Egon WillighagenMay 21, 2024
new blog: "New paper: From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials" http://chem-bla-ics.linkedchemistry.info/2024/05/20/from-papers-to-rdf.html #riskGone #NanoSolveIT
New paper: From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials

Making something FAIR is hard, particularly when you do more than making something findable. We’ve seen before that making something usefully findable requires deep indexing, and already that continues to be difficult, because we are not seeing it enough. So, when I thought convert a paper led by Hoet’s lab in Leuven into machine-actionable RDF to make it FAIR, I gravely underestimated the amount of work. Jeaphianne et al. did an awesome job on this work (doi:10.1186/s13321-024-00833-0).

chem-bla-ics
Egon WillighagenMay 16, 2024

happy to see this paper by Ammar Ammar is now out!

"FAIR assessment of nanosafety data reusability with community standards" https://doi.org/10.1038/s41597-024-03324-x

Do we really need another FAIR framework?

YES! This one directly links maturity with reuse case scenarios. Data can be mature enough for one reuse, while be immature for another. This paper brings this open door into the semantic world. #fair #openscience #reuse #nanosafetyCluster #nanoSolveIT #riskGone #chemistry

BiGCaT BioinformaticsMay 2, 2024
new paper by Jeaphianne van Rijn et al.: "From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials" https://doi.org/10.1186/s13321-024-00833-0 #nanomaterial #RiskGone #NanoSolveIT #SbD4Nano #rdf
From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials - Journal of Cheminformatics

Abstract Adverse Outcome Pathways (AOPs) have been proposed to facilitate mechanistic understanding of interactions of chemicals/materials with biological systems. Each AOP starts with a molecular initiating event (MIE) and possibly ends with adverse outcome(s) (AOs) via a series of key events (KEs). So far, the interaction of engineered nanomaterials (ENMs) with biomolecules, biomembranes, cells, and biological structures, in general, is not yet fully elucidated. There is also a huge lack of information on which AOPs are ENMs-relevant or -specific, despite numerous published data on toxicological endpoints they trigger, such as oxidative stress and inflammation. We propose to integrate related data and knowledge recently collected. Our approach combines the annotation of nanomaterials and their MIEs with ontology annotation to demonstrate how we can then query AOPs and biological pathway information for these materials. We conclude that a FAIR (Findable, Accessible, Interoperable, Reusable) representation of the ENM-MIE knowledge simplifies integration with other knowledge. Scientific contribution This study introduces a new database linking nanomaterial stressors to the first known MIE or KE. Second, it presents a reproducible workflow to analyze and summarize this knowledge. Third, this work extends the use of semantic web technologies to the field of nanoinformatics and nanosafety.

BioMed Central
Egon WillighagenMar 5, 2024
Maria Dusinska is given a very concise and detailed overview of risk assessment for nanomaterials #ANTHOS24 #toxicology #RiskGone #Sabydoma
Egon WillighagenSep 17, 2023

new blog post ("Using FAIR to select data for reuse" https://chem-bla-ics.linkedchemistry.info/2023/09/17/using-fair-for-reuse.html), about very interesting research by Irini Furxhi, Ammar Ammar, me, and others: "A data reusability assessment in the nanosafety domain based on the NSDRA framework followed by an exploratory quantitative structure activity relationships (QSAR) modeling targeting cellular viability" https://doi.org/10.1016/j.impact.2023.100475

#FAIR #chemistry #nanosolveit #RiskGONE

Using FAIR to select data for reuse

This paper got published in July already, but I had not had the time yet to blog about this exciting work by Irini Furxhi and Ammar Ammar: A data reusability assessment in the nanosafety domain based on the NSDRA framework followed by an exploratory quantitative structure activity relationships (QSAR) modeling targeting cellular viability (doi:10.1016/j.impact.2023.100475)

chem-bla-ics
Show threadEgon WillighagenJun 15, 2023
@iseult is now discussing the #RiskGone results from WP6. One of the systems they use for toxicity is Daphnia... for future use, we've started creating @wikipathways pages for molecular processes, thanks to Marvin's work, linkable to AOPs. https://daphnia.wikipathways.org/
Redirecting…

Show threadEgon WillighagenJun 15, 2023

some #RiskGone project results are reported onn the @EU_Commission CORDIS database entry for the project: https://cordis.europa.eu/project/id/814425/results

I think more will follow soon.

Risk Governance of Nanotechnology | RiskGONE Project | Results | H2020 | CORDIS | European Commission

Deliverables, publications, datasets, software, exploitable results

CORDIS | European Commission
Egon WillighagenJun 15, 2023
attending the final #RiskGONE meeting. listening the results presentations of the work packages