Semantic search and integration of nanotechnology and nanotoxicology datasets require knowledge of existing information (or data) resources. This section is a list of resources assembled and discussed through the activities of the NCI caBIG® Nanotechnology Working Group and expanded by contributions of members of this group. The focus is on online information resources that have been designed to share experimental data and other information related to the description, characterization, toxicity and safe handling of nanomaterials, which are necessary for advancing the field of nanomedicine.
In , we list the different online resources and compare them with respect to their focus areas and the type of information gathered in each resource. These resources are publicly accessible and the link to access each resource is also given in . Although these resources are independent of each other, they are complementary to each other with respect to the scope of information shared and the purpose of each resource. In the following sections, we briefly summarize the scope, purpose and some of the unique capabilities of each resource. The groups and organizations, associated with the development of each resource, are also listed as shown in . Collectively, members of these groups and organizations have collaborated to create a Nanoinformatics 2020 Roadmap53
, which is the first broad-based community effort to articulate the comprehensive needs and goals to establish an effective system of nanoinformatics data, tools, and infrastructure. Such a program will enable the community to improve and “travel” on the road to understanding, development, and beneficial application of nanotechnology.
Online information resources relevant to nanotechnology and nanomedicine.
Groups/organizations associated with different information resources.
caNanoLab database portal
caNanoLab is a web-based application designed for facilitating data sharing in the nanomedicine research community. It was particularly developed to allow researchers or data curators to deposit data on nanomaterials and their characterizations to be made available to the broader cancer research community. It is an open source software package that uses caBIG® grid infrastructure and can be freely downloaded from the project website (http://gforge.nci.nih.gov/frs/?group+id=69
). Multiple organizations or labs can locally install caNanoLab and connect to the caBIG® grid to submit and share their data.
Currently, there exists one centralized caNanoLab site which can be used by researchers with a variety of levels of expertise and resources. caNanoLab is extensible and provides support for entering and sharing different types of information generated from pre-clinical studies of nanoparticles, which include the following: protocols for preparation and characterization of nanomaterials; chemical composition of nanomaterial samples; data from physicochemical characterization of nanomaterials, which include size, molecular weight, shape, physical state, surface chemistry, purity, solubility and relaxivity; data from in vitro characterization of nanomaterials, which include cytotoxicity, blood contact properties, oxidative stress, immune cell function, etc.; publication and reports. caNanoLab is being extended to provide support for capturing in vivo characterization data such as pharmacokinetics and toxicology.
caNanoLab is designed to enable users to submit and share data in a secure way. Data providers have options to allow limited or unlimited access to their data entered into the caNanoLab database. One does not need to have a user account to view publicly accessible data through caNanoLab portal. As of January 9, 2011, 41 protocols, 878 nanomaterial samples, and 1072 publications are publicly accessible through the caNanoLab portal. Thus, caNanoLab provides an essential element for satisfying the data sharing needs of the nanomedicine community significantly by providing the resource to support sharing, and accessing data within and across labs and organizations.
Nanomaterial Biological Interactions Knowledgebase
The Nanomaterial Biological Interactions (NBI) knowledgebase was developed in 2008 to directly address the need for a comparative, integrative database information system, driven by the desire to promote the safe development of nanomaterials and nanotechnologies. NBI knowledgebase is functionally comprised of two components: a nanomaterial library and analysis tools. The nanomaterial library serves as a repository for annotated data that characterize the physicochemical properties (size, shape, charge, composition, functionalization, and agglomeration state), synthesis methods, and biological effects (at molecular, cellular and organism levels) of nanomaterials. One can search for data in the nanomaterial library by material class, shape, size and surface charge. Data displayed are color-coded to allow users to quickly assess the relative impact of nanomaterials visually. Analysis tools have the capability to generate heat maps and plots, which are being used to compare the biological effects of different types of nanoparticles that have been investigated in toxicity studies using embryonic zebrafish. The knowledgebase has functionalities intended for performing several informatics-related and computational tasks, such as: storing, integrating, organizing, and visualizing the data; comparing the properties of different types of nanomaterials; determining structure-activity relationships from the data; and predicting biological effects of nanomaterials for which empirical data are unavailable.
