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News

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

Sep 22 2017

PhenoTips 1.3.3 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3.3 release. In this is release, the following issues have been resolved:

Pedigree editor:

  • PT-3272 - Upon deletion of a pedigree node, its carrier genes are still present in the legend
  • PT-3320 - Pedigree node hover boxes do not fade out when they should in some cases
  • PT-3321 - Drop-down autocomplete doesn't follow the search bar in pedigree editor
  • PT-3355 - Some functionality is broken in IE9 (most notably pedigree editor can not be opened)
  • PT-3385 - Unauthenticated users can't save new pedigree
  • PT-3438 - Pedigree editor breaks when using non-default date input format
  • PT-3248 - Rename "disorders" to "final diagnosis" in pedigree editor
  • PT-3275 - Improve info text in pedigree legend box
  • PT-3357 - In pedigree editor do not show A&W options on hoverboxes for patients which are read-only for current user

Family charts:

  • PT-2804 - All families should only list current user's families
  • PT-2815 - Family updates and patient JSON updates should be performed under the correct user
  • PT-2824 - "Families shared with me" are missing some families with shared patients

Patient records:

  • PT-3315 - Phenotypes from the predefined list disappear from phenotype selection after JSON import from edit mode
  • PT-3319 - Long custom entries in the genes table cause layout issues
  • PT-3338 - In the excel export, paternal ethnicity should be left, maternal ethnicity should be right
  • PT-3345 - When importing a new patient, a new owner object is created even if the owner already exists
  • PT-3353 - Terms added from the ontology browser are always added in the main clinical symptoms section, regardless of where the browser was triggered from
  • PT-3408 - Wrong failure reported when guest users delete their records
  • PT-3416 - Loading spinner doesn't display properly in export modal
  • PT-3377 - Remove negative phenotypes from Gene panel section

See the full list of changes on JIRA.