the ASINA project published a new paper, about making their project output more FAIR. e.g. https://doi.org/10.5281/zenodo.17052010 and context in https://doi.org/10.1016/j.impact.2025.100583

They have been using European Registry of Materials (ERM) identifier, and I have started updating two resources we started during #NanoCommons and #NanoSolveIT: https://nanocommons.github.io/datasets/ and https://nanocommons.github.io/erm-database/ (and still using #bioschemas)

ASINA Dataset: LC2_σ_Exposure_campaigns

ERM is added to the original dataset. Human safety - exposure dataset captures occupational exposure data from Near-Field (NF), Far-Field (FF), and inside spray coating machinery monitoring campaigns, providing insights into aerosol generation during NEP coating process. Measurements were obtained using Scanning Mobility Particle Sizer (SMPS) and Optical Particle Counter (OPC) to assess processing conditions and aerosol behaviour in industrial settings. Key aerosol-related parameters include particle number concentration in NF as an indicator of worker exposure, with SDs. Background conditions were assessed across various operational states, including when the spray process was inactive, ventilation running, and oven in operation. Particle size information of the process emissions in NF provides insight into the dynamic behaviour of aerosol particles indoors and in the human lungs. NM mass concentrations were measured in NF, inside the spray coating, and FF using Teflon filters, with Ti concentrations analysed by ICP-MS. Values were normalized by air volume (m³) to calculate NM mass concentrations (µg/m³), with SDs reflecting variability. The metadata folder contains extensive raw data, structured across three monitoring campaigns, with both on-line and off-line measurements in time-series formats. It includes NANEOS and OPC data, along with detailed records of additional parameters, offering a comprehensive source for exposure analysis. A detailed descriptor breakdown in Table S9. It is important to note that some metadata files contain additional data from monitoring campaigns; however, the necessary information to include the key descriptors that define each experiment was not available. As a result, these data could not be integrated into the Descriptors tab, where all results were systematically merged. This limitation affects the ability to directly link certain metadata records to the structured dataset but does not compromise the availability of raw exposure data. 

Zenodo

In 2 weeks from now, Ammar Ammar will defend his PhD thesis on "Enhancing the Interoperability and Reusability of Nanosafety Data" at Maastricht University. See also https://scholar.google.com/citations?user=8ZmXyZcAAAAJ&hl=en&inst=13291755310766122872&oi=ao

Following the defense, we will hold a mini-symposium around the topic of his thesis, including talk by Jose Emilio Labra Gayo. Ammar's research was part of the RiskGONE Project and #NanoSolveIT projects.

Sign up here: https://edu.nl/whawy

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

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

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
I indexed three more #NanoSolveIT datasets for their European Registry of Materials identifiers. We now have 163 identifiers in the databases, linking to project deliverables, data sets (so, 3 more today), articles, and other online resources. https://nanocommons.github.io/erm-database/ #chemistry
ERM Identifier Database

This database provides information about materials with an European Registry of Materials (ERM) identifer for which information was disclosed.

ERM Identifier Database

The EU NanoSafety Cluster has now released more then 50 open-licensed datasets about #nanosafety: https://nanocommons.github.io/datasets/

We passed this milestone by a big release by the #NanoSolveIT project during their final meeting in August.

#fairData #openData #chemistry #biology

datasets

Overview of archived datasets with an open license

datasets

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
it's a bit running from meeting to meeting right now, but the #nanosolveit project meeting and #osf2023nl are only just over but already packing for #lipidhack23

In my way to the next meeting #nsit2023

This is the final #NanoSolveIT meeting, in which we worked in new solutions for FAIR nanosafety data, machine readable Reuse metrics linked to real use cases, knowledge graphs to support the research, and general RSE work, like better systems biology solutions for the cloud