BOQA

Bayesian Ontology Query Algorithm (PMID:22843981)

Run tests

We use Maven Surefire plugin to run tests:

./mvnw test

Distribute CLI

The compilation of JAR files, generation of sources and Javadoc, as well as packaging into distribution ZIP file requires activation of the release profile:

./mvnw -Prelease package 

Input data

In BOQA analyses, observed phenotypic features of individuals are compared with annotated disease-phenotype associations. We use the following HPO resources:

1. Disease-phenotype associations: phenotype.hpoa

2. HPO: hp.json

3. Disease-gene associations: genes_to_disease.txt

Use the following command to download these files from the latest release:

java -jar boqa-cli/target/boqa-cli-0.1.0.jar download -d ./data 

The files are downloaded to a subdirectory ./data/latest_<time_stamp>.

To download a specific release, use the following command;

java -jar boqa-cli/target/boqa-cli-0.1.0.jar download -d ./data -r v2025-05-06 

The files are downloaded into a subdirectory of ./data named after the release.

4. Phenopackets containing phenotypic features observed in individuals: phenopacket-store

wget -O data/all_phenopackets.zip https://github.com/monarch-initiative/phenopacket-store/releases/latest/download/all_phenopackets.zip
unzip data/all_phenopackets.zip -d data

Run CLI

Run the following to run the CLI:

./mvnw -Prelease package

java -jar boqa-cli/target/boqa-cli-0.1.0.jar --help