Nanoinformatics: Difference between revisions

'''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 [[Dispersity|nonuniform]] collections of particles that have distributions of physical properties that must be specified. The nanoinformatics infrastructure includes [[Ontology (information science)|ontologies]] for nanomaterials, file formats, and data repositories.

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 relationship]]s in a similar manner to [[bioinformatics]].

[[File:Nanoinformatics as a convergence.jpg|thumb|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 [[Particle size|size]], [[shape]], [[Surface science|surface properties]], [[crystallinity]], and [[Dispersion (chemistry)|dispersion state]]. In addition, preparations of nanoparticles are often [[Dispersity|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.<ref name=":3">{{Cite journal|last1=Hassellöv|first1=Martin|last2=Readman|first2=James W.|last3=Ranville|first3=James F.|last4=Tiede|first4=Karen|date=2008-07-01|title=Nanoparticle analysis and characterization methodologies in environmental risk assessment of engineered nanoparticles|journal=Ecotoxicology|language=en|volume=17|issue=5|pages=344–361|doi=10.1007/s10646-008-0225-x|issn=0963-9292|pmid=18483764|s2cid=25291395}}</ref><ref name=":7">{{Cite journal|last1=Powers|first1=Kevin W.|last2=Palazuelos|first2=Maria|last3=Moudgil|first3=Brij M.|last4=Roberts|first4=Stephen M.|date=2007-01-01|title=Characterization of the size, shape, and state of dispersion of nanoparticles for toxicological studies|journal=Nanotoxicology|volume=1|issue=1|pages=42–51|doi=10.1080/17435390701314902|s2cid=137174566|issn=1743-5390}}</ref> The context of nanoinformatics is that effective development and implementation of the imaginedpotential applications of nanotechnology requires the harnessing of information at the intersection of safety, health, well-being, and productivity; [[risk management]]; and emerging nanotechnology.<ref name=":2" /><ref name=":4">{{Cite book|title=Nanotechnology Environmental Health and Safety: Risks, Regulation, and Management |lastlast1=Hoover|firstfirst1=M.D.|last2=Cash|first2=L.J. |last3=Feitshans|first3=I.L|last4=Hendren|first4=C.O.|last5=Harper|first5=S.L. |publisher=Elsevier|year=2018|isbn=9780128135884|editor-last=Hull|editor-first=M.S.|edition=3rd|location=Oxford|pages=83–117|chapter=A Nanoinformatics Approach to Safety, Health, Well-being, and Productivity|doi=10.1016/B978-0-12-813588-4.00005-1|editor-last2=Bowman|editor-first2=D.M.}}</ref>[[File:Nanoinformatics as a Life Cycle.jpg|thumb|A graphical representation of a working definition of nanoinformatics as a life-cycle process]]

Although nanotechnology is the subject of significant experimentation, mostmuch of the data isare not stored in a standardized formatformats or sharedbroadly accessible. Nanoinformatics initiatives seek to coordinate developments of data standards and informatics methods.<ref name=":1" />

In the context of information science, an [[Ontology (information science)|ontology]] is a formal [[Representation (systemics)|representation]] of knowledge within a [[Domain of discourse|domain]], using hierarchies of terms including their definitions, attributedattributes, and relations. Ontologies provide a common terminology in a machine-readable framework that facilitates sharing and [[Knowledge discovery|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.<ref name=":0" /><ref>{{cite journal |last1=Maojo |first1=Victor |last2=Fritts |first2=Martin |last3=Martin-Sanchez |first3=Fernando |last4=De la Iglesia |first4=Diana |last5=Cachau |first5=Raul E. |last6=Garcia-Remesal |first6=Miguel |last7=Crespo |first7=Jose |last8=Mitchell |first8=Joyce A. |last9=Anguita |first9=Alberto |last10=Baker |first10=Nathan |last11=Barreiro |first11=Jose Maria |last12=Benitez |first12=Sonia E. |last13=De la Calle |first13=Guillermo |last14=Facelli |first14=Julio C. |last15=Ghazal |first15=Peter |last16=Geissbuhler |first16=Antoine |last17=Gonzalez-Nilo |first17=Fernando |last18=Graf |first18=Norbert |last19=Grangeat |first19=Pierre |last20=Hermosilla |first20=Isabel |last21=Hussein |first21=Rada |last22=Kern |first22=Josipa |last23=Koch |first23=Sabine |last24=Legre |first24=Yannick |last25=Lopez-Alonso |first25=Victoria |last26=Lopez-Campos |first26=Guillermo |last27=Milanesi |first27=Luciano |last28=Moustakis |first28=Vassilis |last29=Munteanu |first29=Cristian |last30=Otero |first30=Paula |last31=Pazos |first31=Alejandro |last32=Perez-Rey |first32=David |last33=Potamias |first33=George |last34=Sanz |first34=Ferran |last35=Kulikowski |first35=Casimir |title=Nanoinformatics: developing new computing applications for nanomedicine |journal=Computing |date=7 March 2012 |volume=94 |issue=6 |pages=521–539 |doi=10.1007/s00607-012-0191-2|pmid=22942787 |pmc=3430140 |s2cid=1770704 }}</ref>

