Concept Maps in TeSS
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The implementation study focuses on integrating ELIXIR registries to enhance user experience for life scientists in finding and utilizing resources through intuitive graphical representations of scientific workflows. Key design considerations include workflow structure, tool configuration, and the importance of narrative context. The study highlights various use cases, features for user interaction, and acknowledges the contributions of leaders and development team members involved in the project.
Concept Maps in TeSS
- 1. Implementation Study: ELIXIR Registry Integration from a User Perspective Niall Beard ELIXIR All Hands Meeting 17th – 20th June 2019
- 6. Registry Integration •Each of these registries has a clear use case. •Can we combine our registries data to produce a useful application? •Slot together the jigsaw pieces to produce a beautiful picture.
- 8. https://elixir-europe.org/about-us/implementation-studies/elixir-integration- user-perspective The goal of this implementation study is to provide the life-scientist end-user with a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.
- 9. Potential Use Cases •Figure in Publication • Created by an Author wishing to disseminate a new data analysis pipeline •Training Material Content • Created by a Trainer to guide students step- by-step through a tutorial •Workflow Documentation • Created by a Developer to document each stage of a workflow
- 10. Design Considerations •The structure of a workflow is `data is passed into an operation which produces data`. This may repeat across multiple operations •Some stages of a workflow are required, some are optional. •A choice of tools can execute an operation. •Tool configuration usage is bespoke to the workflow. •Some Data is in a recognized format. •Narrative text is important to help contextualize information
- 11. Design – The EDAM ontology architecture
- 12. Data Topic Operation Operation Data Condition description Narrative text Narrative text Tool paramete Narrative text Tool parameters Narrative text
- 13. •Sandbox TeSS • https://tess.oerc.ox.ac.uk/concept_maps/sequence-translation-and- product-identification •Standalone version • https://concept-maps-9669f.firebaseapp.com
- 14. User Features •Graphical Editor •Register API Integrations •Export/Import as JSON file •EDAM Selection tool •Realtime Markdown renderer •Documentation within pages •Connection validation tools •Source code is integratable into other platforms
- 15. Extensions Workflow Convertor made at Biohackathon ‘18
- 16. Other types of “Training Workflow” •Tutorials • Structural Bioinformatics Workflows – (Lee Larcombe) • https://tess.elixir-europe.org/workflows/fork-structural- bioinformatics-1-getting-a-structure-for-a-protein-of-interest •https://tess.elixir-europe.org/workflows/fork-structural- bioinformatics-2-exploring-predictions-of-protein-functional- sites-using-funfams-in-cath-gene3d-9655793d-1cee-4164-a0c2- c7104ddb44c4 •https://tess.elixir-europe.org/workflows/fork-structural- bioinformatics-3-predicting-the-effect-of-mutation-on-protein- function • EMBER Tutorial – (Teresa Attwood) • https://tess.elixir-europe.org/workflows/sequence-translation •Learning Paths – Implementation Study Funded
- 17. Acknowledgements • Implementation Study leaders; • Frederik Coppens ELIXIR-BE • Hedi Peterson ELIXIR-EE • Niall Beard ELIXIR-UK •Dev Team; • Ivan Kuzmin ( with special thanks to) • Niall Beard • Tong Li • Aleksandra Nenadic