Nanoinformatics is the application of
informatics
Informatics is the study of computational systems, especially those for data storage and retrieval. According to ACM ''Europe and'' ''Informatics Europe'', informatics is synonymous with computer science and computing as a profession, in which ...
to
nanotechnology
Nanotechnology, also shortened to nanotech, is the use of matter on an atomic, molecular, and supramolecular scale for industrial purposes. The earliest, widespread description of nanotechnology referred to the particular technological goal o ...
. 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
Cheminformatics (also known as chemoinformatics) refers to use of physical chemistry theory with computer and information science techniques—so called "''in silico''" techniques—in application to a range of descriptive and prescriptive problem ...
in that
nanomaterials
*
Nanomaterials describe, in principle, materials of which a single unit is sized (in at least one dimension) between 1 and 100 nm (the usual definition of nanoscale).
Nanomaterials research takes a materials science-based approach to nan ...
usually involve
nonuniform collections of particles that have distributions of physical properties that must be specified. The nanoinformatics infrastructure includes
ontologies
In computer science and information science, an ontology encompasses a representation, formal naming, and definition of the categories, properties, and relations between the concepts, data, and entities that substantiate one, many, or all domains ...
for nanomaterials, file formats, and data repositories.
Nanoinformatics has applications for improving workflows in fundamental research, manufacturing, and
environmental health
Environmental health is the branch of public health concerned with all aspects of the natural and built environment affecting human health. In order to effectively control factors that may affect health, the requirements that must be met in ...
, allowing the use of high-throughput data-driven methods to analyze broad sets of experimental results.
Nanomedicine
Nanomedicine is the medical application of nanotechnology. Nanomedicine ranges from the medical applications of nanomaterials and BioBrick, biological devices, to Nanoelectronics, nanoelectronic biosensors, and even possible future applicatio ...
applications include analysis of nanoparticle-based pharmaceuticals for
structure–activity relationship The structure–activity relationship (SAR) is the relationship between the chemical structure of a molecule and its biological activity. This idea was first presented by Crum-Brown and Fraser in 1865.
The analysis of SAR enables the determination o ...
s in a similar manner to
bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...
.
Background
![Nanoinformatics as a convergence](https://upload.wikimedia.org/wikipedia/commons/e/e6/Nanoinformatics_as_a_convergence.jpg)
While conventional chemicals are specified by their
chemical composition
A chemical composition specifies the identity, arrangement, and ratio of the elements making up a compound.
Chemical formulas can be used to describe the relative amounts of elements present in a compound. For example, the chemical formula for ...
, and
concentration
In chemistry, concentration is the abundance of a constituent divided by the total volume of a mixture. Several types of mathematical description can be distinguished: '' mass concentration'', ''molar concentration'', ''number concentration'', an ...
, nanoparticles have other physical properties that must be measured for a complete description, such as
size
Size in general is the Magnitude (mathematics), magnitude or dimensions of a thing. More specifically, ''geometrical size'' (or ''spatial size'') can refer to linear dimensions (length, width, height, diameter, perimeter), area, or volume ...
,
shape
A shape or figure is a graphics, graphical representation of an object or its external boundary, outline, or external Surface (mathematics), surface, as opposed to other properties such as color, Surface texture, texture, or material type.
A pl ...
,
surface properties,
crystallinity
Crystallinity refers to the degree of structural order in a solid. In a crystal, the atoms or molecules are arranged in a regular, periodic manner. The degree of crystallinity has a big influence on hardness, density, Transparency and translucen ...
, 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
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 o ...
and their representation in an informatics system.
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.
![Nanoinformatics as a Life Cycle](https://upload.wikimedia.org/wikipedia/commons/9/9f/Nanoinformatics_as_a_Life_Cycle.jpg)
One working definition of nanoinformatics developed through the community-based Nanoinformatics 2020 Roadmap
and subsequently expanded
is:
* Determining which information is relevant to meeting the safety, health, well-being, and productivity objectives of the nanoscale science, engineering, and technology community;
* Developing and implementing effective mechanisms for collecting, validating, storing, sharing, analyzing, modeling, and applying the information;
* Confirming that appropriate decisions were made and that desired mission outcomes were achieved as a result of that information; and finally
* Conveying experience to the broader community, contributing to generalized knowledge, and updating standards and training.
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.
Ontologies
![ENanoMapper ontology Hastings et al 2015 J Biomed Semantics 6-10 fig 2](https://upload.wikimedia.org/wikipedia/commons/c/c5/ENanoMapper_ontology_Hastings_et_al_2015_J_Biomed_Semantics_6-10_fig_2.gif)
In the context of information science, an
ontology
In metaphysics, ontology is the philosophical study of being, as well as related concepts such as existence, becoming, and reality.
