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News

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.

Aug 23 2017

PhenoTips 1.4 Milestone 1 Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.4 Milestone 1 release. The highlights of the release are:

Pedigree editor

  • Colouring of disorders, phenotypes and genes can be turned on/off for the whole group or per individual item in the pedigree legend
  • Improved pedigree legend box
  • All abnormalities/annotations associated with person are highlighted in the legend while hovering over an individual's symbol in the pedigree
  • Allowed assigning "Alive and Well" status to a group of people
  • Corrected problem with missing person's details when exporting to PNG and SVG

PedigreeColouring.png

Patient and family records

Data tables

  • New and improved data filtering: Advanced filters are replaced with FILTERS panel located on the far left side of All patient/family records pages
  • Collaborators are added to the patient's FILTERS panel
  • 'Owner', 'Visibility' and "Collaborators" are now available for displaying in the patients table (they are not shown by default)

AdvancedFilters.png

Patient form

  • Text mining: HPO terms are now extracted from "Indication for referral" and "Medical history" and displayed as phenotype suggestions under SUGGESTIONS FROM CLINICAL NOTES box
  • Renamed "Molecular diagnosis" to "Final diagnosis"
  • Added info button to selected phenotypes, clinical and final diagnoses
  • Improved layout of the Gene panels section
  • Added new option to filter out genes that have been ruled out in gene panels (turned on by default)
  • Corrected several problems involving entering phenotype details

TextMining.png

GenePanels.png

Push/Export/Import

  • Added ability to push, export and import medical reports, additional images and documents
  • Improved and more user friendly export dialog
  • Various fixes involving Excel export file

ExportDialog.png

Vocabularies

  • Added support for vocabulary categories
    • instead of searching only a specific vocabulary, for example "OMIM", it is now possible to search in all vocabularies of a certain type, for example "diseases"
    • added REST API endpoints /vocabularies/categories; vocabularies/categories/{category}; vocabularies/categories/{category}?suggest)
  • More robust vocabulary reindexing operation is no longer leaving system in a bad state (e.g. after failure)
  • Suggest widgets for vocabularies are now working on the filters for groups' owned and shared cases tables, and for study cases
  • Gene suggestions are now showing the exact input provided (if found) as a first option

Permissions

  • Several improvements in case permissions module is not installed:
    • Patients and family tables are now displayed on the homepage
    • Fields 'owner' and 'visibility' are removed from advanced filters
    • All patients are now shown in the "Browse Patients" table
  • Permissions manager dialog can be extended with custom sharing options
  • Removal of one's own account as managing collaborator no longer throws exceptions

Other

  • Java 1.8 is now required
  • Removed FAMILIES SHARED WITH ME widget from the home page
  • Gene Panels JSON is now more concise

See the full list of changes in JIRA.

Jul 24 2017

PhenoTips 1.3.2 (stable) Released

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.3.2 release. In this is release, the following 19 issues have been resolved:

  • PT-3221 - Gene Comments panel is too short, Strategy panel too long
  • PT-3265 - getTerm in HGNC vocabulary should match on exact input provided
  • PT-3273 - Gene strategies and variant evidence have an extra semicolon when exported to Excel
  • PT-3278 - Export doesn't take into account the filters for genes and for clinical diagnosis
  • PT-3279 - "Delete all x" option does not work in the Advanced Search and in the Export dialog
  • PT-3284 - Suggestions do not work on the filters for groups' owned and shared cases tables, and for study cases
  • PT-3287 - In the advanced data filters, when filtering by more than one owner no results are returned
  • PT-3294 - A phenotype can appear as both positive and negative in the "Current selection" in certain conditions
  • PT-3295 - Selecting from the quick search suggestions a phenotype that is already selected and had details attached appears to cause the loss of the details
  • PT-3297 - Phenotype details re-appear in view mode, with no pre-notice in edit mode about the extra data
  • PT-3304 - "New patient" button in the browse patient page should be underlined on mouse hover
  • PT-3305 - Empty family tables displayed on the homepage when the permissions module is not installed
  • PT-3306 - No patients table displayed on the homepage when the permissions module is not installed
  • PT-3307 - A&W box does not clear in some situations, causing problems with export to png
  • PT-3308 - Export to PNG SVG initiated in pedigree editor is missing person's details other than internalID
  • PT-3309 - Remove quotation marks from Export to PNG/SVG buttons
  • PT-3311 - TermsForGene.toJSON should create a summary for each term instead of calling term.toJSON
  • PT-3313 - Not all patients are shown in the "All Patients" table when the permissions module is not installed
  • PT-3314 - When the permissions module is not installed, do not show the 'owner' and 'visibility' advanced filters