1
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Jeliazkova N, Longhin E, El Yamani N, Rundén-Pran E, Moschini E, Serchi T, Vrček IV, Burgum MJ, Doak SH, Cimpan MR, Rios-Mondragon I, Cimpan E, Battistelli CL, Bossa C, Tsekovska R, Drobne D, Novak S, Repar N, Ammar A, Nymark P, Di Battista V, Sosnowska A, Puzyn T, Kochev N, Iliev L, Jeliazkov V, Reilly K, Lynch I, Bakker M, Delpivo C, Sánchez Jiménez A, Fonseca AS, Manier N, Fernandez-Cruz ML, Rashid S, Willighagen E, D Apostolova M, Dusinska M. A template wizard for the cocreation of machine-readable data-reporting to harmonize the evaluation of (nano)materials. Nat Protoc 2024:10.1038/s41596-024-00993-1. [PMID: 38755447 DOI: 10.1038/s41596-024-00993-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 02/20/2024] [Indexed: 05/18/2024]
Abstract
Making research data findable, accessible, interoperable and reusable (FAIR) is typically hampered by a lack of skills in technical aspects of data management by data generators and a lack of resources. We developed a Template Wizard for researchers to easily create templates suitable for consistently capturing data and metadata from their experiments. The templates are easy to use and enable the compilation of machine-readable metadata to accompany data generation and align them to existing community standards and databases, such as eNanoMapper, streamlining the adoption of the FAIR principles. These templates are citable objects and are available as online tools. The Template Wizard is designed to be user friendly and facilitates using and reusing existing templates for new projects or project extensions. The wizard is accompanied by an online template validator, which allows self-evaluation of the template (to ensure mapping to the data schema and machine readability of the captured data) and transformation by an open-source parser into machine-readable formats, compliant with the FAIR principles. The templates are based on extensive collective experience in nanosafety data collection and include over 60 harmonized data entry templates for physicochemical characterization and hazard assessment (cell viability, genotoxicity, environmental organism dose-response tests, omics), as well as exposure and release studies. The templates are generalizable across fields and have already been extended and adapted for microplastics and advanced materials research. The harmonized templates improve the reliability of interlaboratory comparisons, data reuse and meta-analyses and can facilitate the safety evaluation and regulation process for (nano) materials.
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Affiliation(s)
| | - Eleonora Longhin
- Health Effects Laboratory, Department of Environmental Chemistry & Health Effects, The Climate and Environmental Research Institute NILU, Kjeller, Norway
| | - Naouale El Yamani
- Health Effects Laboratory, Department of Environmental Chemistry & Health Effects, The Climate and Environmental Research Institute NILU, Kjeller, Norway
| | - Elise Rundén-Pran
- Health Effects Laboratory, Department of Environmental Chemistry & Health Effects, The Climate and Environmental Research Institute NILU, Kjeller, Norway
| | - Elisa Moschini
- Environmental Health group, Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Tommaso Serchi
- Environmental Health group, Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | | | - Michael J Burgum
- In Vitro Toxicology Group, Faculty of Medicine, Health and Life Sciences, Institute of Life Sciences, Swansea University Medical School, Singleton Park, Swansea, Wales, UK
| | - Shareen H Doak
- In Vitro Toxicology Group, Faculty of Medicine, Health and Life Sciences, Institute of Life Sciences, Swansea University Medical School, Singleton Park, Swansea, Wales, UK
| | | | | | - Emil Cimpan
- Department of Computer Science, Electrical Engineering and Mathematical Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | | | - Cecilia Bossa
- Environment and Health Department, Istituto Superiore di Sanità, Rome, Italy
| | - Rositsa Tsekovska
- Medical and Biological Research Laboratory, Roumen Tsanev Institute of Molecular Biology-Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Damjana Drobne
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sara Novak
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Neža Repar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ammar Ammar
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Veronica Di Battista
- BASF SE, Material Physics, Carl Bosch straße, Ludwigshafen, Germany
- Department of Environmental and Resource Engineering, DTU, Kgs. Lyngby, Denmark
| | - Anita Sosnowska
- QSAR Lab Ltd., Gdańsk, Poland
- University of Gdańsk, Faculty of Chemistry, Gdansk, Poland
| | - Tomasz Puzyn
- QSAR Lab Ltd., Gdańsk, Poland
- University of Gdańsk, Faculty of Chemistry, Gdansk, Poland
| | - Nikolay Kochev
- Ideaconsult Ltd., Sofia, Bulgaria
- Department of Analytical Chemistry and Computer Chemistry, Faculty of Chemistry, University of Plovdiv, Plovdiv, Bulgaria
| | | | | | - Katie Reilly
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Martine Bakker
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | | | - Araceli Sánchez Jiménez
- Spanish National Institute of Health and Safety, Centro Nacional de Verificación de Maquinaria, Barakaldo, Spain
| | - Ana Sofia Fonseca
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Nicolas Manier
- Ecotoxicology of Substances and Environmental Matrices Unit, French National Institute for Industrial Environment and Risks, Verneuil-en-Halatte, France
| | - María Luisa Fernandez-Cruz
- Department of Environment and Agronomy, National Institute for Agriculture and Food Research and Technology, Spanish National Research Council, Madrid, Spain
| | - Shahzad Rashid
- Institute of Occupational Medicine, Research Avenue North, Edinburgh, UK
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Margarita D Apostolova
- Medical and Biological Research Laboratory, Roumen Tsanev Institute of Molecular Biology-Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria Dusinska
- Health Effects Laboratory, Department of Environmental Chemistry & Health Effects, The Climate and Environmental Research Institute NILU, Kjeller, Norway.
