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News

Oct 24 2017

PhenoTips 1.3.5 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3.5 release.
In this is release, the following items have been addressed:

New Feature

PT-3451 - Add a "My groups" gadget on the homepage

Bug fixes and improvements

PT-3104 - Different/inconsistent behavior when filtering in Advanced data filtering and Export
PT-3450 - Filtering by member in the phenotips-groups macro ignores the Administrators subgroup
PT-3452 - Enable support for free-text diagnoses in the patient record form and in the pedigree editor
PT-3460 - Non-categorized custom phenotypes disappear from saved patient record

Oct 17 2017

PhenoTips 1.4 Milestone 2 Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.4 Milestone 2 release. The highlights of the release are:

Patient data

  • Patient records can be filtered by the study they belong to
  • Improved look and functionality of patient and family directories
  • New and improved cancers UI in pedigree editor
  • Pedigree editor is now using standardized vocabulary for cancers
  • By default negative phenotypes are removed from Gene panel section
  • Free-text diagnoses in patient form and in pedigree editor are now supported
  • Implemented family permissions

REST API

  • Allowed method PATCH on patient resources
  • Allowed explicit updates, overwrites and merges when updating patient records
  • Added REST API for family permissions

Vocabularies

  • Administrators can permanently redefine the location of vocabulary sources
  • Improved vocabulary reindex process

Text mining

  • Administrators can configure the text-mining service either locally (CTAKES) or remotely through services.phenotips.org (CTAKES and NCR)

Bug fixes

  • Families shared with me are missing some families with shared patients
  • Drop-down autocomplete doesn't follow the search bar in pedigree editor
  • Layout issue in the first tab of the pedigree editor node menu
  • Gene panels should display HGNC gene symbol rather that its alias
  • Under high load, no HPO terms are extracted from clinical notes
  • Loading spinner doesn't display properly in export modal
  • Pedigree editor breaks when using non-default date input format
  • In some cases, using a decade for DOB in a pedigree breaks the editor
  • When using dd-mm-yyyy for pedigree date format (both input and display), using decades in the pedigree breaks the editor
  • Genes should be stored internally as Ensembl IDs, not HGNC IDs
  • Problems with guest users:
    - missing "owner" access on guest-owned patient records
    - wrong failure reported when deleting records

See the full list of changes in JIRA.

Oct 12 2017

PhenoTips 1.3.4 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3.4 release. In this is release, the following issues have been resolved:

  • Pedigree editor
    PT-3446 - In some cases, using a decade for DOB in a pedigree breaks the editor
    PT-3449 - When using dd-mm-yyyy for pedigree date format (both input and display), using decades in the pedigree breaks the editor

  • Permissions
    PT-3444 - DefaultCollaborator objects with null user cannot be added to any hashed collection
    PT-3447 - DefaultOwner objects with null user cannot be compared