Making something FAIR is hard, particularly when you do more than making something findable. We’ve seen before that\nmaking something usefully findable requires deep indexing,\nand already that continues to be difficult, because we are not seeing it enough.\nSo, when I thought convert a paper led by Hoet’s lab in Leuven\ninto machine-actionable RDF to make it FAIR, I gravely underestimated the amount of work.\nJeaphianne et al. did an awesome job on this work\n(doi:10.1186/s13321-024-00833-0).
\n\nThe idea was simple: write up which nanomaterial (type) activates which molecular initiating event.\nIt would simply annotate each material with a unique identifier to link it to databases like\neNanoMapper and NanoCommons\nand it would use unique identifiers for the\nAdverse Outcome Pathway) (AOP) key events.\nAs such, it would make a direct link in the growing linked open data cloud between the AOPs\nand the nanomaterial databases.
\n\nUnfortunately, it was quickly discovered that actually reusing this new datasets requires rich annotation (metadata!)\nof the materials and the materials from the source paper were not yet in material databases.\nAnd then the cumbersome start was started, resulting in a very rich data model describing the\nkey events, the materials, the assays used, and the original papers themselves:
\n\n\n
Ammar, A., Bonaretti, S., Winckers, L., Quik, J., Bakker, M., Maier, D., Lynch, I., van Rijn, J., & Willighagen, E. (2020). A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences.
Nanomaterials,
10(10), 2068. https://doi.org/10.3390/nano10102068
CrossRef Scholia\n
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., & Willighagen, E. (2015). The eNanoMapper database for nanomaterial safety information.
Beilstein Journal of Nanotechnology,
6, 1609–1634. https://doi.org/10.3762/bjnano.6.165
CrossRef Scholia\n
Maier, D., Exner, T. E., Papadiamantis, A. G., Ammar, A., Tsoumanis, A., Doganis, P., Rouse, I., Slater, L. T., Gkoutos, G. V., Jeliazkova, N., Ilgenfritz, H., Ziegler, M., Gerhard, B., Kopetsky, S., Joshi, D., Walker, L., Svendsen, C., Sarimveis, H., Lobaskin, V., … Lynch, I. (2023). Harmonising knowledge for safer materials via the “NanoCommons” Knowledge Base.
Frontiers in Physics,
11. https://doi.org/10.3389/fphy.2023.1271842
CrossRef Scholia\n
Martens, M., Evelo, C. T., & Willighagen, E. L. (2022). Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content.
Applied In Vitro Toxicology,
8(1), 2–13. https://doi.org/10.1089/aivt.2021.0010
CrossRef Scholia\n
Murugadoss, S. (2021). A strategy towards the generation of testable adverse outcome pathways for nanomaterials.
ALTEX. https://doi.org/10.14573/altex.2102191
CrossRef Scholia\n
van Rijn, J. P. M., Martens, M., Ammar, A., Cimpan, M. R., Fessard, V., Hoet, P., Jeliazkova, N., Murugadoss, S., Vinković Vrček, I., & Willighagen, E. L. (2024). From papers to RDF-based integration of physicochemical data and adverse outcome pathways for nanomaterials.
Journal of Cheminformatics,
16(1). https://doi.org/10.1186/s13321-024-00833-0
CrossRef Scholia\n
van Rijn, J., Afantitis, A., Culha, M., Dusinska, M., Exner, T. E., Jeliazkova, N., Longhin, E. M., Lynch, I., Melagraki, G., Nymark, P., Papadiamantis, A. G., Winkler, D. A., Yilmaz, H., & Willighagen, E. (2022). European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials.
Journal of Cheminformatics,
14(1). https://doi.org/10.1186/s13321-022-00614-7
CrossRef Scholia\n
![\"\"](\"/assets/images/13321_2024_833_Fig1_HTML.png\")