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2
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Wyrzykowska E, Mikolajczyk A, Lynch I, Jeliazkova N, Kochev N, Sarimveis H, Doganis P, Karatzas P, Afantitis A, Melagraki G, Serra A, Greco D, Subbotina J, Lobaskin V, Bañares MA, Valsami-Jones E, Jagiello K, Puzyn T. Representing and describing nanomaterials in predictive nanoinformatics. Nat Nanotechnol 2022; 17:924-932. [PMID: 35982314 DOI: 10.1038/s41565-022-01173-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Engineered nanomaterials (ENMs) enable new and enhanced products and devices in which matter can be controlled at a near-atomic scale (in the range of 1 to 100 nm). However, the unique nanoscale properties that make ENMs attractive may result in as yet poorly known risks to human health and the environment. Thus, new ENMs should be designed in line with the idea of safe-and-sustainable-by-design (SSbD). The biological activity of ENMs is closely related to their physicochemical characteristics, changes in these characteristics may therefore cause changes in the ENMs activity. In this sense, a set of physicochemical characteristics (for example, chemical composition, crystal structure, size, shape, surface structure) creates a unique 'representation' of a given ENM. The usability of these characteristics or nanomaterial descriptors (nanodescriptors) in nanoinformatics methods such as quantitative structure-activity/property relationship (QSAR/QSPR) models, provides exciting opportunities to optimize ENMs at the design stage by improving their functionality and minimizing unforeseen health/environmental hazards. A computational screening of possible versions of novel ENMs would return optimal nanostructures and manage ('design out') hazardous features at the earliest possible manufacturing step. Safe adoption of ENMs on a vast scale will depend on the successful integration of the entire bulk of nanodescriptors extracted experimentally with data from theoretical and computational models. This Review discusses directions for developing appropriate nanomaterial representations and related nanodescriptors to enhance the reliability of computational modelling utilized in designing safer and more sustainable ENMs.
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Affiliation(s)
| | - Alicja Mikolajczyk
- QSAR Lab Ltd, Gdańsk, Poland
- Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | | | - Nikolay Kochev
- Ideaconsult Ltd, Sofia, Bulgaria
- Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, Plovdiv, Bulgaria
| | - Haralambos Sarimveis
- School of Chemical Engineering, National Technical University of Athens, Zografou, Athens, Greece
| | - Philip Doganis
- School of Chemical Engineering, National Technical University of Athens, Zografou, Athens, Greece
| | - Pantelis Karatzas
- School of Chemical Engineering, National Technical University of Athens, Zografou, Athens, Greece
| | | | - Georgia Melagraki
- Division of Physical Sciences and Applications, Hellenic Military Academy, Vari, Greece
| | - Angela Serra
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
| | - Dario Greco
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Julia Subbotina
- School of Physics, University College Dublin, Belfield, Dublin, Ireland
| | - Vladimir Lobaskin
- School of Physics, University College Dublin, Belfield, Dublin, Ireland
| | - Miguel A Bañares
- Instituto de Catálisis y Petroleoquimica, ICP CSIC, Madrid, Spain
| | - Eugenia Valsami-Jones
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Karolina Jagiello
- QSAR Lab Ltd, Gdańsk, Poland
- Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Tomasz Puzyn
- QSAR Lab Ltd, Gdańsk, Poland.
- Laboratory of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.
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3
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Kochev N, Jeliazkova N, Tancheva G. Ambit-SLN: an Open Source Software Library for Processing of Chemical Objects via SLN Linear Notation. Mol Inform 2021; 40:e2100027. [PMID: 34342942 DOI: 10.1002/minf.202100027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/19/2021] [Indexed: 11/11/2022]
Abstract
SLN (SYBYL Line Notation) is the most comprehensive and rich linear notation for representation of chemical objects of various kinds facilitating a wide range of cheminformatics algorithms. Though, it is not the most popular linear notation nowadays, SLN has capabilities for supporting the most challenging tasks of the present day cheminformatics research. We present Ambit-SLN, a new software library for cheminformatics processing of chemical objects via linear notation SLN. Ambit-SLN is developed as a part of the cheminformatics platform AMBIT. It is an open-source tool, distributed under LGPL license, written in Java and based on the Chemistry Development Kit. Ambit-SLN includes a parser for the full SLN syntax of chemical structures and substructure search queries including support for macro and Markush atoms, global and local dictionaries and user defined properties which can be stored and used by the Ambit data model. The Ambit-SLN library includes functionalities for substructure matching based on SLN query strings and utilities for conversion of SLN objects to other chemical formats such as SMILES and SMARTS. The functionality for Markush atom expansion can be used for generation of combinatorial structure sets.
