Comments (5)
Ah you are right; I take that back. There I no InChIKey
in the drug file and I have been using pert_iname
to merge the two lists. This means, I have not been annotating these two compounds with their respective MOAs/targets. Thanks for bringing this to my attention.
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cc @niranjchandrasekaran @shntnu - in case either of you have run into this issue and solved it before
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Thanks @gwaygenomics for figuring this out! It will be helpful when I am losing my mind over why the lists aren't matching.
On a side note: Usually, I merge the two lists ( When Shantanu and I did that, we ran into another issue where there were multiple samples
and drugs
) using InChIKey
.pert_iname
mapping to the same InChIKey
and InChIKey
and smiles
did not match 1:1. We have taken this approach to overcome the problems and the cleaned up samples
file is here. This file also contains additional vendor availability information, which may not be useful to you.
Edit: I have been merging the two lists with pert_iname
and not with InChIKey
. But the rest of the paragraph is accurate for deduplicating the samples
list.
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oh interesting! Thanks for sharing @niranjchandrasekaran.
Where are you retrieving the drug
file from? On the repurposing homepage in CLUE (https://clue.io/repurposing) the drug
file does not have an InChIKey
column.
This is the source of data in this repo (#5 (comment)) - maybe it is different in JUMP?
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no longer an issue. Solved specifically in #8 (comment) and implemented in #7
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Related Issues (20)
- Java dependency in environment.yml HOT 3
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- Delete column names after spherizing HOT 6
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