The NBI aims to offer industry, academia and regulatory agencies a mechanism to rationally inquire about nanomaterial exposure effects in biological systems. Computational approaches using experimental data are critical to gain knowledge and understanding of the fundamental principles that govern nanomaterial-biological interactions. Systematic analysis of disparate data on nanomaterial-biological interactions and computational optimization of the NBI knowledgebase have the potential to provide global capabilities to identify structure and design principles of high-performance, environmentally-benign nanomaterials that can be then applied to the development of future nanotechnology products. This knowledge has significant implications for the emerging fields of nanomedicine, nanotoxicology, green nanoscience and nanotechnology.
Molecular Imaging and Contrast Agent Database
The Molecular Imaging and Contrast Agent Database (MICAD) is an online resource that provides information about imaging and contrast agents used with in vitro, animal or human studies that have been published in peer-reviewed scientific journals. MICAD also provides information about nanoparticles that are intended for use as imaging and contrast agents. There are 929 agents listed in MICAD as of January 5, 2011. Information about each agent is summarized in a book chapter format, and these book chapters are organized into five sections. The first section discusses detection methods, including techniques such magnetic resonance imaging, optical imaging, positron emission tomography, single photon emission computed tomography, ultrasound, X-ray, and computed tomography. The second section focuses on the source of signal/contrast; i.e., the active component in the agent. The third section describes the type of agent (e.g., protein, peptide, nanoparticle, metal, ligand, etc.), while the fourth section describes the target category (e.g., non-targeted, lipid, receptors, enzymes, antigens, etc.). Finally, the fifth section describes the scope of study; e.g., in vitro, rodents, humans, etc.
InterNano is a web portal designed for sharing information on advances in applications, devices, metrology, and nanomaterials, in order to facilitate the commercial development and/or marketable applications of nanotechnology. InterNano gathers information from multiple sources, adds original commentaries on these sources, and provides news highlights, feature articles and assessments of the current state of practice in nanomanufacturing. InterNano uses a taxonomy to index articles and organize information about topics of interest to the nanomanufacturing community, including nanomanufacturing processes; tools; nanoscale-sized and nanostructured objects; characterization techniques; environmental, health, and safety aspects; social and economic implications; informatics and standards for nanomanufacturing; commercialization, regulation, and intellectual property. This online resource demonstrates the effective use of taxonomies to organize and share information among researchers and practitioners, thereby facilitating the development and application of nanotechnology-based methods.
The International Council of Nanotechnology (ICON) is an international organization, established in 2004, and is comprised of stakeholders from industry, academia, government and non-governmental organizations. The mission of the organization is to develop and communicate information regarding potential risks of nanotechnology to human health and environment, and further to minimize the risks while maximizing societal benefits of nanotechnology. The ICON website hosts several information resources such as GoodNanoGuide and nano-EHS virtual journal.
The GoodNanoGuide is an online resource based on a wiki-software platform, which serves as a collaborative platform for occupational safety professionals around the world to contribute, exchange and obtain up-to-date information about safe handling of nanomaterials, and the occupational risks associated with exposure to nanomaterials. In particular, the GoodNanoGuide is a place to share information about good workplace practices and protocols for handling nanomaterials. Current information is provided at three levels, designed according to the expertise and knowledge of the user. The first level is the “basic” level, designed for users who are new to nanotechnology and want to know about the efforts in developing good workplace practices for nanomaterials. The second level is the “intermediate” level, designed for users who know about nanotechnology and want to know more about good workplace practices for handling nanomaterials. The third level is an “advanced” level, designed for experts who want to know about good workplace practices for multiple and similar types of nanomaterials. Information about protocols and standards for occupational safety and health can be organized in GoodNanoGuide under three categories: general, material-specific and operation-specific.
