Nanoinformatics

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Nanoinformatics is the application of informatics to nanotechnology. It is an interdisciplinary field that develops methods and software tools for understanding nanomaterials, their properties, and their interactions with biological entities, and using that information more efficiently. It differs from cheminformatics in that nanomaterials usually involve nonuniform collections of particles that have distributions of physical properties that must be specified. The nanoinformatics infrastructure includes ontologies for nanomaterials, file formats, and data repositories.

Contents

Nanoinformatics has applications for improving workflows in fundamental research, manufacturing, and environmental health, allowing the use of high-throughput data-driven methods to analyze broad sets of experimental results. Nanomedicine applications include analysis of nanoparticle-based pharmaceuticals for structure–activity relationships in a similar manner to bioinformatics.

Background

Context of nanoinformatics as a convergence of science and practice at the nexus of safety, health, well-being, and productivity; risk management; and emerging nanotechnology. Nanoinformatics as a convergence.jpg
Context of nanoinformatics as a convergence of science and practice at the nexus of safety, health, well-being, and productivity; risk management; and emerging nanotechnology.

While conventional chemicals are specified by their chemical composition, and concentration, nanoparticles have other physical properties that must be measured for a complete description, such as size, shape, surface properties, crystallinity, and dispersion state. In addition, preparations of nanoparticles are often non-uniform, having distributions of these properties that must also be specified. These molecular-scale properties influence their macroscopic chemical and physical properties, as well as their biological effects. They are important in both the experimental characterization of nanoparticles and their representation in an informatics system. [1] [2] The context of nanoinformatics is that effective development and implementation of potential applications of nanotechnology requires the harnessing of information at the intersection of safety, health, well-being, and productivity; risk management; and emerging nanotechnology. [3] [4]

A graphical representation of a working definition of nanoinformatics as a life-cycle process Nanoinformatics as a Life Cycle.jpg
A graphical representation of a working definition of nanoinformatics as a life-cycle process

One working definition of nanoinformatics developed through the community-based Nanoinformatics 2020 Roadmap [5] and subsequently expanded [3] is:

Data representations

Although nanotechnology is the subject of significant experimentation, much of the data are not stored in standardized formats or broadly accessible. Nanoinformatics initiatives seek to coordinate developments of data standards and informatics methods. [5]

Ontologies

An overview of the eNanoMapper nanomaterial ontology ENanoMapper ontology Hastings et al 2015 J Biomed Semantics 6-10 fig 2.gif
An overview of the eNanoMapper nanomaterial ontology

In the context of information science, an ontology is a formal representation of knowledge within a domain, using hierarchies of terms including their definitions, attributes, and relations. Ontologies provide a common terminology in a machine-readable framework that facilitates sharing and discovery of data. Having an established ontology for nanoparticles is important for cancer nanomedicine due to the need of researchers to search, access, and analyze large amounts of data. [6] [7]

The NanoParticle Ontology is an ontology for the preparation, chemical composition, and characterization of nanomaterials involved in cancer research. It uses the Basic Formal Ontology framework and is implemented in the Web Ontology Language. It is hosted by the National Center for Biomedical Ontology and maintained on GitHub. [6] The eNanoMapper Ontology is more recent and reuses wherever possible already existing domain ontologies. As such, it reuses and extends the NanoParticle Ontology, but also the BioAssay Ontology, Experimental Factor Ontology, Unit Ontology, and ChEBI. [8]

File formats

Flowchart depicting the ways to identify different components of a material sample to guide the creation of an ISA-TAB-Nano Material file ISA-TAB-Nano flowchart.jpg
Flowchart depicting the ways to identify different components of a material sample to guide the creation of an ISA-TAB-Nano Material file

ISA-TAB-Nano is a set of four spreadsheet-based file formats for representing and sharing nanomaterial data, [9] [10] based on the ISA-TAB metadata standard. [11] In Europe, other templates have been adopted that were developed by the Institute of Occupational Medicine, [12] and by the Joint Research Centre for the NANoREG project. [13]

Tools

Nanoinformatics is not limited to aggregating and sharing information about nanotechnologies, but has many complementary tools, some originating from chemoinformatics and bioinformatics. [14] [15]