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Affiliation(s)
- Nikolay Kochev
- University of Plovdiv, Faculty of Chemistry, Department of Analytical Chemistry and Computer Chemistry, 24 Tsar Assen Str., 4000, Plovdiv, Bulgaria.,Ideaconsult Ltd., 4 Angel Kanchev Str, 1000, Sofia, Bulgaria
| | - Nina Jeliazkova
- Ideaconsult Ltd., 4 Angel Kanchev Str, 1000, Sofia, Bulgaria
| | - Gergana Tancheva
- University of Plovdiv, Faculty of Chemistry, Department of Analytical Chemistry and Computer Chemistry, 24 Tsar Assen Str., 4000, Plovdiv, Bulgaria
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4
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Jeliazkova N, Apostolova MD, Andreoli C, Barone F, Barrick A, Battistelli C, Bossa C, Botea-Petcu A, Châtel A, De Angelis I, Dusinska M, El Yamani N, Gheorghe D, Giusti A, Gómez-Fernández P, Grafström R, Gromelski M, Jacobsen NR, Jeliazkov V, Jensen KA, Kochev N, Kohonen P, Manier N, Mariussen E, Mech A, Navas JM, Paskaleva V, Precupas A, Puzyn T, Rasmussen K, Ritchie P, Llopis IR, Rundén-Pran E, Sandu R, Shandilya N, Tanasescu S, Haase A, Nymark P. Towards FAIR nanosafety data. Nat Nanotechnol 2021; 16:644-654. [PMID: 34017099 DOI: 10.1038/s41565-021-00911-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
Nanotechnology is a key enabling technology with billions of euros in global investment from public funding, which include large collaborative projects that have investigated environmental and health safety aspects of nanomaterials, but the reuse of accumulated data is clearly lagging behind. Here we summarize challenges and provide recommendations for the efficient reuse of nanosafety data, in line with the recently established FAIR (findable, accessible, interoperable and reusable) guiding principles. We describe the FAIR-aligned Nanosafety Data Interface, with an aggregated findability, accessibility and interoperability across physicochemical, bio-nano interaction, human toxicity, omics, ecotoxicological and exposure data. Overall, we illustrate a much-needed path towards standards for the optimized use of existing data, which avoids duplication of efforts, and provides a multitude of options to promote safe and sustainable nanotechnology.
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Affiliation(s)
| | - Margarita D Apostolova
- Medical and Biological Research Laboratory, Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | | | - Andrew Barrick
- Mer Molécules Santé, Université Catholique de l'Ouest, Angers, France
| | | | | | - Alina Botea-Petcu
- Institute of Physical Chemistry 'Ilie Murgulescu' of the Romanian Academy, Bucharest, Romania
| | - Amélie Châtel
- Mer Molécules Santé, Université Catholique de l'Ouest, Angers, France
| | | | - Maria Dusinska
- Department of Environmental Chemistry, Health Effects Laboratory, Norwegian Institute for Air Research, Kjeller, Norway
| | - Naouale El Yamani
- Department of Environmental Chemistry, Health Effects Laboratory, Norwegian Institute for Air Research, Kjeller, Norway
| | - Daniela Gheorghe
- Institute of Physical Chemistry 'Ilie Murgulescu' of the Romanian Academy, Bucharest, Romania
| | - Anna Giusti
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Roland Grafström
- Department of Toxicology, Misvik Biology, Turku, Finland
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maciej Gromelski
- Group of Environmental Chemometrics, Faculty of Chemistry, University of Gdansk, Gdańsk, Poland
- QSAR Lab Ltd, Gdańsk, Poland
| | | | | | | | - Nikolay Kochev
- Ideaconsult Ltd, Sofia, Bulgaria
- Faculty of Chemistry, Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, Plovdiv, Bulgaria
| | - Pekka Kohonen
- Department of Toxicology, Misvik Biology, Turku, Finland
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Nicolas Manier
- Expertise and Assays in Ecotoxicology Unit, French National Institute for Industrial Environment and Risks, Verneuil-en-Halatte, France
| | - Espen Mariussen
- Department of Environmental Chemistry, Health Effects Laboratory, Norwegian Institute for Air Research, Kjeller, Norway
| | - Agnieszka Mech
- Joint Research Centre, European Commission, Ispra, Italy
| | - José María Navas
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Vesselina Paskaleva
- Ideaconsult Ltd, Sofia, Bulgaria
- Faculty of Chemistry, Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, Plovdiv, Bulgaria
| | - Aurica Precupas
- Institute of Physical Chemistry 'Ilie Murgulescu' of the Romanian Academy, Bucharest, Romania
| | - Tomasz Puzyn
- Group of Environmental Chemometrics, Faculty of Chemistry, University of Gdansk, Gdańsk, Poland
- QSAR Lab Ltd, Gdańsk, Poland
| | | | | | | | - Elise Rundén-Pran
- Department of Environmental Chemistry, Health Effects Laboratory, Norwegian Institute for Air Research, Kjeller, Norway
| | - Romica Sandu
- Institute of Physical Chemistry 'Ilie Murgulescu' of the Romanian Academy, Bucharest, Romania
| | - Neeraj Shandilya
- Netherlands Organisation for Applied Scientific Research (TNO), Utrecht, Netherlands
| | - Speranta Tanasescu
- Institute of Physical Chemistry 'Ilie Murgulescu' of the Romanian Academy, Bucharest, Romania
| | - Andrea Haase
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Penny Nymark
- Department of Toxicology, Misvik Biology, Turku, Finland.
