Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research

Abstract

Nanotechnology represents an area of particular promise and significant opportunity across multiple scientific disciplines. Ongoing nanotechnology research ranges from the characterization of nanoparticles and nanomaterials to the analysis and processing of experimental data seeking correlations between nanoparticles and their functionalities and side effects. Due to their special properties, nanoparticles are suitable for cellular-level diagnostics and therapy, offering numerous applications in medicine, e.g. development of biomedical devices, tissue repair, drug delivery systems and biosensors. In nanomedicine, recent studies are producing large amounts of structural and property data, highlighting the role for computational approaches in information management. While in vitro and in vivo assays are expensive, the cost of computing is falling. Furthermore, improvements in the accuracy of computational methods (e.g. data mining, knowledge discovery, modeling and simulation) have enabled effective tools to automate the extraction, management and storage of these vast data volumes. Since this information is widely distributed, one major issue is how to locate and access data where it resides (which also poses data-sharing limitations). The novel discipline of nanoinformatics addresses the information challenges related to nanotechnology research. In this paper, we summarize the needs and challenges in the field and present an overview of extant initiatives and efforts.

Nanocuration workflows: Establishing best practices for identifying, inputting, and sharing data to inform decisions on nanomaterials

“…Data quality and completeness is the topic of another article in this series and, thus, will not be discussed at length in this article. Nevertheless, understanding these concepts in various repositories is necessary for researchers or others using the data since different levels of quality or completeness are required for different uses of data (e.g., research prioritization, screening level decisions about hazard, quantitative risk assessment) [ 3 – 4 ].…”

NaDev: An Annotated Corpus to Support Information Extraction from Research Papers on Nanocrystal Devices

“…For example, the Greener Nano 2012: Nanoinformatics Tools and Resources Workshop [13] aimed at establishing a better understanding of state-of-the-art approaches to nanoinformatics and clearly defining the immediate and projected informatics infrastructure needs for the nanotechnology community. De la Iglesia et al also discussed the needs and challenges, as well as extant initiatives and international efforts, in the field [2].…”

“…Nanoinformatics is a newly developing interdisciplinary research domain that aims to use information technology to support research in the nanoscience field [1], [2]. Nanoinformatics is the science and practice of determining which information is relevant to the nanoscale science and engineering community and then developing and implementing effective mechanisms for collecting, validating, storing, sharing, analyzing, modeling, and applying this information [3].…”

Using natural language processing techniques to inform research on nanotechnology

“…Extracting information usually comes from two different sources: (1) literature to which natural language processing methods are applied, and (2) experimental data to which data modeling methods, such as those used in HDAT and NanoMiner, are applied [5,6]. Despite being a largely overlooked area of informatics, several reviews have been published that list the different databases and tools currently available [7][8][9][10][11]. In this review, we focus on the tools that utilize natural language processing.…”