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Add EGFR test case for evaluation code #178

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agitter opened this issue Aug 18, 2024 · 0 comments
Open

Add EGFR test case for evaluation code #178

agitter opened this issue Aug 18, 2024 · 0 comments

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@agitter
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agitter commented Aug 18, 2024

We can include an EGFR gold standard from the TPS paper. I found a good source for that dataset. It is not in the main TPS repository, but it is in the gitter-lab fork. The file is https://github.com/gitter-lab/tps/blob/ca7cafd1e1c17f45ddea07c3fb54d0d70b86ff45/data/resources/eight-egfr-reference-all.txt

It was added in pull request gitter-lab/tps#3 via commit gitter-lab/tps@ab3d866, which gives details about where I obtained the file locally. I have some other local information about the eight original pathway databases that were combined to create this file, shown here along with their edge overlaps with various network predictions (from my evaluation/2016-03-30 directory).
gold_standard_comparison

This file has nodes only, which should be sufficient for now. I may be able to get the edge lists if we want those too. We should remove the nodes with the _PSEUDONODE suffix before adding the gold standard list.

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