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
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5
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Kochev N, Jeliazkova N, Paskaleva V, Tancheva G, Iliev L, Ritchie P, Jeliazkov V. Your Spreadsheets Can Be FAIR: A Tool and FAIRification Workflow for the eNanoMapper Database. Nanomaterials (Basel) 2020; 10:nano10101908. [PMID: 32987901 PMCID: PMC7601422 DOI: 10.3390/nano10101908] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/17/2020] [Accepted: 09/20/2020] [Indexed: 11/30/2022]
Abstract
The field of nanoinformatics is rapidly developing and provides data driven solutions in the area of nanomaterials (NM) safety. Safe by Design approaches are encouraged and promoted through regulatory initiatives and multiple scientific projects. Experimental data is at the core of nanoinformatics processing workflows for risk assessment. The nanosafety data is predominantly recorded in Excel spreadsheet files. Although the spreadsheets are quite convenient for the experimentalists, they also pose great challenges for the consequent processing into databases due to variability of the templates used, specific details provided by each laboratory and the need for proper metadata documentation and formatting. In this paper, we present a workflow to facilitate the conversion of spreadsheets into a FAIR (Findable, Accessible, Interoperable, and Reusable) database, with the pivotal aid of the NMDataParser tool, developed to streamline the mapping of the original file layout into the eNanoMapper semantic data model. The NMDataParser is an open source Java library and application, making use of a JSON configuration to define the mapping. We describe the JSON configuration syntax and the approaches applied for parsing different spreadsheet layouts used by the nanosafety community. Examples of using the NMDataParser tool in nanoinformatics workflows are given. Challenging cases are discussed and appropriate solutions are proposed.
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Affiliation(s)
- Nikolay Kochev
- Department of Analytical Chemistry and Computer Chemistry, Faculty of Chemistry, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria; (V.P.); (G.T.)
- Ideaconsult Ltd., 4 Angel Kanchev St, 1000 Sofia, Bulgaria; (L.I.); (V.J.)
- Correspondence: (N.K.); (N.J.)
| | - Nina Jeliazkova
- Ideaconsult Ltd., 4 Angel Kanchev St, 1000 Sofia, Bulgaria; (L.I.); (V.J.)
- Correspondence: (N.K.); (N.J.)
| | - Vesselina Paskaleva
- Department of Analytical Chemistry and Computer Chemistry, Faculty of Chemistry, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria; (V.P.); (G.T.)
| | - Gergana Tancheva
- Department of Analytical Chemistry and Computer Chemistry, Faculty of Chemistry, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria; (V.P.); (G.T.)
| | - Luchesar Iliev
- Ideaconsult Ltd., 4 Angel Kanchev St, 1000 Sofia, Bulgaria; (L.I.); (V.J.)
| | - Peter Ritchie
- Institute of Occupational Medicine, Research Avenue North, Riccarton, Edinburgh EH14 4AP, UK;
| | - Vedrin Jeliazkov
- Ideaconsult Ltd., 4 Angel Kanchev St, 1000 Sofia, Bulgaria; (L.I.); (V.J.)
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6
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de Bruyn Kops C, Stork C, Šícho M, Kochev N, Svozil D, Jeliazkova N, Kirchmair J. GLORY: Generator of the Structures of Likely Cytochrome P450 Metabolites Based on Predicted Sites of Metabolism. Front Chem 2019; 7:402. [PMID: 31249827 PMCID: PMC6582643 DOI: 10.3389/fchem.2019.00402] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/17/2019] [Indexed: 01/10/2023] Open
Abstract
Computational prediction of xenobiotic metabolism can provide valuable information to guide the development of drugs, cosmetics, agrochemicals, and other chemical entities. We have previously developed FAME 2, an effective tool for predicting sites of metabolism (SoMs). In this work, we focus on the prediction of the chemical structures of metabolites, in particular metabolites of xenobiotics. To this end, we have developed a new tool, GLORY, which combines SoM prediction with FAME 2 and a new collection of rules for metabolic reactions mediated by the cytochrome P450 enzyme family. GLORY has two modes: MaxEfficiency and MaxCoverage. For MaxEfficiency mode, the use of predicted SoMs to restrict the locations in the molecule at which the reaction rules could be applied was explored. For MaxCoverage mode, the predicted SoM probabilities were instead used to develop a new scoring approach for the predicted metabolites. With this scoring approach, GLORY achieves a recall of 0.83 and can predict at least one known metabolite within the top three ranked positions for 76% of the molecules of a new, manually curated test set. GLORY is freely available as a web server at https://acm.zbh.uni-hamburg.de/glory/, and the datasets and reaction rules are provided in the Supplementary Material.