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]].<ref name=":0">{{cite journal |last1=Thomas |first1=Dennis G. |last2=Pappu |first2=Rohit V. |last3=Baker |first3=Nathan A. |title=NanoParticle Ontology for cancer nanotechnology research |journal=Journal of Biomedical Informatics |date=February 2011 |volume=44 |issue=1 |pages=59–74 |doi=10.1016/j.jbi.2010.03.001|pmid=20211274 |pmc=3042056 }}</ref> 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]].<ref>{{cite journal|last1=Hastings|first1=Janna|last2=Jeliazkova|first2=Nina|last3=Owen|first3=Gareth|last4=Tsiliki|first4=Georgia|last5=Munteanu|first5=Cristian R|last6=Steinbeck|first6=Christoph|last7=Willighagen|first7=Egon|date=21 March 2015|title=eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment|journal=Journal of Biomedical Semantics|volume=6|issue=1|pages=10|doi=10.1186/s13326-015-0005-5|pmid=25815161|pmc=4374589 |doi-access=free }}</ref>

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.<ref>{{Cite journal|lastlast1=Thomas|firstfirst1=Dennis G|last2=Gaheen|first2=Sharon|last3=Harper|first3=Stacey L|last4=Fritts|first4=Martin|last5=Klaessig|first5=Fred|last6=Hahn-Dantona|first6=Elizabeth|last7=Paik|first7=David|last8=Pan|first8=Sue|last9=Stafford|first9=Grace A|date=2013|title=ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format|url=http://bmcbiotechnol.biomedcentral.com/articles/10.1186/1472-6750-13-2|journal=BMC Biotechnology|language=en|volume=13|issue=1|pages=2|doi=10.1186/1472-6750-13-2|issn=1472-6750|pmc=3598649|pmid=23311978 |doi-access=free }}</ref><ref>{{cite journal |last1=Marchese Robinson |first1=Richard L |last2=Cronin |first2=Mark T D |last3=Richarz |first3=Andrea-Nicole |last4=Rallo |first4=Robert |title=An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology |journal=Beilstein Journal of Nanotechnology |date=5 October 2015 |volume=6 |pages=1978–1999 |doi=10.3762/bjnano.6.202|pmid=26665069 |pmc=4660926 }}</ref> based on the [[ISA-TAB]] metadata standard.<ref>{{cite journal |last1=González-Beltrán |first1=Alejandra |last2=Maguire |first2=Eamonn |last3=Sansone |first3=Susanna-Assunta |last4=Rocca-Serra |first4=Philippe |title=linkedISA: semantic representation of ISA-Tab experimental metadata |journal=BMC Bioinformatics |date=27 November 2014 |volume=15 |issue=S14 |pages=S4 |doi=10.1186/1471-2105-15-S14-S4|pmid=25472428 |pmc=4255742 |doi-access=free }}</ref> In Europe, other templates have been adopted that were developed by the [[Institute of Occupational Medicine]],<ref name=":6" /> and by the [[Joint Research Centre]] for the NANoREG project.<ref>{{cite book |last1=Totaro |first1=Sara |last2=Crutzen |first2=Hugues |last3=Sintes |first3=Juan Riego |title=Data logging templates for the environmental, health and safety assessment of nanomaterials |date=2017 |isbn=978-92-79-62614-2 |url=http://publications.jrc.ec.europa.eu/repository/handle/JRC103178 |access-date=30 May 2019}}</ref>

