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CHANGELOG.md

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loinc2hpo Changelog

current

  • v 1.1.8

v1.1.8

  • Update to phenol 1.5.0

loinc2hpo-core

  • Adding enums for FHIR observation codes

v0.0.2

loinc2hpogui

  • Added FHIR to HPO conversion dialog

loinc2hpo-core

  • added FHIR parsing

v1.0.1

This is the first official release. Many features are added.

loinc2hpogui

Multiple features are added. This will be the baseline for future tracking.

loinc2hpo-core

  • The core change is completely switching to FHIR to parse observation and patient resources.

  • Redesigned the annotation class.

    • Use Code (system/namespace, code) to ensure uniqueness
    • An HPO term for a coded result is wrapped in a class that also indicate whether the term should be negated.
    • A complete annotation for a Loinc code contains many Code - (HPO term, isNegated) list.

  • Redesigned the logic process from observation to HPO term.

    • The app first looks at whether the observation has an interpretation field.

      • If it does, it will first try to find an annotation for the interpretation code directly;
      • if it fails, it will try to convert convert the interpretation code to the internal code and then find the corresponding HPO term.

    • If the app fails the last step, it will try to use the raw value and interpret it with the reference ranges.

v1.0.2

  • Build Jar with all dependencies with maven-assembly-plugin

  • Add META-INF/services to Core module because it appears that is what Jar requires

v1.0.3

  • Refactor pom files.

  • Refactor gitignore file.

v1.0.4

  • Allow adding multiple labels to Github issues

  • Disable the function to clear annotation fields during manual query

  • Loinc entries change color if they have been annotated

  • Add tooltips to HPO listview and treeview

  • Allow user to switch to previously selected Loinc list

  • Allow user to categorize Loinc entries

v1.1.0

  • New develop version

Additional changes for this version

  • Change menu Edit to Configuration
  • update tutorial

  • Create new features that allow user to manipulate a session

  • Automatically retrieve information from auto-saved data for last session

v1.1.1

  • Session data now only saves terms for low, intermediate, and high value, instead for all 6 internal codes

  • Basic and Advanced data are stored separately

v1.1.2

  • Session data now saves to a universal TSV file

  • Restrict internal mappings

    Qn will not be mapped to "Presence" or "Absence" and Ord (of "Presence" type) will not be mapped to "high", "low", "normal"

  • Internal codes changed match FHIR

    "system" is renamed to "FHIR"; Code for "presence" changed from "P" to "POS", code for "not presence" changed from "NP" to "NEG" to be consistent with FHIR

  • Show version in "About" message

  • Refactor to remove deprecated classes

  • Allow user to specify the path to hp OWL and Obo

v1.1.3

  • Add function to simulate patient data (patient and observation resources)

  • Add function to allow uploading simulated data to hapi-fhir server

  • Add function to allow downloading patient data from fhir server

v1.1.4

  • Add function to restart the app when necessary

  • Prevent app from crashing when user's local HPO is outdated

  • Added classes to appTempData patient phenopacket (phenotype only)

  • Refactored to use phenol 1.0.0

v1.1.5

  • Add feature to copy annotation for one LOINC and paste to multiple selections of similar LOINC

  • Add function to annotate LOINC panels

  • Add function to convert FHIR messages for LOINC panels

  • Add a LOINC list for tests with "unspecified specimen". Messages on those should be not converted to HPO.

v1.1.6

  • Add feature to allow easy addition of LOINC lists: allow user to change colors of LOINC lists

  • Added HPO parser for owl format.

  • Refactored to use phenol 1.2.6

v1.1.7

  • Add algorithms to appTempData patients