SCT_SubOntTerms

A script to obtain a tsv file with the Snomed CT child terms and codes from a list of seed codes.

For example we would use this script if we want to get the terms and child snocmed ids of the code "272115004", whose descriptor is "Synchronicities".

As a result of the script you would get a tsv file with the following format, containing the codes "255215002" and "255237009" (children of the above code) as well as their descriptors and synonyms:

255215002 asynchronous (qualifier)
255215002 asynchronous
255215002 Asynchronous (qualifier value)
255215002 Asynchronous
255237009 asynchronous (qualifier)
255237009 synchronous
255237009 Synchronous (qualifier value)
255237009 Synchronous

Getting Started

This script has been developed with Python 3.6.9 in order to achieve compatibility with the rest of the TeMU tools.

Installation

1. Clone the repo

   git clone https://github.com/luisgasco/sct_subontterms.git

2. Create a new virtual environment

   python3 -m venv .env

3. Activate the new environment

   source .env/bin/activate

4. Install the requirements

   pip install -r requirements.txt

Usage

The sct_subontterms.py script has the following options:

• Relationships file (-r or --rel_file): Path to the SnomedCT Relationship file in RF2 format.
• Concepts file (-c or --concept_file): Path to the SnomedCT Concept file in RF2 format
• Output tsv (-o or --output_file): File in which you want to save the results (it can be a path/filename.tsv).
• List of seed codes (-l or --code_list): List of codes separated by commas.
• Root code to consider in SnomedCT (--root_code): Snomed concept id from which you want to generate the ontology file. For example if you want to consider only the branch "Pharmaceutical / biologic product" you should use the code "373873005", if you want to use the whole snomed ontology you should use the code "138875005".Defaults to "138875005"
• Relationship types to consider in SnomedCT (--rel_types): Type of relationship to consider when building the ontology. Use string "116680003" if you only want to consider "Is a" relationships, use "all" if you want to consider all types of relationships (including concept model attributes).Defaults to "116680003"

Examples:

python sct_subontterms.py -r "/Path/to/Full/Terminoology/sct2_Relationship_Full_INT_20210731.txt" \
    -c "/Path/to/Full/Terminoology/sct2_Description_SpanishExtensionFull-es_INT_20210430.txt" \
    -o "output_terms.tsv" \
    -l 258695005,272103003,7389001

You can download de Snomed-CT RF2 files here. The relationship file can be found in the International Edition version.