Nanoinformatics is not limited to aggregating and sharing information about nanotechnologies, but has many complementary tools, some originating from [[Cheminformatics|chemoinformatics]] and [[bioinformatics]].<ref>{{cite journal |last1=Melagraki |first1=Georgia |last2=Afantitis |first2=Antreas |title=Computational toxicology: From cheminformatics to nanoinformatics |journal=Food and Chemical Toxicology |date=February 2018 |volume=112 |pages=476–477 |doi=10.1016/j.fct.2018.01.014|pmid=29331732 }}</ref><ref>{{cite journal |last1=Panneerselvam |first1=Suresh |last2=Choi |first2=Sangdun |title=Nanoinformatics: Emerging Databases and Available Tools |journal=International Journal of Molecular Sciences |date=25 April 2014 |volume=15 |issue=5 |pages=7158–7182 |doi=10.3390/ijms15057158|pmid=24776761 |pmc=4057665 |doi-access=free }}</ref>

Nanoinformatics is especially applicableuseful toin 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.<ref name=":0" /> Nanoinformatics can enable [[structure–activity relationship]] modelling for nanoparticle-based drugs.<ref name=":0" /> Nanoinformatics and biomolecular nanomodeling provide a route for effective cancer treatment.<ref>{{Cite journal|lastlast1=Sharma|firstfirst1=Neha|last2=Sharma|first2=Mala|last3=Sajid Jamal|first3=Qazi M.|last4=Kamal|first4=Mohammad A.|last5=Akhtar|first5=Salman|date=2019-04-25|title=Nanoinformatics and biomolecular nanomodeling: a novel move en route for effective cancer treatment|url=https://www.ncbi.nlm.nih.gov/pubmed/31025282|journal=Environmental Science and Pollution Research International|volume=27|issue=16|pages=19127–19141|doi=10.1007/s11356-019-05152-8|issn=1614-7499|pmid=31025282|s2cid=133607980}}</ref> Nanoinformatics also enables a data-driven approach to the design of materials to meet health and environmental needs.<ref>{{Cite book|title=Nanotechnology Environmental Health and Safety: Risks, Regulation, and Management|last=Rajan|first=Krishnan|publisher=Elsevier|year=2018|isbn=978-0-12-813588-4|editor-last=Hull|editor-first=M.S.|edition=3rd|location=Oxford|pages=119-150119–150|chapter=Data-Driven Materials Design for Health and Environmental Needs|doi=10.1016/B978-0-12-813588-4.00005-1|editor-last2=Bowman|editor-first2=D.M.}}</ref>

Viewed as a workflow process,<ref [1]{{Citation needed|datename=May":7" 2019}},/> nanoinformatics deconstructs experimental studies using data, [[metadata]], [[Controlled vocabulary|controlled vocabularies]] and [[Ontology (information science)|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, [[Certified reference materials|reference materials]], [[Modelmodel organism|model organisms]]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.[2]<ref>{{CitationCite neededbook|datetitle=MaySpringer 2019handbook of model-based science|last1=Frigg|first1=Roman|last2=Nguyen|first2=James|publisher=Springer|year=2017|isbn=9783319305264|editor-last=Magnani|editor-first=Lorenzo|location=Cham, Switzerland|pages=49–102|chapter=Models and representation|oclc=987910975|editor-last2=Bertolotti|editor-first2=Tommaso}}</ref>

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 pharmacokinetic modelling|physiologically based toxicokinticstoxicokinetics]], PBTK).<ref>{{Cite book|title=Physiologically Based Pharmacokinetic (PBPK) Modeling and Simulations : [3Principles,4] Methods, and Applications in the Pharmaceutical Industry|last=Peters, Sheila Annie.|date=2011|publisher=Wiley|isbn=978-0470484067|location=Hoboken, N.J.|oclc=794619804}}</ref><ref>{{CitationCite neededjournal|last1=Fujita|first1=Toshio|last2=Winkler|first2=David A.|date=May2016-02-22|title=Understanding 2019the Roles of the "Two QSARs"|journal=Journal of Chemical Information and Modeling|volume=56|issue=2|pages=269–274|doi=10.1021/acs.jcim.5b00229|issn=1549-960X|pmid=26754147}}.</ref> Each of these has been explored for [[small molecule]] [[drug development]] with a supporting body of literature.