Databases and repositories

Over the last couple of years, various databases have been made available. [16]

caNanoLab, developed by the U.S. National Cancer Institute, focuses on nanotechnologies related to biomedicine. [17] The NanoMaterials Registry, maintained by RTI International, is a curated database of nanomaterials, and includes data from caNanoLab. [18]

The eNanoMapper database, a project of the EU NanoSafety Cluster, is a deployment of the database software developed in the eNanoMapper project. [19] It has since been used in other settings, such as the EU Observatory for NanoMaterials (EUON). [20] [21]

Other databases include the Center for the Environmental Implications of NanoTechnology's NanoInformatics Knowledge Commons (NIKC) [22] and NanoDatabank, [23] PEROSH's Nano Exposure & Contextual Information Database (NECID), [24] Data and Knowledge on Nanomaterials (DaNa), [25] and Springer Nature's Nano database. [26]

Applications

Nanoinformatics has applications for improving workflows in fundamental research, manufacturing, and environmental health, allowing the use of high-throughput data-driven methods to analyze broad sets of experimental results. [5]

Nanoinformatics is especially useful in nanoparticle-based cancer diagnostics and therapeutics. They are very diverse in nature due to the combinatorially large numbers of chemical and physical modifications that can be made to them, which can cause drastic changes in their functional properties. This leads to a combinatorial complexity that far exceeds, for example, genomic data. [6] Nanoinformatics can enable structure–activity relationship modelling for nanoparticle-based drugs. [6] Nanoinformatics and biomolecular nanomodeling provide a route for effective cancer treatment. [27] Nanoinformatics also enables a data-driven approach to the design of materials to meet health and environmental needs. [28]

Modeling and NanoQSAR

Viewed as a workflow process, [2] nanoinformatics deconstructs experimental studies using data, metadata, controlled vocabularies and ontologies to populate databases so that trends, regularities and theories will be uncovered for use as predictive computational tools. Models are involved at each stage, some material (experiments, reference materials, model organisms) and some abstract (ontology, mathematical formulae), and all intended as a representation of the target system. Models can be used in experimental design, may substitute for experiment or may simulate how a complex system changes over time. [29]

At present, nanoinformatics is an extension of bioinformatics due to the great opportunities for nanotechnology in medical applications, as well as to the importance of regulatory approvals to product commercialization. In these cases, the models target, their purposes, may be physico-chemical, estimating a property based on structure (quantitative structure–property relationship, QSPR); or biological, predicting biological activity based on molecular structure (quantitative structure–activity relationship, QSAR) or the time-course development of a simulation (physiologically based toxicokinetics, PBTK). [30] [31] Each of these has been explored for small molecule drug development with a supporting body of literature.

Particles differ from molecular entities, especially in having surfaces that challenge nomenclature system and QSAR/PBTK model development. For example, particles do not exhibit an octanol–water partition coefficient, which acts as a motive force in QSAR/PBTK models; and they may dissolve in vivo or have band gaps. [32] Illustrative of current QSAR and PBTK models are those of Puzyn et al. [33] and Bachler et al. [34] The OECD has codified regulatory acceptance criteria, [35] and there are guidance roadmaps [5] [12] with supporting workshops [36] to coordinate international efforts.

Communities

Communities active in nanoinformatics include the European Union NanoSafety Cluster, [37] The U.S. National Cancer Institute National Cancer Informatics Program's Nanotechnology Working Group, [38] [39] and the US–EU Nanotechnology Communities of Research. [40]

Nanoinformatics roles, responsibilities, and communication interfaces Nanoinformatics Roles and Responsibilities.jpg
Nanoinformatics roles, responsibilities, and communication interfaces

Individuals who engage in nanoinformatics can be viewed as fitting across four categories of roles and responsibilities for nanoinformatics methods and data: [4] [41] [42]

In some instances, the same individuals perform all four roles. More often, many individuals must interact, with their roles and responsibilities extending over significant distances, organizations, and time. Effective communication is important across each of the twelve links (in both directions across each of the six pairwise interactions) that exist among the various customers, creators, curators, and analysts. [4]

