Authors: Martin Himly
Contributors: Marvin Martens, Haralambos Sarimveis, Philip Doganis, Iseult Lynch
Building on the hugely successful set of webinars and online training events that NanoCommons ran in 2020 as part of our adaption to the Covid-19 travel restrictions, a similar series of virtual training events and hackathons is planned for 2021. While the exact dates for some are still be finalised, we present here a teaser of what is coming your way! The formats will vary from webinar style presentations to more hands-on guided activities where the NanoCommons tools and services are presented and participants have the opportunity to work with real datasets and to apply the tools and approaches directly. Some of the successful events from last year will also be re-run this year to widen the pool of users for the tools and approaches.
On Tuesday 23rd March 2021, NanoCommons and NanoSolveIT will offer a webinar on the use of linked data resources such as WikiPathways and AOP-Wiki. Linked data is basically structured data which is interlinked with other data so it becomes more useful through semantic queries. One way of doing this is through the integration of databases through RDF (Resource Description Framework, the standard model for data interchange) using the newly developed User Interfaces for WikiPathways and AOP-Wiki, providing a variety of useful features to facilitate exploring the databases and linking their data with other resources. The new features include a flexible, auto-populated query panel, SPARQL syntax highlighting, permalinks for SPARQL queries, and full-screen mode. The webinar will focus on the usability of the interface by walking through the various functionalities, and showing a variety of example queries against the WikiPathways1 and AOP-Wiki data2. Furthermore, federated queries across resources will be executed to illustrate the strength of linked data. The webinar is for everyone who wants to learn how to use linked data resources such as WikiPathways and AOP-Wiki, and no preparations are necessary. The expected duration is 45 minutes with time for discussion and support with queries afterwards.
On Tuesday 13th April, 2021, NanoCommons will offer an entry-level workshop on in silico nanotoxicology, providing users with easy (no installations required) access to Jaqpot3, a powerful and versatile nanotoxicological in silico prediction platform, enabled through powerful Google Colab notebooks. Users will receive training from the expert team from the National Technical University of Athens, who developed the platform, on how to develop a Quantitative Structure-Activity Relationship (QSAR) model and publish it as a web application through the Jaqpot platform with minimal programming skills requirements. Models built on Jaqpot can be used over the graphical user interface or across platforms over the API and can be shared to groups with controlled access and rights.
Next, in May 2021 (exact date to be confirmed) NanoCommons and SmartNanoTox will offer a training session dedicated to the concept of adverse outcome pathways and molecular initiating events. A number of prediction models for molecular initiating events, such as (i) disruption of lung surfactant functionality, (ii) lysosomal destabilization, and (iii) oxidation of cell membrane have been generated by the SmartNanoTox team, waiting for experimental validation based on data from other researchers in the field. Combining in vitro data with results from in silico modeling our learning may be enriched and contribute to read-across to other types of nanomaterials showing similar characteristics. Moreover, in silico models may in the future be optimized based on such correlation attempts.
Also during the spring, a series of guidance workshops and hackathons will be offered for nanoscientists to support the upload of their experimental data and the relevant metadata4 to the NanoCommons Knowledge Base and thus to comply with the criteria of data FAIRness. This activity will assist attendees in finding the correct ontology terms for their data, provide a quick and easy process to add missing ontology terms, and will enable attendees to get DataCite unique identifiers for their datasets to include in their publications or to link existing publication to the datasets in NanoCommons. NanoCommons will award an EU Nanosafety Data Curation Prize among the participants of the entire training series, with an overall prize and two runner-up prizes available. Participation can also be used to gain experience as a data shepherd as per the concept defined by NanoCommons4 which spans experimental and computational expertise and herds data throughout the datalife cycle to ensure it is managed and made available for re-use by others.
For further details and to stay tuned with our training activities please join the mailing list of NSC WG-A. A comprehensive set of educational resources (recorded webinars, tutorials, etc.) can be viewed in the NanoCommons User Guidance Handbook, and more information on events, services and presentation materials can be found in the NanoCommons infrastructure. Training events are also listed in the ELIXIR TeSS database.
- Martens M, Ammar A, Riutta A, Waagmeester A, Slenter DN, Hanspers K, Miller RA, Digles D, Lopes EN, Ehrhart F, Dupuis LJ, Winckers LA, Coort SL, Willighagen EL, Evelo CT, Pico AR, Kutmon M. WikiPathways: connecting communities, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D613–D621, https://doi.org/10.1093/nar/gkaa1024
- Martens, M; Evelo, C; Willighagen, E. (2021): Providing Adverse Outcome Pathways from the AOP-Wiki in Semantic Web Format to Increase Usability and Accessibility of the Content. ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.13524191.v1
- Chomenidis C, Drakakis G, Tsiliki G, Anagnostopoulou E, Valsamis A, Doganis P, Sopasakis P, Sarimveis H. Jaqpot Quattro: A Novel Computational Web Platform for Modeling and Analysis in Nanoinformatics. J Chem Inf Model. 2017 Sep 25;57(9):2161-2172. doi: 10.1021/acs.jcim.7b00223. Epub 2017 Sep 11. PMID: 28812890.
Papadiamantis AG, Klaessig FC, Exner TE, Hofer S, Hofstaetter N, Himly M, Williams MA, Doganis P, Hoover MD, Afantitis A, Melagraki G, Nolan TS, Rumble J, Maier D, Lynch I. Metadata Stewardship in Nanosafety Research: Community-Driven Organisation of Metadata Schemas to Support FAIR Nanoscience Data. Nanomaterials. 2020; 10(10):2033. https://doi.org/10.3390/nano10102033