Create Turtle file of AOP Wiki XML

elixir-europe / toxicology-community

Repository to coordinate the work of the Toxicology Community.

https://elixir-europe.org/communities/toxicology

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Create Turtle file of AOP Wiki XML #24

Closed marvinm2 closed 4 years ago

marvinm2 commented 6 years ago

The initial step towards a semantic integration of AOP Wiki (https://aopwiki.org/downloads), eventually allowing SPARQL queries on the contents of this database.

egonw commented 6 years ago

My recommendations:

[x] create a GitHub repo for the code that does the transformation
[ ] set up a Jenkins job based on this repo that 1. downloads the AOPWiki data, 2. runs the code from the repo to create Turtle
[ ] define a number of tests that make sure the Turtle is reasonable

Check the license of AOPWiki... it's Open, right? If not, delete the turtle from the Jenkins job workspace.

egonw commented 5 years ago

ping @marvinm2, can you update this issue report with the current status, progress, pointers?

marvinm2 commented 5 years ago

A script is created for ttl generation, which is valid Turtle. SPARQL queries can be done, and it is presented in a poster at SWAT4HCLS: https://doi.org/10.6084/m9.figshare.7735067.v1

However, some elements are missing/lacking annotations, and we plan to add more elements to the RDF, such as metabolite identifiers for stressors and links to data sets for KEs (ToxCast)

egonw commented 5 years ago

The paper is being written up.