History

One of the first mentions of nanoinformatics was in the context of handling information about nanotechnology. [43]

An early international workshop with substantial discussion of the need for sharing all types of information on nanotechnology and nanomaterials was the First International Symposium on Occupational Health Implications of Nanomaterials held 12–14 October 2004 at the Palace Hotel, Buxton, Derbyshire, UK. [44] The workshop report [44] included a presentation on Information Management for Nanotechnology Safety and Health [45] that described the development of a Nanoparticle Information Library (NIL) and noted that efforts to ensure the health and safety of nanotechnology workers and members of the public could be substantially enhanced by a coordinated approach to information management. The NIL subsequently served as an example for web-based sharing of characterization data for nanomaterials. [46]

The National Cancer Institute prepared in 2009 a rough vision of, what was then still called, nanotechnology informatics, [47] outlining various aspects of what nanoinformatics should comprise. This was later followed by two roadmaps, detailing existing solutions, needs, and ideas on how the field should further develop: the Nanoinformatics 2020 Roadmap [5] and the EU US Roadmap Nanoinformatics 2030. [12]

A 2013 workshop on nanoinformatics described current resources, community needs and the proposal of a collaborative framework for data sharing and information integration. [48]

See also

Related Research Articles

<span class="mw-page-title-main">Nanotechnology</span> Field of science involving control of matter on atomic and (supra)molecular scales

Nanotechnology was defined by the National Nanotechnology Initiative as the manipulation of matter with at least one dimension sized from 1 to 100 nanometers (nm). At this scale, commonly known as the nanoscale, surface area and quantum mechanical effects become important in describing properties of matter. The definition of nanotechnology is inclusive of all types of research and technologies that deal with these special properties. It is therefore common to see the plural form "nanotechnologies" as well as "nanoscale technologies" to refer to the broad range of research and applications whose common trait is size. An earlier description of nanotechnology referred to the particular technological goal of precisely manipulating atoms and molecules for fabrication of macroscale products, also now referred to as molecular nanotechnology.

Nanomedicine is the medical application of nanotechnology. Nanomedicine ranges from the medical applications of nanomaterials and biological devices, to nanoelectronic biosensors, and even possible future applications of molecular nanotechnology such as biological machines. Current problems for nanomedicine involve understanding the issues related to toxicity and environmental impact of nanoscale materials.

Nanosensors are nanoscale devices that measure physical quantities and convert these to signals that can be detected and analyzed. There are several ways proposed today to make nanosensors; these include top-down lithography, bottom-up assembly, and molecular self-assembly. There are different types of nanosensors in the market and in development for various applications, most notably in defense, environmental, and healthcare industries. These sensors share the same basic workflow: a selective binding of an analyte, signal generation from the interaction of the nanosensor with the bio-element, and processing of the signal into useful metrics.

<span class="mw-page-title-main">Nanomaterials</span> Materials whose granular size lies between 1 and 100 nm

Nanomaterials describe, in principle, materials of which a single unit is sized between 1 and 100 nm.

<span class="mw-page-title-main">Nanobiotechnology</span> Intersection of nanotechnology and biology

Nanobiotechnology, bionanotechnology, and nanobiology are terms that refer to the intersection of nanotechnology and biology. Given that the subject is one that has only emerged very recently, bionanotechnology and nanobiotechnology serve as blanket terms for various related technologies.

The impact of nanotechnology extends from its medical, ethical, mental, legal and environmental applications, to fields such as engineering, biology, chemistry, computing, materials science, and communications.

Nanotoxicology is the study of the toxicity of nanomaterials. Because of quantum size effects and large surface area to volume ratio, nanomaterials have unique properties compared with their larger counterparts that affect their toxicity. Of the possible hazards, inhalation exposure appears to present the most concern, with animal studies showing pulmonary effects such as inflammation, fibrosis, and carcinogenicity for some nanomaterials. Skin contact and ingestion exposure are also a concern.

The following outline is provided as an overview of and topical guide to nanotechnology:

Green nanotechnology refers to the use of nanotechnology to enhance the environmental sustainability of processes producing negative externalities. It also refers to the use of the products of nanotechnology to enhance sustainability. It includes making green nano-products and using nano-products in support of sustainability.

