shahimessaid/comp-loinc

CompLOINC LinkML

Computable OWL Formalization of LOINC

Website

Repository Structure

• comp-loinc/ - Python package for this project
  • data/ - LOINC Input data and output OWL Files
    • code_files/ - LOINC Code Files
    • part_files/ - LOINC Part Files
    • output/ - OWL Output Files
      • owl_component_files/ - OWL Component Files
      • merged_loinc.owl - Merged OWL File
      • merged_reasoned_loinc.owl - Merged and Reasoned OWL File
  • project/ - project files (do not edit these)
  • src/ - source files (edit these)
    • comp_loinc
      • schema -- LinkML schema
      • datamodel -- generated Python datamodel
      • cli -- command line interface
      • ingest -- ingest code
      • mapping -- mapping code for extracting mappings from the loin fhir server
      • ROBOT -- ROBOT tools for OWL Operations
  • tests/ - Python tests

Developer Documentation

Use the `make` command to generate project artefacts:

• make all: make everything
• make deploy: deploys site

Credits

This project was made with linkml-project-cookiecutter.

Prerequisities

1. Python 3.9.7+
2. Required LOINC Files For now, these files are downloadable from GoogleDrive. They need to be put in these locations:

• data/part_files/ComponentTree.tsv
• data/code_files/LOINC.csv
• data/code_files/LoincPartlink_Primary.csv

Setup

1. Clone this repository.
2. install poetry
3. run poetry install

Usage

Commands 1.1 - 1.5 are meant to be run sequentially.

Alternatively, you can run all of them at once using default values by running python src/comp_loinc/cli/main.py all.

Help text can be run via python src/comp_loinc/cli/main.py --help. You can see help text for a specific command, including information about its parameters, by running python src/comp_loinc/cli/main.py COMMAND_NAME --help.

1.0. loinc_release: Download the latest LOINC release files and put them in the correct locations. Zip LoincRelease needs to be in the data/loinc_release directory.

python src/comp_loinc/main.py loinc_release

1.1. parts: Build the part ontology from the intermediate Part Hierarchy files

python src/comp_loinc/main.py parts --schema-file src/comp_loinc/schema/part_schema.yaml --part-directory data/part_files --output data/output/owl_component_files/part_ontology.owl

1.2. codes: Build the code classes from the intermediate Part Hierarchy files

python src/comp_loinc/main.py codes --schema-file src/comp_loinc/schema/code_schema.yaml --code-directory data/code_files --output data/output/owl_component_files/code_classes.owl

1.3. composed: Build the composed class axioms for the reasoner to group classes (this is pretty bespoke, and hardcoded at the moment)

python src/comp_loinc/main.py composed --schema-file src/comp_loinc/schema/grouping_classes_schema.yaml --composed-classes-data-file data/composed_classes_data.yaml --output data/output/owl_component_files/composed_component_classes.owl

1.4. map: Get Mappings from the LOINC FHIR Server and use SSSOM to convert to OWL (Requires LOINC FHIR Server credentials)

python src/comp_loinc/main.py map --username username --password password --output loinc2chebi.owl

1.5. merge: Merge all owl files into single merged ontology

python src/comp_loinc/main.py merge --owl-directory data/output/owl_component_files/ --output data/output/merged_loinc.owl

1.6. reason: Run the reasoner using elk to create the composed code classes

python src/comp_loinc/main.py reason --output latest/comp_loinc.owl

2. Open the merged and reasoned owl file in Protégé for viewing

Open data/output/merged_reasoned_loinc.owl