Nanoinformatics: a new area of research in nanomedicine

Figures & data

Table 1 Nanoinformatics challenges proposed by three recent initiatives

Nanoinformatics 2020 Roadmap (2010)^Citation79	The ACTION-Grid White Paper (2010)^Citation80	A Research Strategy for Environmental, Health, and Safety Aspects of Engineered Nanomaterials (2012)^Citation81
Nanomaterial data gap workshops for discussing how to facilitate the exchange of data and information about engineered nanomaterials: their physicochemical properties, behavior in the environment, biological activity, etc	Creation of a nanoinformatics infrastructure to collect, curate, annotate, organize, and archive the available data	Identify minimum characterization principles to develop standardized descriptors (that is, metadata) for engineered nanomaterials (ENMs)
Development of a meta-ontology for nanoinformatics from existing ontologies and structured databases, dealing with issues such as interoperability and federation and demonstrating its applicability across multiple domains	Design of extended web nano portals, linking groups and information around the world to facilitate data sharing	Establish uniform metadata to describe ENM manufacturing and distribution processes and to correlate lot-to-lot variability of ENM properties
Minimum information recommendations: minimal information required for nanomaterial characterization, quality assurance processes for data collection and curation, ranking system for quality and completeness of data/datasets	Development of repositories/databases of use cases, resources, nanotoxicity data and, clinical trial experiments or on nano facilitating the reuse of data – such as ArrayExpress for genomic data	Develop ontologies and data formats to allow relevant data on gene and protein expression to be correlated with ENM toxicity mechanisms and, in particular, to develop an ontology “crawler” to aid in mapping relationships among ontologies
A meta-crawler for searching nano-related information on the Web, serving as an interface to relevant ontologies (browse and search), resources (semantic search), materials (structural search), literature (links back to relevant terminologies), and news	Incorporation of regulatory aspects: standards, issues related to open data and source tools, quality control	Develop strategies for federating nanotechnology databases to allow seamless data exposure and data sharing while protecting intellectual property rights
Simulation challenge: development of simulation and modeling tools for nanotechnology, targeting specific materials and using standard nanostructures that are well characterized to compare and validate calculation tools	Translational nanoinformatics: linking basic research from the lab to the bedside and nano-information to the Electronic Health Record	Develop new mechanisms for digital archiving and annotating and updating of methods, data, tools, and models to spur rapid and efficient formation of new targeted national and international scientific collaborations

Figure 1 Impact of nanoinformatics in different topics, modified from an earlier version presented by the authors in The ACTION-Grid White Paper.⁸⁰

Abbreviations: AMIA, American Medical Informatics Association; BMI, biomedical informatics; EFMI, European Federation for Medical Informatics; IMIA, International Medical Informatics Association; ISCB, International Society for Computational Biology; NSF, National Science Foundation; US NIH, National Institutes of Health.

Figure 2 Screenshot of the Nanoparticles Toxicity Searcher, using “quantum dots” as an example.