Nano-EHS database and virtual journal
The nano-EHS virtual journal is a publicly accessible database, listing peer-reviewed articles related to environmental, health and safety issues of nanotechnology. The articles are classified such that they can be searched under nine categories of information: particle type (e.g., carbon, metal, oxide, semiconductor, etc.); article type (e.g., applications, commentaries, exposure, hazard, policy reports, environmental fate and transport); exposure pathway (e.g., inhalation, injection, dermal/mucous membrane, etc.); method of study (in vitro, in vivo, ex vivo, environmental study, computational and system modeling, synthesis, material analysis and applications); exposure or hazard target (e.g., aquatic ecosystem, atmospheric ecosystem, etc.); risk exposure group (e.g., consumers, ecosystem, general population, industrial/research worker, other/unspecified); target audience (e.g. general public, public policy, technical research); content emphasis (e.g., peer reviewed journal article, review); and, production method (e.g., engineered, incidental, or both).
The database provides tools for analysis and report generation and allows for individual annotations by database users regarding data quality and usefulness. The analysis tool can be used to obtain information about the distribution of publications for selected categories at a given time or over a period of time. One can search for a list of publications among selected categories, and save the list as a report in PDF or Excel format using the report-generating tool (http://icon.rice.edu/report.cfm
Nanoparticle Information Library
The Nanoparticle Information Library (NIL) is an online database, developed for organizing, linking and sharing information pertaining to the occupational health and safety aspects of nanomaterials.54
The database is intended to help occupational health professionals, industrial users, worker groups, and researchers to organize and share information about nanomaterials, including their properties associated with health and safety. Information in NIL is organized by structure, primary composing elements, and synthesis method of each nanomaterial. Information covered in the NIL includes basic physical properties of a nanomaterial, applications demonstrating the intended use of a nanomaterial, publications associated with or relevant to a nanomaterial, and points of contact for additional information about a nanomaterial, or for potential research collaborations.
The NIL was developed by the National Institute for Occupational Safety and Health (NIOSH), which is the federal agency responsible for improving health and safety at the workplace. NIOSH conducts research, provides guidance and authoritative recommendations, gathers and disseminates information, and evaluates workplace health hazards. The NIOSH nanotechnology website (www.cdc.gov/niosh/topics/nanotech
) includes online access to Approaches to Safe Nanotechnology: Managing the Health and Safety Concerns Associated with Engineered Nanomaterials, which reviews what is currently known about nanoparticle toxicity, process emissions and exposure assessment, engineering controls, and personal protective equipment.
Nanowerk is a web portal and Twitter feed that provides comprehensive information about nanotechnology and nanoscale science. It includes educational resources for nanotechnology and nanomaterials, a news section related to business and research in nanotechnology, a database that contains physical information (e.g., particle size, purity, synthesis methods, characterization methods, etc.) provided by companies on nanomaterials, and several other resources for the nanotechnology community.
SAFENANO provides information and consultancy services to help identify and manage the potential risks that arise due to the development and use of nanotechnology-enabled products on human health, safety and environment. It has a searchable database of publications that are classified as reports, policies, conference proceedings, research papers, guidance papers, policies, standards, and organizations.
The Nanotechnology Citizen Engagement Organization (NanoCEO) is an independent citizen organization founded to educate the community about nanotechnology issues through events, meetings and the NanoCEO website; to facilitate the engagement of citizens in discussing the implications of nanotechnology for the benefit of the general public, and to enable the community to address nanotechnology issues.
The NanoCEO website gathers useful information (articles, reviews, studies) about the health and environmental effects of nanomaterials, occupational health and safety issues surrounding nanomaterials, and general information about nanotechnology and its applications. This is a useful resource of information like GoodNanoGuide and SAFENANO, and provides more comprehensive, up-to-date information relevant for scientists working in the area of nanotoxicology.
