Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations

Karcher, Sandra; Willighagen, Egon L.; Rumble, John; Ehrhart, Friederike; Evelo, Chris T.; Fritts, Martin; Gaheen, Sharon; Harper, Stacey L.; Hoover, Mark D.; Jeliazkova, Nina; Lewinski, Nastassja; Marchese Robinson, Richard L.; Mills, Karmann C.; Mustad, Axel P.; Thomas, Dennis G.; Tsiliki, Georgia; Hendren, Christine Ogilvie

doi:10.1016/j.impact.2017.11.002

Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations

Journal Article · Mon Jan 01 04:00:00 EST 2018 · NanoImpact

DOI:https://doi.org/10.1016/j.impact.2017.11.002· OSTI ID:1439666

Karcher, Sandra; Willighagen, Egon L.; Rumble, John; Ehrhart, Friederike; Evelo, Chris T.; Fritts, Martin; Gaheen, Sharon; Harper, Stacey L.; Hoover, Mark D.; Jeliazkova, Nina; Lewinski, Nastassja; Marchese Robinson, Richard L.; Mills, Karmann C.; Mustad, Axel P.; Thomas, Dennis G.; Tsiliki, Georgia; Hendren, Christine Ogilvie

Many groups within the broad field of nanoinformatics are already developing data repositories and analytical tools driven by their individual organizational goals. Integrating these data resources across disciplines and with non-nanotechnology resources can support multiple objectives by enabling the reuse of the same information. Integration can also serve as the impetus for novel scientific discoveries by providing the framework to support deeper data analyses. This article discusses current data integration practices in nanoinformatics and in comparable mature fields, and nanotechnology-specific challenges impacting data integration. Based on results from a nanoinformatics-community-wide survey, recommendations for achieving integration of existing operational nanotechnology resources are presented. Nanotechnology-specific data integration challenges, if effectively resolved, can foster the application and validation of nanotechnology within and across disciplines. This paper is one of a series of articles by the Nanomaterial Data Curation Initiative that address data issues such as data curation workflows, data completeness and quality, curator responsibilities, and metadata.

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (US)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1439666

Report Number(s):: PNNL-SA-128856

Journal Information:: NanoImpact, Journal Name: NanoImpact Journal Issue: C Vol. 9; ISSN 2452-0748

Country of Publication:: United States

Language:: English

References (63)

