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.

1. Implementation Study:
ELIXIR Registry Integration from a
User Perspective
Niall Beard
ELIXIR All Hands Meeting
17th – 20th June 2019

2. ELIXIR Platforms
https://www.dtls.nl/elixir-nl/about-elixir-nl/

3. Training Platform Registry
https://bio.tools

4. Interoperability Registry
https://fairsharing.org

5. Training Platform Registry
https://tess.elixir-europe.org

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.

7. https://elixir-europe.org/about-us/implementation-studies/elixir-integration-
user-perspective

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