Java library to map LOINC-encoded test results to Human Phenotype Ontology
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README.md

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LOINC2HPO annotation

If you want to access the LOINC to HPO mapping, refer to loinc2hpoAnnotation repo.

If you want to contribute to LOINC to HPO mapping, read below.

org.monarchinitiative.loinc2hpo

Java library to map LOINC-encoded test results to Human Phenotype Ontology.

There are currently two modules, a core module and a graphical user interface (GUI) module. loinc2hpogui is a JavaFX app that intends to help with biocuration of LOINC code to HPO term mappings. To build and run the GUI, use the following command.

$ mvn clean package
$ java -jar loinc2hpogui/target/Loinc2HpoGui-jar-with-dependencies.jar 

To run the library code, enter the following

$ java -jar loinc2hpo-core/target/Loinc2HpoLib.jar download

This will download the hp.obo file (You need to manually download the LOINC Core Table file). There is a demo function that currently doesn't do anything

$ java -jar loinc2hpo-core/target/Loinc2HpoLib.jar demo

documentation

Please refer to http://loinc2hpo.readthedocs.io/en/latest/.

spring framework app

We are developing a separate app that will specialize in one functionality of this app - converting FHIR observations into HPO terms. The new app will be coded with the Spring framework and we strive to achieve enterprise-level quality. Please refer to the app with the following link: https://github.com/OCTRI/fhir2hpo

funding

We gratefully acknowledge funding by NCATS (CD2H project), 1U24TR002306 A NATIONAL CENTER FOR DIGITAL HEALTH INFORMATICS INNOVATION