Event types: Workshops and courses
Content provider: OpenRiskNet
Demonstration on data curation and creation of pre-reasoned datasets in the OpenRiskNet framework
18 March 2019Demonstration on data curation and creation of pre-reasoned datasets in the OpenRiskNet framework https://openrisknet.org/events/58/ https://tess.elixir-europe.org/events/demonstration-on-data-curation-and-creation-of-pre-reasoned-datasets-in-the-openrisknet-framework In the process of utilising the analysis tools available in the OpenRiskNet e-infrastructure, data needs to be accessed from different sources and various formats. In this webinar we will use examples to introduce attendees to the OpenRiskNet data handling and curation process. This will include methods for data access, upload, and extraction for further downstream analysis. Some specific examples we will be exploring include: * A workflow using the text mining capability for data extraction from a public database; * Demonstration of extraction of data from a public database for a specific endpoint (e.g. drug induced liver injury) and combine with other data (e.g. omics data) to get a better grouping for target prediction. 2019-03-18 16:00:00 UTC 2019-03-18 17:00:00 UTC OpenRiskNet Data submission, annotation, and curation Toxicology  Registration: https://attendee.gotowebinar.com/register/1969650133692000781   workshops_and_courses  
How to describe OpenRiskNet services and their functionality by semantic annotation
13 May 2019How to describe OpenRiskNet services and their functionality by semantic annotation https://openrisknet.org/events/64/ https://tess.elixir-europe.org/events/how-to-describe-openrisknet-services-and-their-functionality-by-semantic-annotation Providing the data and software services within OpenRiskNet virtual environment and make the functionality available via application programming interfaces (APIs) already allows for the development of advanced workflows providing solutions to complex risk assessment tasks (demonstrated in the case studies webinars). However, identification and selection of the most appropriate service, understanding their functionality and format the input and output still need manual investigation and programming/scripting skills. To be able to automate these tasks, OpenRiskNet is exploring semantic annotation on different levels. After a short introduction to ontologies applicable to service annotation, we will first demonstrate high-level annotation, which gives the information for the OpenRiskNet registry service to index the service and to make it findable for users and gives basic categorisation like dataset, algorithm and model. Then we will show low level annotation, which will be used for dataset and input/output harmonisation so that the user but more important other services can understand the information provided/required and how to access it. Finally, first approaches to define the middle layer providing metadata describing the service in more detail like available toxicity domains, available endpoint as well as gene/pathway/AOP associations will be shown. 2019-05-13 16:00:00 UTC 2019-05-13 17:00:00 UTC OpenRiskNet Ontology and terminology    workshops_and_courses first_come_first_served 
Use of Nextflow tool for toxicogenomics-based prediction and mechanism identification in OpenRiskNet e-infrastructure
27 May 2019Use of Nextflow tool for toxicogenomics-based prediction and mechanism identification in OpenRiskNet e-infrastructure https://openrisknet.org/events/65/ https://tess.elixir-europe.org/events/use-of-nextflow-tool-for-toxicogenomics-based-prediction-and-mechanism-identification-in-openrisknet-e-infrastructure Predictive toxicology and risk assessments increasingly rely on Big Data analyses for more informed decision making. Toxicogenomics uses transcriptomic readouts to predict the characteristics of compounds based on the gene-expression profiling of cells in response to exposure. These large genomic analysis place new computational demands on researchers with the handling of datasets, the combining of tools and the reproducible deployment of an analysis presenting significant challenges. This webinar highlights how these challenges can be overcome using the open source workflow management tool Nextflow within the OpenRiskNet e-infrastructure. Using the toxicogenomics example, we will show how a workflow can be created, deployed and shared across Kubernetes-based environments. 2019-05-27 16:00:00 UTC 2019-05-27 17:00:00 UTC OpenRiskNet Toxicology    workshops_and_courses first_come_first_served toxicogenomics
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