Developing Data Collections for (Q)SAR Modelling of Nanomaterials

<p>This is a poster delivered at the 16th International Workshop on Quantitative Structure Activity Relationships in Environmental and Health Sciences (QSAR2014), 16-20th June 2014, Milan, Italy: <a href="http://qsar2014.insilico.eu/">http://qsar2014.insilico.eu/</a></p> <p>Disclaimers:</p> <p>(1) this presentation has not undergone peer review</p> <p>(2) this presentation may report preliminary results which may have been revised in subsequent publications</p> <p>(3) no endorsement by third parties should be inferred</p> <p>Presentation abstract:</p><p> There are an increasing number of (Q)SAR models to predict the toxicity and properties of nanomaterials [1]. Indeed, in light of perceived uncertainties regarding their potential health and environmental effects, as well as the drive towards reduced use of animals for toxicity testing, the European Commission has funded a number of projects looking at computational prediction of nanomaterial toxicity. The NanoPUZZLES (www.nanopuzzles.eu) and NanoBRIDGES (www.nanobridges.eu) projects are two such activities charged with developing grouping, read-across and (Q)SAR approaches for modelling of nanomaterial toxicity. These approaches require adequate quantities of high quality toxicological and physicochemical data on well-characterised nanomaterials, which are being collected in both projects. These data need to be available within an electronic database in a consistent and interoperable manner to best support modelling. The NanoPUZZLES project is organising collected data in a suitable electronic format that will be made available to modellers via a publicly accessible database in accordance with the previously noted requirements. Specifically, data are being curated from public domain sources and organised using data collection templates based upon a proposal for a global data exchange standard: ISA-TAB-Nano [2,3]. In order to facilitate their use for modelling and, in particular, their integration with other datasets for future modelling efforts, it is essential that the data are recorded in a standardised fashion. To achieve this objective, the data collection templates being employed record (meta)data using terms linked to ontologies wherever possible. These ontology terms are being retrieved via the BioPortal online resource [4]. Moreover, it is important that modellers are able to assess the quality of (subsets of) the available data. To facilitate this, proposals for assigning data quality scores are being developed. Finally, an overview of the potential usefulness for modelling of some public domain sources, for selected endpoints, will be presented based upon a recent survey of the scientific literature.</p><p> <br></p><p> The research leading to these results has received funding from the European Union Seventh Framework Programme [FP7/2007-2013] under grant agreement n° 309837 (NanoPUZZLES project) and from the NanoBRIDGES project (FP7-PEOPLE-2011-IRSES, Grant Agreement no. 295128).</p><ol><li><p>Winkler, D.A..; Mombelli, E.; Pietroiusti, A.; Tran, L.; Worth, A.; Fadeel, B.; McCall, M.J. <i>Toxicology</i>, <i>313</i>, <b>2013</b>, 15-23.</p></li><li><p>Thomas, D.G.; Gaheen, S.; Harper, S.L.; Fritts, M.; Klaessig, F.; Hahn-Dantona, E.; Paik, D.; Pan, S.; Staffiord, G.A.; Freund, E.T.; Klemm, J.D.; Baker, N.A. <i>BMC Biotechnol.</i>, <i>13</i>, <b>2013</b>, 2.</p></li><li><p>https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano [last accessed 9th of April 2014]</p></li><li><p>Whetzel, P.L.; Noy, N.F.; Shah, N.H.; Alexander, P.R.; Nyulas, C.; Tudorache, T.; Musen, M.A. <i>Nucleic Acids Res.</i>, <i>39</i>, <b>2011</b>, W541-W545.</p></li></ol><p> <br></p

Collection of toxicity, physicochemical and characterisation data to enable modelling of nanomaterial effects

This is a poster presentation delivered at the Nanosafety 2013 conference, November 2013, Saarbruecken, Germany: http://nanosafety.inm-gmbh.de/<br><br>Disclaimers:<br><br>(1) this presentation has not undergone peer review<br><br>(2) this presentation may report preliminary results which may have been revised in subsequent publications<br><br>(3) no endorsement by third parties should be inferred<br><br>Presentation abstract:<br> <p>A number of EU projects have been established to address concerns about the potential health risks posed by nanomaterials. The NanoPUZZLES project is developing new computational methods for predicting the toxicity of nanomaterials based on Quantitative Structure-Activity Relationships (QSARs), chemical category formation and read-across approaches. Successful application of these approaches requires sufficient quantities of high quality toxicological and physicochemical data on well-characterised nanomaterials to be organised self-consistently within an electronic database. NanoPUZZLES is contributing to the development of such a database based on data curated from public domain sources.</p> <p>Initial data collection efforts within NanoPUZZLES yielded a significant number of data points from various peer-reviewed publications. By extending the Klimisch criteria for toxicological data quality assessment, criteria for assessing the quality of data reported for nanomaterials, as well as the suitability of datasets for building QSARs, were developed. However, organising nanomaterial data remains a challenge. The current focus of data collection efforts within NanoPUZZLES is the exploration and evaluation of standards for organising experimental data for nanomaterials: the recently published ISA-Tab-Nano file format is of particular interest. The need for a unique identifier for nanomaterials and minimum information standards for a nanomaterials database is also being addressed. </p> <p>Funding through the European Commission 7th Framework Program NanoPUZZLES (FP7-NMP-2012-SMALL-6, Grant Agreement no. 309837) and NanoBRIDGES (FP7-PEOPLE-2011-IRSES, Grant Agreement no. 295128) projects is gratefully acknowledged.</p><p>N.B. The spreadsheet images provided in this poster, of provisional NanoPUZZLES files, are used with permission from Microsoft. </p> <br