Because of the ongoing controversy on the implications of nanotechnology, there is significant debate concerning whether nanotechnology or nanotechnology-based products merit special government regulation. This mainly relates to when to assess new substances prior to their release into the market, community and environment.

<span class="mw-page-title-main">Pollution from nanomaterials</span>

The International Organization for Standardization defines Engineered Nanomaterials, or ENMS, as materials with external dimensions between 1 and 100nm, the nanoscale, or having an internal surface structure at these dimensions. Nanoparticles can be both incidental and engineered. Incidental nanoparticles include particles from dust storms, volcanic eruptions, forest fires, and ocean water evaporation. Engineered nanoparticles (EMMs) are nanoparticles that are made for use in cosmetics or pharmaceuticals like ZnO and TiO2. They are also found from sources such as cigarette smoke and building demolition. Engineered nanoparticles have become increasingly important for many applications in consumer and industrial products, which has resulted in an increased presence in the environment. This proliferation has instigated a growing body of research into the effects of nanoparticles on the environment.

The applications of nanotechnology, commonly incorporate industrial, medicinal, and energy uses. These include more durable construction materials, therapeutic drug delivery, and higher density hydrogen fuel cells that are environmentally friendly. Being that nanoparticles and nanodevices are highly versatile through modification of their physiochemical properties, they have found uses in nanoscale electronics, cancer treatments, vaccines, hydrogen fuel cells, and nanographene batteries.

<span class="mw-page-title-main">Toxicology of carbon nanomaterials</span> Overview of toxicology of carbon nanomaterials

Toxicology of carbon nanomaterials is the study of toxicity in carbon nanomaterials like fullerenes and carbon nanotubes.

The EU NanoSafety Cluster (NSC) is a cluster of European Commission-funded projects in the funding programs FP6 (2002–2006), FP7 (2007–2013), and Horizon 2020 aka H2020 (2014–2020) and Horizon Europe framework programmes, aimed at harmonizing the research done in these projects. The cluster coordinates work done by the NanoSafety Cluster projects to study and establish the safety of nanomaterials. The coordination by the cluster is organized in half-yearly meetings and various working groups. An example of a result of the NanoSafety Cluster's harmonization was the prioritization of which nanomaterials to study. The NSC has become a reference actor for consumers' associations in the field.

The health and safety hazards of nanomaterials include the potential toxicity of various types of nanomaterials, as well as fire and dust explosion hazards. Because nanotechnology is a recent development, the health and safety effects of exposures to nanomaterials, and what levels of exposure may be acceptable, are subjects of ongoing research. Of the possible hazards, inhalation exposure appears to present the most concern, with animal studies showing pulmonary effects such as inflammation, fibrosis, and carcinogenicity for some nanomaterials. Skin contact and ingestion exposure, and dust explosion hazards, are also a concern.

A radioactive nanoparticle is a nanoparticle that contains radioactive materials. Radioactive nanoparticles have applications in medical diagnostics, medical imaging, toxicokinetics, and environmental health, and are being investigated for applications in nuclear nanomedicine. Radioactive nanoparticles present special challenges in operational health physics and internal dosimetry that are not present for other substances, although existing radiation protection measures and hazard controls for nanoparticles generally apply.

<span class="mw-page-title-main">Characterization of nanoparticles</span> Measurement of physical and chemical properties of nanoparticles

The characterization of nanoparticles is a branch of nanometrology that deals with the characterization, or measurement, of the physical and chemical properties of nanoparticles. Nanoparticles measure less than 100 nanometers in at least one of their external dimensions, and are often engineered for their unique properties. Nanoparticles are unlike conventional chemicals in that their chemical composition and concentration are not sufficient metrics for a complete description, because they vary in other physical properties such as size, shape, surface properties, crystallinity, and dispersion state.