Table 2 Important events in the nanoinformatics field over the past 5 years

Nanoinformatics events and activities	Date
Past
Launch of the first version of the caNanoLab Portal, a research framework for biomedical nanotechnology data sharing. National Cancer Institute	March 2007
Nanoinformatics Workshop. Arlington, VA	June 2007
Launch of NanoMedNet, a platform for education and training in nanomedicine for medical professionals	August 2007
The Network for Computational Nanotechnology receive a grant of USD$18.25 million from the National Science Foundation to support the nanoHub project, focused on computer simulation at the nano level	September 2007
Establishment of NanoSafe Inc, Virginia Tech Corporate Research Center’s KnowledgeWorks Business Accelerator	October, 2007
Research Challenges for Nanomanufacturing Systems. Arlington, VA	February 2008
Launch of NanoImpactNet, a multidisciplinary European network on the health and environmental impact of nanomaterials	April 2008
Launch of ACTION-Grid, first European initiative on Nanoinformatics	June 2008
NSTI Nanotech Conference organized by Nano Science and Technology Institute (NSTI). Boston, MA
Launch of the International Alliance for NanoEHS Harmonization at Nanotox 2008 Conference. Zurich, Switzerland	September 2008
Launch of the first working version of the NanoParticle Ontology. NCI Cancer Biomedical Informatics Grid (caBIG^®) Nanotechnology Working Group	December 2008
Publication of the white paper Ontologies in cancer nanotechnology research. caBIG, National Cancer Institute	January 2009
Publication of the white paper The need for minimum information standards for development and advancement of nanomaterials as cancer diagnostics and therapeutics. caBIG, National Cancer Institute	February 2009
Publication of the white paper Nanotechnology Informatics White Paper.^Citation83 caBIG, National Cancer Institute
Nanotech Conference and Expo 2009 organized by NSTI. Houston, TX	May 2009
1D Heterostructure Tool, new tool for the simulation of heterostructures at the atomic scale
Launch of GoodNanoGuide, an Internet-based collaboration platform about handling nanomaterials in an occupational setting. International Council on Nanotechnology (ICON)	June 2009
Inclusion of Medical Nanoinformatics in the “Recommendations of the International Medical Informatics Association (IMIA) on Education in Biomedical and Health Informatics”	January 2010
Synergies in Nanoscale Manufacturing and Research Workshop. Ithaca, NY
Report to the President and Congress on the Third Assessment of the National Nanotechnology Initiative. President’s Council of Advisors on Science and Technology (PCAST)^Citation78	March 2010
Nanoinformatics publication in Pediatrics Research (first in a medical journal) by Maojo et al “Nanoinformatics and DNA-based computing: catalyzing nanomedicine”^Citation24	May 2010
Development of nano-TAB as ASTM standard (ASTM WK28974) initiated, standard for identifying nanomaterials and characterizations in a tab-delimited format
NanoTech Conference and Expo 2010. Anaheim, CA	June 2010
Launch of the Collaboratory for Structural Nanobiology. National Cancer Institute and University of Talca
Publication of the National Nanotechnology Initiative Signature Initiative: Nanoelectronics for 2020 and Beyond	July 2010
Publication of The ACTION-Grid White Paper on Nanoinformatics.^Citation80 ACTION-Grid Consortium, approved by the European Commission	September 2010
Destination Nano! Premier nanomanufacturing Conference, UMass Lowell. Lowell, MA
Launch of the Nanoscience Portal. National Science Foundation
“Nanoinformatics: making sense out of nanotechnology information.” International Council on Nanotechnology
Publication of the report Nanotechnology Research Directions for Societal Needs in 2020. National Science Foundation
5th General Assembly and Annual Forum of the European Technology Platform on Nanomedicine. Milan, Italy	October 2010
Nanoinformatics 2010. Arlington, VA
Nanoinformatics review in Methods of Information in Medicine by de la Iglesia et al, “International efforts in nanoinformatics research applied to nanomedicine”	November 2010
Nanotechnology Innovation Summit, Washington DC. National Nanotechnology Initiative	December 2010
Establishment of QNano, integrated hub to support Europe’s nanosafety research community	February 2011
Publication of the National Nanotechnology Initiative Strategic Plan. National Science and Technology Council
Publication of the Nanoinformatics 2020 Roadmap.^Citation79 National Nanomanufacturing Network	April 2011
5th Concertation and Consultation Workshop on Micro-Nano-Bio-Convergence Systems 2011. Mondragon, Spain
Nanoinformatics publication in Biological Research by González-Nilo et al, “Nanoinformatics: an emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology”	May 2011
Publication of the Materials Genome Initiative Report Materials Genome Initiative for Global Competitiveness. National Sciences and Technology Council, Washington DC	June 2011
NanoTech Conference and Expo 2011. Boston, MA
Nanoinformatics publication in Wiley Interdisciplinary Reviews, Nanomedicine and Nanobiotechnology by Thomas et al, “Informatics and standards for nanomedicine technology”^Citation70	October 2011
Final specification of the nano-TAB standard	November 2011
Nanoinformatics 2011, Arlington, VA	December 2011
A Research Strategy for Environmental, Health, and Safety Aspects of Engineered Nanomaterials released.^Citation81 National Research Council	January 2012
Launch of the ISA-TAB-Nano (first version), general purpose framework that provides a standard means to communicate data on nanomaterial properties and experiments. Nano Working Group, National Cancer Institute
European Summit for Clinical Nanomedicine 2012. Basel, Switzerland	April 2012
Future events
6th Concertation and Consultation Workshop on Micro-Nano-Bio-Convergence Systems 2012. Athens, Greece. European Commission	May 2012
Nanofair 2012 – 9th International Nanotechnology Symposium. Dresden, Germany	June 2012
8th NanoBio-Europe conference. Varese, Italy
NanoTech Conference and Expo 2012. Santa Clara, CA
9th International Conference on Nanosciences and Nanotechnologies (NN12). Thessaloniki, Greece	July 2012
International Conference on Nanoscience + Technology (ICN+T2012). Paris, France
Nanoinformatics 2012	To be determined

