PhenoTips » News » PhenoTips 1.4 Milestone 4 Released

PhenoTips 1.4 Milestone 4 Released

Jun 15 2018

The PhenoTips development team is happy to announce the availability of the PhenoTips 1.4 Milestone 4 release. The highlights of the release are:

Improvements

Patients data

  • Families now support members that are not assigned to an individual in the pedigree
  • Added owner, collaborators and visibility to family directory filters
  • Renamed "Report date" to "Creation date" on the landing page
  • Permissions: Clicking on the new owner field automatically select "Transfer ownership to another user or group"
  • Added info button to Mode of inheritance
  • Removed "Global" from Global mode of inheritance and Global age of onset
  • Added alternative names, inheritance, onset, and prevalence in ORDO diagnosis info-box
  • Display human-readable symptoms and not symptoms in ORDO and OMIM diagnosis info-boxes
  • Added validation of PubMed IDs and details about the article are now shown
  • Added Rejected candidate gene status
  • Renamed Negative to Tested negative status
  • Gene lookup now supports free text option at the bottom as the other lookups do
  • Improved labeling/default for variants in Genotype section
  • Gene panels section:
      - renamed section title to Suggested Genes
      - now more user friendly
      - shows the number of genes associated with each phenotype,
      - sorts phenotypes by number of associated genes in descending order,
      - nonstandard terms are marked with an icon
      - rejected genes are now displayed with a strike-through
      - Rejected Candidate is added to existing Exclude Negative Genes filter
  • Same visual arrangements in PED export dialog as in pedigree legend
  • More robust save functionality
  • Uniform look for lookup fields in advanced filters and export/push dialog

Administration/System

  • Added ability to consent/push/export genes and variants separately
  • Vocabulary version is now updated upon successful reindexing
  • New vocabularies can be installed as extensions
  • New support for auditing who viewed and edited records
  • Added ability to show external identifiers in place of internal ones in the Patient and Family record forms
  • Upgraded XWiki to 7.4.6

Defects

  • Problems when reindexing vocabularies:
      - an installed vocabulary from a source included inside a jar
      - a vocabulary from a source included inside a jar
      - vocabularies with special characters in their source URL
  • Gray out Cancer tab for view only users
  • View-only collaborators are presented with the option to change the study of a patient record
  • Users that are not subscribed to any studies cannot see when a patient record belongs to a study
  • When a patient is deleted the "push to remote servers" data is not removed
  • Cannot delete a family via REST
  • Group cases are not displayed in Admin/Group/Cases
  • Resolve text mining issues and turn it on by default
  • Free text option appended to the phenotype lookup, when input (phenotype) has exact match in the suggestion list
  • Free text entered as an ethnicity does not get suggested anymore
  • Nonstandard features get copied to features array in the pedigree JSON representation
  • Export as JSON is missing the Referrer (report creator) info
  • Phenotype suggestions aren't displayed if OMIM suggestions aren't enabled
  • Non-functional "Go to search page" displayed in the quick-search results
  • PED export omits cancers entered in the new cancer tab
  • Clearing Referrer and Last Author fields in families' advanced filters does not automatically refresh the results
  • Bugs in pedigree patient drop legend and unlinked patient handling
  • Typed gene name doesn't get replaced with the proper Ensembl ID after displaying gene information
  • Logging out while in edit mode can lock the object for 30 minutes
  • Unauthenticated users can edit the PatientTemplate and FamilyTemplate
  • PhenoTips won't run on Windows if username contains space character
  • PhenoTips doesn't run on Java 9
  • XSS vulnerability in patient form data

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

 Ask for free support (by volunteers):
support@phenotips.org
 Inquire about commercial support:
info@gene42.com
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@phenotips

PhenoTips® is an exclusive trademark of Gene42 Inc.