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Affiliation(s)
- Christina de Bruyn Kops
- Department of Computer Science, Center for Bioinformatics (ZBH), Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany
| | - Conrad Stork
- Department of Computer Science, Center for Bioinformatics (ZBH), Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany
| | - Martin Šícho
- Department of Computer Science, Center for Bioinformatics (ZBH), Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany.,CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Nikolay Kochev
- Ideaconsult Ltd., Sofia, Bulgaria.,Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, Plovdiv, Bulgaria
| | - Daniel Svozil
- CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Prague, Czechia
| | | | - Johannes Kirchmair
- Department of Computer Science, Center for Bioinformatics (ZBH), Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany.,Department of Chemistry, University of Bergen, Bergen, Norway.,Computational Biology Unit (CBU), University of Bergen, Bergen, Norway
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7
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Honma M, Kitazawa A, Cayley A, Williams RV, Barber C, Hanser T, Saiakhov R, Chakravarti S, Myatt GJ, Cross KP, Benfenati E, Raitano G, Mekenyan O, Petkov P, Bossa C, Benigni R, Battistelli CL, Giuliani A, Tcheremenskaia O, DeMeo C, Norinder U, Koga H, Jose C, Jeliazkova N, Kochev N, Paskaleva V, Yang C, Daga PR, Clark RD, Rathman J. Improvement of quantitative structure-activity relationship (QSAR) tools for predicting Ames mutagenicity: outcomes of the Ames/QSAR International Challenge Project. Mutagenesis 2019; 34:3-16. [PMID: 30357358 PMCID: PMC6402315 DOI: 10.1093/mutage/gey031] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/20/2018] [Indexed: 11/12/2022] Open
Abstract
The International Conference on Harmonization (ICH) M7 guideline allows the use of in silico approaches for predicting Ames mutagenicity for the initial assessment of impurities in pharmaceuticals. This is the first international guideline that addresses the use of quantitative structure–activity relationship (QSAR) models in lieu of actual toxicological studies for human health assessment. Therefore, QSAR models for Ames mutagenicity now require higher predictive power for identifying mutagenic chemicals. To increase the predictive power of QSAR models, larger experimental datasets from reliable sources are required. The Division of Genetics and Mutagenesis, National Institute of Health Sciences (DGM/NIHS) of Japan recently established a unique proprietary Ames mutagenicity database containing 12140 new chemicals that have not been previously used for developing QSAR models. The DGM/NIHS provided this Ames database to QSAR vendors to validate and improve their QSAR tools. The Ames/QSAR International Challenge Project was initiated in 2014 with 12 QSAR vendors testing 17 QSAR tools against these compounds in three phases. We now present the final results. All tools were considerably improved by participation in this project. Most tools achieved >50% sensitivity (positive prediction among all Ames positives) and predictive power (accuracy) was as high as 80%, almost equivalent to the inter-laboratory reproducibility of Ames tests. To further increase the predictive power of QSAR tools, accumulation of additional Ames test data is required as well as re-evaluation of some previous Ames test results. Indeed, some Ames-positive or Ames-negative chemicals may have previously been incorrectly classified because of methodological weakness, resulting in false-positive or false-negative predictions by QSAR tools. These incorrect data hamper prediction and are a source of noise in the development of QSAR models. It is thus essential to establish a large benchmark database consisting only of well-validated Ames test results to build more accurate QSAR models.
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Affiliation(s)
- Masamitsu Honma
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Tonomachi, Kawasaki-ku, Kanagawa, Japan
| | - Airi Kitazawa
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Tonomachi, Kawasaki-ku, Kanagawa, Japan
| | - Alex Cayley
- Lhasa Limited, Granary Wharf House, Canal Wharf, Leeds, UK
| | | | - Chris Barber
- Lhasa Limited, Granary Wharf House, Canal Wharf, Leeds, UK
| | - Thierry Hanser
- Lhasa Limited, Granary Wharf House, Canal Wharf, Leeds, UK
| | | | | | | | | | - Emilio Benfenati
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via G. La Masa19 Milano, Italy
| | - Giuseppa Raitano
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via G. La Masa19 Milano, Italy
| | - Ovanes Mekenyan
- Laboratory of Mathematical Chemistry, As. Zlatarov University, Bourgas, Bulgaria
| | - Petko Petkov
- Laboratory of Mathematical Chemistry, As. Zlatarov University, Bourgas, Bulgaria
| | - Cecilia Bossa
- Istituto Superiore di Sanita', Viale Regina Elena, Rome, Italy
| | - Romualdo Benigni
- Istituto Superiore di Sanita', Viale Regina Elena, Rome, Italy.,Alpha-Pretox, Via G. Pascoli, Rome, Italy
| | | | | | | | | | - Ulf Norinder