Figure 3 Timeline of events and activities depicted in Table 2.

Abbreviations: Biol Res, Biological Research; CSN, Collaboratory for Structural Nanobiology; IANH, International Alliance for NanoEHS Harmonization; ICON, International Council on Nanotechnology; ICN, International Conference on Nanoscience; MNBS, Micro-Nano-Bio Systems; NNI, National Nanotechnology Initiative; NNN, National Nanomanufacturing Network; NRC, National Research Council; NSTI, Nano Science and Technology Institute; NSF, National Science Foundation; PCAST, President’s Council of Advisors on Science and Technology.

Table A1 Summary of current nanoinformatics initiatives and projects

Name/acronym	Description	Institution	Geographical area	Start year
Initiatives and scientific networks
Nano Science and Technology Institute (NSTI)	It integrates nano and other technologies through education, conventions, business publishing, and research services	NSTI	USA	1997
NanoBioTechnology Center	Experts on nanobiotechnology: biomolecular devices, cellular microdynamics, cell–surface interactions, cell biology, etc	National Science Foundation (NSF)	USA	2000
National Nanotechnology Initiative (NNI)	Central point of communication, cooperation, and collaboration for all US federal agencies engaged in nanotechnology research	25 US governmental agencies	USA	2000
Global Nanotechnology Network	Platform for addressing shared global challenges through nanoscale science, engineering, development, and education	Diverse nanotechnology stakeholders from industry, academia, and government	International	2001
International Council on Nanotechnology (ICON)	Portal for information about the environmental, health, and safety aspects of nanotechnology	Rice University	USA	2004
National Cancer Institute (NCI) Alliance for nanotechnology in Cancer	Committed to build a community of researchers dedicated to using nanotechnology to advance the fight against cancer	NCI, US National Institutes of Health (NIH)	USA	2004
Alliance for NanoHealth	Promotes nano-based approaches, nano-resources, and tools to battle against cancer, heart diseases, or diabetes	Texas Medical Center (Houston, TX)	USA	2005
European Technology Platform on Nanomedicine	Led by industry together with the European Commission (EC) for the application of nanotechnology in health care	EC	Europe	2005
Nanoforum	European Nanotechnology Gateway	Former Fifth RTD Framework Programme, now an European Economic Interest Group	Europe	2005
Nanomedicine Roadmap Initiative	Nanomachinery of the cell to control and manipulate molecules and supramolecular assemblies in living cells	US NIH	USA	2005
Nanotechnology Characterization Laboratory	A NCI-supported lab to perform and standardize nanomaterials intended for cancer therapeutics and diagnostics	NCI, US NIH	USA	2005
Nanotechnologies Industries Association	It represents the industries’ views, interfaces with governments, consultation on regulation, standards, media and public	Group of companies from a variety of industry sectors	International	2005
Project on Emerging Nanotechnologies	Designed to minimize potential risks to health and environment, identifying gaps in knowledge and regulatory processes	Pew Charitable Trusts, Woodrow Wilson International Center for Scholars	USA	2005
Safer Nanomaterials and Nanomanufacturing Initiative	New nanomaterials and nanomanufacturing approaches that offer a high level of performance, yet pose minimal harm	Universities of Oregon, Pacific Northwest Lab, Oregon Nanoscience and Mircrotechnologies Institute	USA	2005
Nanosciences, Nanotechnologies, Materials and new Production Technologies Programme	EC program which funds research, development, demonstration, and coordination projects	EC under FP7	Europe	2006
National Institute for Nanotechnology	Integrated, multidisciplinary, involves researchers in physics, chemistry, engineering, biology, informatics, and medicine	National Research Council of Canada and the University of Alberta	Canada	2006
