The challenges associated with developing data collections to support modelling of nanomaterial effects
Disclaimers:
(1) this presentation has not undergone peer review
(2) this presentation may report preliminary results which may have been revised in subsequent publications
(3) no endorsement by third parties should be inferred
Presentation abstract:
In light of perceived uncertainties regarding the potential health and environmental effects of nanomaterials, as well as the legislative impetus towards reduced use of animals for toxicity testing, the European Commission has funded a number of projects aimed at developing computational models for predicting nanomaterial effects. The NanoPUZZLES (www.nanopuzzles.eu) project is one such activity which aims to develop new in silico approaches to predict the harmful effects of nanomaterials based on grouping, read-across and Quantitative Structure-Activity Relationships (QSARs). To apply these approaches, adequate quantities of high quality toxicological and physicochemical information on well-characterised nanomaterials is required. This needs to be organised within an electronic database in a consistent and interoperable manner. NanoPUZZLES is contributing to the development of such a database based on data curated from public domain sources. This presentation will discuss the challenges associated with collecting these data and organising them appropriately to support modelling. The strategy developed within NanoPUZZLES to solve these challenges will be presented as a case study. It is imperative that relevant references are identified and selected for data extraction. Appropriate selection criteria should take into account data quality as well as the usefulness of the data for developing models. These data must be recorded using a standardised, machine readable format, which would allow them to be integrated within a queryable database. In order to promote data standardisation, the identification and/or development of appropriate ontologies is valuable. The strategy developed within NanoPUZZLES is based upon a survey of the relevant scientific literature. The results of this survey will be presented, offering insights into the nature of the data available from these sources. Possible criteria, reported in the literature, for assessing the quality of these data as well as their usefulness for modelling will be reviewed. Following consideration of the challenges associated with recording nanomaterial structures to support modelling, a scheme for assigning quality scores to nanomaterial structures will be proposed. A proposed data collection/exchange standard, ISA-TAB-Nano, which supports the use of ontologies, will be discussed. The derivation of data collection templates based on this standard within NanoPUZZLES will be presented. Finally, the work being carried out in this area within the NanoPUZZLES project will be placed in the context of wider European and global efforts.
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).
N.B. The spreadsheet images provided in this poster, of provisional NanoPUZZLES files, are used with permission from Microsoft.