- Swetox, Karolinska Institutet, Unit of Toxicology Sciences, Södertälje, Sweden.,Department of Computer and Systems Sciences, Stockholm University, SE Kista, Sweden
| | - Hiromi Koga
- Fujitsu Kyushu Systems Limited, Higashihie, Hakata-ku, Fukuoka, Japan
| | - Ciloy Jose
- Fujitsu Kyushu Systems Limited, Higashihie, Hakata-ku, Fukuoka, Japan
| | | | - Nikolay Kochev
- IdeaConsult Ltd., A. Kanchev str., Sofia, Bulgaria.,Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, Plovdiv, Bulgaria
| | - Vesselina Paskaleva
- Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, Plovdiv, Bulgaria
| | - Chihae Yang
- Molecular Networks GmbH and Altamira LLC, Neumeyerstrasse Nürnberg, Germany and Candlewood Drive, Columbus, OH, USA
| | | | | | - James Rathman
- Molecular Networks GmbH and Altamira LLC, Neumeyerstrasse Nürnberg, Germany and Candlewood Drive, Columbus, OH, USA.,Chemical and Biomolecular Engineering, The Ohio State University, W. Woodruff Ave. Columbus, OH, USA
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8
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Cassani S, Kovarich S, Papa E, Roy PP, Rahmberg M, Nilsson S, Sahlin U, Jeliazkova N, Kochev N, Pukalov O, Tetko IV, Brandmaier S, Durjava MK, Kolar B, Peijnenburg W, Gramatica P. Evaluation of CADASTER QSAR Models for the Aquatic Toxicity of (Benzo)triazoles and Prioritisation by Consensus Prediction. Altern Lab Anim 2019; 41:49-64. [DOI: 10.1177/026119291304100107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Stefano Cassani
- QSAR Research Unit in Environmental Chemistry and Ecotoxicology, DiSTA, University of Insubria, Varese, Italy
| | - Simona Kovarich
- QSAR Research Unit in Environmental Chemistry and Ecotoxicology, DiSTA, University of Insubria, Varese, Italy
| | - Ester Papa
- QSAR Research Unit in Environmental Chemistry and Ecotoxicology, DiSTA, University of Insubria, Varese, Italy
| | - Partha Pratim Roy
- QSAR Research Unit in Environmental Chemistry and Ecotoxicology, DiSTA, University of Insubria, Varese, Italy
| | - Magnus Rahmberg
- IVL Swedish Environmental Research Institute Ltd, Stockholm, Sweden
| | - Sara Nilsson
- IVL Swedish Environmental Research Institute Ltd, Stockholm, Sweden
| | - Ullrika Sahlin
- School of Natural Sciences, Linnaeus University, Kalmar, Sweden
| | | | - Nikolay Kochev
- University of Plovdiv, Department of Analytical Chemistry and Computer Chemistry, Plovdiv, Bulgaria
| | - Ognyan Pukalov
- University of Plovdiv, Department of Analytical Chemistry and Computer Chemistry, Plovdiv, Bulgaria
| | - Igor V. Tetko
- Helmholtz-Zentrum München, German Research Centre for Environmental Health, Munich, Germany
| | - Stefan Brandmaier
- Helmholtz-Zentrum München, German Research Centre for Environmental Health, Munich, Germany
| | | | - Boris Kolar
- Public Health Institute Maribor, Maribor, Slovenia
| | - Willie Peijnenburg
- National Institute of Public Health and the Environment (RIVM), Laboratory for Ecological Risk Assessment, Bilthoven, The Netherlands
- Leiden University, Institute of Environmental Sciences (CML), Department of Conservation Biology, Leiden, The Netherlands
| | - Paola Gramatica
- QSAR Research Unit in Environmental Chemistry and Ecotoxicology, DiSTA, University of Insubria, Varese, Italy
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9
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Kochev N, Paskaleva V, Pukalov O, Jeliazkova N. Ambit-GCM: An Open-source Software Tool for Group Contribution Modelling. Mol Inform 2019; 38:e1800138. [PMID: 30654426 DOI: 10.1002/minf.201800138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 12/18/2018] [Indexed: 11/06/2022]
Abstract
Ambit-GCM is a new software tool for group contribution modelling (GCM), developed as a part of the chemoinformatics platform AMBIT. It is an open-source tool distributed under LGPL license, written in Java and based on the Chemistry Development Kit. Ambit-GCM provides an environment for creating models of molecular properties using additive schemes of zero, first or second orders. Ambit-GCM supports a set of local atomic attributes used for dynamic configuration of desired atom descriptions, which are applied to define fragments of different sizes. All defined groups are exhaustively generated for each molecule from a training set of compounds and combined to form the basic set of GCM fragments. Additionally, Ambit-GCM users can define correction factors via custom SMARTS notations or add externally calculated molecular descriptors. A molecular property model is obtained as a sum over all found groups by multiplying each group or correction factor frequency to its corresponding contribution. Multiple linear regression analysis (MLRA) is used for group contributions calculation. Ambit-GCM performs full statistical characterization of the obtained MLRA models via various validation techniques: external tests validation, cross validation, y-scrambling, etc. The software can be optionally used only for molecule fragmentation combined with an external statistical modelling package for further processing. Ambit-GCM example usage and test cases are given.
