighagen EL, Bakker MI, Quik JTK. FAIR assessment tools: evaluating use and performance. NanoImpact 2022; 27:100402. [PMID: 35717894 DOI: 10.1016/j.impact.2022.100402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Publishing research data using a findable, accessible, interoperable, and reusable (FAIR) approach is paramount to further innovation in many areas of research. In particular in developing innovative approaches to predict (eco)toxicological risks in (nano or advanced) material design where efficient use of existing data is essential. The use of tools assessing the FAIRness of data helps the future improvement of data FAIRness and therefore their re-use. This paper reviews ten FAIR assessment tools that have been evaluated and characterized using two datasets from the nanomaterials and microplastics risk assessment domain. The tools were grouped into four categories: online and offline self-assessment survey based, online (semi-) automated and other tools. We found that the online self-assessment tools can be used for a quick scan of a user's dataset due to their ease of use, little need for experience and short time investment. When a user is looking to assess full databases, and not just datasets, for their FAIRness, (semi-)automated tools are more practical. The offline assessment tools were found to be limited and unreliable due to a lack of guidance and an under-developed state. To further characterize the usability, two datasets were run through all tools to check the similarity in the tools' results. As most of the tools differ in their implementation of the FAIR principles, a large variety in outcomes was obtained. Furthermore, it was observed that only one tool gives recommendations to the user on how to improve the FAIRness of the evaluated dataset. This paper gives clear recommendations for both the user and the developer of FAIR assessment tools.
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Affiliation(s)
- N A Krans
- National Institute for Public Health and the Environment (RIVM), Centre for Safety of Substances and Products, Bilthoven, the Netherlands
| | - A Ammar
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands.
| | - P Nymark
- Institute of Environmental Medicine, Karolinska Institute, 171 77 Stockholm, Sweden
| | - E L Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - M I Bakker
- National Institute for Public Health and the Environment (RIVM), Centre for Safety of Substances and Products, Bilthoven, the Netherlands
| | - J T K Quik
- National Institute for Public Health and the Environment (RIVM), Centre for Sustainability, Environment and Health, Bilthoven, the Netherlands
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Mech A, Rasmussen K, Jantunen P, Aicher L, Alessandrelli M, Bernauer U, Bleeker EAJ, Bouillard J, Di Prospero Fanghella P, Draisci R, Dusinska M, Encheva G, Flament G, Haase A, Handzhiyski Y, Herzberg F, Huwyler J, Jacobsen NR, Jeliazkov V, Jeliazkova N, Nymark P, Grafström R, Oomen AG, Polci ML, Riebeling C, Sandström J, Shivachev B, Stateva S, Tanasescu S, Tsekovska R, Wallin H, Wilks MF, Zellmer S, Apostolova MD. Insights into possibilities for grouping and read-across for nanomaterials in EU chemicals legislation. Nanotoxicology 2018; 13:119-141. [DOI: 10.1080/17435390.2018.1513092] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- A. Mech
- Directorate F – Health, Consumers and Reference Materials, JRC, European Commission's Joint Research Centre, Ispra, Italy
| | - K. Rasmussen
- Directorate F – Health, Consumers and Reference Materials, JRC, European Commission's Joint Research Centre, Ispra, Italy
| | - P. Jantunen
- Directorate F – Health, Consumers and Reference Materials, JRC, European Commission's Joint Research Centre, Ispra, Italy
| | - L. Aicher
- Department of Pharmaceutical Sciences and Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland
| | | | - U. Bernauer
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - E. A. J. Bleeker
- National Institute for Public Health and the Environment (RIVM), RIVM, Bilthoven, the Netherlands
| | - J. Bouillard
- Parc Technologique ALATA, INERIS, Verneuil-en-Halatte, France
| | | | - R. Draisci
- Istituto Superiore di Sanità, ISS, Roma, Italy
| | - M. Dusinska
- Norwegian Institute for Air Research, NILU, Kjeller, Norway
| | - G. Encheva
- Institute of Molecular Biology – BAS, IMB-BAS, Sofia, Bulgaria