Ontology addresses questions like how entities are grouped into categories and which of these entities exis ...
is a formal representation of knowledge within a
domain
Domain may refer to:
Mathematics
*Domain of a function, the set of input values for which the (total) function is defined
**Domain of definition of a partial function
**Natural domain of a partial function
**Domain of holomorphy of a function
* Do ...
, 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
Discovery may refer to:
* Discovery (observation), observing or finding something unknown
* Discovery (fiction), a character's learning something unknown
* Discovery (law), a process in courts of law relating to evidence
Discovery, The Discovery ...
of data. Having an established ontology for nanoparticles is important for cancer
nanomedicine
Nanomedicine is the medical application of nanotechnology. Nanomedicine ranges from the medical applications of nanomaterials and BioBrick, biological devices, to Nanoelectronics, nanoelectronic biosensors, and even possible future applicatio ...
due to the need of researchers to search, access, and analyze large amounts of data.
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
Basic Formal Ontology (BFO) is a top-level ontology developed by Barry Smith and his associates for the purposes of promoting interoperability among domain ontologies built in its terms through a process of downward population. A guide to buil ...
framework and is implemented in the
Web Ontology Language
The Web Ontology Language (OWL) is a family of knowledge representation languages for authoring ontologies. Ontologies are a formal way to describe taxonomies and classification networks, essentially defining the structure of knowledge for variou ...
. It is hosted by the
National Center for Biomedical Ontology The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing, and is funded by the NIH. Among the goals of the NCBO are to provide tools for discovery and access of biomedical ontologies, which are a t ...
and maintained on
GitHub
GitHub, Inc. () is an Internet hosting service for software development and version control using Git. It provides the distributed version control of Git plus access control, bug tracking, software feature requests, task management, continuous ...
.
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
Chemical Entities of Biological Interest, also known as ChEBI, is a chemical database and ontology of molecular entities focused on 'small' chemical compounds, that is part of the Open Biomedical Ontologies (OBO) effort at the European Bioinf ...
.
File formats
![ISA-TAB-Nano flowchart](https://upload.wikimedia.org/wikipedia/commons/e/e5/ISA-TAB-Nano_flowchart.jpg)
ISA-TAB-Nano is a set of four spreadsheet-based file formats for representing and sharing nanomaterial data, based on the
ISA-TAB metadata standard. In Europe, other templates have been adopted that were developed by the
Institute of Occupational Medicine The Institute of Occupational Medicine (IOM) was founded in 1969 by the National Coal Board (NCB) as an independent charity in the UK and retains this charitable purpose and status today. The "Institute" has a subsidiary, IOM Consulting Limited, whi ...
,
and by the
Joint Research Centre
The Joint Research Centre (JRC) is the European Commission's science and knowledge service which employs scientists to carry out research in order to provide independent scientific advice and support to European Union (EU) policy. The JRC is ...
for the NANoREG project.
Tools
Nanoinformatics is not limited to aggregating and sharing information about nanotechnologies, but has many complementary tools, some originating from
chemoinformatics
Cheminformatics (also known as chemoinformatics) refers to use of physical chemistry theory with computer and information science techniques—so called "''in silico''" techniques—in application to a range of descriptive and prescriptive proble ...
and
bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...
.
Databases and repositories
Over the last couple of years, various databases have been made available.
caNanoLab, developed by the U.S.
National Cancer Institute
The National Cancer Institute (NCI) coordinates the United States National Cancer Program and is part of the National Institutes of Health (NIH), which is one of eleven agencies that are part of the U.S. Department of Health and Human Services. ...
, focuses on nanotechnologies related to biomedicine. The NanoMaterials Registry, maintained by
RTI International
Research Triangle Institute, trading as RTI International, is a nonprofit organization headquartered in the Research Triangle Park in North Carolina. RTI provides research and technical services. It was founded in 1958 with $500,000 in funding f ...
, is a curated database of nanomaterials, and includes data from caNanoLab.
The eNanoMapper database, a project of the EU NanoSafety Cluster, is a deployment of the database software developed in the eNanoMapper project. It has since been used in other settings, such as the EU Observatory for NanoMaterials (EUON).
Other databases include the Center for the Environmental Implications of NanoTechnology's NanoInformatics Knowledge Commons (NIKC) and NanoDatabank,
PEROSH's Nano Exposure & Contextual Information Database (NECID), Data and Knowledge on Nanomaterials (DaNa), and
Springer Nature
Springer Nature or the Springer Nature Group is a German-British academic publishing company created by the May 2015 merger of Springer Science+Business Media and Holtzbrinck Publishing Group's Nature Publishing Group, Palgrave Macmillan, and Macm ...
's Nano database.
Applications
Nanoinformatics has applications for improving workflows in fundamental research, manufacturing, and
environmental health
Environmental health is the branch of public health concerned with all aspects of the natural and built environment affecting human health. In order to effectively control factors that may affect health, the requirements that must be met in ...
, allowing the use of high-throughput data-driven methods to analyze broad sets of experimental results.
