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knowledgesystems / pipelines-scrum

Repository for tracking uncategorizable issues related to backend pipelines work
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assemble all production data #1283

Closed sheridancbio closed 1 month ago

sheridancbio commented 2 months ago

Done Condition (What do we need? Why do we need it? Keep this is small as possible!)

all necessary objects and properties are capture from the current oncrtree production versions (preferably rdf downloads from topbraid)

Technical Description (How are we going to achieve the above)

Potential Issues

Dependencies

Technical Requirements

Outside People/Teams

Changes

sheridancbio commented 1 month ago

Frozen versions do not change once frozen. There are .rdf dumps for all the frozen versions:

oncotree_latest_stable is a synonym for stable release oncotree_2021_11_02

The two other versions are oncotree_candidate_release and oncotree_development: For oncotree_candidate_release, downloaded rdf files were searched. This new version has 4 additional oncotree codes compared to oncotree_2021_11_02:

No downloaded version had all 4 of these additional codes, but several had 3 of the 4. Among these, the most concordant showed that the parent of GBC is ICPN (rather than BILIARY_TRACT). Also the parent of CHOL is IPN (rather than BILIARY_TRACT). An importable version of oncotree_candidate_release was synthesized by adding an additional element for for NRCC to the most concordant version.

For oncotree_development, it was surprising to see that none of {NRCC, MDSWP, MPNWP, or NVRINT} were present despite them being in oncotree_candiate_release. Instead, oncotree developement added:

This was synthesized from the .rdf file from oncotree_latest_stable.

sheridancbio commented 1 month ago

In the mapping file, MLNFLT3ABL1 was assigned URI ONC000921 and MLNJAK2 was assigned URI ONC000922.