Closed vthorsson closed 11 months ago
cdebrowser
In the data model, external database references in Source that point to cdebrowser (CDE Browser) are now invalid. E.g. The current row “Primary Diagnosis” has https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161032&version=1.0 as the Source. That now leads to a Retirement notice for the CDE Browser. They also provide a link format . For the above, this seems to be the valid replacement https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6161032%20and%20ver_nr=1.0
Need to replace https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId={CDE_ID}&version={CDE_VERSION} with https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID={CDE_ID}%20and%20ver_nr={CDE_VERSION}
HTAN.model.csv
HTAN.model.jsonld
main
ncihtan/HTAN-data-curator
Should be able to find and replace
Need to re-do after merging this PR: https://github.com/ncihtan/data-models/pull/292
We should open a FAIR data ticket on source not being included in the JSON-LD
Proposed change
Replace URIs containing
cdebrowser
with currently valid stringsDiscussion link
Initial discussion on https://htanworkspace.slack.com/archives/C03E345AMLK/p1690227558135099
How important is this feature?
When will use cases depending on this become relevant?
Additional context
In the data model, external database references in Source that point to cdebrowser (CDE Browser) are now invalid. E.g. The current row “Primary Diagnosis” has https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId=6161032&version=1.0 as the Source. That now leads to a Retirement notice for the CDE Browser. They also provide a link format . For the above, this seems to be the valid replacement https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=6161032%20and%20ver_nr=1.0
Need to replace https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?publicId={CDE_ID}&version={CDE_VERSION} with https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID={CDE_ID}%20and%20ver_nr={CDE_VERSION}
Implementation checklist
HTAN.model.csv
editied and pushedHTAN.model.jsonld
validated and created by Github actionmain
ncihtan/HTAN-data-curator
(if required)