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Affiliation(s)
- Nikolay Kochev
- Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, 24 Tsar Assen St., Plovdiv, 4000, Bulgaria
| | - Vesselina Paskaleva
- Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, 24 Tsar Assen St., Plovdiv, 4000, Bulgaria
| | - Ognyan Pukalov
- Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, 24 Tsar Assen St., Plovdiv, 4000, Bulgaria
| | - Nina Jeliazkova
- Ideaconsult Ltd, 4 Angel Kanchev Str., Sofia, 1000, Bulgaria
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10
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Kochev N, Jeliazkova N, Tsakovska I. CHAPTER 3. Chemoinformatics Representation of Chemical Structures – A Milestone for Successful Big Data Modelling in Predictive Toxicology. Issues in Toxicology 2019. [DOI: 10.1039/9781782623656-00069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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Angelova S, Paskaleva V, Kochev N, Antonov L. DFT study of hydrazone-based molecular switches: the effect of different stators on the on/off state distribution. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1548717] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Silvia Angelova
- Bulgarian Academy of Sciences, Institute of Organic Chemistry with Centre of Phytochemistry Sofia, Bulgaria
| | - Vesselina Paskaleva
- Faculty of Chemistry, University of Plovdiv ‘Paisii Hilendarski’, Plovdiv, Bulgaria
| | - Nikolay Kochev
- Faculty of Chemistry, University of Plovdiv ‘Paisii Hilendarski’, Plovdiv, Bulgaria
| | - Liudmil Antonov
- Bulgarian Academy of Sciences, Institute of Organic Chemistry with Centre of Phytochemistry Sofia, Bulgaria
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12
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Kochev N, Avramova S, Jeliazkova N. Ambit-SMIRKS: a software module for reaction representation, reaction search and structure transformation. J Cheminform 2018; 10:42. [PMID: 30128804 PMCID: PMC6102164 DOI: 10.1186/s13321-018-0295-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 08/11/2018] [Indexed: 11/15/2022] Open
Abstract
Ambit-SMIRKS is an open source software, enabling structure transformation via the SMIRKS language and implemented as an extension of Ambit-SMARTS. As part of the Ambit project it builds on top of The Chemistry Development Kit (The CDK). Ambit-SMIRKS provides the following functionalities: parsing of SMIRKS linear notations into internal reaction (transformation) representations based on The CDK objects, application of the stored reactions against target (reactant) molecules for actual transformation of the target chemical objects, reaction searching, stereo information handling, product post-processing, etc. The transformations can be applied on various sites of the reactant molecule in several modes: single, non-overlapping, non-identical, non-homomorphic or externally specified list of sites utilizing efficient substructure searching algorithm. Ambit-SMIRKS handles the molecules stereo information and supports basic chemical stereo elements implemented in The CDK library. The full SMARTS logical expressions syntax for reactions specification is supported, including recursive SMARTS expressions as well as additional syntax extensions. Since its initial development for the purpose of metabolite generation within Toxtree, the Ambit-SMIRKS module was used in various chemoinformatics projects, both developed by the authors of the package and by external teams. We show several use cases of the Ambit-SMIRKS software including standardization of large chemical databases and pathway transformation database and prediction. Ambit-SMIRKS is distributed as a Java library under LGPL license. More information on use cases and applications, including download links is available at http://ambit.sourceforge.net/smirks .
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Affiliation(s)
- Nikolay Kochev
- Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, 24 Tsar Assen St., 4000 Plovdiv, Bulgaria
- Ideaconsult Ltd, 4 A. Kanchev Str., 1000 Sofia, Bulgaria
| | - Svetlana Avramova
- Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, 24 Tsar Assen St., 4000 Plovdiv, Bulgaria
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13
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Sun J, Jeliazkova N, Chupakhin V, Golib-Dzib JF, Engkvist O, Carlsson L, Wegner J, Ceulemans H, Georgiev I, Jeliazkov V, Kochev N, Ashby TJ, Chen H. Erratum to: ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics. J Cheminform 2017; 9:41. [PMID: 29086166 PMCID: PMC5471272 DOI: 10.1186/s13321-017-0222-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 05/24/2017] [Indexed: 11/10/2022] Open
Affiliation(s)
- Jiangming Sun
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D Gothenburg, 43183, Mölndal, Sweden.
| | - Nina Jeliazkova
- Ideaconsult Ltd., 4. Angel Kanchev Str., 1000, Sofia, Bulgaria
| | - Vladimir Chupakhin
- Computational Biology, Discovery Sciences, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2349, Beerse, Belgium
| | - Jose-Felipe Golib-Dzib
- Computational Biology, Discovery Sciences, Janssen Cilag SA, Calle Río Jarama, 71A, 45007, Toledo, Spain
| | - Ola Engkvist
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D Gothenburg, 43183, Mölndal, Sweden
| | - Lars Carlsson
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D Gothenburg, 43183, Mölndal, Sweden
| | - Jörg Wegner
- Computational Biology, Discovery Sciences, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2349, Beerse, Belgium
| | - Hugo Ceulemans
- Computational Biology, Discovery Sciences, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2349, Beerse, Belgium
| | - Ivan Georgiev
- Ideaconsult Ltd., 4. Angel Kanchev Str., 1000, Sofia, Bulgaria
| | | | - Nikolay Kochev
- Ideaconsult Ltd., 4. Angel Kanchev Str., 1000, Sofia, Bulgaria.,Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, Plovdiv, Bulgaria
| | | | - Hongming Chen
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D Gothenburg, 43183, Mölndal, Sweden.