PubChem Substance and Compound databases Kim, Sunghwan; Thiessen, Paul A.; Bolton, Evan E. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv951	journal	September 2015
DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs Knox, C.; Law, V.; Jewison, T. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq1126	journal	November 2010
Application of an Informatics-Based Decision-Making Framework and Process to the Assessment of Radiation Safety in Nanotechnology Hoover, Mark D.; Myers, David S.; Cash, Leigh J. Health Physics, Vol. 108, Issue 2 https://doi.org/10.1097/HP.0000000000000250	journal	January 2015
Jaqpot Quattro: A Novel Computational Web Platform for Modeling and Analysis in Nanoinformatics Chomenidis, Charalampos; Drakakis, Georgios; Tsiliki, Georgia Journal of Chemical Information and Modeling, Vol. 57, Issue 9 https://doi.org/10.1021/acs.jcim.7b00223	journal	August 2017
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services van Iersel, Martijn P.; Pico, Alexander R.; Kelder, Thomas BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-5	journal	January 2010
A Database Perspective on Consuming Linked Data on the Web Hartig, Olaf; Langegger, Andreas Datenbank-Spektrum, Vol. 10, Issue 2 https://doi.org/10.1007/s13222-010-0021-7	journal	August 2010
The Semantic Web Berners-Lee, Tim; Hendler, James; Lassila, Ora Scientific American, Vol. 284, Issue 5 https://doi.org/10.1038/scientificamerican0501-34	journal	May 2001
Nanomaterial registry: database that captures the minimal information about nanomaterial physico-chemical characteristics Mills, Karmann C.; Murry, Damaris; Guzan, Kimberly A. Journal of Nanoparticle Research, Vol. 16, Issue 2 https://doi.org/10.1007/s11051-013-2219-8	journal	January 2014
Dependence of QSAR Models on the Selection of Trial Descriptor Sets: A Demonstration Using Nanotoxicity Endpoints of Decorated Nanotubes Shao, Chi-Yu; Chen, Sing-Zuo; Su, Bo-Han Journal of Chemical Information and Modeling, Vol. 53, Issue 1 https://doi.org/10.1021/ci3005308	journal	December 2012
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment Hastings, Janna; Jeliazkova, Nina; Owen, Gareth Journal of Biomedical Semantics, Vol. 6, Issue 1 https://doi.org/10.1186/s13326-015-0005-5	journal	March 2015
InChI, the IUPAC International Chemical Identifier Heller, Stephen R.; McNaught, Alan; Pletnev, Igor Journal of Cheminformatics, Vol. 7, Issue 1 https://doi.org/10.1186/s13321-015-0068-4	journal	May 2015
Current situation on the availability of nanostructure–biological activity data Oksel, C.; Ma, C. Y.; Wang, X. Z. Taylor & Francis https://doi.org/10.6084/m9.figshare.1292888.v2	dataset	January 2015
Environmental impacts of nanomaterials: providing comprehensive information on exposure, transport and ecotoxicity - the project DaNa2.0 Kühnel, Dana; Marquardt, Clarissa; Nau, Katja Environmental Sciences Europe, Vol. 26, Issue 1 https://doi.org/10.1186/s12302-014-0021-6	journal	October 2014
Emerging practices for mapping and linking life sciences data using RDF — A case series Marshall, M. Scott; Boyce, Richard; Deus, Helena F. Journal of Web Semantics, Vol. 14 https://doi.org/10.1016/j.websem.2012.02.003	journal	July 2012
The Nanoparticle Information Library (NIL): A Prototype for Linking and Sharing Emerging Data Miller, Arthur L.; Hoover, Mark D.; Mitchell, David M. Journal of Occupational and Environmental Hygiene, Vol. 4, Issue 12 https://doi.org/10.1080/15459620701683947	journal	October 2007
The European Commission's recommendation on the definition of nanomaterial makes an impact Rauscher, Hubert; Sokull-Klüttgen, Birgit; Stamm, Hermann Nanotoxicology, Vol. 7, Issue 7 https://doi.org/10.3109/17435390.2012.724724	journal	August 2012
The description of nanomaterials: A multi-disiciplinary uniform description system Rumble, John; Freiman, Steve; Teague, Clayton 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) https://doi.org/10.1109/BIBM.2014.6999372	conference	November 2014
A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury Kohonen, Pekka; Parkkinen, Juuso A.; Willighagen, Egon L. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15932	journal	July 2017
The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports Wohlgemuth, G.; Haldiya, P. K.; Willighagen, E. Bioinformatics, Vol. 26, Issue 20 https://doi.org/10.1093/bioinformatics/btq476	journal	September 2010
NanoParticle Ontology for cancer nanotechnology research Thomas, Dennis G.; Pappu, Rohit V.; Baker, Nathan A. Journal of Biomedical Informatics, Vol. 44, Issue 1 https://doi.org/10.1016/j.jbi.2010.03.001	journal	February 2011
Informatics and standards for nanomedicine technology Thomas, Dennis G.; Klaessig, Fred; Harper, Stacey L. Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology, Vol. 3, Issue 5 https://doi.org/10.1002/wnan.152	journal	June 2011
