Chang, Jiakang

Drakakis, Georgios

Ehrhart, Friederike

Gebele, Denis

Helma, Christoph

Jeliazkova, Nina

Kohonen, Pekka

Nymark, Penny

Owen, Gareth

Rautenberg, Micha

Rieswijk, Linda

Sarimveis, Haralambos

Willighagen, Egon

English

Maastricht University Research Portal

   Answering scientific questions with linked Europeannanosafety dataCitation for published version (APA):Willighagen, E., Rautenberg, M., Gebele, D., Rieswijk, L., Ehrhart, F., Chang, J., Drakakis, G., Nymark,P., Kohonen, P., Owen, G., Sarimveis, H., Helma, C., & Jeliazkova, N. (2016). Answering scientificquestions with linked European nanosafety data. In Semantic Web Applications and Tools for LifeSciences 2016 (Vol. 1795). Article 126520 https://ceur-ws.org/Vol-1795/paper40.pdfDocument status and date:Published: 01/01/2016Document Version:Publisher's PDF, also known as Version of recordDocument license:TavernePlease check the document version of this publication:• A submitted manuscript is the version of the article upon submission and before peer-review. There canbe important differences between the submitted version and the official published version of record.People interested in the research are advised to contact the author for the final version of the publication,or visit the DOI to the publisher's website.• The final author version and the galley proof are versions of the publication after peer review.• The final published version features the final layout of the paper including the volume, issue and pagenumbers.Link to publicationGeneral rightsCopyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyrightowners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with theserights.• Users may download and print one copy of any publication from the public portal for the purpose of private study or research.• You may not further distribute the material or use it for any profit-making activity or commercial gain• You may freely distribute the URL identifying the publication in the public portal.If the publication is distributed under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license above,please follow below link for the End User Agreement:www.umlib.nl/taverne-licenseTake down policyIf you believe that this document breaches copyright please contact us at:repository@maastrichtuniversity.nlproviding details and we will investigate your claim.Download date: 13 Dec. 2023Answering scientific questions with linkedEuropean nanosafety dataEgon Willighagen1, Micha Rautenberg2, Denis Gebele2, Linda Rieswijk1,Friederike Ehrhart1, Jiakang Chang3, Georgios Drakakis4, Penny Nymark5,Pekka Kohonen5, Gareth Owen3, Haralambos Sarimveis4, Christoph Helma2,and Nina Jeliazkova61 Maastricht University, Maastricht, NL2 in silico toxicology gmbh, Freiburg, DE3 EMBL-EBI, Hinxton, UK4 National Technical University of Athens, Athens, GR5 Misvik Biology, Turku, FI6 IdeaConsult Ltd., Sofia, BGNanomaterials are increasingly used in healthcare and consumer products.The European community seeks solutions to assess the safety of these materialswith experimental research data. Ideally, read across and predictive toxicologyapproaches can then be used to answer questions if a class of metal oxides isgenotoxic or not. If successful, this will replace animal testing in bringing newnanomaterials to the market.The eNanoMapper project (http://enanomapper.net/) is an FP7 project de-veloping an ontology and database solutions for the data generated in the EUNanoSafety Cluster [2, 3]. This includes extracts of experimental data from,for example, cell line experiments, environmental toxicity studies, and high-throughput screening results. More important, however, is that this data is nolonger static but can be queried and analysed. That is, to make the best use ofthis data, integration with other life science databases is needed, such as proteinsequence database like Uniprot and compound databases such as ChEMBL [7],UniProt [5] and PubChem [1]. Doing so allows us to test scientific hypothesessuch as about the genotoxicity of metal oxides, whether chemically similar nano-materials have similar bioactivities, or whether protein coronas contain prefer-ably proteins involved in specific biological processes.Semantic Web standards are an increasingly central interoperability layerlinking experimental data to scientific knowledge. eNanoMapper has been work-ing on extending the semantics of the database software to import and exportdata in a serialization based on the Resource Description Framework (RDF) andthe eNanoMapper ontology. The RDF data is made available as dereferenceabledata and via a SPARQL endpoint (https://sparql.enanomapper.net/) and witha graphical query interface (https://query.enanomapper.net/). These technolo-gies are then used to support the research data management in the community.First, data completeness [4] is checked by using SPARQL queries, thereby high-lighting missing data, and allowing support of pattern recognition [6]. Second,the scientific questions predefined by the eNanoMapper project, such as men-tioned earlier in this abstract, are supported by SPARQL queries aggregatingthe relevant data. Finally, the eNanoMapper RDF is enriched with links to otherLinked Open Data Cloud resources (e.g. ChEMBL, PubChem) to support fur-ther nanosafety research.Source code for various components of this work are available from GitHubat https://github.com/enanomapper/.References1. Fu, G., Batchelor, C., Dumontier, M., Hastings, J., Willighagen, E., Bolton, E.: Pub-ChemRDF: towards the semantic annotation of PubChem compound and substancedatabases. Journal of Cheminformatics 7(1), 34+ (Jul 2015)2. Hastings, J., Jeliazkova, N., Owen, G., Tsiliki, G., Munteanu, C.R., Steinbeck, C.,Willighagen, E.: eNanoMapper: harnessing ontologies to enable data integrationfor nanomaterial risk assessment. Journal of Biomedical Semantics 6(1), 10+ (Mar2015)3. Jeliazkova, N., Chomenidis, C., Doganis, P., Fadeel, B., Grafström, R., Hardy, B.,Hastings, J., Hegi, M., Jeliazkov, V., Kochev, N., Kohonen, P., Munteanu, C.R.,Sarimveis, H., Smeets, B., Sopasakis, P., Tsiliki, G., Vorgrimmler, D., Willigha-gen, E.: The eNanoMapper database for nanomaterial safety information. BeilsteinJournal of Nanotechnology 6, 1609–1634 (Jul 2015)4. Marchese Robinson, R.L., Lynch, I., Peijnenburg, W., Rumble, J., Klaessig, F., Mar-quardt, C., Rauscher, H., Puzyn, T., Purian, R., Åberg, C., Karcher, S., Vriens, H.,Hoet, P., Hoover, M.D., Hendren, C.O., Harper, S.L.: How should the completenessand quality of curated nanomaterial data be evaluated? Nanoscale 8(19), 9919–9943(2016)5. The UniProt Consortium: Activities at the universal protein resource (UniProt).Nucleic Acids Research 42(D1), D191–D198 (Jan 2014)6. Willighagen, E., Alvarsson, J., Andersson, A., Eklund, M., Lampa, S., Lapins, M.,Spjuth, O., Wikberg, J.: Linking the resource description framework to cheminfor-matics and proteochemometrics. Journal of Biomedical Semantics 2(Suppl 1), S6+(2011)7. Willighagen, E.L., Waagmeester, A., Spjuth, O., Ansell, P., Williams, A.J.,Tkachenko, V., Hastings, J., Chen, B., Wild, D.J.: The ChEMBL database as linkedopen data. Journal of Cheminformatics 5(1), 23+ (May 2013)

Answering scientific questions with linked European nanosafety data

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Answering scientific questions with linked European nanosafety data

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