Project on Emerging Nanotechnologies
The Project on Emerging Nanotechnologies (PEN) was established in April 2005 with a mission to help ensure that as nanotechnologies advance, the potential risks to health and environment are minimized, potential benefits are realized, and public and consumer engagement remains strong. The project aims to achieve this mission by collaborating with government, industry, policy makers, and others to identify gaps in knowledge and regulatory processes, and to develop strategies to close these gaps. Results from research, meetings, and events carried out in the project, are made publicly available in the form of publications on the website.
The National Toxicology Program (NTP) is an interagency program established in 1978, and it coordinates the toxicology testing programs within the US federal government Department of Health and Human Services (DHHS). This program develops and tests new and improved methods to evaluate the toxicological properties of manufactured chemicals that are of concern to public health and safety. The program has expanded to include toxicological studies on nanomaterials to address the potential health risks associated with the manufacture and use of nanomaterials.
Toxicology information about chemicals and nanomaterials, generated under the NTP program, are provided to health, regulatory and research agencies, scientific and medical communities, and the public. Abstracts, reports and data from toxicology studies are accessible through the NTP website hosted by the NIEHS. The NTP database provides access to data belonging to different types of studies, such as, bioassay pathology studies, developmental toxicity, immunotoxicity, and genetic toxicology. In particular, pathology, body weight changes, and survival results from 13-week and 2-year studies in mice and rats are also made available on the website.
In 2002, the National Science Foundation funded a six-university initiative to establish the Network for Computational Nanotechnology (NCN) for connecting those who develop simulation tools with those who use them. The NCN has developed a science gateway called the nano-HUB, to support and enable research, education and collaboration by sharing and offering simulation tools, resources, and services.55, 56
Nano-HUB has over 160,000 users from over 170 countries. Users can log on, access state-of-the-art simulation software, run interactive graphical or batch simulations, and view results online.56
A unique feature of nanoHUB is that users who share the simulation software on nano-HUB do not have to download, install, support or maintain the software. Nano-HUB provides the computational resources needed for carrying out several simulation tasks, and there is no burden on the user to manage accounts or access specific machines.56
The website also hosts online courses (short or full) and tutorials that encourage cross-disciplinary education. In addition, it also hosts tools for collaborating on research, education and software development. Overall, the nano-HUB resource demonstrates how integration of computational resources can support and enable research, education, and collaboration in a multidisciplinary field such as nanotechnology, and therefore has the potential to transform research, collaboration and education in nanomedicine.
The National Center for Biomedical Ontology (NCBO) BioPortal provides a service that indexes online information resources, including nanomaterial-specific resources such as caNanoLab and MICAD, as well as many others. The data present in these indexed resources can be searched and retrieved using terms from ontologies and controlled vocabularies that are stored in the NCBO BioPortal repository (discussed later in this manuscript). Therefore, the NCBO BioPortal is a valuable resource that enables the use of ontologies and controlled vocabularies to semantically search, organize and retrieve data from the different data resources important to nanomedicine.
Nanotechnology and the law
A growing number of online resources (e.g., blogs.law.widener.edu/nanolaw/, forecastingnanolaw.net, nanolawreport.com, and nanotortlaw.com), texts (e.g., Nanotechnology Law57
and the International Handbook on Regulating Nanotechnologies58
), and journals (e.g., Nanotechnology Law
; nanolabweb.com) are addressing how national and international laws are being applied, adapted, or developed for nanotechnology-related issues.
Efforts are underway to establish a web-based registry that provides a public resource of curated information on the biological and environmental interactions of well-characterized nanomaterials (https://www.fbo.gov/index?s=opportunity&mode=form&tab=core&id=14b7e72c5b28b20 d9dc45da7234282bf&_cview=0
). The Nanomaterials Registry is being developed by RTI International under a multi-year project contract funded by the National Institute of Biomedical Imaging and Bioengineering (NIBIB), NIEHS, and NCI. It is expected that the registry will help improve data quality, facilitate data sharing and validation, enhance the development of new models, assays, standards, and manufacturing methods, and accelerate the translation of new nanomaterials for biomedical and environmental applications.