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Biohackathon-TeSS-ConceptMaps.pptx
README.md

README.md

Import workflows into TeSS Concept Maps

### Representative: Niall Beard

Community


ELIXIR Training Platform

Leads


Niall beard

Background information


TeSS has been developing a new feature called Concept Maps (demo: https://tess.oerc.ox.ac.uk/concept_maps). Concept Maps provide a conceptual representation of data analysis pipelines. The Concept Map is a medium for educating researchers about the steps a typical Workflow comrpises of, and informing them about what tools, databases, standards, and other resources are available to use when constructing one.

Each step of a Training Workflow in TeSS is annotated with an EDAM term. There are two step types; Data and Operations.

  • Data steps are annotated with an EDAM Data and EDAM Format term, and contain links to available databases through the FAIRSharing registry.
  • Operation steps are annotated with an EDAM Operation term, and contain links to tools from the bio.tools registry.

This task will look at devising a way to import workflows (CWL or Galaxy) into TeSS to turn the Computational Workflows into Conceptual Training Workflows that can educate and inform bioinformatics researchers.

tuxedo tuxedo concept map

Expected outcomes


  1. Manually construct a Concept Map based on a Galaxy Workflow
  2. Make the Concept Map again, but this time - automatically, by:
  • Annotating the Galaxy/CWL workflow with EDAM terms (Operation and Data).
  • Parse the workflow (CWL or Galaxy) using Ruby.
  • Create a connected graph representation of the workflow in memory.
  • Use TeSS's existing modified Cytoscape JS plugin to plot the connected graph onto a canvas ready to be annotated, assigned resources from bio.tools, FAIRSharing, and TeSS, and saved.

Expected audience


Programmers, workflow experts. Cytoscape JS, CWL/Galaxy, Ruby programmers (other languages welcome) Expected hacking days: 4 days, 3 days, 2 days

Related works and references


TeSS Concept Maps prototype, ELIXIR Implementation Study on Registry integration from a User Perspective (training workflows Annotation of Galaxy tools with EDAM terms

GitHub or any other public repositories of your FOSS products (if any)


TeSS Concept Maps JS

Hackers


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