Configuration

The app requires the following configurations the first time you run it.

Mandatory Settings

  • Download the Loinc Core Table from loinc.org. Follow instructions from the loinc.org website. You need to register before you can download the document. The current version is Loinc Version 2.63 (2017/12/15 release).
  • Configure the path to the Loinc core table. From the menu bar, click “Configuration” - “Set path to Loinc Core Table file” and point to the LoincTableCore.csv file.
  • Download HPO file. From the menu bar, click “Configuration” - “Download HPO file”. The files (HPO in .obo and .owl formats) will be automatically downloaded.
  • Set the path to auto-saved data. First clone the repository for loinc2hpoAnnotation from Github (https://github.com/TheJacksonLaboratory/loinc2hpoAnnotation)[https://github.com/TheJacksonLaboratory/loinc2hpoAnnotation]. Then from the menu bar, click “Configuration” - “Set path to Auto-saved Data”, point to the loinc2hpoAnnotation folder.

Restart the app to apply all settings

Optional Settings

The following setting are strongly recommended. Not specifying them will not affect the operation of the app.

  • Set biocurator ID. From the menu bar, click “Configuration” - “Set biocurator ID”, specify your biocurator ID. If you are not assigned one, create one for yourself with the following format: organization name first followed by :, then your name/id.
  • Once you are done, click “Configuration” - “Show settings” to view all your settings. The first two settings should NOT be null in order for the app to work correctly.
  • Use customized hpo. If you prefer to use your own versions of hpo, click “Configuration” - “Change hpo.owl” to set the path to your hpo.owl file; use the button below to set the path to the hpo.obo file. An important note: inconsistencies of hpo.owl and hpo.obo files will lead to errors, so make sure your hpo OWL and OBO files are serialized from the same HPO. For details, refer to https://github.com/TheJacksonLaboratory/loinc2hpoAnnotation/blob/master/README.md#annotating-with-newly-created-hpo-terms

Change Settings

The settings will be saved to a local file so that you do not need to repeat the above steps every time you run the app. This applies even after you upgrade to a newer version of the app. Should you decide to change the settings, follow the above steps accordingly to overwrite the original settings.