Demo Data for Cross Study App

[iwwwish]

Hi,

Thank you, Kevin & colleagues for creating the Cross Study R Shiny app. I have trouble getting the app working with internal SEND datasets. Specifically, the FW domain data could not be summarized across studies (due to pool ID and USUBJID discrepancy) but when I completely skipped FW domain, it started to complain about differences in the number of levels for other domains.

Could you share the de-identified SEND datasets that were used for the publication on this repo? The corresponding DOI link from the publication does not work anymore. Thank you!

Best regards,
Vishal

[William-Houser]

Hi Vishal, I just confirmed that I could load 10 of the studies that are on phuse-scripts/data/send at master * phuse-org/phuse-scripts * GitHub<https://github.com/phuse-org/phuse-scripts/tree/master/data/send> The studies we analyzed for this publication are not included here (yet), but they contain some SEND data that might be useful examples for you. I placed these directories and their contents under C:/001/SQLliteSEND/phuse/ on my computer and ran this script: library(sendigR) library(RSQLite) # create the database initEnvironment(dbType='sqlite', dbPath='C:/001/SQLliteSEND/phuse.db', dbCreate=TRUE, ctFile='C:/001/SQLliteSEND/SEND Terminology 2023-12-15.xls') # Create an empty SQLite database and create the SEND schema myDbToken <- initEnvironment(dbType = 'sqlite', dbPath ='C:/001/SQLliteSEND/phuse.db', dbCreate = FALSE) dbCreateSchema(myDbToken) dbCreateIndexes(myDbToken) dbImportStudies(myDbToken,'C:/001/SQLliteSEND/phuse',overWrite=FALSE,checkRequiredVars=TRUE,verbose=TRUE,logFilePath='C:/001/SQLliteSEND/') Not all the folders contain studies and not all the studies include *.xpt files, but I ended up with 10 distinct studyid values in dm. Here are the messages that were displayed when running the script:

source("C:/001/SQLliteSEND/CreateDB.R")

[1] "CBER-POC-Pilot-Study1-Vaccine: OK with warning(s): Non-SEND XPT file(s) ignored: is.xpt,suppis.xpt" [1] "CBER-POC-Pilot-Study2-Vaccine: OK" Error in log_warning() : could not find function "log_warning" [1] "CBER-POC-Pilot-Study3-Gene-Therapy: OK with warning(s): Non-SEND XPT file(s) ignored: is.xpt" [1] "CBER-POC-Pilot-Study4-Vaccine: Cancelled: Missing xpt file(s): dm.xpt" [1] "CBER-POC-Pilot-Study5: Cancelled: Failed to parse C:/001/SQLliteSEND/phuse/CBER-POC-Pilot-Study5/lb.xpt: Unable to read from file." [1] "CDISC-Safety-Pharmacology-POC: OK" [1] "CJ16050: OK" [1] "CJ16050/RE Function in Rats/CJ16050_SEND Package: Cancelled: No xpt files found" [1] "CJ16050/RE Function in Rats/CJ16050_SEND Package/CJ16050/tabulation: Cancelled: The study exists in the database, but it is specified not to overwrite existing studies" [1] "CJ16050/RE Function in Rats/CJ16050_SEND Package/Study Protocol and Report: Cancelled: No xpt files found" [1] "CJUGSEND00: OK" [1] "FFU-Contribution-to-FDA: OK" [1] "instem: OK" [1] "instem/Xlsx: Cancelled: No xpt files found" [1] "instem/Xpt: Cancelled: The study exists in the database, but it is specified not to overwrite existing studies" [1] "JSON-CBER-POC-Pilot-Study3-Gene-Therapy: Cancelled: No xpt files found" [1] "Nimble: OK" [1] "PDS: OK with warning(s): Additional columns in domain CL has been ignored: CLREFID" [1] "PDS/Xpt: Cancelled: The study exists in the database, but it is specified not to overwrite existing studies" [1] "PDS/Xpt/legacy: Cancelled: Missing xpt file(s): dm.xpt,ts.xpt,tx.xpt" [1] "PointCross: Cancelled: the condition has length > 1" [1] "PointCross/PC201708_XPT: Cancelled: the condition has length > 1" [1] "SENDIG3.1.1excel: Cancelled: No xpt files found"

I hope this helps.

…

-Bill. From: Vishal Siramshetty ***@***.***> Sent: Thursday, December 5, 2024 7:08 PM To: phuse-org/BioCelerate ***@***.***> Cc: Subscribed ***@***.***> Subject: [phuse-org/BioCelerate] Demo Data for Cross Study App (Issue #34) [Use CAUTION when opening links/attachments] Hi, Thank you, Kevin & colleagues for creating the Cross Study R Shiny app. I have trouble getting the app working with internal SEND datasets. Specifically, the FW domain data could not be summarized across studies (due to pool ID and USUBJID discrepancy) but when I completely skipped FW domain, it started to complain about differences in the number of levels for other domains. Could you share the de-identified SEND datasets that were used for the publication<https://academic.oup.com/toxsci/article/200/2/277/7690167> on this repo? The corresponding DOI<https://doi.org/10.5061/dryad.s1rn8pkgr> link from the publication does not work anymore. Thank you! Best regards, Vishal - Reply to this email directly, view it on GitHub<#34>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AESDPOHQJR7NYQJSTDO2PGL2EDTFDAVCNFSM6AAAAABTDS5GD2VHI2DSMVQWIX3LMV43ASLTON2WKOZSG4ZDCNZSGU2DOMI>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.******@***.***>>

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