eNanoMapper - A Database and Ontology Framework for Nanomaterials Design and Safety Assessment
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Enanomapper is a collaborative project aimed at creating a database and ontology framework for the design and safety assessment of engineered nanomaterials (ENMs). Key objectives include developing modular infrastructure for data management, creating ontologies for ENM categorization, and facilitating interdisciplinary collaboration in nanoscience and toxicology. The project involves multiple partners and emphasizes a linked data approach to promote safe-by-design development of nanomaterials.
![The Experimental graph
Source
Name
Characteristics
[organism]
Characteristics
[strain]
Protocol
REF
Sample
Name
Factor Value
[limiting
nutrient]
Factor
Value
[rate]
Unit
culture1 Saccharomyces
cerevisiae
FY1679 growth
protocol
C-0.07-
aliquot1
carbon 0.07 l/hour
culture4 Saccharomyces
cerevisiae
FY1679 growth
protocol
N-0.07-
aliquot1
nitrogen 0.07 l/hour
culture5 Saccharomyces
cerevisiae
FY1679 growth
protocol
N-0.1-
aliquot1
nitrogen 0.1 l/hour
Source name Sample Name
Protocol REF
Characteristics
[organism]
Processed by
Characteristics
[strain]
Factor Value
[limiting nutrient]
Factor Value
[rate] Unit
Protocol Parameter](https://image.slidesharecdn.com/150813enanomapperacsboston-150818141251-lva1-app6891/85/eNanoMapper-A-Database-and-Ontology-Framework-for-Nanomaterials-Design-and-Safety-Assessment-19-320.jpg)
![References
Jeliazkova N, Chomenidis C, Doganis P, Fadeel B, Grafström R, Hardy B, Hastings J, Hegi M,
Jeliazkov V, Kochev N, Kohonen P, Munteanu CR, Sarimveis H, Smeets B, Sopasakis P, Tsiliki
G, Vorgrimmler D, Willighagen E. The eNanoMapper database for nanomaterial safety
information. Beilstein Journal of Nanotechnology, 2015 [in press]
Hastings J, Jeliazkova N, Owen O, Tsiliki G, Munteanu CR, Steinbeck C, Willighagen E.
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk
assessment, Journal of Biomedical Semantics, 2015, 6:10
Hastings J, Willighagen E, Owen G, Jeliazkova N, Steinbeck C. eNanoMapper: Opportunities
and challenges in using ontologies to enable data integration for nanomaterial risk
assessment. In Proceedings of the ISMB Bio-Ontologies SIG meeting, Boston, USA, July 11-
12 2014.
Kohonen P, Ceder R, Smit I, Hongisto V, Myatt G, Hardy B, Spjuth O, Grafström R. Cancer
biology, toxicology and alternative methods development go hand-in-hand. Basic Clin
Pharmacol Toxicol. 2014 Jul;115(1):50-8.](https://image.slidesharecdn.com/150813enanomapperacsboston-150818141251-lva1-app6891/85/eNanoMapper-A-Database-and-Ontology-Framework-for-Nanomaterials-Design-and-Safety-Assessment-34-320.jpg)
eNanoMapper - A Database and Ontology Framework for Nanomaterials Design and Safety Assessment
- 1. eNanoMapper - A Database and Ontology Framework for Nanomaterials Design and Safety Assessment ACS Meeting, Boston, USA, 18 August 2015 Presented by Barry Hardy (Douglas Connect) as Coordinator and in representation of work carried out by eNanoMapper and its partners. Any opinions or comments are made as personal statements and are not to taken as indicating any official position of any organisation. Barry dot Hardy –(at)/- douglasconnect dot com www.enanomapper.net
- 2. Collaborating Partners on eNanoMapper Douglas Connect, Switzerland (Coordinator) In Silico Toxicology, Switzerland Ideaconsult, Bulgaria Karolinska Instituet, Sweden VTT, Finland Maastricht University, Netherlands National Technical University of Athens, Greece Associate Partners EMBL-EBI, UK
- 3. Main objectives of eNanoMapper • Modular infrastructure for data storage, sharing and searching, based on open standards and semantic web technologies, minimum information standards and established security solutions • Development of ontologies for the categorisation and characterisation of Engineered Nanomaterials (ENMs) in collaboration with other projects • Creation of new computational models in nanomaterials safety through the implementation of interfaces for toxicity modelling and prediction algorithms which may process all data made available through eNanoMapper (e.g. using algorithms available from the OpenTox project or statistical/data mining software)
- 4. Main objectives of eNanoMapper • Meta analysis of nano-bio interactions supporting “safe-by- design” ENMs development by pursuing a Linked Data approach which integrates data and metadata originating from diverse sources within nanoscience, chemistry, biology and toxicology • Creation of tools for the exchange, quality assurance and reporting of research protocols and data for regulatory purposes • Creation of a community framework for interdisciplinary collaboration