<span class="mw-page-title-main">Titanium dioxide nanoparticle</span>

Titanium dioxide nanoparticles, also called ultrafine titanium dioxide or nanocrystalline titanium dioxide or microcrystalline titanium dioxide, are particles of titanium dioxide with diameters less than 100 nm. Ultrafine TiO2 is used in sunscreens due to its ability to block ultraviolet radiation while remaining transparent on the skin. It is in rutile crystal structure and coated with silica or/and alumina to prevent photocatalytic phenomena. The health risks of ultrafine TiO2 from dermal exposure on intact skin are considered extremely low, and it is considered safer than other substances used for ultraviolet protection.

Thomas J. Webster is an American biomedical engineer, researcher, and entrepreneur. Throughout his over 25-year academic career, his research group has produced several books and book chapters. He has over 1350 publications and has an H-index of 118. This high H-index places him amongst the top 1% of researchers in his field.

Moein Moghimi is a British professor and researcher in the fields of nanomedicine, drug delivery and biomaterials. He is currently the professor of Pharmaceutics and Nanomedicine at the School of Pharmacy and the Translational and Clinical Research Institute at Newcastle University. He is also an adjoint professor at the Skaggs School of Pharmacy, University of Colorado Denver.

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  42. ↑ Woodall, George M.; Hoover, Mark D.; Williams, Ronald; Benedict, Kristen; Harper, Martin; Soo, Jhy-Charm; Jarabek, Annie M.; Stewart, Michael J.; Brown, James S. (2017). "Interpreting Mobile and Handheld Air Sensor Readings in Relation to Air Quality Standards and Health Effect Reference Values: Tackling the Challenges". Atmosphere. 8 (10): 182. Bibcode:2017Atmos...8..182W. doi: 10.3390/atmos8100182 . ISSN   2073-4433. PMC   5662140 . PMID   29093969.
  43. ↑ Porter, Alan L.; Youtie, Jan; Shapira, Philip; Schoeneck, David J. (3 August 2007). "Refining search terms for nanotechnology". Journal of Nanoparticle Research. 10 (5): 715–728. doi:10.1007/s11051-007-9266-y. S2CID   56232588.
  44. 1 2 Mark, David, ed. (2004). Nanomaterials: A risk to health at Work? Report of Presentations at Plenary and Workshop Sessions and Summary of Conclusions from the First International Symposium on Occupational Health Implications of Nanomaterials held 12-14 October 2004 at the Palace Hotel, Buxton, Derbyshire, UK (PDF). Buxton, UK: Health and Safety Laboratory.
  45. ↑ Hoover, Mark D.; Miller, Arthur L.; Lowe, Nathan T.; Stefaniak, Aleksandr B.; Day, Gregory L.; Linch, Kenneth D. (2004). "Information Management for Nanotechnology Safety and Health" (PDF). In Mark, David (ed.). Nanomaterials: A risk to health at Work? Report of Presentations at Plenary and Workshop Sessions and Summary of Conclusions from the First International Symposium on Occupational Health Implications of Nanomaterials held 12-14 October 2004 at the Palace Hotel, Buxton, Derbyshire, UK. Buxton, UK: Health and Safety Laboratory. p. 110.
  46. ↑ Miller, Arthur L.; Hoover, Mark D.; Mitchell, David M.; Stapleton, Brian P. (2007). "The Nanoparticle Information Library (NIL): a prototype for linking and sharing emerging data". Journal of Occupational and Environmental Hygiene. 4 (12): D131–134. doi:10.1080/15459620701683947. ISSN   1545-9624. PMID   17924276. S2CID   7518070.
  47. ↑ Baker, Nathan (February 2009). Nanotechnology Informatics White Paper.
  48. ↑ Harper, Stacey L.; Hutchison, James E.; Baker, Nathan; Ostraat, Michele; Tinkle, Sally; Steevens, Jeffrey; Hoover, Mark D.; Adamick, Jessica; Rajan, Krishna (2013). "Nanoinformatics workshop report: Current resources, community needs, and the proposal of a collaborative framework for data sharing and information integration". Computational Science & Discovery. 6 (1): 14008. Bibcode:2013CS&D....6a4008H. doi:10.1088/1749-4699/6/1/014008. ISSN   1749-4699. PMC   3895330 . PMID   24454543.
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