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biothings / biothings_explorer

TRAPI service for BioThings Explorer
https://explorer.biothings.io
Apache License 2.0
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Query BTE/Translator for all edges in DrugMechDB #181

Open andrewsu opened 3 years ago

andrewsu commented 3 years ago

DrugMechDB (https://github.com/SuLab/DrugMechDB) is a database of drug mechanisms expressed as paths (or small graphs) through a knowledge graph. Let's take each edge in DrugMechDB, formulate a TRAPI query, and see if BTE can find it. Output will be some sort of report that describes what percentage of DrugMechDB edges are found, stratified by edge type.

Mike created an initial analysis in this repo https://github.com/SuLab/DMDB_Analysis/tree/main/1_code and in particular this notebook https://github.com/SuLab/DMDB_Analysis/blob/main/1_code/4_dmdb_bte_trapi_analysis.ipynb. Would be good to finish/finalize this.

newgene commented 3 years ago

final result will depend on the fix of #185

r76941156 commented 3 years ago

Final result will depend on the fix of #212

andrewsu commented 2 years ago

Rebooting this issue as a rotation project for Hanbing. Let's start with cell 20 in https://github.com/SuLab/DMDB_Analysis/blob/main/1_code/1_basic_dmdb_analysis.ipynb, which lists the common metapaths used in DrugMechDB. Starting with one of the more common metapaths, let's create a corresponding TRAPI query and see how many examples BTE (and/or other Translator tools) can retrieve.