Loinc2hpo Documentation

Loinc2hpo is a JavaFX app designed to convert FHIR observations into HPO terms. The app has three core functionalities:

• help mapping LOINC codes into candidate HPO terms
• help retrieve patient observations
• convert patient observations into HPO terms

Mapping LOINC to HPO terms requires significant efforts from biocurators. Loinc2hpo tries to simplify the process by automatically finding the best matching terms using Sparql query. With this app, collaborators can easily split LOINC codes of interest into smaller tasks and share their annotations.

• Introduction to LOINC
  • Parts of LOINC entry
  • Common LOINC codes
• Introduction to FHIR
  • Resources
• Our Mission
• Working logic
  • Mapping LOINC to candidate HPO terms
  • Retrieve Resources from EHR systems
  • Convert Observations into HPO terms
• Annotation Logic
  • Qn
  • Ord
  • Nom
  • Nar and other types
• Install & running
• Configuration
  • Mandatory Settings
  • Optional Settings
  • Change Settings
• Tutorial
  • Overview
  • Annotation
  • Converting Observations to HPO terms
• Consumption Tutorial
  • Overview
  • Installation
• Contact

GitHub repo

The source code of Loinc2hpo can be found at GitHub: https://github.com/monarch-initiative/loinc2hpo