Communities active in nanoinformatics include the [[European Union]] [[EU NanoSafety Cluster|NanoSafety Cluster]],<ref>{{Cite web|url=https://www.nanosafetycluster.eu/|title=About the NanoSafety Cluster|last=|first=|date=|website=EU NanoSafety Cluster|archive-url=|archive-date=|dead-url=|access-date=2019-05-28}}</ref> The U.S. [[National Cancer Institute]] National Cancer Informatics Program's Nanotechnology Working Group,<ref>{{Cite web|url=https://nciphub.org/groups/nanowg|title=Nanotechnology Working Group|last=|first=|date=|website=National Cancer Informatics Program Hub|archive-url=|archive-date=|dead-url=|access-date=2019-05-28}}</ref><ref>{{Cite web|url=https://wiki.nci.nih.gov/display/ICR/Nanotechnology+Working+Group|title=Nanotechnology Working Group|last=|first=|date=|website=U.S. National Cancer Institute|archive-url=|archive-date=|dead-url=|access-date=2019-05-28}}</ref> and the US–EU Nanotechnology Communities of Research.<ref>{{Cite web|url=https://us-eu.org/|title=US–EU Nanotechnology Communities of Research|last=|first=|date=|website=US–EU Nanotechnology Communities of Research|language=en-US|archive-url=|archive-date=|dead-url=|access-date=2019-05-28}}</ref>[[File:Nanoinformatics Roles and Responsibilities.jpg|thumb|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:<ref name=":4" /><ref>{{Cite journal|lastlast1=Hendren|firstfirst1=Christine Ogilvie|last2=Powers|first2=Christina M.|last3=Hoover|first3=Mark D.|last4=Harper|first4=Stacey L.|date=2015|title=The Nanomaterial Data Curation Initiative: A collaborative approach to assessing, evaluating, and advancing the state of the field|url=https://www.ncbi.nlm.nih.gov/pubmed/26425427|journal=Beilstein Journal of Nanotechnology|volume=6|pages=1752–1762|doi=10.3762/bjnano.6.179|issn=2190-4286|pmid=26425427|viapmc=4578388}}</ref><ref>{{Cite journal|lastlast1=Woodall|firstfirst1=George M.|last2=Hoover|first2=Mark D.|last3=Williams|first3=Ronald|last4=Benedict|first4=Kristen|last5=Harper|first5=Martin|last6=Soo|first6=Jhy-Charm|last7=Jarabek|first7=Annie M.|last8=Stewart|first8=Michael J.|last9=Brown|first9=James S.|date=2017|title=Interpreting Mobile and Handheld Air Sensor Readings in Relation to Air Quality Standards and Health Effect Reference Values: Tackling the Challenges|url=https://www.ncbi.nlm.nih.gov/pubmed/29093969|journal=Atmosphere|volume=8|issue=10|pages=182|doi=10.3390/atmos8100182|issn=2073-4433|pmid=29093969|viapmc=5662140|bibcode=2017Atmos...8..182W|doi-access=free}}</ref>

One of the first mentions of nanoinformatics was in the context of handling information about nanotechnology.<ref>{{cite journal|last1=Porter|first1=Alan L.|last2=Youtie|first2=Jan|last3=Shapira|first3=Philip|last4=Schoeneck|first4=David J.|date=3 August 2007|title=Refining search terms for nanotechnology|journal=Journal of Nanoparticle Research|volume=10|issue=5|pages=715–728|doi=10.1007/s11051-007-9266-y|s2cid=56232588}}</ref>

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.<ref name=":5">{{Cite book|url=https://www.hsl.gov.uk/media/394200/nanosymrep_final.pdf|title=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.|publisher=Health and Safety Laboratory|year=2004|editor-last=Mark|editor-first=David|location=Buxton, UK}}</ref> The workshop report<ref name=":5" /> included a presentation on Information Management for Nanotechnology Safety and Health<ref>{{Cite book|chapter-url=https://www.hsl.gov.uk/media/394200/nanosymrep_final.pdf|title=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|last1=Hoover|first1=Mark D.|last2=Miller|first2=Arthur L.|last3=Lowe|first3=Nathan T.|last4=Stefaniak|first4=Aleksandr B.|last5=Day|first5=Gregory L.|last6=Linch|first6=Kenneth D.|publisher=Health and Safety Laboratory|year=2004|editor-last=Mark|editor-first=David|location=Buxton, UK|pages=110|chapter=Information Management for Nanotechnology Safety and Health}}</ref> 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.<ref>{{Cite journal|last1=Miller|first1=Arthur L.|last2=Hoover|first2=Mark D.|last3=Mitchell|first3=David M.|last4=Stapleton|first4=Brian P.|date=2007|title=The Nanoparticle Information Library (NIL): a prototype for linking and sharing emerging data|journal=Journal of Occupational and Environmental Hygiene|volume=4|issue=12|pages=D131–134|doi=10.1080/15459620701683947|issn=1545-9624|pmid=17924276|s2cid=7518070}}</ref>

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