Bioconductor: open software development for computational biology and bioinformatics Gentleman, Robert C.; Carey, Vincent J.; Bates, Douglas M. Genome Biology, Vol. 5, Issue 10, p. R80 https://doi.org/10.1186/gb-2004-5-10-r80	journal	September 2004
AMBIT RESTful web services: an implementation of the OpenTox application programming interface Jeliazkova, Nina; Jeliazkov, Vedrin Journal of Cheminformatics, Vol. 3, Issue 1 https://doi.org/10.1186/1758-2946-3-18	journal	May 2011
A journey to Semantic Web query federation in the life sciences Cheung, Kei-Hoi; Frost, H. Robert; Marshall, M. Scott BMC Bioinformatics, Vol. 10, Issue S10 https://doi.org/10.1186/1471-2105-10-S10-S10	journal	October 2009
Chemical databases: curation or integration by user-defined equivalence? Hersey, Anne; Chambers, Jon; Bellis, Louisa Drug Discovery Today: Technologies, Vol. 14 https://doi.org/10.1016/j.ddtec.2015.01.005	journal	July 2015
Proactively designing nanomaterials to enhance performance and minimise hazard Harper, Stacey L.; Dahl, Jennifer A.; Maddux, Bettye L. S. International Journal of Nanotechnology, Vol. 5, Issue 1 https://doi.org/10.1504/IJNT.2008.016552	journal	January 2008
Minimum information about a microarray experiment (MIAME)—toward standards for microarray data Brazma, Alvis; Hingamp, Pascal; Quackenbush, John Nature Genetics, Vol. 29, Issue 4 https://doi.org/10.1038/ng1201-365	journal	December 2001
PubChem BioAssay: 2014 update Wang, Yanli; Suzek, Tugba; Zhang, Jian Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt978	journal	November 2013
The Nanomaterial Data Curation Initiative: A collaborative approach to assessing, evaluating, and advancing the state of the field Hendren, Christine Ogilvie; Powers, Christina M.; Hoover, Mark D. Beilstein Journal of Nanotechnology, Vol. 6 https://doi.org/10.3762/bjnano.6.179	journal	January 2015
Challenges and Opportunities of Open Data in Ecology Reichman, O. J.; Jones, M. B.; Schildhauer, M. P. Science, Vol. 331, Issue 6018 https://doi.org/10.1126/science.1197962	journal	February 2011
NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information Sioutos, Nicholas; Coronado, Sherri de; Haber, Margaret W. Journal of Biomedical Informatics, Vol. 40, Issue 1 https://doi.org/10.1016/j.jbi.2006.02.013	journal	February 2007
Extracting more value from data silos: using the semantic web to link chemistry and biology for innovation Eyres, Tim P. EMBnet.journal, Vol. 19, Issue B https://doi.org/10.14806/ej.19.b.725	journal	October 2013
Nanoscale reference materials for environmental, health and safety measurements: needs, gaps and opportunities Stefaniak, Aleksandr B.; Hackley, Vincent A.; Roebben, Gert Nanotoxicology, Vol. 7, Issue 8 https://doi.org/10.3109/17435390.2012.739664	journal	October 2012
ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format Thomas, Dennis G.; Gaheen, Sharon; Harper, Stacey L. BMC Biotechnology, Vol. 13, Issue 1 https://doi.org/10.1186/1472-6750-13-2	journal	January 2013
Nanocuration workflows: Establishing best practices for identifying, inputting, and sharing data to inform decisions on nanomaterials Powers, Christina M.; Mills, Karmann A.; Morris, Stephanie A. Beilstein Journal of Nanotechnology, Vol. 6 https://doi.org/10.3762/bjnano.6.189	journal	January 2015
An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology Marchese Robinson, Richard L.; Cronin, Mark T. D.; Richarz, Andrea-Nicole Beilstein Journal of Nanotechnology, Vol. 6 https://doi.org/10.3762/bjnano.6.202	journal	January 2015
Environmental impacts of nanomaterials: providing comprehensive information on exposure, transport and ecotoxicity - the project DaNa2.0 Kühnel, D.; Marquardt, C.; Nau, K. Karlsruhe https://doi.org/10.5445/ir/1000046381	text	January 2014
Bioconductor : open software development for computational biology and bioinformatics C., Gentleman, Robert; J., Carey, Vincent; M., Bates, Douglas BioMed Central https://doi.org/10.21256/zhaw-1907	text	January 2004
A Systematic Approach for Evaluating the Quality of Experimental Toxicological and Ecotoxicological Data Klimisch, H. -J; Andreae, M.; Tillmann, U. Regulatory Toxicology and Pharmacology, Vol. 25, Issue 1 https://doi.org/10.1006/rtph.1996.1076	journal	February 1997
A Definition Framework for the Terms Nanomaterial and Nanoparticle Boholm, Max; Arvidsson, Rickard NanoEthics, Vol. 10, Issue 1 https://doi.org/10.1007/s11569-015-0249-7	journal	January 2016
Linked open drug data for pharmaceutical research and development Samwald, Matthias; Jentzsch, Anja; Bouton, Christopher Journal of Cheminformatics, Vol. 3, Issue 1 https://doi.org/10.1186/1758-2946-3-19	journal	May 2011
UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers Chambers, Jon; Davies, Mark; Gaulton, Anna Journal of Cheminformatics, Vol. 6, Issue 1 https://doi.org/10.1186/s13321-014-0043-5	journal	September 2014
Nanotechnology in the real world: Redeveloping the nanomaterial consumer products inventory Vance, Marina E.; Kuiken, Todd; Vejerano, Eric P. Beilstein Journal of Nanotechnology, Vol. 6 https://doi.org/10.3762/bjnano.6.181	journal	January 2015
Data Sharing Longo, Dan L.; Drazen, Jeffrey M. New England Journal of Medicine, Vol. 374, Issue 3 https://doi.org/10.1056/NEJMe1516564	journal	January 2016
Toward principles for the design of ontologies used for knowledge sharing? Gruber, Thomas R. International Journal of Human-Computer Studies, Vol. 43, Issue 5-6 https://doi.org/10.1006/ijhc.1995.1081	journal	November 1995
How should the completeness and quality of curated nanomaterial data be evaluated? Marchese Robinson, Richard L.; Lynch, Iseult; Peijnenburg, Willie Nanoscale, Vol. 8, Issue 19 https://doi.org/10.1039/c5nr08944a	journal	January 2016
Current situation on the availability of nanostructure–biological activity data Oksel, C.; Ma, C. Y.; Wang, X. Z. SAR and QSAR in Environmental Research, Vol. 26, Issue 2 https://doi.org/10.1080/1062936X.2014.993702	journal	January 2015
ChEBI in 2016: Improved services and an expanding collection of metabolites Hastings, Janna; Owen, Gareth; Dekker, Adriano Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1031	journal	October 2015
The EBI RDF platform: linked open data for the life sciences Jupp, S.; Malone, J.; Bolleman, J. Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btt765	journal	January 2014
'Omics Data Sharing Field, D.; Sansone, S. -A.; Collis, A. Science, Vol. 326, Issue 5950 https://doi.org/10.1126/science.1180598	journal	October 2009
Considerations about the implementation of a public knowledge base regarding nanotechnology Kimmig, Daniel; Marquardt, Clarissa; Nau, Katja Computational Science & Discovery, Vol. 7, Issue 1 https://doi.org/10.1088/1749-4699/7/1/014001	journal	January 2014
The FAIR Guiding Principles for scientific data management and stewardship Wilkinson, Mark D.; Dumontier, Michel; Aalbersberg, IJsbrand Jan Scientific Data, Vol. 3, Issue 1 https://doi.org/10.1038/sdata.2016.18	journal	March 2016
Scientific Lenses to Support Multiple Views over Linked Chemistry Data Batchelor, Colin; Brenninkmeijer, Christian Y. A.; Chichester, Christine The Semantic Web – ISWC 2014 https://doi.org/10.1007/978-3-319-11964-9_7	book	January 2014
BioPortal: ontologies and integrated data resources at the click of a mouse Noy, N. F.; Shah, N. H.; Whetzel, P. L. Nucleic Acids Research, Vol. 37, Issue Web Server https://doi.org/10.1093/nar/gkp440	journal	May 2009
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification Juty, N.; Le Novere, N.; Laibe, C. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1097	journal	December 2011
Acute toxicity of 31 different nanoparticles to zebrafish (Danio rerio) tested in adulthood and in early life stages – comparative study Kovrižnych, Jevgenij A.; Sotníková, Ružena; Zeljenková, Dagmar Interdisciplinary Toxicology, Vol. 6, Issue 2 https://doi.org/10.2478/intox-2013-0012	journal	June 2013
The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web Hastings, Janna; Chepelev, Leonid; Willighagen, Egon PLoS ONE, Vol. 6, Issue 10 https://doi.org/10.1371/journal.pone.0025513	journal	October 2011
Extracting more value from data silos: using the semantic web to link chemistry and biology for innovation Eyres, Tim P. EMBnet.journal, Vol. 19, Issue B https://doi.org/10.14806/ej.19.B.725	journal	October 2013
The eNanoMapper database for nanomaterial safety information Jeliazkova, Nina; Chomenidis, Charalampos; Doganis, Philip Beilstein Journal of Nanotechnology, Vol. 6 https://doi.org/10.3762/bjnano.6.165	journal	January 2015
Entrez Gene: gene-centered information at NCBI Maglott, D. Nucleic Acids Research, Vol. 33, Issue Database issue https://doi.org/10.1093/nar/gki031	journal	December 2004
Open PHACTS: semantic interoperability for drug discovery Williams, Antony J.; Harland, Lee; Groth, Paul Drug Discovery Today, Vol. 17, Issue 21-22 https://doi.org/10.1016/j.drudis.2012.05.016	journal	November 2012
Impact of storage conditions and storage time on silver nanoparticles' physicochemical properties and implications for their biological effects Izak-Nau, E.; Huk, A.; Reidy, B. RSC Advances, Vol. 5, Issue 102 https://doi.org/10.1039/c5ra10187e	journal	January 2015
Impact of storage conditions and storage time on silver nanoparticles' physicochemical properties and implications for their biological effects Izak-Nau, E.; Huk, A.; Reidy, B. RSC Advances, Vol. 5, Issue 102 https://doi.org/10.1039/C5RA10187E	journal	January 2015