National Network of Nanomedicine Development Centers	Initiative to determine the physical properties of cellular and subcellular components	US NIH	USA	2006
SAFENANO	Europe’s center of excellence on nanotechnology hazard and risk, facilitating responsible development of safe nanomaterials	Institute of Occupational Medicine (IOM)	Europe	2006
Technology cooperative framework on nanoscale analytical and measurement methods	Initiative for interlaboratory comparison on nanoparticle size. Characterization among ten laboratories from six member economies	Asia-Pacific Economy Cooperation Industrial Science and Technology Working Group	International (Asia-Pacific)	2005
ACTION-Grid	International project on health care and nanoinformatics between Latin America, the Western Balkans, and the European Union (EU)	EC under FP7	EU. Africa, USA, Latin America	2008
European Foundation for Clinical Nanomedicine	Initiative for prevention, diagnosis, and therapy through nanomedicine as well as exploration of its implications	Nonprofit institution, with researchers from the EU and USA	USA	2008
ICPCNanoNet	Collaboration between organizations and scientists in the EU and International Cooperation Partner Countries (ICPC)	EC under FP7	EU and partner countries	2008
Institute of Electrical and Electronics Engineers (IEEE) Nanotechnology Council	IEEE group on nanotechnology	IEEE	International	2008
International Alliance for NanoEHS Harmonization	Scientists from the EU, Japan, and the USA to establish reproducible approaches for dealing with nanoparticle hazards	Peer-group of scientists that voluntarily collaborate	International (Europe, Japan, and the USA)	2008
NanoPediatrics Program	Focused on the development and use of nanomedicine for the care of children	Mattel Children’s Hospital, University of California Los Angeles, CA	USA	2008
National Nanomanufacturing Network	Alliance of academic, government, and industry partners to promote nanomanufacturing workshops and exchanges	NSF	USA	2008
Cancer Biomedical Informatics Grid (caBIG^®) Nanotechnology Working Group	Rational design of nanomaterials and discovering nanoparticle toxicity; development of standards and ontologies	NCI, US NIH	USA	2009
EU Nanosafety Cluster	EC’s initiative to maximize synergies between the Sixth Framework Programme (FP6) and Seventh Framework Programme (FP7) projects, addressing nanosafety	Compendium of EC-funded projects	Europe	2009
Ibero-American Network of Convergent Technologies for Health	Research on the social impact of converging technologies (Nano-Bio-Info-Cogno) in Ibero-America	Latin-American Science and Technology Development Programme	Latin America, Spain, and Portugal	2009
NanoCom	To bridge the gap between laboratory-based and industrial applications in nanotechnology	EC through FP7. Coordinator: University of Nottingham	Europe	2009
Nanotechnology Informatics White Paper^Citation83	White paper covering the history of nanotechnology and the application of nanotechnology in the biomedical field	National Characterization Laboratory, US NCI	USA	2009
ObservatoryNano	European observatory for science-based and economic expert analysis of nanotechnologies,	EC-FP7. Coordinator: Institute of Nanotechnology, UK	Europe	2009
MINAM 2.0	Brings together micro- and nano-related organizations	EC-FP7. Coordinator: Karlsruher Institut Für Technologie	Europe	2010
NanoGEM	Evaluates the hazards of industrially relevant nanomaterials and nanoparticles contained in processed products	Institute of Energy and Environmental Technology	Germany	2010
ProNano	Coaching services to research institutions or persons interested in the commercial exploitation of nanotechnologies	EC-FP7. Coordinator: Zabala Innovation Consulting, SA	Europe	2010