- 5. OpenTox and Open Components and Standards Feature GET POST PUT DELETE Compound GET POST PUT DELETE Dataset GET POST PUT DELETE Ontology GET POST PUT DELETE Algorithm GET POST PUT DELETE Model GET POST PUT DELETE AppDomain GET POST PUT DELETE Validation GET POST PUT DELETE Report GET POST PUT DELETE www.opentox.org/dev/apis/api-1.2 Investigation (Study, Assay) GET POST PUT DELETE <-New API addition from ToxBank Authorisation & Authentication GET POST PUT DELETE
- 6. A Toxicology Ontology Roadmap • See perspectives and roadmap published in A Toxicology Ontology Roadmap ALTEX 29(2), 129- 137 and Toxicology Ontology Perspectives 139 - 156 (2012) • Available online in Open Access mode from www.altex.ch • Barry Hardy (Douglas Connect and OpenTox), Gordana Apic (Cambridge Cell Networks), Philip Carthew (Unilever), Dominic Clark (EMBL-EBI), David Cook (AstraZeneca), Ian Dix (AstraZeneca & Pistoia Alliance), Sylvia Escher (Fraunhofer Institute for Toxicology & Experimental Medicine), Janna Hastings (EMBL-EBI), David J. Heard (Novartis), Nina Jeliazkova (Ideaconsult), Philip Judson (Lhasa Ltd.), Sherri Matis-Mitchell (AstraZeneca), Dragana Mitic (Cambridge Cell Networks), Glenn Myatt (Leadscope), Imran Shah (US EPA), Ola Spjuth (University of Uppsala), Olga Tcheremenskaia (Istituto Superiore di Sanità), Luca Toldo (Merck KGaA), David Watson (Lhasa Ltd.), Andrew White (Unilever), Chihae Yang (Altamira) Based on Proceedings from the Toxicology Ontology Roadmap Workshop EMBL-EBI Industry Programme Workshop 16 -17th November 2010, Hinxton, UK
- 8. Ontology assembled from multiple sources 4,456 classes
- 10. eNanoMapper Ontology in BioPortal bioportal.bioontology.org/ontologies/ENM
- 11. Browse classes
- 12. View metadata (synonyms, ID)
- 13. eNanoMapper Ontology in Protegé Open in Protegé purl.enanomapper.org/onto/enanomapper.owl
- 14. Browse, Search
- 17. REST Application Programming Interface API documentation (Swagger-UI) Interactive API queries 17 http://enanomapper.github.io/API/
- 18. Prototype database (NM components) 18 Protein Corona Data set DOI:10.1021/nn406018q Coating Coating Core data.enanomapper.net
- 19. The Experimental graph Source Name Characteristics [organism] Characteristics [strain] Protocol REF Sample Name Factor Value [limiting nutrient] Factor Value [rate] Unit culture1 Saccharomyces cerevisiae FY1679 growth protocol C-0.07- aliquot1 carbon 0.07 l/hour culture4 Saccharomyces cerevisiae FY1679 growth protocol N-0.07- aliquot1 nitrogen 0.07 l/hour culture5 Saccharomyces cerevisiae FY1679 growth protocol N-0.1- aliquot1 nitrogen 0.1 l/hour Source name Sample Name Protocol REF Characteristics [organism] Processed by Characteristics [strain] Factor Value [limiting nutrient] Factor Value [rate] Unit Protocol Parameter
- 20. ENM data in Ambit 20
- 21. Protocol service
- 22. Analysis & Modelling http://enanomapper.ntua.gr:8080/jaqpot/swagger/ https://github.com/enanomapper/imageAnalysis , First prototype: http://enanomapper.ntua.gr:8880/imageAnalysis/
- 24. Modelling Infrastructure • Web service standards for modelling: http://enanomapper.ntua.gr:8080/jaqpot/swagger/
- 26. Development of NanoQSAR models for predicting cell association using corona information (OpenTox models) 26
- 27. Prototype database: Phys chem & Tox (NanoWiki) 27
- 28. Importing data: NanoWiki • Export data from an existing database • Import data into the eNM platform • Test if it works 28
- 31. Chemical substructure search 31 NanoWiki Protein Corona dataset Coating
- 32. NanoEHS – EU-US Communities of Research 1. Exposure 2. Eco Toxicity 3. Risk Assessment 4. Risk Management 5. Human Health 6. Data and Modelling 7. Characterisation Encourage joint programs of work that leverage EU and US resources.
- 33. Project partners
- 34. References Jeliazkova N, Chomenidis C, Doganis P, Fadeel B, Grafström R, Hardy B, Hastings J, Hegi M, Jeliazkov V, Kochev N, Kohonen P, Munteanu CR, Sarimveis H, Smeets B, Sopasakis P, Tsiliki G, Vorgrimmler D, Willighagen E. The eNanoMapper database for nanomaterial safety information. Beilstein Journal of Nanotechnology, 2015 [in press] Hastings J, Jeliazkova N, Owen O, Tsiliki G, Munteanu CR, Steinbeck C, Willighagen E. eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment, Journal of Biomedical Semantics, 2015, 6:10 Hastings J, Willighagen E, Owen G, Jeliazkova N, Steinbeck C. eNanoMapper: Opportunities and challenges in using ontologies to enable data integration for nanomaterial risk assessment. In Proceedings of the ISMB Bio-Ontologies SIG meeting, Boston, USA, July 11- 12 2014. Kohonen P, Ceder R, Smit I, Hongisto V, Myatt G, Hardy B, Spjuth O, Grafström R. Cancer biology, toxicology and alternative methods development go hand-in-hand. Basic Clin Pharmacol Toxicol. 2014 Jul;115(1):50-8.
- 35. FP7-eNanoMapper "eNanoMapper - A Database and Ontology Framework for Nanomaterials Design and Safety Assessment” • Grant Agreement: 604134 • Duration: 36 months (1 Feb 2014 – 31 Jan 2016)