joeflack4 / comp-loinc

CompLOINC LinkML

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/CHEM_HIERARCHY_REVISED.TSV
• data/part_files/METHOD_CHEM_HIERARCHY.TSV
• data/part_files/PROPERTY_CHEM_HIERARCHY.TSV
• data/part_files/SYSTEM_CHEM_HIERARCHY.TSV
• data/part_files/TIME_CHEM_HIERARCHY.TSV

Setup

1. Clone this repository.
2. From repo directory, run: pip install -r requirements.txt

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 comp_loinc/build.py all.

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

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

python comp_loinc/build.py parts --schema-file ./model/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 comp_loinc/build.py codes --schema-file ./model/schema/code_schema.yaml --part-directory ./data/part_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 comp_loinc/build.py composed --schema-file model/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. merge: Merge all of the owl files into single merged ontology

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

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

python comp_loinc/build.py reason --merged-owl data/output/merged_loinc.owl --owl-reasoner elk --output data/output/merged_reasoned_loinc.owl

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

Open data/output/merged_reasoned_loinc.owl