University of California Center for Environmental Implications of Nanotechnology	Development of environmental decision-making tools for managing engineered nanomaterials across a wide spectrum of nano/bio interfaces in cells, bacteria, etc	NSF, Environmental Protection Agency, California NanoSystems Institute, University of California	USA	2010
Materials Genome Initiative	To develop an infrastructure to accelerate advanced materials discovery and deployment in the United States	National Science and Technology Council	USA	2011
Technology Platform NanoFutures	A European Technology Integrating and Innovation Platform, multi-sectorial	EC	Europe	2011
Euro-Nano-Tox	Portal for researchers and industry seeking critical toxicological data for nano-structured materials	BioNanoNet Forschungsgesellschaft mbH	Austria	2011
Data repositories and standards
ICON Environmental, Health and Safety Database	Contains summaries (abstracts) and citations	Rice University, ICON	USA	2004
Molecular Imaging and Contrast Agent Database (MICAD)	Online source of scientific information regarding molecular imaging and contrast agents	NCBI, US NIH	USA	2004
Nanotechnology Standards Panel	Development of standards in nanotechnology including nomenclature/terminology; materials properties and testing	American National Standards Institute	USA	2004
ISO TC 229	Developing standards for the understanding and control of matter and processes at the nanoscale to create improved materials	International Association for Standardization (ISO)	International	2005
National Toxicology Program Database	Toxicology information about chemicals and nanoscale materials, abstracts, reports, and data from toxicology studies	NIH, National Institute for Occupational Safety and Health (NIOSH), US Food and Drug Administration	USA	2005
American Society for Testing and Materials (ASTM) Nanotechnology	ASTM standards for nanotechnology as well as nanotechnology terminology, property testing, and issues of health and safety	ASTM	USA	2006
caNanoLab Database	Annotation of nanomaterials with characterizations resulting from physico-chemical and in vitro assays	NCI, US NIH	USA	2006
SAFENANO Database	Data resource on nanotechnology hazard and risk	IOM	UK	2006
Organisation for Economic Co-operation and Development (OECD) Database on Research into Safety of Manufactured Nanomaterials	Collects research projects that address environmental, human health, and safety issues of manufactured nanomaterials	OECD	International	2007
British Standards Institute (BSI) Nanotechnology	Documents relevant to nanotechnology, addressing nanotechnology terminology, health and safety issues, and product labeling	BSI	UK	2008
Collaboratory for Structural Nanobiology	Nanoparticle structure files and related research data, as well as resources for the visualization of nanoparticles	NCI, US NIH, Universidad de Talca (Chile)	USA, Latin America	2008
ISO Nano Terminology	It lists unambiguous terms and definitions related to particles in the field of nanotechnologies	ISO	International	2008
MINChar	A community initiative to improve the utility of nanotoxicology studies through effective nanomaterial characterization	The Dow Chemical Company, Evonik Industries, Rice University, ICON, BASF Corporation, NIOSH, Clemson University, Woodrow Wilson International Center for Scholars, National Institute of Environmental Health Sciences (NIEHS), DuPont	USA	2008
NanoParticle Ontology	An ontology with basic physical, chemical and functional nano characteristics, as used in cancer diagnosis and therapy	caBIG	USA	2008
Cancer Open Biomedical Resource Project	Toolset for information retrieval for cancer nanotechnology-related information using biomedical ontologies	National Center for Biomedical Ontology through US NIH (NIH)	USA	2009
Nanomaterials Registry	Public resource of curated information on biological and environmental interactions of nanomaterials	NIBIB, NIEHS, NCI	USA	2009
Nanoparticle Information Library	Nanoparticle library to organize and share information on nanomaterials, including health and safety-associated properties	NIOSH	USA	2009
