Informatics Tool to Explore the Nanomaterial-Biological Interactions Knowledgebase

By Sandra Karcher

Carnegie Mellon University

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Welcome to the resource: Informatics Tool to Explore the Nanomaterial-Biological Interactions Knowledgebase!

N4mics was developed to enable cross-study exploration of the NBI Knowledgebase with the goal of identifying relationships between nanomaterial characteristics and biological responses. N4mics allows the user to select nanomaterials and biological responses to investigate and to specify how those data will be aggregated and visualized. Access to the N4mics tool and to some of the supporting information is restricted to members of the group Exploring the NBI with N4mics.

Go to the N4mics tool. 

It is recommended that new visitors review the Presentation.pdf file, a PowerPoint presentation saved to pdf format with the presentation narrative provided as notes. The file is publicly accessible and provides an overview of the motivation for this work, briefly describes the results generated by the N4mics tool, and demonstrates the use of the tool interface.

N4mics offers three primary options for visualizing data. The visualizations generated using the primary options display distinct labels across the x-axis based on the user selected grouping method (by nanomaterial, response, or characteristic(s)). The tool aggregates data for display as follows: (1) two sets of graphs are provided; a set that shows the concentration of exposure where selected responses reached a target percent response, and a corresponding set that shows the full range of responses; (2) the maximum percent response for each concentration of exposure interval is shown using a color ramp; and (3) the maximum percent response for each selected sublethal response is shown using a color ramp for responses that were observed at concentrations of exposure less than or equal to a user selected threshold. Examples of the graphs are shown below.

When the user opts to aggregate data across the x-axis by nanomaterial, N4mics offers two bonus features: 1) logistic regression to fit the mortality curves, and 2) calculation of characteristic similarity scores. More information on using the bonus features is available inside the N4mics tool.

Supporting Information

Presentation.pdf - This is a three part PowerPoint presentation (Nanoinformatics: Part I - The Big Picture; Part 2 - N4mics Options and Features; Part 3 - Using N4mics), saved to pdf format with the presentation narrative provided as notes.

Fishers_Exact_Test.pdf - Some of the visualizations generated by the N4mics tool provide information on the statistical significance of observing dead and/or abnormal fish in the assays based on the Fisher's Exact Test. Information on how the Fisher's Exact Test was used is provided in this file.

NBI_Excel_File_Format.pdf - The NBI data used in this tool were provided via Microsoft Excel files. This pdf file describes the format of those Excel files.

NBI_Nano_Characteristics.pdf - This file contains a table of the nanomaterials in the NBI at the time this tool was developed and includes information on the characteristics used by the N4mics tool. - The NBI data used in the N4mics tool containing one Excel file for each nanomaterial studied. - A python file that can extract the characteristics (used in N4mics) and the associated responses out of the NBI spreadsheets and put them into a pipe delimited text file.

Understanding_Aggregation.pdf - This file provides information on how to appropriately interpret the visualizations and on the computational algorithms used to prepare and aggregate data. 

Users_Guide.pdf - This document provides instructions on how to navigate within the N4mics tool and explains how to select options for aggregating and visualizing data.

Visualizations_Examples.pdf - Some example visualizations are provided in this document.

Why_Zebrafish.pdf - The NBI provides results of experimental studies performed using zebrafish. This file briefly explains the advantages of working with zebrafish.