| | - G. Flament
- Nanotechnology Industries Association, NIA, Woluwe-Saint-Pierre, Brussels, Belgium
| | - A. Haase
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Y. Handzhiyski
- Institute of Molecular Biology – BAS, IMB-BAS, Sofia, Bulgaria
| | - F. Herzberg
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - J. Huwyler
- Department of Pharmaceutical Sciences and Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland
| | - N. R. Jacobsen
- National Research Centre for the Working Environment, NRCWE, Copenhagen, Denmark
| | | | | | - P. Nymark
- Institute for Environmental Medicine, KI, Karolinska Institutet, Stockholm, Sweden
- Toxicology Division, Misvik Biology, Turku, Finland
| | - R. Grafström
- Institute for Environmental Medicine, KI, Karolinska Institutet, Stockholm, Sweden
- Toxicology Division, Misvik Biology, Turku, Finland
| | - A. G. Oomen
- National Institute for Public Health and the Environment (RIVM), RIVM, Bilthoven, the Netherlands
| | - M. L. Polci
- Istituto Superiore di Sanità, ISS, Roma, Italy
| | - C. Riebeling
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - J. Sandström
- Department of Pharmaceutical Sciences and Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland
| | - B. Shivachev
- Institute of Molecular Biology – BAS, IMB-BAS, Sofia, Bulgaria
| | - S. Stateva
- Institute of Molecular Biology – BAS, IMB-BAS, Sofia, Bulgaria
| | - S. Tanasescu
- Romanian Academy, Institute of Physical Chemistry “Ilie Murgulescu”, IPC, Bucharest, Romania
| | - R. Tsekovska
- Institute of Molecular Biology – BAS, IMB-BAS, Sofia, Bulgaria
| | - H. Wallin
- National Institute of Occupational Health, STAMI, Gydas vei 8, Oslo, 0363, Norway
| | - M. F. Wilks
- Department of Pharmaceutical Sciences and Swiss Centre for Applied Human Toxicology (SCAHT), University of Basel, Basel, Switzerland
| | - S. Zellmer
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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Kilic G, Fadeel B, Farcal L, Sarimveis H, Doganis P, Drakakis G, Tsiliki G, Chomenidis C, Helma C, Rautenberg M, Gebele D, Jeliazkova N, Kochev N, Owen G, Chang J, Willighagen E, Ehrhart F, Rieswijk L, Hongisto V, Nymark P, Kohonen P, Grafström R, Hardy B. eNanoMapper – A database and ontology framework for design and safety assessment of nanomaterials. Toxicol Lett 2016. [DOI: 10.1016/j.toxlet.2016.06.1481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Wikman H, Ruosaari S, Nymark P, Sarhadi VK, Saharinen J, Vanhala E, Karjalainen A, Hollmén J, Knuutila S, Anttila S. Gene expression and copy number profiling suggests the importance of allelic imbalance in 19p in asbestos-associated lung cancer. Oncogene 2007; 26:4730-7. [PMID: 17297452 DOI: 10.1038/sj.onc.1210270] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Asbestos is a pulmonary carcinogen known to give rise to DNA and chromosomal damage, but the exact carcinogenic mechanisms are still largely unknown. In this study, gene expression arrays were performed on lung tumor samples from 14 heavily asbestos-exposed and 14 non-exposed patients matched for other characteristics. Using a two-step statistical analysis, 47 genes were revealed that could differentiate the tumors of asbestos-exposed from those of non-exposed patients. To identify asbestos-associated regions with DNA copy number and expressional changes, the gene expression data were combined with comparative genomic hybridization microarray data. As a result, a combinatory profile of DNA copy number aberrations and expressional changes significantly associated with asbestos exposure was obtained. Asbestos-related areas were detected in 2p21-p16.3, 3p21.31, 5q35.2-q35.3, 16p13.3, 19p13.3-p13.1 and 22q12.3-q13.1. The most prominent of these, 19p13, was further characterized by microsatellite analysis in 62 patients for the differences in allelic imbalance (AI) between the two groups of lung tumors. 79% of the exposed and 45% of the non-exposed patients (P=0.008) were found to be carriers of AI in their lung tumors. In the exposed group, AI in 19p was prevalent regardless of the histological tumor type. In adenocarcinomas, AI in 19p appeared to occur independently of the asbestos exposure.
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Affiliation(s)
- H Wikman
- Finnish Institute of Occupational Health, Helsinki, Finland
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