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Need for text mining / mapping for AOP-Wiki contents #37

Closed marvinm2 closed 4 years ago

marvinm2 commented 5 years ago

There is a need for identification of genes, proteins, metabolites described in text in Key Events and Key Event Relationships.

Also, methods and approaches are described on how to test for a Key Event. Extracting this data would be useful as well.

AOP-Wiki RDF Virtuoso docker should allow extracting these pieces of text.

Which tools would fit this purpose?

egonw commented 5 years ago

I recommend looking at the ContentMine stack. if we're going to take this forward.

egonw commented 5 years ago

Marvin, please add which items you like to extract. For genes (human, mouse) there is already existing code. For other things, a dictionary (=list of words it should recognize) would make it trivial too.