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14
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Sun J, Jeliazkova N, Chupakin V, Golib-Dzib JF, Engkvist O, Carlsson L, Wegner J, Ceulemans H, Georgiev I, Jeliazkov V, Kochev N, Ashby TJ, Chen H. ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics. J Cheminform 2017; 9:17. [PMID: 28316655 PMCID: PMC5340785 DOI: 10.1186/s13321-017-0203-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/24/2017] [Indexed: 12/02/2022] Open
Abstract
Chemogenomics data generally refers to the activity data of chemical compounds on an array of protein targets and represents an important source of information for building in silico target prediction models. The increasing volume of chemogenomics data offers exciting opportunities to build models based on Big Data. Preparing a high quality data set is a vital step in realizing this goal and this work aims to compile such a comprehensive chemogenomics dataset. This dataset comprises over 70 million SAR data points from publicly available databases (PubChem and ChEMBL) including structure, target information and activity annotations. Our aspiration is to create a useful chemogenomics resource reflecting industry-scale data not only for building predictive models of in silico polypharmacology and off-target effects but also for the validation of cheminformatics approaches in general.
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Affiliation(s)
- Jiangming Sun
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D Gothenburg, 43183 Mölndal, Sweden
| | - Nina Jeliazkova
- Ideaconsult Ltd., 4. Angel Kanchev Str., 1000 Sofia, Bulgaria
| | - Vladimir Chupakin
- Computational Biology, Discovery Sciences, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2349 Beerse, Belgium
| | - Jose-Felipe Golib-Dzib
- Computational Biology, Discovery Sciences, Janssen Cilag SA, Calle Río Jarama, 71A, 45007 Toledo, Spain
| | - Ola Engkvist
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D Gothenburg, 43183 Mölndal, Sweden
| | - Lars Carlsson
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D Gothenburg, 43183 Mölndal, Sweden
| | - Jörg Wegner
- Computational Biology, Discovery Sciences, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2349 Beerse, Belgium
| | - Hugo Ceulemans
- Computational Biology, Discovery Sciences, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2349 Beerse, Belgium
| | - Ivan Georgiev
- Ideaconsult Ltd., 4. Angel Kanchev Str., 1000 Sofia, Bulgaria
| | | | - Nikolay Kochev
- Ideaconsult Ltd., 4. Angel Kanchev Str., 1000 Sofia, Bulgaria.,Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, Plovdiv, Bulgaria
| | | | - Hongming Chen
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D Gothenburg, 43183 Mölndal, Sweden
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15
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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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16
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Jeliazkova N, Chomenidis C, Doganis P, Fadeel B, Grafström R, Hardy B, Hastings J, Hegi M, Jeliazkov V, Kochev N, Kohonen P, Munteanu CR, Sarimveis H, Smeets B, Sopasakis P, Tsiliki G, Vorgrimmler D, Willighagen E. The eNanoMapper database for nanomaterial safety information. Beilstein J Nanotechnol 2015; 6:1609-34. [PMID: 26425413 PMCID: PMC4578352 DOI: 10.3762/bjnano.6.165] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/03/2015] [Indexed: 05/20/2023]
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 (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs. RESULTS The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API), and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms. CONCLUSION We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the "representational state transfer" (REST) API enables building user friendly interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure-activity relationships for nanomaterials (NanoQSAR).
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Affiliation(s)
| | | | - Philip Doganis
- National Technical University of Athens, School of Chemical Engineering, Athens, Greece
| | | | | | - Barry Hardy
- Douglas Connect GmbH, Zeiningen, Switzerland
| | - Janna Hastings
- European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
| | - Markus Hegi
- Douglas Connect GmbH, Zeiningen, Switzerland
| | | | - Nikolay Kochev
- Ideaconsult Ltd., Sofia, Bulgaria
- Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, Plovdiv, Bulgaria
| | | | - Cristian R Munteanu
- Department of Bioinformatics, NUTRIM, Maastricht University, Maastricht, The Netherlands
- Computer Science Faculty, University of A Coruna, A Coruña, Spain
| | - Haralambos Sarimveis
- National Technical University of Athens, School of Chemical Engineering, Athens, Greece
| | - Bart Smeets
- Department of Bioinformatics, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Pantelis Sopasakis
- National Technical University of Athens, School of Chemical Engineering, Athens, Greece
- IMT Institute for Advanced Studies Lucca, Lucca, Italy
| | - Georgia Tsiliki
- National Technical University of Athens, School of Chemical Engineering, Athens, Greece
| | | | - Egon Willighagen
- Department of Bioinformatics, NUTRIM, Maastricht University, Maastricht, The Netherlands
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17
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Jeliazkova N, Kochev N. AMBIT-SMARTS: Efficient Searching of Chemical Structures and Fragments. Mol Inform 2011; 30:707-20. [DOI: 10.1002/minf.201100028] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Accepted: 05/02/2011] [Indexed: 11/08/2022]
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18
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Bhhatarai B, Teetz W, Liu T, Öberg T, Jeliazkova N, Kochev N, Pukalov O, Tetko IV, Kovarich S, Papa E, Gramatica P. CADASTER QSPR Models for Predictions of Melting and Boiling Points of Perfluorinated Chemicals. Mol Inform 2011; 30:189-204. [DOI: 10.1002/minf.201000133] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 02/03/2011] [Indexed: 11/06/2022]
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