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.
Nanoinformatics can enable
structure–activity relationship The structure–activity relationship (SAR) is the relationship between the chemical structure of a molecule and its biological activity. This idea was first presented by Crum-Brown and Fraser in 1865.
The analysis of SAR enables the determination o ...
modelling for nanoparticle-based drugs.
Nanoinformatics and biomolecular nanomodeling provide a route for effective cancer treatment. Nanoinformatics also enables a data-driven approach to the design of materials to meet health and environmental needs.
Modeling and NanoQSAR
Viewed as a workflow process,
nanoinformatics deconstructs experimental studies using data,
metadata
Metadata is "data that provides information about other data", but not the content of the data, such as the text of a message or the image itself. There are many distinct types of metadata, including:
* Descriptive metadata – the descriptive ...
,
controlled vocabularies
Control may refer to:
Basic meanings Economics and business
* Control (management), an element of management
* Control, an element of management accounting
* Comptroller (or controller), a senior financial officer in an organization
* Controlling ...
and
ontologies
In computer science and information science, an ontology encompasses a representation, formal naming, and definition of the categories, properties, and relations between the concepts, data, and entities that substantiate one, many, or all domains ...
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 organism
A model organism (often shortened to model) is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workin ...
s) 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.
At present, nanoinformatics is an extension of
bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...
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
Quantitative structure–activity relationship models (QSAR models) are regression or classification models used in the chemical and biological sciences and engineering. Like other regression models, QSAR regression models relate a set of "predic ...
, QSAR) or the time-course development of a simulation (
physiologically based toxicokinetics, PBTK). Each of these has been explored for
small molecule
Within the fields of molecular biology and pharmacology, a small molecule or micromolecule is a low molecular weight (≤ 1000 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs ar ...
drug development
Drug development is the process of bringing a new pharmaceutical drug to the market once a lead compound has been identified through the process of drug discovery. It includes preclinical research on microorganisms and animals, filing for re ...
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. Illustrative of current QSAR and PBTK models are those of Puzyn et al. and Bachler et al. The
OECD
The Organisation for Economic Co-operation and Development (OECD; french: Organisation de coopération et de développement économiques, ''OCDE'') is an intergovernmental organisation with 38 member countries, founded in 1961 to stimulate e ...
has codified regulatory acceptance criteria, and there are guidance roadmaps
with supporting workshops to coordinate international efforts.
Communities
Communities active in nanoinformatics include the
European Union
The European Union (EU) is a supranational political and economic union of member states that are located primarily in Europe. The union has a total area of and an estimated total population of about 447million. The EU has often been des ...
NanoSafety Cluster, The U.S.
National Cancer Institute
The National Cancer Institute (NCI) coordinates the United States National Cancer Program and is part of the National Institutes of Health (NIH), which is one of eleven agencies that are part of the U.S. Department of Health and Human Services. ...
National Cancer Informatics Program's Nanotechnology Working Group, and the US–EU Nanotechnology Communities of Research.
![Nanoinformatics Roles and Responsibilities](https://upload.wikimedia.org/wikipedia/commons/e/e8/Nanoinformatics_Roles_and_Responsibilities.jpg)
Individuals who engage in nanoinformatics can be viewed as fitting across four categories of roles and responsibilities for nanoinformatics methods and data:
* Customers, who need either the methods to create the data, the data itself, or both, and who specify the scientific applications and characterization methods and data needs for their intended purposes;
* Creators, who develop relevant and reliable methods and data to meet the needs of customers in the nanotechnology community;
* Curators, who maintain and ensure the quality of the methods and associated data; and
* Analysts, who develop and apply methods and models for data analysis and interpretation that are consistent with the quality and quantity of the data and that meet customers’ needs.
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.
History
One of the first mentions of nanoinformatics was in the context of handling information about nanotechnology.
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
Buxton is a spa town in the Borough of High Peak, Derbyshire, England. It is England's highest market town, sited at some above sea level. , Derbyshire, UK.
The workshop report
included a presentation on Information Management for Nanotechnology Safety and Health 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.
The National Cancer Institute prepared in 2009 a rough vision of, what was then still called, nanotechnology informatics, 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''
and the ''EU US Roadmap Nanoinformatics 2030''.
A 2013 workshop on nanoinformatics described current resources, community needs and the proposal of a collaborative framework for data sharing and information integration.
See also
*
Cheminformatics
Cheminformatics (also known as chemoinformatics) refers to use of physical chemistry theory with computer and information science techniques—so called "''in silico''" techniques—in application to a range of descriptive and prescriptive problem ...
*
Materials informatics Materials informatics is a field of study that applies the principles of informatics to materials science and engineering to improve the understanding, use, selection, development, and discovery of materials. This is an emerging field, with a goal ...
References
External links
* {{Scholia-inline, Q61911710, topic
Information science by discipline
Nanotechnology