PhenoTips » News » PhenoTips 1.4 Milestone 1 Released

PhenoTips 1.4 Milestone 1 Released

Aug 23 2017

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.

Availability

PhenoTips® is freely available under the terms of the the GNU Affero General Public License, version 3.0.

 Download the latest release
 Play with our demo
 Get the source code

Contact

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support@phenotips.org
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info@gene42.com
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