Looks like we still need the high-level study metadata?

[seandavi]

The equivalent of this:

ftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs000001/phs000001.v3.p1/GapExchange_phs000001.v3.p1.xml

[rbutleriii]

I think we are working on parsing the dbgapr and adding the info from NIH Common Data Elements. For the CDE i should have something later this morning. Turned out to be quite useful.

[seandavi]

Awesome!

[jameslhao]

I’ve made some changes to dbgapr code so that it can display metainfo by object accession without the requirement of data files present in the project data directory. The following should work now. library('dbgapr') # create class obj c <- Commons() # Create user project directory prjConfig(c, prjDir="~/dbGaPR") # update obj to include proj info c <- Commons() # view proj info getPrjDir(c, showErr = TRUE) # download metainfo files not limited to the studies that have data files ftpDownload(c, dataStudyOnly=F) # view metainfo by accession df <- accInfo(c, acc='phs000001.v3.p1') # by study accession df <- accInfo(c, acc='pht000370.v2') # by dataset accession df <- accInfo(c, acc='phv00000084.v2') # by variable accession From: Robert Butler [mailto:[email protected]] Sent: Tuesday, August 15, 2017 7:59 AM To: NCBI-Hackathons/ComplexPhenotypes <[email protected]> Cc: Subscribed <[email protected]> Subject: Re: [NCBI-Hackathons/ComplexPhenotypes] Looks like we still need the high-level study metadata? (#8) I think we are working on parsing the dbgapr and adding the info from NIH Common Data Elements. For the CDE i should have something later this morning. Turned out to be quite useful. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#8 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AQKZJHdDcjsWFG0YpZujJP4nIw1N-pjHks5sYYgCgaJpZM4O3dTd>.

[davemcg]

CDE doesn't have study level info. I think we'll need to parse the xml for it.

[seandavi]

Yep. I agree. Parsing XML looks like the way to go.