Nano-TAB	Data-sharing challenges in nanotechnology by identifying nanomaterials and characterizations in a tab-delimited format	NCI, US NIH	USA	2009
DaNa	Acquisition, evaluation, and public-oriented presentation of society-relevant data and findings relating to nanomaterials	DECHEMA eV	Germany	2010
Nanomaterial-Biological Interactions Knowledgebase	Repository for annotated data on nanomaterial characterization synthesis methods and nanomaterial–biological interactions	Oregon universities and Microtechnologies Institute	USA	2010
Nano-QSAR	Initiative for applying structure– activity relationships (SARs) to predict properties of nanomaterials	NCI, US NIH	USA	2010
European Repository of Reference Nanomaterials	Nanomaterial repository with a collection representing 25 different types of nanomaterials	EC’s Joint Research Centre	Europe	2011
InterNano NanoManufacturing Taxonomy	Central digital repository of nanomanufacturing research and trade information for the nanomanufacturing community	Coordinated by the National Nanomanufacturing Network	USA	2011
ISA-TAB-Nano (ASTM WK28974)	Standard format for representing information on nanomaterials and small molecules along with their assay characterization data	NCI, US NIH	USA	2012
Collaborative platforms
Network for Computational Nanotechnology (NCN)	Cyber-resource for nanotechnology theory, modeling, and simulation	NSF	USA	2002
Nano Network	Consortium of resources available to companies	ONAMI	USA	2003
caNanoLab	Data-sharing portal designed to facilitate information sharing in the biomedical nanotechnology research community	NCI, US NIH	USA	2006
InterNano	Information clearinghouse for the nanomanufacturing community	Coordinated by the National Nanomanufacturing Network and funded by the NSF	USA	2007
NANOSAFE Inc	An extensive network of experts in the fields of nanoscience and engineering, industrial and environmental health and safety, toxicology, and risk assessment	Virginia Tech Corporate Research Center’s KnowledgeWorks Business Accelerator	USA	2007
GoodNanoGuide	Collaboration platform designed to enhance the ability of experts to exchange ideas on how best to handle nanomaterials	Rice University	USA	2009
NanoHub – NCN	Framework with a set of tools for online simulation and more for nanotechnology	NSF	USA	2009
QNano	EU-funded infrastructure for nanomaterial safety testing	EC through FP7	Europe	2011
Dissemination and information portals
Nano Tech Wire	Latest nanotechnology news	NNI, NSTI, FEI Company, Veeco, Zyvex	USA	2003
ICON nanoEHS Virtual Journal	The Virtual Journal of Nanotechnology Environment, Health and Safety	Rice University, ICON (ICON)	USA	2004
NanoWerk	Committed to educating, informing, and inspiring people about nanosciences and nanotechnologies	NanoWerk LLC	USA	2005
PEN Environmental, Health and Safety Inventory	An inventory of current research involving nanotechnology health and environmental implications	Pew Charitable Trusts, Woodrow Wilson International Center for Scholars	USA	2005
PEN Nanotechnology Medical Applications	Web-based resource to better understand current and future applications of nanotechnology in various fields of medicine	Pew Charitable Trusts, Woodrow Wilson International Center for Scholars	USA	2005
TryNano	Information resource for anyone interested in learning about nanoscience and nanotechnology, oriented to the general public	IBM, IEEE, New York Hall of Science	International	2007
Nanotechnology Risk Resources	References to papers, articles, and books on (or related to) potential health and environmental risks of nanomaterials	Nanotechnology Citizens Engagement Organization	USA	2010
National Institute of Standards and Technology (NIST) Nanotechnology Portal	Portal about nanotechnology-related research conducted in NIST’s laboratories that develops measurements and standards	NIST	USA	2010

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