Features
Command line arguments
| Command | Alternate | Description |
|---|---|---|
| --schema | -s | Database schema to use |
| --emr | -e | EMR/Database to use as input for ETL |
| --num | -n | Top n depending on the context |
| --cui | -c | CUIs to use as input (multiple) |
| --cdm | -d | CDM concepts to use as input (multiple) |
| --fun | -f | Function to execute |
| --cid | -i | Set of IDs to use (Contextual |
| --fun | -f | Function to execute (similar/create/etl/anchor |
F1: Create CDM schema
- Hephaestus can create a CDM schema for you
python main.py -s myschema -f create
F2: Expand concept set with anchors from Cui2Vec
- See this article:
- In Hephaestus anchors are identified using Cui2Vec
- Integrates with ATLAS
How to use
python main.py -s ohdsi -i 2 -n 20 -f anchor
-s is for schema -i is the concept_set_id in ATLAS -n is the Topn -f function name to execute, anchor in this case.
F3: Find similar concepts using Cui2Vec
python main.py -d 140168 -n 20 -f similar