Cited By (11)

Practices and Trends of Machine Learning Application in Nanotoxicology Furxhi, Irini; Murphy, Finbarr; Mullins, Martin Nanomaterials, Vol. 10, Issue 1 https://doi.org/10.3390/nano10010116	journal	January 2020
Toward Rigorous Materials Production: New Approach Methodologies Have Extensive Potential to Improve Current Safety Assessment Practices Nymark, Penny; Bakker, Martine; Dekkers, Susan Small, Vol. 16, Issue 6 https://doi.org/10.1002/smll.201904749	journal	January 2020
Harmonizing across environmental nanomaterial testing media for increased comparability of nanomaterial datasets Geitner, Nicholas K.; Ogilvie Hendren, Christine; Cornelis, Geert Environmental Science: Nano, Vol. 7, Issue 1 https://doi.org/10.1039/c9en00448c	journal	January 2020
A Method for Extending Ontologies with Application to the Materials Science Domain Li, Huanyu; Armiento, Rickard; Lambrix, Patrick Data Science Journal, Vol. 18 https://doi.org/10.5334/dsj-2019-050	journal	January 2019
Computational Design of Nucleic Acid-Based Bioreceptor for Contaminants of Emerging Concern Arrigo, Patrizio; Baroni, Debora Sensors in Water Pollutants Monitoring: Role of Material https://doi.org/10.1007/978-981-15-0671-0_12	book	October 2019
Contribution of mesocosm testing to a single-step and exposure-driven environmental risk assessment of engineered nanomaterials Auffan, Mélanie; Masion, Armand; Mouneyrac, Catherine NanoImpact, Vol. 13 https://doi.org/10.1016/j.impact.2018.12.005	journal	January 2019
Fifteen years of nanoEHS research advances science and fosters a vibrant community Friedersdorf, Lisa E.; Bjorkland, Rhema; Klaper, Rebecca D. Nature Nanotechnology, Vol. 14, Issue 11 https://doi.org/10.1038/s41565-019-0574-z	journal	November 2019
Best practices from nano-risk analysis relevant for other emerging technologies Grieger, Khara; Jones, Jacob L.; Hansen, Steffen Foss Nature Nanotechnology, Vol. 14, Issue 11 https://doi.org/10.1038/s41565-019-0572-1	journal	November 2019
A One Health approach to managing the applications and implications of nanotechnologies in agriculture Lombi, Enzo; Donner, Erica; Dusinska, Maria Nature Nanotechnology, Vol. 14, Issue 6 https://doi.org/10.1038/s41565-019-0460-8	journal	June 2019
Nanotoxicology data for in silico tools: a literature review Furxhi, Irini; Murphy, Finbarr; Mullins, Martin Nanotoxicology, Vol. 14, Issue 5 https://doi.org/10.1080/17435390.2020.1729439	journal	February 2020
Building an International Consensus on Multi-Disciplinary Metadata Standards: A CODATA Case History in Nanotechnology Rumble, John; Broome, John; Hodson, Simon Data Science Journal, Vol. 18 https://doi.org/10.5334/dsj-2019-012	journal	January 2019

Similar Records

Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations

Journal Article · Wed Jan 10 19:00:00 EST 2018 · NanoImpact · OSTI ID:1737352

Standardizng Data

Journal Article · Mon Feb 04 23:00:00 EST 2013 · Nature Nanotechnology, 8(2):73-74 · OSTI ID:1063695

Nanotechnology: Promises and challenges for tomorrow

Conference · Mon Feb 28 23:00:00 EST 2000 · OSTI ID:752165

Related Subjects

data integration
databases
nanoinformatics
nanomaterials
nanotechnology
web services

Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations

Citation Formats

References (63)

Cited By (11)

Similar Records

Related Subjects