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FAIRplus / the-fair-cookbook

The FAIR cookbook, containing recipes to make your data more FAIR. Find the rendered version on:
https://faircookbook.elixir-europe.org/
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New recipe request: hands-on recipe on ETL-RDF #173

Open FuqiX opened 3 years ago

FuqiX commented 3 years ago

Following our discussion in Cookbook Dash 3.

This recipe is an implementation example for #160 , showing step-by-step guide on how to use one of the tools to convert to RDF.

To write this recipe, we need:

Some ideas collected from the cookbook meeting:

  1. Recipe on how to use YARRRML
  2. Recipe on how to use OpenRefine
    • Option 1 : using public phenotypic data in biosamples, and the Phenopacket data standards to demonstrate the workflow
    • Option 2: using public sample metadata in csv format which complies with the ENA checklists, converts to RDF
    • Option 3: Use FAIRplus IMI project example data sets and data models

Hi, @eelkevanderhorst @proccaserra I created this new recipe request so that we won't lose the discussions. Please feel free to edit.

Note (EH): for option 3, @robertgiessmann would be happy to provide an anonymized tumor growth data set (xenograft mouse model).

sgtp commented 3 years ago

I may have some material on using OR and Wikidata to share. But this is more tech infrastructure than a specific use case. Do you plan to connect OR to a local instance of Wikidata in this recipe?

JolandaS commented 3 years ago

I will take up the writing of the OpenRefine recipe. I will make a first set up (based on work done before) and will contact you @robertgiessmann on implementing it on your data.

JolandaS commented 2 years ago

@proccaserra Andrea (@sgtp) and I have had a call on this. We both have started writing down our experiences (see also this folder). Once we have finished that, we would like to discuss with you what the best angle is for a recipe.