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remove drugs from CTRP dataset #241

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sgosline opened this issue Oct 29, 2024 · 7 comments · May be fixed by #252
Open

remove drugs from CTRP dataset #241

sgosline opened this issue Oct 29, 2024 · 7 comments · May be fixed by #252
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@jjacobson95
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data update

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@sgosline
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remove these drugs:
BRD-K03911514
BRD-K07442505
BRD-K13185470
BRD-K16130065
BRD-K20514654
BRD-K27188169
BRD-K55473186
YL54
BRD-K58730230
BRD-K79669418
BRD-K99584050
@sgosline sgosline self-assigned this Oct 29, 2024
@sgosline sgosline assigned jjacobson95 and unassigned sgosline Nov 13, 2024
@sgosline sgosline moved this to In progress in CoderData Nov 13, 2024
@sgosline
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@jjacobson95 why dont you go ahead and add these before starting the build process.

@jjacobson95
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jjacobson95 commented Nov 13, 2024 •
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Are these in the current data? I'm not finding them in the broad_sanger drugs file in the 0.1.40 build.

To Reproduce, run the following:

Bash

coderdata download --prefix broad_sanger_drugs.tsv.gz
gunzip broad_sanger_drugs.tsv.gz

Python

all_drugs = pd.read_csv("broad_sanger_drugs.tsv",sep="\t")

brd_list = [
    "BRD-K03911514",
    "BRD-K07442505",
    "BRD-K13185470",
    "BRD-K16130065",
    "BRD-K20514654",
    "BRD-K27188169",
    "BRD-K55473186",
    "YL54",
    "BRD-K58730230",
    "BRD-K79669418",
    "BRD-K99584050"
]

# filter by items in the list above
all_drugs = all_drugs[all_drugs.chem_name.isin(brd_list)]
print(all_drugs) # empty

# check for lowercase versions of drugs in list
brd_list = [item.lower() for item in brd_list] 
all_drugs = all_drugs[all_drugs.chem_name.isin(brd_list)]
print(all_drugs) # also empty

Resulting Empty Dataframe:
Screenshot 2024-11-13 at 1 28 57 PM

@jjacobson95
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jjacobson95 commented Nov 13, 2024 •
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I will still build in code to remove them if they exist, just wondering where they are coming from here.

@sgosline
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Maybe they drop out in the pubchem or structure mapping. We can just cloes this if they are not there.

@jjacobson95
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It could be that they were missing due to the incompleteness of the previous build. I already added it to the pipeline in the drop_drugs branch so it shouldn't hurt to have.

@sgosline
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So can we close this?

@sgosline sgosline moved this from In progress to Done in CoderData Nov 22, 2024
@jjacobson95 jjacobson95 linked a pull request Nov 22, 2024 that will close this issue
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@jjacobson95
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Once we merge PR #252, this will close.

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@jjacobson95 jjacobson95

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data update
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CoderData
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Drugs, BeatAML, CanSMILES Updates PNNL-CompBio/coderdata
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@sgosline @jjacobson95